Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: At_chr3

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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31

Warning! 3062571 characters in sequence are not A, C, G, or T


File 106 of 290

Found at i:36295545 original size:27 final size:27

Alignment explanation

Indices: 36295503--36295672 Score: 207 Period size: 27 Copynumber: 6.3 Consensus size: 27 36295493 GACCCCAGTT ** * * 36295503 TGTAAAATTATTGAAATACCACGGTAG 1 TGTAAAATTATCAAAATACCCCTGTAG * * 36295530 TGTAAAATTATCGAAATACCCTTGTAG 1 TGTAAAATTATCAAAATACCCCTGTAG * * 36295557 TGTTAAATTACCAAAATACCCCTGTAG 1 TGTAAAATTATCAAAATACCCCTGTAG * * 36295584 TGTAAAATCACCAAAATACCCCTGTAG 1 TGTAAAATTATCAAAATACCCCTGTAG * 36295611 TGTAAAATTATCAAAATACCCTTGTAG 1 TGTAAAATTATCAAAATACCCCTGTAG * 36295638 TGTAAAATTA-CTGAAATACCCCTGTAG 1 TGTAAAATTATC-AAAATACCCCTGTAG * 36295665 GGTAAAAT 1 TGTAAAAT 36295673 GGCTATTTTT Statistics Matches: 126, Mismatches: 16, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 26 1 0.01 27 125 0.99 ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29 Consensus pattern (27 bp): TGTAAAATTATCAAAATACCCCTGTAG Found at i:36295638 original size:81 final size:81 Alignment explanation

Indices: 36295516--36295672 Score: 251 Period size: 81 Copynumber: 1.9 Consensus size: 81 36295506 AAAATTATTG * * 36295516 AAATACCACGGTAGTGTAAAATTATCGAAATACCCTTGTAGTGTTAAATTACCAAAATACCCCTG 1 AAATACCACGGTAGTGTAAAATTATCAAAATACCCTTGTAGTGTAAAATTACCAAAATACCCCTG * 36295581 TAGTGTAAAATCACCA 66 TAGGGTAAAATCACCA * * ** 36295597 AAATACCCCTGTAGTGTAAAATTATCAAAATACCCTTGTAGTGTAAAATTACTGAAATACCCCTG 1 AAATACCACGGTAGTGTAAAATTATCAAAATACCCTTGTAGTGTAAAATTACCAAAATACCCCTG 36295662 TAGGGTAAAAT 66 TAGGGTAAAAT 36295673 GGCTATTTTT Statistics Matches: 69, Mismatches: 7, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 81 69 1.00 ACGTcount: A:0.39, C:0.18, G:0.14, T:0.28 Consensus pattern (81 bp): AAATACCACGGTAGTGTAAAATTATCAAAATACCCTTGTAGTGTAAAATTACCAAAATACCCCTG TAGGGTAAAATCACCA Found at i:36297657 original size:7 final size:7 Alignment explanation

Indices: 36297647--36297675 Score: 58 Period size: 7 Copynumber: 4.1 Consensus size: 7 36297637 ATGAATGATA 36297647 AGGGATG 1 AGGGATG 36297654 AGGGATG 1 AGGGATG 36297661 AGGGATG 1 AGGGATG 36297668 AGGGATG 1 AGGGATG 36297675 A 1 A 36297676 TTAGAAATGT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 22 1.00 ACGTcount: A:0.31, C:0.00, G:0.55, T:0.14 Consensus pattern (7 bp): AGGGATG Found at i:36297660 original size:21 final size:21 Alignment explanation

Indices: 36297636--36297675 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 21 36297626 AGGAGAGAAT * 36297636 GATGAATGATAAGGGATGAGG 1 GATGAAGGATAAGGGATGAGG * * 36297657 GATGAGGGATGAGGGATGA 1 GATGAAGGATAAGGGATGA 36297676 TTAGAAATGT Statistics Matches: 16, Mismatches: 3, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 21 16 1.00 ACGTcount: A:0.35, C:0.00, G:0.47, T:0.17 Consensus pattern (21 bp): GATGAAGGATAAGGGATGAGG Found at i:36298895 original size:25 final size:24 Alignment explanation

Indices: 36298867--36298916 Score: 59 Period size: 22 Copynumber: 2.1 Consensus size: 24 36298857 TATGGCTCAA 36298867 GATATACTACTATGGCTCAACATAG 1 GATATA-TACTATGGCTCAACATAG * * 36298892 G--ATATGCTATGGCTCGACATAG 1 GATATATACTATGGCTCAACATAG 36298914 GAT 1 GAT 36298917 GGGTTTCATG Statistics Matches: 21, Mismatches: 2, Indels: 5 0.75 0.07 0.18 Matches are distributed among these distances: 22 17 0.81 23 3 0.14 25 1 0.05 ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28 Consensus pattern (24 bp): GATATATACTATGGCTCAACATAG Found at i:36308371 original size:43 final size:43 Alignment explanation

Indices: 36308201--36308372 Score: 145 Period size: 43 Copynumber: 4.0 Consensus size: 43 36308191 ACATAGGATT * * * ** * 36308201 TCGATATGTGATTTCATGTAAGACCACGTCTCAGACGTTGCCA 1 TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA * * * * 36308244 TCGAT-TTGAGATTTAC-TGTAAGACCATGTCTGGGACATCGACA 1 TCGATATT-TGA-TTACATGTAAGACCATGTCTGGGACGTTGGCA * * * * * 36308287 TCG-TATTTGATTTCGTGTAAGACCTTGTTTGGGATAG-TGGCA 1 TCGATATTTGATTACATGTAAGACCATGTCTGGGA-CGTTGGCA * 36308329 TCGATATTTGATTACATATAAGACCATGTCTGGGACGTTGGCA 1 TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA 36308372 T 1 T 36308373 TGTACGAGCT Statistics Matches: 99, Mismatches: 23, Indels: 14 0.73 0.17 0.10 Matches are distributed among these distances: 41 3 0.03 42 28 0.28 43 65 0.66 44 3 0.03 ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34 Consensus pattern (43 bp): TCGATATTTGATTACATGTAAGACCATGTCTGGGACGTTGGCA Found at i:36313762 original size:40 final size:39 Alignment explanation

Indices: 36313686--36313766 Score: 108 Period size: 40 Copynumber: 2.1 Consensus size: 39 36313676 AACGACTTAC ** 36313686 CGGCTAAAATGGCACTTAGTGTGCGGTTCGAAATAGCTT 1 CGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTT * * * 36313725 CGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCTT 1 CGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCTT 36313765 CG 1 CG 36313767 ACTATATTTA Statistics Matches: 36, Mismatches: 5, Indels: 1 0.86 0.12 0.02 Matches are distributed among these distances: 39 9 0.25 40 27 0.75 ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28 Consensus pattern (39 bp): CGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTT Found at i:36313824 original size:28 final size:28 Alignment explanation

Indices: 36313781--36313855 Score: 80 Period size: 28 Copynumber: 2.7 Consensus size: 28 36313771 TATTTATATA * * * 36313781 AATGGAACTTAATGTGC-AAAGTATCAAG 1 AATGGCACTTAGTGTGCGAAA-CATCAAG * * 36313809 GATGGCACTTAGTGTGCGAAACATCCAG 1 AATGGCACTTAGTGTGCGAAACATCAAG * 36313837 AATAGCACTTAGTGTGCGA 1 AATGGCACTTAGTGTGCGA 36313856 GGTATAGAGT Statistics Matches: 39, Mismatches: 7, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 28 36 0.92 29 3 0.08 ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24 Consensus pattern (28 bp): AATGGCACTTAGTGTGCGAAACATCAAG Found at i:36316657 original size:50 final size:50 Alignment explanation

Indices: 36316589--36316719 Score: 192 Period size: 50 Copynumber: 2.6 Consensus size: 50 36316579 TGATATGTGT 36316589 CAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGAAAAAAGGAGAGC 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAAAAAA-GAGAGC * * * * * * 36316639 CAGTGTAAGACCATGTCTGGGATATGGCATCGGCCTCTATATAAGAGAGT 1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAAAAAAGAGAGC 36316689 CAGTGTAAGACCATGTCTGGGACATGGCATC 1 CAGTGTAAGACCATGTCTGGGACATGGCATC 36316720 CACTCGATAT Statistics Matches: 73, Mismatches: 7, Indels: 2 0.89 0.09 0.02 Matches are distributed among these distances: 50 67 0.92 51 6 0.08 ACGTcount: A:0.30, C:0.20, G:0.30, T:0.21 Consensus pattern (50 bp): CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGAAAAAAGAGAGC Found at i:36316790 original size:43 final size:44 Alignment explanation

Indices: 36316691--36316810 Score: 129 Period size: 43 Copynumber: 2.7 Consensus size: 44 36316681 AAGAGAGTCA 36316691 GTGTAAGACCATGTCTGGGACATGGCATCCACTCGATATGTGATTAC 1 GTGTAAGACCATGTCTGGGACATGGCAT---CTCGATATGTGATTAC * * 36316738 ATGTAAGACCATGTCTGGGACATTGGCAT-T-G-TATTGTGATTTC 1 GTGTAAGACCATGTCTGGGACA-TGGCATCTCGATA-TGTGATTAC * * 36316781 GTGTAAGACCTTGTGTGGGACAGTGGCATC 1 GTGTAAGACCATGTCTGGGACA-TGGCATC 36316811 GATATAACAT Statistics Matches: 64, Mismatches: 6, Indels: 9 0.81 0.08 0.11 Matches are distributed among these distances: 42 2 0.03 43 34 0.53 44 1 0.02 47 21 0.33 48 6 0.09 ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31 Consensus pattern (44 bp): GTGTAAGACCATGTCTGGGACATGGCATCTCGATATGTGATTAC Found at i:36320384 original size:41 final size:41 Alignment explanation

Indices: 36320339--36320463 Score: 223 Period size: 41 Copynumber: 3.0 Consensus size: 41 36320329 GGTAAAAGTG 36320339 TGAATAAATTAAAAATATGGACTGATATGAGCATGTATAAA 1 TGAATAAATTAAAAATATGGACTGATATGAGCATGTATAAA * 36320380 TGAATAAATTAAAAATATGGACTGATATGAGCATGTATGAA 1 TGAATAAATTAAAAATATGGACTGATATGAGCATGTATAAA * 36320421 TGAATAAATTAAAAATATGGACTGATATGAGCATATATCAAA 1 TGAATAAATTAAAAATATGGACTGATATGAGCATGTAT-AAA 36320463 T 1 T 36320464 TCGGATAGCT Statistics Matches: 80, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 41 77 0.96 42 3 0.04 ACGTcount: A:0.48, C:0.06, G:0.17, T:0.30 Consensus pattern (41 bp): TGAATAAATTAAAAATATGGACTGATATGAGCATGTATAAA Found at i:36320879 original size:40 final size:39 Alignment explanation

Indices: 36320820--36320895 Score: 116 Period size: 40 Copynumber: 1.9 Consensus size: 39 36320810 GACTTATCGG 36320820 CTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCGA 1 CTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCGA * * * 36320859 CTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCTT 1 CTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCTT 36320896 TGGCTATATT Statistics Matches: 33, Mismatches: 3, Indels: 1 0.89 0.08 0.03 Matches are distributed among these distances: 39 6 0.18 40 27 0.82 ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30 Consensus pattern (39 bp): CTAAAATGGCACTTAGTGTGCAATTCGAAATAGCTTCGA Found at i:36326197 original size:26 final size:26 Alignment explanation

Indices: 36326166--36326218 Score: 97 Period size: 26 Copynumber: 2.0 Consensus size: 26 36326156 GTGTCTATGG * 36326166 ATTGAATTGAATGATTTTTTGAATAA 1 ATTGAATTGAATGATTTGTTGAATAA 36326192 ATTGAATTGAATGATTTGTTGAATAA 1 ATTGAATTGAATGATTTGTTGAATAA 36326218 A 1 A 36326219 AGAATTAACT Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43 Consensus pattern (26 bp): ATTGAATTGAATGATTTGTTGAATAA Found at i:36326686 original size:43 final size:42 Alignment explanation

Indices: 36326531--36326687 Score: 122 Period size: 43 Copynumber: 3.7 Consensus size: 42 36326521 TGCATTTTCG * 36326531 TGTAAGACCACGTCTGAGACGTTGGCATCA-ACTTATGATTTACA 1 TGTAAGACCATGTCTGAGACGTTGGCATCATA-TT-TGA-TTACA * ** * * * ** * * 36326575 TGCAAGATGATGTGTGGGACATCAGCATCATATTTGATTTCG 1 TGTAAGACCATGTCTGAGACGTTGGCATCATATTTGATTACA * * 36326617 TGTAAGACCCTATCTGGGAGA-G-TGGCATCGATATTTGATTACA 1 TGTAAGACCATGTCT--GAGACGTTGGCATC-ATATTTGATTACA 36326660 TGTAAGACCATGTCTGAGACGTTGGCAT 1 TGTAAGACCATGTCTGAGACGTTGGCAT 36326688 TGTACAAGCT Statistics Matches: 82, Mismatches: 25, Indels: 13 0.68 0.21 0.11 Matches are distributed among these distances: 41 4 0.05 42 18 0.22 43 33 0.40 44 26 0.32 45 1 0.01 ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31 Consensus pattern (42 bp): TGTAAGACCATGTCTGAGACGTTGGCATCATATTTGATTACA Found at i:36337348 original size:19 final size:18 Alignment explanation

Indices: 36337320--36337359 Score: 53 Period size: 19 Copynumber: 2.2 Consensus size: 18 36337310 ATGAAATTTT 36337320 AATTAGTATTATGAGATAA 1 AATTAGTATTATGAGA-AA * * 36337339 AATTATTATTATTAGAAA 1 AATTAGTATTATGAGAAA 36337357 AAT 1 AAT 36337360 AATACTGTAT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 18 5 0.26 19 14 0.74 ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40 Consensus pattern (18 bp): AATTAGTATTATGAGAAA Found at i:36344001 original size:27 final size:27 Alignment explanation

Indices: 36343970--36344147 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 36343960 TAAATTGTAC 36343970 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 36343997 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 36344023 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 36344051 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 36344079 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 36344106 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 36344133 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 36344148 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:36344084 original size:82 final size:81 Alignment explanation

Indices: 36343971--36344126 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 36343961 AAATTGTACA * * 36343971 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 36344035 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 36344052 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 36344117 TGCGAGTTGA 65 TGCGAATTGA 36344127 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:36344138 original size:82 final size:81 Alignment explanation

Indices: 36343967--36344147 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 36343957 GATTAAATTG * * 36343967 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 36344032 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 36344048 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 36344112 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 36344130 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 36344148 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:36352191 original size:27 final size:27 Alignment explanation

Indices: 36352160--36352337 Score: 205 Period size: 27 Copynumber: 6.6 Consensus size: 27 36352150 TAAATTGTAC 36352160 AGCACTAAGTGTGCGATTTGACTATGT 1 AGCACTAAGTGTGCGATTTGACTATGT * ** * 36352187 TGCACTAAGTGTGCGAAATGAATATG- 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 36352213 ATGCACTAAGTGTGCGAATTGACCATGC 1 A-GCACTAAGTGTGCGATTTGACTATGT * 36352241 GGCACTAAGTGTGCGAGTTTGACTATGT 1 AGCACTAAGTGTGCGA-TTTGACTATGT * * 36352269 AGCACTAAGTGTGCGATTTGATTACGT 1 AGCACTAAGTGTGCGATTTGACTATGT * * * 36352296 AGCACTAAGTGTGCGAGTTGATTATAT 1 AGCACTAAGTGTGCGATTTGACTATGT * 36352323 AGCACTGAGTGTGCG 1 AGCACTAAGTGTGCG 36352338 GACTCAATAT Statistics Matches: 129, Mismatches: 19, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 27 106 0.82 28 23 0.18 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (27 bp): AGCACTAAGTGTGCGATTTGACTATGT Found at i:36352274 original size:82 final size:81 Alignment explanation

Indices: 36352161--36352316 Score: 233 Period size: 82 Copynumber: 1.9 Consensus size: 81 36352151 AAATTGTACA * * 36352161 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG 1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG 36352225 TGCGAATTGACCATGCG 65 TGCGAATTGACCATGCG ** * 36352242 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG 1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG * 36352307 TGCGAGTTGA 65 TGCGAATTGA 36352317 TTATATAGCA Statistics Matches: 67, Mismatches: 6, Indels: 3 0.88 0.08 0.04 Matches are distributed among these distances: 81 15 0.22 82 51 0.76 83 1 0.01 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29 Consensus pattern (81 bp): GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT GCGAATTGACCATGCG Found at i:36352328 original size:82 final size:81 Alignment explanation

Indices: 36352157--36352337 Score: 229 Period size: 82 Copynumber: 2.2 Consensus size: 81 36352147 GATTAAATTG * * 36352157 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA 1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA 36352222 GTGTGCGAATTGACCA 66 GTGTGCGAATTGACCA * * ** * 36352238 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT 1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT * ** 36352302 AAGTGTGCGAGTTGATTA 64 AAGTGTGCGAATTGACCA * * 36352320 TATAGCACTGAGTGTGCG 1 TACAGCACTAAGTGTGCG 36352338 GACTCAATAT Statistics Matches: 84, Mismatches: 14, Indels: 3 0.83 0.14 0.03 Matches are distributed among these distances: 81 18 0.21 82 66 0.79 ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30 Consensus pattern (81 bp): TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA GTGTGCGAATTGACCA Found at i:36359283 original size:133 final size:134 Alignment explanation

Indices: 36358945--36359344 Score: 766 Period size: 134 Copynumber: 3.0 Consensus size: 134 36358935 AACTAGCTCC * 36358945 AGCTAGCCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG 1 AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG 36359010 AA-TTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAAAGT 66 AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAAAGT 36359074 GATA 131 GATA 36359078 AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG 1 AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG * 36359143 AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAGAGT 66 AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAAAGT 36359208 GATA 131 GATA 36359212 AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG 1 AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG * 36359277 AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATCTGTAAAGT 66 AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAAAGT 36359342 GAT 131 GAT 36359345 TTTTGTTAGA Statistics Matches: 262, Mismatches: 4, Indels: 1 0.98 0.01 0.00 Matches are distributed among these distances: 133 66 0.25 134 196 0.75 ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43 Consensus pattern (134 bp): AGCTAGTCCGTACCTTCATTTTTGAATCTGTTAAAAATTTTAGAAGTTTCCATTGATGAATCCTG AATTTTTTTTAATGAATACCATGTATTTGAAGCTTTGATTGTGTTGTTTAATGAATTTGTAAAGT GATA Found at i:36361603 original size:48 final size:48 Alignment explanation

Indices: 36361488--36361709 Score: 215 Period size: 48 Copynumber: 4.7 Consensus size: 48 36361478 GTAAGATTCT * * * * 36361488 AATGCCATATCCCAGACATGGTCTTACATGGGATCACAAATCGAAGCC 1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGCC * * * * 36361536 GAT---A-G-CCTAG-CTATGGTCTTACACGATG-TCTCATATCGATGCC 1 AATGCCATGTCCCAGAC-ATGGTCTTACATG-GGATCTCATATCGATGCC * * * * 36361579 AATGCCATATCCCAGATATGGTCTTACATGGGATCACATGTCGATGCC 1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGCC * * * * 36361627 AATTCCATGTCCCATACATGGTATTACATGGGATCTCATAACGATGCC 1 AATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGCC * * 36361675 AATGCCATGTCCTAGGCATGGTCTTACATGGGATC 1 AATGCCATGTCCCAGACATGGTCTTACATGGGATC 36361710 ACACATAACC Statistics Matches: 136, Mismatches: 29, Indels: 18 0.74 0.16 0.10 Matches are distributed among these distances: 42 1 0.01 43 30 0.22 44 1 0.01 45 1 0.01 46 1 0.01 47 1 0.01 48 101 0.74 ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27 Consensus pattern (48 bp): AATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGCC Found at i:36364860 original size:46 final size:46 Alignment explanation

Indices: 36364810--36364982 Score: 212 Period size: 46 Copynumber: 3.7 Consensus size: 46 36364800 TGGTTGAGCA 36364810 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * 36364856 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G * 36364901 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * 36364949 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA 1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA 36364983 GGGGCGGGTT Statistics Matches: 109, Mismatches: 8, Indels: 20 0.80 0.06 0.15 Matches are distributed among these distances: 42 2 0.02 43 5 0.05 45 7 0.06 46 57 0.52 47 29 0.27 48 3 0.03 50 4 0.04 51 2 0.02 ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29 Consensus pattern (46 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:36364966 original size:93 final size:93 Alignment explanation

Indices: 36364807--36364977 Score: 308 Period size: 93 Copynumber: 1.8 Consensus size: 93 36364797 GGATGGTTGA * * 36364807 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT 36364872 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG 36364900 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG 36364964 TTGAGTCCGAGTTC 65 TTGAGTCCGAGTTC 36364978 ACTTAGGGGC Statistics Matches: 75, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 92 4 0.05 93 71 0.95 ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:36369221 original size:68 final size:67 Alignment explanation

Indices: 36369149--36369298 Score: 171 Period size: 67 Copynumber: 2.2 Consensus size: 67 36369139 CATCATGTGT * * * * 36369149 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC 1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC 36369211 ATGTAG 62 ATGTAG ** * * 36369217 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT 1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT 36369282 AG 66 AG 36369284 ACAAGAGAGCTACGA 1 ACAAGAGAGCTACGA 36369299 GATAAACTGG Statistics Matches: 70, Mismatches: 9, Indels: 7 0.81 0.10 0.08 Matches are distributed among these distances: 64 20 0.29 65 7 0.10 66 4 0.06 67 26 0.37 68 13 0.19 ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21 Consensus pattern (67 bp): ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT AG Found at i:36369254 original size:64 final size:64 Alignment explanation

Indices: 36369173--36369356 Score: 194 Period size: 67 Copynumber: 2.8 Consensus size: 64 36369163 AGACATTATG * * 36369173 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT 1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA * * * * * * 36369237 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT 1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT 36369302 AA 63 AA * * * * 36369304 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC 1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC 36369357 CGAACTATAT Statistics Matches: 98, Mismatches: 17, Indels: 11 0.78 0.13 0.09 Matches are distributed among these distances: 62 1 0.01 63 19 0.19 64 21 0.21 65 8 0.08 66 16 0.16 67 31 0.32 68 2 0.02 ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23 Consensus pattern (64 bp): ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA Found at i:36370880 original size:13 final size:13 Alignment explanation

Indices: 36370862--36370888 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 36370852 TGTCTCAACT 36370862 GACTTTGGGACAC 1 GACTTTGGGACAC 36370875 GACTTTGGGACAC 1 GACTTTGGGACAC 36370888 G 1 G 36370889 GGCGTGTGGA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22 Consensus pattern (13 bp): GACTTTGGGACAC Found at i:36371503 original size:89 final size:89 Alignment explanation

Indices: 36371388--36371565 Score: 329 Period size: 89 Copynumber: 2.0 Consensus size: 89 36371378 AAAGAAAATT 36371388 TCCTGGGATTTCTTTCAGAGTGAGTTGAAAAAGATGTATGGCGAGAAATGGTATCTAGACAAGAA 1 TCCTGGGATTTCTTTCAGAGTGAGTTGAAAAAGATGTATGGCGAGAAATGGTATCTAGACAAGAA 36371453 AAAGATAGAATTTCTTGAGTTATG 66 AAAGATAGAATTTCTTGAGTTATG * * * 36371477 TCCTGGGATTTCTTTCAGAGTGAGTTGAAAATGATGTATGTCGGGAAATGGTATCTAGACAAGAA 1 TCCTGGGATTTCTTTCAGAGTGAGTTGAAAAAGATGTATGGCGAGAAATGGTATCTAGACAAGAA 36371542 AAAGATAGAATTTCTTGAGTTATG 66 AAAGATAGAATTTCTTGAGTTATG 36371566 ACAAGGAATT Statistics Matches: 86, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 89 86 1.00 ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31 Consensus pattern (89 bp): TCCTGGGATTTCTTTCAGAGTGAGTTGAAAAAGATGTATGGCGAGAAATGGTATCTAGACAAGAA AAAGATAGAATTTCTTGAGTTATG Found at i:36373873 original size:26 final size:26 Alignment explanation

Indices: 36373844--36373906 Score: 110 Period size: 26 Copynumber: 2.4 Consensus size: 26 36373834 AGAGTATGCT 36373844 CCCTGATTATGTACC-CTGATGGGTAC 1 CCCTGATTATGTACCTC-GATGGGTAC 36373870 CCCTGATTATGTACCTCGATGGGTAC 1 CCCTGATTATGTACCTCGATGGGTAC 36373896 CCCTGATTATG 1 CCCTGATTATG 36373907 AATTGACAGT Statistics Matches: 36, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 26 35 0.97 27 1 0.03 ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32 Consensus pattern (26 bp): CCCTGATTATGTACCTCGATGGGTAC Found at i:36377159 original size:39 final size:40 Alignment explanation

Indices: 36377064--36377325 Score: 337 Period size: 39 Copynumber: 6.7 Consensus size: 40 36377054 TTGAATGATG * 36377064 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT * 36377102 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT 1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT 36377143 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT 36377182 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * * 36377221 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT * 36377260 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT * * 36377299 AACCGGGCTATGTCCCGAAGGCATTTG 1 -TCCGGGCTAAGTCCCGAAGGCATTTG 36377326 AACGAGGAGC Statistics Matches: 203, Mismatches: 11, Indels: 17 0.88 0.05 0.07 Matches are distributed among these distances: 39 132 0.65 40 59 0.29 41 11 0.05 42 1 0.00 ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT Found at i:36384469 original size:18 final size:18 Alignment explanation

Indices: 36384429--36384490 Score: 52 Period size: 18 Copynumber: 3.4 Consensus size: 18 36384419 CTTGGCCCAT * * 36384429 TGCAGTAAAAGTAAATGG 1 TGCAGTAAAAGTAATTAG * * 36384447 AGCAGTAATAGTAATTAG 1 TGCAGTAAAAGTAATTAG * * * 36384465 TGCAGCAACAGTAATCAG 1 TGCAGTAAAAGTAATTAG * 36384483 TACAGTAA 1 TGCAGTAA 36384491 CAGTTTAAAC Statistics Matches: 34, Mismatches: 10, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 18 34 1.00 ACGTcount: A:0.44, C:0.11, G:0.23, T:0.23 Consensus pattern (18 bp): TGCAGTAAAAGTAATTAG Found at i:36384492 original size:18 final size:18 Alignment explanation

Indices: 36384449--36384494 Score: 56 Period size: 18 Copynumber: 2.6 Consensus size: 18 36384439 GTAAATGGAG * * * 36384449 CAGTAATAGTAATTAGTG 1 CAGTAACAGTAATCAGTA * 36384467 CAGCAACAGTAATCAGTA 1 CAGTAACAGTAATCAGTA 36384485 CAGTAACAGT 1 CAGTAACAGT 36384495 TTAAACAATA Statistics Matches: 23, Mismatches: 5, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24 Consensus pattern (18 bp): CAGTAACAGTAATCAGTA Found at i:36384905 original size:26 final size:26 Alignment explanation

Indices: 36384851--36384975 Score: 137 Period size: 27 Copynumber: 4.7 Consensus size: 26 36384841 CCTCACATAG * 36384851 GGGCAAAACAGTCAATTTACC-ATGCAA 1 GGGCAAAACAGTCATTTTACCTAT--AA *** 36384878 GGGCATTTCAGTCATTTTACCTATAA 1 GGGCAAAACAGTCATTTTACCTATAA 36384904 GGGCAAAACAGTCATTTTACCTCATAA 1 GGGCAAAACAGTCATTTTACCT-ATAA * * 36384931 GAGCAAAACAGTCATTTTACC-ACATA 1 GGGCAAAACAGTCATTTTACCTATA-A * 36384957 GGGCAAAATAGTCATTTTA 1 GGGCAAAACAGTCATTTTA 36384976 TTGATTACGG Statistics Matches: 84, Mismatches: 11, Indels: 7 0.82 0.11 0.07 Matches are distributed among these distances: 25 2 0.02 26 39 0.46 27 41 0.49 28 2 0.02 ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27 Consensus pattern (26 bp): GGGCAAAACAGTCATTTTACCTATAA Found at i:36384923 original size:53 final size:52 Alignment explanation

Indices: 36384844--36384975 Score: 142 Period size: 53 Copynumber: 2.5 Consensus size: 52 36384834 ATAAATACCT * * *** 36384844 CACATAGGGGCAAAACAGTCAATTTACCATGC-AAGGGCATTTCAGTCATTTTAC 1 CACATA-GGGCAAAACAGTCATTTTACC-T-CAAAGAGCAAAACAGTCATTTTAC * 36384898 C-TATAAGGGCAAAACAGTCATTTTACCTCATAAGAGCAAAACAGTCATTTTAC 1 CACAT-AGGGCAAAACAGTCATTTTACCTCA-AAGAGCAAAACAGTCATTTTAC * 36384951 CACATAGGGCAAAATAGTCATTTTA 1 CACATAGGGCAAAACAGTCATTTTA 36384976 TTGATTACGG Statistics Matches: 66, Mismatches: 8, Indels: 9 0.80 0.10 0.11 Matches are distributed among these distances: 51 1 0.02 52 1 0.02 53 60 0.91 54 4 0.06 ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27 Consensus pattern (52 bp): CACATAGGGCAAAACAGTCATTTTACCTCAAAGAGCAAAACAGTCATTTTAC Found at i:36388788 original size:16 final size:16 Alignment explanation

Indices: 36388769--36388799 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 36388759 CTTCTTCACT 36388769 TACTCACTTACTTAAA 1 TACTCACTTACTTAAA * 36388785 TACTTACTTACTTAA 1 TACTCACTTACTTAA 36388800 TCAAATTTAT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42 Consensus pattern (16 bp): TACTCACTTACTTAAA Found at i:36388805 original size:20 final size:20 Alignment explanation

Indices: 36388766--36388805 Score: 53 Period size: 20 Copynumber: 2.0 Consensus size: 20 36388756 AAACTTCTTC * * 36388766 ACTTACTCACTTACTTAAAT 1 ACTTACTCACTTAATCAAAT * 36388786 ACTTACTTACTTAATCAAAT 1 ACTTACTCACTTAATCAAAT 36388806 TTATTAATAC Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 20 17 1.00 ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40 Consensus pattern (20 bp): ACTTACTCACTTAATCAAAT Found at i:36388916 original size:23 final size:24 Alignment explanation

Indices: 36388878--36388922 Score: 74 Period size: 23 Copynumber: 1.9 Consensus size: 24 36388868 TTTGCTCTTC * 36388878 TAGCATGAACTTGTCTTACCTTTT 1 TAGCATGAACTCGTCTTACCTTTT 36388902 TAGCAT-AACTCGTCTTACCTT 1 TAGCATGAACTCGTCTTACCTT 36388923 ACCTTACCTT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 23 14 0.70 24 6 0.30 ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42 Consensus pattern (24 bp): TAGCATGAACTCGTCTTACCTTTT Found at i:36390920 original size:30 final size:29 Alignment explanation

Indices: 36390886--36390942 Score: 96 Period size: 30 Copynumber: 1.9 Consensus size: 29 36390876 ATCGGAAGCT * 36390886 TTGGCACTAAGTGTGTGATTTAAACTAGAC 1 TTGGCACTAAGTGTGCGATTT-AACTAGAC 36390916 TTGGCACTAAGTGTGCGATTTAACTAG 1 TTGGCACTAAGTGTGCGATTTAACTAG 36390943 CTTCGGCTAC Statistics Matches: 26, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 29 6 0.23 30 20 0.77 ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33 Consensus pattern (29 bp): TTGGCACTAAGTGTGCGATTTAACTAGAC Found at i:36400614 original size:28 final size:27 Alignment explanation

Indices: 36400551--36400702 Score: 232 Period size: 27 Copynumber: 5.6 Consensus size: 27 36400541 ATATTAAGTC * * 36400551 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT 36400578 CGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT * 36400606 CGCACACTTAGTGCTACATAGTCAACT 1 CGCACACTTAGTGCTACATAATCAACT * 36400633 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT * * 36400661 CGCACACTTAGTGCTACATAGTCAATT 1 CGCACACTTAGTGCTACATAATCAACT 36400688 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 36400703 GCACAATTTA Statistics Matches: 119, Mismatches: 4, Indels: 4 0.94 0.03 0.03 Matches are distributed among these distances: 27 66 0.55 28 53 0.45 ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:36400635 original size:55 final size:55 Alignment explanation

Indices: 36400551--36400727 Score: 264 Period size: 55 Copynumber: 3.2 Consensus size: 55 36400541 ATATTAAGTC * * * 36400551 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT 1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT * 36400606 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT * * * * * 36400661 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAACC 1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT 36400717 CGCACACTTAG 1 CGCACACTTAG 36400728 CGCCAATCTC Statistics Matches: 111, Mismatches: 10, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 55 95 0.86 56 16 0.14 ACGTcount: A:0.32, C:0.29, G:0.14, T:0.25 Consensus pattern (55 bp): CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT Found at i:36406430 original size:33 final size:33 Alignment explanation

Indices: 36406393--36406466 Score: 78 Period size: 33 Copynumber: 2.2 Consensus size: 33 36406383 CCTACCAAGG * * * 36406393 TCTTACACTCATAATGCCATAACCTAGTTATGA 1 TCTTACACTCAGAATGCCATAACCCAGCTATGA * * 36406426 TCTTATCA-TCAGGATGCCATAGCCCAGCTATGA 1 TCTTA-CACTCAGAATGCCATAACCCAGCTATGA * 36406459 TTTTACAC 1 TCTTACAC 36406467 ATATACATAT Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 32 2 0.06 33 29 0.88 34 2 0.06 ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32 Consensus pattern (33 bp): TCTTACACTCAGAATGCCATAACCCAGCTATGA Found at i:36408174 original size:43 final size:43 Alignment explanation

Indices: 36408119--36408279 Score: 161 Period size: 43 Copynumber: 3.7 Consensus size: 43 36408109 TGCCAACGTA * * 36408119 CCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCCACTGTC 1 CCAGACAG-GGTCTTACACGAAATCAAATATCGATGCCACTGTC * * 36408162 CCAAACAGGGTCTTACACGAAATCAAATAT-GATGCCAATGTC 1 CCAGACAGGGTCTTACACGAAATCAAATATCGATGCCACTGTC * * * 36408204 CTAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTC 1 CCAGACAGGGTCTTACACG-AAATC-AAATATCGATGCC-ACTGTC * * 36408248 CCAGAC-GTGGTCTTACATGAAATCACATATCG 1 CCAGACAG-GGTCTTACACGAAATCAAATATCG 36408280 GAATCCTATG Statistics Matches: 97, Mismatches: 14, Indels: 14 0.78 0.11 0.11 Matches are distributed among these distances: 42 28 0.29 43 41 0.42 44 27 0.28 45 1 0.01 ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25 Consensus pattern (43 bp): CCAGACAGGGTCTTACACGAAATCAAATATCGATGCCACTGTC Found at i:36408249 original size:86 final size:85 Alignment explanation

Indices: 36408108--36408277 Score: 204 Period size: 86 Copynumber: 2.0 Consensus size: 85 36408098 AGCTCGTACA * * 36408108 ATGCCAACGTACCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAACAG-GG 1 ATGCCAACGTACCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAAC-GTGG 36408172 TCTTACACGAAATCAAATATG 65 TCTTACACGAAATCAAATATG * * * 36408193 ATGCCAATGT-CCTAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGACG 1 ATGCCAACGTACC-AGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTCCCAAACG * * 36408255 TGGTCTTACATGAAATCACATAT 62 TGGTCTTACACGAAATCAAATAT 36408278 CGGAATCCTA Statistics Matches: 73, Mismatches: 7, Indels: 9 0.82 0.08 0.10 Matches are distributed among these distances: 84 2 0.03 85 26 0.36 86 41 0.56 87 4 0.05 ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25 Consensus pattern (85 bp): ATGCCAACGTACCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAAACGTGGT CTTACACGAAATCAAATATG Found at i:36410676 original size:39 final size:39 Alignment explanation

Indices: 36410642--36410738 Score: 142 Period size: 39 Copynumber: 2.5 Consensus size: 39 36410632 CCGGATTCCA * 36410642 TTCCAGCACATA-CTCTGCGGACTTGAAGTCCGGATATAT 1 TTCCAGCACATAGC-CTGCGGACTTCAAGTCCGGATATAT * 36410681 TTCCAGTACATAGCCTGCGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT * * 36410720 TCCCAGCATATAGCCTGCG 1 TTCCAGCACATAGCCTGCG 36410739 TGTAACACCC Statistics Matches: 52, Mismatches: 5, Indels: 2 0.88 0.08 0.03 Matches are distributed among these distances: 39 51 0.98 40 1 0.02 ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27 Consensus pattern (39 bp): TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT Found at i:36420966 original size:39 final size:39 Alignment explanation

Indices: 36420922--36421195 Score: 431 Period size: 39 Copynumber: 7.0 Consensus size: 39 36420912 CCGGATTCCA * * 36420922 TTCCAGCACGTAGCCTACGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 36420961 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 36421000 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 36421039 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 36421078 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT * * * * * 36421117 TCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATAA 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT * * * * * * 36421156 TCCCAGCATATAGCTTGCGGACCTCATGTCTGGATATAT 1 TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT 36421195 T 1 T 36421196 CCCGATATCA Statistics Matches: 225, Mismatches: 10, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 39 225 1.00 ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26 Consensus pattern (39 bp): TTCCAGCACATAGCCTGCGGACTTCAAGTCCGGATATAT Found at i:36423864 original size:13 final size:13 Alignment explanation

Indices: 36423846--36423881 Score: 72 Period size: 13 Copynumber: 2.8 Consensus size: 13 36423836 TACTCGTAAA 36423846 CACATATCGAAGT 1 CACATATCGAAGT 36423859 CACATATCGAAGT 1 CACATATCGAAGT 36423872 CACATATCGA 1 CACATATCGA 36423882 TGCCATGGTC Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 23 1.00 ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22 Consensus pattern (13 bp): CACATATCGAAGT Found at i:36435579 original size:13 final size:13 Alignment explanation

Indices: 36435561--36435588 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 36435551 TATATATATA 36435561 AAAGAAACAAAAG 1 AAAGAAACAAAAG 36435574 AAAGAAACAAAAG 1 AAAGAAACAAAAG 36435587 AA 1 AA 36435589 TAAAAAGAGG 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:0.79, C:0.07, G:0.14, T:0.00 Consensus pattern (13 bp): AAAGAAACAAAAG Found at i:36436382 original size:15 final size:14 Alignment explanation

Indices: 36436359--36436408 Score: 73 Period size: 15 Copynumber: 3.4 Consensus size: 14 36436349 TTTATTAAAT 36436359 TTATATTGATTGATA 1 TTATATTGATTGA-A * 36436374 TTATTTTGATTGAA 1 TTATATTGATTGAA 36436388 TTTATATTGATTGAA 1 -TTATATTGATTGAA 36436403 TTATAT 1 TTATAT 36436409 AATATACATG Statistics Matches: 32, Mismatches: 2, Indels: 3 0.86 0.05 0.08 Matches are distributed among these distances: 14 7 0.22 15 25 0.78 ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56 Consensus pattern (14 bp): TTATATTGATTGAA Found at i:36436810 original size:23 final size:23 Alignment explanation

Indices: 36436780--36436866 Score: 92 Period size: 21 Copynumber: 4.0 Consensus size: 23 36436770 GCTTTATCGA * * 36436780 TCAGGCACTTTATGTGTCGTATT 1 TCAGGCACCTCATGTGTCGTATT * 36436803 TCAGGCACCTCGTGTGTCGTA-- 1 TCAGGCACCTCATGTGTCGTATT * 36436824 TCAGGCACCTCGTGTGTCGT-TT 1 TCAGGCACCTCATGTGTCGTATT * * 36436846 T-AGGCACTTTATGTGTCGTAT 1 TCAGGCACCTCATGTGTCGTAT 36436867 ACTGATCAGG Statistics Matches: 55, Mismatches: 6, Indels: 7 0.81 0.09 0.10 Matches are distributed among these distances: 21 35 0.64 22 2 0.04 23 18 0.33 ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38 Consensus pattern (23 bp): TCAGGCACCTCATGTGTCGTATT Found at i:36439731 original size:5 final size:6 Alignment explanation

Indices: 36439715--36439741 Score: 54 Period size: 6 Copynumber: 4.5 Consensus size: 6 36439705 CATTCCCTTG 36439715 ATTTTT ATTTTT ATTTTT ATTTTT ATT 1 ATTTTT ATTTTT ATTTTT ATTTTT ATT 36439742 CCAACCTCTT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 21 1.00 ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81 Consensus pattern (6 bp): ATTTTT Found at i:36441361 original size:47 final size:46 Alignment explanation

Indices: 36441310--36441404 Score: 109 Period size: 46 Copynumber: 2.0 Consensus size: 46 36441300 TAAGCACATT * * * 36441310 TTTGTTTTGACAACTTAACTGCAACTATAGTGGCTCGACCACATATA 1 TTTGTTCTGACAACTTAACTG-AAATATAGTGGCTCGACCAAATATA * * ** * 36441357 TTTGTTCTGATATCTTAGTTGAAATATAGTGGCTTGACCAAATATA 1 TTTGTTCTGACAACTTAACTGAAATATAGTGGCTCGACCAAATATA 36441403 TT 1 TT 36441405 CGATATGGTA Statistics Matches: 40, Mismatches: 8, Indels: 1 0.82 0.16 0.02 Matches are distributed among these distances: 46 24 0.60 47 16 0.40 ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39 Consensus pattern (46 bp): TTTGTTCTGACAACTTAACTGAAATATAGTGGCTCGACCAAATATA Found at i:36446330 original size:29 final size:29 Alignment explanation

Indices: 36446297--36446353 Score: 71 Period size: 29 Copynumber: 2.0 Consensus size: 29 36446287 CTGTGTCACC * * 36446297 CACACAGTCTCAG-ACATGCCCGTGTGGCT 1 CACACAGTCT-AGCACATGACCATGTGGCT * 36446326 CACACGGTCTAGCACATGACCATGTGGC 1 CACACAGTCTAGCACATGACCATGTGGC 36446354 ATCGACAGTT Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 28 2 0.08 29 22 0.92 ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19 Consensus pattern (29 bp): CACACAGTCTAGCACATGACCATGTGGCT Found at i:36449472 original size:52 final size:52 Alignment explanation

Indices: 36449411--36449510 Score: 182 Period size: 52 Copynumber: 1.9 Consensus size: 52 36449401 CGCATACGAT * * 36449411 TAACTCAGATTTTGAAGTTAGAGCTCCTCTATCTTTTTATTAATATCATCAC 1 TAACTCAGATTTTGAAGTCAGAGCTCCTCTATCTTGTTATTAATATCATCAC 36449463 TAACTCAGATTTTGAAGTCAGAGCTCCTCTATCTTGTTATTAATATCA 1 TAACTCAGATTTTGAAGTCAGAGCTCCTCTATCTTGTTATTAATATCA 36449511 CCACAAATGG Statistics Matches: 46, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 52 46 1.00 ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41 Consensus pattern (52 bp): TAACTCAGATTTTGAAGTCAGAGCTCCTCTATCTTGTTATTAATATCATCAC Found at i:36450088 original size:19 final size:19 Alignment explanation

Indices: 36450064--36450102 Score: 69 Period size: 19 Copynumber: 2.1 Consensus size: 19 36450054 TAAGAATCTT * 36450064 ATCAAATTGAGTGTTACAA 1 ATCAAATTGAATGTTACAA 36450083 ATCAAATTGAATGTTACAA 1 ATCAAATTGAATGTTACAA 36450102 A 1 A 36450103 AATGTGTACT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31 Consensus pattern (19 bp): ATCAAATTGAATGTTACAA Found at i:36473909 original size:24 final size:25 Alignment explanation

Indices: 36473857--36473915 Score: 68 Period size: 24 Copynumber: 2.4 Consensus size: 25 36473847 TTTTAGAATA * 36473857 TTTAGTATTTATTAGCATAATATAT 1 TTTAGTATTTATTAGCATAATAAAT * 36473882 TTTA-TATTTATTAGTATAA-AAAT 1 TTTAGTATTTATTAGCATAATAAAT * 36473905 CTTTATTATTT 1 -TTTAGTATTT 36473916 CTTTCTATAT Statistics Matches: 30, Mismatches: 2, Indels: 4 0.83 0.06 0.11 Matches are distributed among these distances: 23 3 0.10 24 18 0.60 25 9 0.30 ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56 Consensus pattern (25 bp): TTTAGTATTTATTAGCATAATAAAT Found at i:36476160 original size:14 final size:14 Alignment explanation

Indices: 36476141--36476190 Score: 50 Period size: 14 Copynumber: 3.5 Consensus size: 14 36476131 TGGTTATGGC 36476141 AGTTAGTAGTTAAT 1 AGTTAGTAGTTAAT * 36476155 AGTTAG-AGCTTAGT 1 AGTTAGTAG-TTAAT 36476169 AGTTATGGTAGTT-AT 1 AGTTA--GTAGTTAAT 36476184 AGTTAGT 1 AGTTAGT 36476191 TAACTATTAC Statistics Matches: 30, Mismatches: 2, Indels: 9 0.73 0.05 0.22 Matches are distributed among these distances: 13 4 0.13 14 15 0.50 15 6 0.20 16 3 0.10 17 2 0.07 ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42 Consensus pattern (14 bp): AGTTAGTAGTTAAT Found at i:36482778 original size:23 final size:22 Alignment explanation

Indices: 36482726--36482778 Score: 56 Period size: 23 Copynumber: 2.4 Consensus size: 22 36482716 TCCACGTCTT * 36482726 TTTCTTTTGTTTCTTTTTCTAA 1 TTTCTTTTCTTTCTTTTTCTAA 36482748 -TTCATTTTCTCTTCTTTCTTC-AA 1 TTTC-TTTTCT-TTCTTT-TTCTAA 36482771 TTTCTTTT 1 TTTCTTTT 36482779 TCACTCTCAA Statistics Matches: 26, Mismatches: 1, Indels: 7 0.76 0.03 0.21 Matches are distributed among these distances: 21 3 0.12 22 5 0.19 23 12 0.46 24 6 0.23 ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70 Consensus pattern (22 bp): TTTCTTTTCTTTCTTTTTCTAA Found at i:36485132 original size:22 final size:23 Alignment explanation

Indices: 36485107--36485166 Score: 63 Period size: 22 Copynumber: 2.7 Consensus size: 23 36485097 TGGACTGAAT 36485107 ATAAAAATTTAAACTAAAT-AAA 1 ATAAAAATTTAAACTAAATAAAA * 36485129 ATAAATAA-ATAAA-TAAATAAAA 1 ATAAA-AATTTAAACTAAATAAAA * 36485151 ATAAAACTTTACAACT 1 ATAAAAATTTA-AACT 36485167 TGGGCCACTT Statistics Matches: 30, Mismatches: 3, Indels: 8 0.73 0.07 0.20 Matches are distributed among these distances: 21 6 0.20 22 19 0.63 23 4 0.13 24 1 0.03 ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27 Consensus pattern (23 bp): ATAAAAATTTAAACTAAATAAAA Found at i:36485134 original size:4 final size:4 Alignment explanation

Indices: 36485116--36485149 Score: 50 Period size: 4 Copynumber: 8.0 Consensus size: 4 36485106 TATAAAAATT 36485116 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA 1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA 36485150 AATAAAACTT Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 4 20 0.71 5 8 0.29 ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24 Consensus pattern (4 bp): TAAA Found at i:36488484 original size:40 final size:40 Alignment explanation

Indices: 36488427--36488509 Score: 123 Period size: 40 Copynumber: 2.1 Consensus size: 40 36488417 ACATCTTCAG * * * 36488427 TTGCACGTACTTTACCCGAGA-AACTTATGTGCATGGATTC 1 TTGCACGTACTTGACCCG-GACAACTTATATGCATGAATTC 36488467 TTGCACGTACTTGACCCGGACAACTTATATGCATGAATTC 1 TTGCACGTACTTGACCCGGACAACTTATATGCATGAATTC 36488507 TTG 1 TTG 36488510 TGTGCATGAA Statistics Matches: 39, Mismatches: 3, Indels: 2 0.89 0.07 0.05 Matches are distributed among these distances: 39 2 0.05 40 37 0.95 ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33 Consensus pattern (40 bp): TTGCACGTACTTGACCCGGACAACTTATATGCATGAATTC Found at i:36489005 original size:28 final size:28 Alignment explanation

Indices: 36488973--36489028 Score: 112 Period size: 28 Copynumber: 2.0 Consensus size: 28 36488963 AGCTGTAAAA 36488973 AATTTATTTATCCTGCATGATATGAAGG 1 AATTTATTTATCCTGCATGATATGAAGG 36489001 AATTTATTTATCCTGCATGATATGAAGG 1 AATTTATTTATCCTGCATGATATGAAGG 36489029 CTAAGTTAAT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 28 28 1.00 ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39 Consensus pattern (28 bp): AATTTATTTATCCTGCATGATATGAAGG Found at i:36494323 original size:23 final size:23 Alignment explanation

Indices: 36494297--36494342 Score: 92 Period size: 23 Copynumber: 2.0 Consensus size: 23 36494287 ATCATGGTTG 36494297 AATTTGGATGATAATCATCTCTT 1 AATTTGGATGATAATCATCTCTT 36494320 AATTTGGATGATAATCATCTCTT 1 AATTTGGATGATAATCATCTCTT 36494343 CTAGATATGA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 23 1.00 ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43 Consensus pattern (23 bp): AATTTGGATGATAATCATCTCTT Found at i:36494637 original size:18 final size:19 Alignment explanation

Indices: 36494614--36494656 Score: 61 Period size: 21 Copynumber: 2.2 Consensus size: 19 36494604 CAGGCAAGCC 36494614 TTTTG-AAGTAGTATTGTA 1 TTTTGTAAGTAGTATTGTA 36494632 TTTTGATTAAGTAGTATTGTA 1 TTTTG--TAAGTAGTATTGTA 36494653 TTTT 1 TTTT 36494657 TGGATGGTTT Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 18 5 0.23 21 17 0.77 ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56 Consensus pattern (19 bp): TTTTGTAAGTAGTATTGTA Found at i:36496991 original size:46 final size:44 Alignment explanation

Indices: 36496898--36496991 Score: 145 Period size: 44 Copynumber: 2.1 Consensus size: 44 36496888 ATTACAACAT 36496898 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC 1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC * 36496942 CATTCCATTCAACCAAACA-ATTGAATTACTGATTACAGTTCTATTC 1 CATTCCATTCAACCAAACACA-AGAA-TACT-ATTACAGTTCTATTC 36496988 CATT 1 CATT 36496992 ACAGCTCTAT Statistics Matches: 46, Mismatches: 1, Indels: 4 0.90 0.02 0.08 Matches are distributed among these distances: 43 1 0.02 44 22 0.48 45 4 0.09 46 19 0.41 ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33 Consensus pattern (44 bp): CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC Found at i:36496994 original size:16 final size:16 Alignment explanation

Indices: 36496973--36497044 Score: 99 Period size: 16 Copynumber: 4.5 Consensus size: 16 36496963 TGAATTACTG 36496973 ATTACAGTTCTATTCC 1 ATTACAGTTCTATTCC * 36496989 ATTACAGCTCTATTCC 1 ATTACAGTTCTATTCC * * 36497005 ATTACAGCTCTATTCA 1 ATTACAGTTCTATTCC * * 36497021 ATTACAGTCCTATTCT 1 ATTACAGTTCTATTCC 36497037 ATTACAGT 1 ATTACAGT 36497045 GAACCAAACG Statistics Matches: 51, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 16 51 1.00 ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40 Consensus pattern (16 bp): ATTACAGTTCTATTCC Found at i:36497640 original size:31 final size:31 Alignment explanation

Indices: 36497605--36497674 Score: 104 Period size: 31 Copynumber: 2.3 Consensus size: 31 36497595 ACCTAGTTAT * * 36497605 CAAGTTTAGAAGCCAATGTGAACATACTTGC 1 CAAGTTCAGAAGCCAATGTGAACATACGTGC * * 36497636 CAAGTTCAGGAGCCAATGTGAACATACGTGT 1 CAAGTTCAGAAGCCAATGTGAACATACGTGC 36497667 CAAGTTCA 1 CAAGTTCA 36497675 AGGGCCATAT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 31 35 1.00 ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24 Consensus pattern (31 bp): CAAGTTCAGAAGCCAATGTGAACATACGTGC Found at i:36498091 original size:15 final size:16 Alignment explanation

Indices: 36498071--36498113 Score: 52 Period size: 16 Copynumber: 2.7 Consensus size: 16 36498061 TTTTAATTAA 36498071 ATAAATATAATTTA-T 1 ATAAATATAATTTATT * 36498086 ATAAATATTATTTTATT 1 ATAAATA-TAATTTATT * 36498103 TTAAATATAAT 1 ATAAATATAAT 36498114 GTTAAAATCA Statistics Matches: 23, Mismatches: 3, Indels: 3 0.79 0.10 0.10 Matches are distributed among these distances: 15 7 0.30 16 9 0.39 17 7 0.30 ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51 Consensus pattern (16 bp): ATAAATATAATTTATT Found at i:36501137 original size:25 final size:26 Alignment explanation

Indices: 36501085--36501139 Score: 87 Period size: 26 Copynumber: 2.2 Consensus size: 26 36501075 TATCTATTAC 36501085 TATTTGATTTTCAATAATTTTACTAT 1 TATTTGATTTTCAATAATTTTACTAT 36501111 TATTTGATTTT-AATAATATTTAC-AT 1 TATTTGATTTTCAATAAT-TTTACTAT 36501136 TATT 1 TATT 36501140 ATGAATGTTG Statistics Matches: 28, Mismatches: 0, Indels: 3 0.90 0.00 0.10 Matches are distributed among these distances: 25 12 0.43 26 16 0.57 ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58 Consensus pattern (26 bp): TATTTGATTTTCAATAATTTTACTAT Found at i:36501687 original size:30 final size:30 Alignment explanation

Indices: 36501653--36501738 Score: 136 Period size: 30 Copynumber: 2.9 Consensus size: 30 36501643 AAAACCCTAG * 36501653 CCACCTTGCCTCCCAATTGCACCTACTCCA 1 CCACCTTGCCTCCCACTTGCACCTACTCCA * 36501683 CCACCTTGCCTCCCACTTGCATCTACTCCA 1 CCACCTTGCCTCCCACTTGCACCTACTCCA ** 36501713 CCACCTTATCTCCCACTTGCACCTAC 1 CCACCTTGCCTCCCACTTGCACCTAC 36501739 ACCATCAAAT Statistics Matches: 51, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 30 51 1.00 ACGTcount: A:0.19, C:0.50, G:0.06, T:0.26 Consensus pattern (30 bp): CCACCTTGCCTCCCACTTGCACCTACTCCA Found at i:36502239 original size:9 final size:9 Alignment explanation

Indices: 36502227--36502305 Score: 50 Period size: 9 Copynumber: 8.1 Consensus size: 9 36502217 GAGAGCTTTG * 36502227 TTTTATTTT 1 TTTTATTAT 36502236 TTTTATTATT 1 TTTTATTA-T 36502246 TTTACTATTAT 1 TTT--TATTAT * 36502257 TTATATTAT 1 TTTTATTAT * 36502266 TATTATTAT 1 TTTTATTAT * 36502275 TTCTCATGTAT 1 TT-TTAT-TAT * 36502286 ATATTATTAT 1 -TTTTATTAT * 36502296 TTATATTAT 1 TTTTATTAT 36502305 T 1 T 36502306 ATATTGTATA Statistics Matches: 54, Mismatches: 10, Indels: 12 0.71 0.13 0.16 Matches are distributed among these distances: 9 29 0.54 10 10 0.19 11 9 0.17 12 6 0.11 ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68 Consensus pattern (9 bp): TTTTATTAT Found at i:36502246 original size:12 final size:12 Alignment explanation

Indices: 36502229--36502307 Score: 61 Period size: 12 Copynumber: 6.3 Consensus size: 12 36502219 GAGCTTTGTT * 36502229 TTATTTTTTTTA 1 TTATTTTTATTA * 36502241 TTATTTTTACTA 1 TTATTTTTATTA * 36502253 TTATTTATATTA 1 TTATTTTTATTA * 36502265 TTATTATTATT- 1 TTATTTTTATTA * 36502276 TCTCATGTATATATTA 1 T-T-AT-T-TTTATTA * 36502292 TTATTTATATTA 1 TTATTTTTATTA 36502304 TTAT 1 TTAT 36502308 ATTGTATATA Statistics Matches: 54, Mismatches: 8, Indels: 10 0.75 0.11 0.14 Matches are distributed among these distances: 11 1 0.02 12 41 0.76 13 3 0.06 14 3 0.06 15 5 0.09 16 1 0.02 ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67 Consensus pattern (12 bp): TTATTTTTATTA Found at i:36502290 original size:21 final size:18 Alignment explanation

Indices: 36502237--36502307 Score: 79 Period size: 18 Copynumber: 3.7 Consensus size: 18 36502227 TTTTATTTTT * * 36502237 TTTATTATTTTTACTATTA 1 TTTA-TATTATTATTATTA 36502256 TTTATATTATTATTATTA 1 TTTATATTATTATTATTA * 36502274 TTTCTCATGTATATATTATTA 1 TTTAT-AT-TAT-TATTATTA 36502295 TTTATATTATTAT 1 TTTATATTATTAT 36502308 ATTGTATATA Statistics Matches: 45, Mismatches: 4, Indels: 7 0.80 0.07 0.12 Matches are distributed among these distances: 18 19 0.42 19 9 0.20 20 5 0.11 21 12 0.27 ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65 Consensus pattern (18 bp): TTTATATTATTATTATTA Found at i:36502427 original size:30 final size:30 Alignment explanation

Indices: 36502393--36502478 Score: 136 Period size: 30 Copynumber: 2.9 Consensus size: 30 36502383 AAAACCCTAG * 36502393 CCACCTTGCCTCCCAATTGCACCTACTCCA 1 CCACCTTGCCTCCCACTTGCACCTACTCCA * 36502423 CCACCTTGCCTCCCACTTGCATCTACTCCA 1 CCACCTTGCCTCCCACTTGCACCTACTCCA ** 36502453 CCACCTTATCTCCCACTTGCACCTAC 1 CCACCTTGCCTCCCACTTGCACCTAC 36502479 ACCATCAAAT Statistics Matches: 51, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 30 51 1.00 ACGTcount: A:0.19, C:0.50, G:0.06, T:0.26 Consensus pattern (30 bp): CCACCTTGCCTCCCACTTGCACCTACTCCA Found at i:36502979 original size:9 final size:9 Alignment explanation

Indices: 36502967--36503045 Score: 50 Period size: 9 Copynumber: 8.1 Consensus size: 9 36502957 GAGAGCTTTG * 36502967 TTTTATTTT 1 TTTTATTAT 36502976 TTTTATTATT 1 TTTTATTA-T 36502986 TTTACTATTAT 1 TTT--TATTAT * 36502997 TTATATTAT 1 TTTTATTAT * 36503006 TATTATTAT 1 TTTTATTAT * 36503015 TTCTCATGTAT 1 TT-TTAT-TAT * 36503026 ATATTATTAT 1 -TTTTATTAT * 36503036 TTATATTAT 1 TTTTATTAT 36503045 T 1 T 36503046 ATATTGTATA Statistics Matches: 54, Mismatches: 10, Indels: 12 0.71 0.13 0.16 Matches are distributed among these distances: 9 29 0.54 10 10 0.19 11 9 0.17 12 6 0.11 ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68 Consensus pattern (9 bp): TTTTATTAT Found at i:36502986 original size:12 final size:12 Alignment explanation

Indices: 36502969--36503047 Score: 61 Period size: 12 Copynumber: 6.3 Consensus size: 12 36502959 GAGCTTTGTT * 36502969 TTATTTTTTTTA 1 TTATTTTTATTA * 36502981 TTATTTTTACTA 1 TTATTTTTATTA * 36502993 TTATTTATATTA 1 TTATTTTTATTA * 36503005 TTATTATTATT- 1 TTATTTTTATTA * 36503016 TCTCATGTATATATTA 1 T-T-AT-T-TTTATTA * 36503032 TTATTTATATTA 1 TTATTTTTATTA 36503044 TTAT 1 TTAT 36503048 ATTGTATATA Statistics Matches: 54, Mismatches: 8, Indels: 10 0.75 0.11 0.14 Matches are distributed among these distances: 11 1 0.02 12 41 0.76 13 3 0.06 14 3 0.06 15 5 0.09 16 1 0.02 ACGTcount: A:0.28, C:0.04, G:0.01, T:0.67 Consensus pattern (12 bp): TTATTTTTATTA Found at i:36503030 original size:21 final size:18 Alignment explanation

Indices: 36502977--36503047 Score: 79 Period size: 18 Copynumber: 3.7 Consensus size: 18 36502967 TTTTATTTTT * * 36502977 TTTATTATTTTTACTATTA 1 TTTA-TATTATTATTATTA 36502996 TTTATATTATTATTATTA 1 TTTATATTATTATTATTA * 36503014 TTTCTCATGTATATATTATTA 1 TTTAT-AT-TAT-TATTATTA 36503035 TTTATATTATTAT 1 TTTATATTATTAT 36503048 ATTGTATATA Statistics Matches: 45, Mismatches: 4, Indels: 7 0.80 0.07 0.12 Matches are distributed among these distances: 18 19 0.42 19 9 0.20 20 5 0.11 21 12 0.27 ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65 Consensus pattern (18 bp): TTTATATTATTATTATTA Found at i:36503057 original size:740 final size:740 Alignment explanation

Indices: 36501638--36503117 Score: 2960 Period size: 740 Copynumber: 2.0 Consensus size: 740 36501628 AAAAAAAAAA 36501638 AAGACAAAACCCTAGCCACCTTGCCTCCCAATTGCACCTACTCCACCACCTTGCCTCCCACTTGC 1 AAGACAAAACCCTAGCCACCTTGCCTCCCAATTGCACCTACTCCACCACCTTGCCTCCCACTTGC 36501703 ATCTACTCCACCACCTTATCTCCCACTTGCACCTACACCATCAAATGGAGAAGAGACATAGAATG 66 ATCTACTCCACCACCTTATCTCCCACTTGCACCTACACCATCAAATGGAGAAGAGACATAGAATG 36501768 ATAAGAAAATGTATGTAAGATGACTATAAAAGCAAAACCAAAAGTCCATTGTAAAAAAAAAAGGA 131 ATAAGAAAATGTATGTAAGATGACTATAAAAGCAAAACCAAAAGTCCATTGTAAAAAAAAAAGGA 36501833 AAGAATTGTATTTTTTAAAAGTTTTTTTGATACAAAAAAAGAGAAGAATGTAAAAGCAAAAGGTT 196 AAGAATTGTATTTTTTAAAAGTTTTTTTGATACAAAAAAAGAGAAGAATGTAAAAGCAAAAGGTT 36501898 TGCAAGCAAATCTGAAATAAAAAAAGCGAGTATTGAAAAAGAAAAGATTCAAACGCGTTAAGGTT 261 TGCAAGCAAATCTGAAATAAAAAAAGCGAGTATTGAAAAAGAAAAGATTCAAACGCGTTAAGGTT 36501963 TTTATTTCTTTTTTCTTTTTATTTTCACTTTTTTTATACATATAAACATTTTTTCTTTTTTTCTT 326 TTTATTTCTTTTTTCTTTTTATTTTCACTTTTTTTATACATATAAACATTTTTTCTTTTTTTCTT 36502028 TTCTTTCAAAAATAGTATACATATATTTAGATATAAAAATAAAAAAGAAAACAAAAAATAATACA 391 TTCTTTCAAAAATAGTATACATATATTTAGATATAAAAATAAAAAAGAAAACAAAAAATAATACA 36502093 TTTTTTAAATTTCTGGCCACCGCGCACGGTGGCCGGCGACGGCGGCAAAGAAGGCGGACGGCGCC 456 TTTTTTAAATTTCTGGCCACCGCGCACGGTGGCCGGCGACGGCGGCAAAGAAGGCGGACGGCGCC 36502158 GGTCCGGCGTCTGGGTACTGACCGGACCATGGTCGGAATGGGGAAAGAGGGAGAGAGTTGAGAGC 521 GGTCCGGCGTCTGGGTACTGACCGGACCATGGTCGGAATGGGGAAAGAGGGAGAGAGTTGAGAGC 36502223 TTTGTTTTATTTTTTTTATTATTTTTACTATTATTTATATTATTATTATTATTTCTCATGTATAT 586 TTTGTTTTATTTTTTTTATTATTTTTACTATTATTTATATTATTATTATTATTTCTCATGTATAT 36502288 ATTATTATTTATATTATTATATTGTATATACACTCTCTATATTTATTTATATTATTACTATCATT 651 ATTATTATTTATATTATTATATTGTATATACACTCTCTATATTTATTTATATTATTACTATCATT 36502353 ATTGTTACTTCTATTATTTTTTATC 716 ATTGTTACTTCTATTATTTTTTATC 36502378 AAGACAAAACCCTAGCCACCTTGCCTCCCAATTGCACCTACTCCACCACCTTGCCTCCCACTTGC 1 AAGACAAAACCCTAGCCACCTTGCCTCCCAATTGCACCTACTCCACCACCTTGCCTCCCACTTGC 36502443 ATCTACTCCACCACCTTATCTCCCACTTGCACCTACACCATCAAATGGAGAAGAGACATAGAATG 66 ATCTACTCCACCACCTTATCTCCCACTTGCACCTACACCATCAAATGGAGAAGAGACATAGAATG 36502508 ATAAGAAAATGTATGTAAGATGACTATAAAAGCAAAACCAAAAGTCCATTGTAAAAAAAAAAGGA 131 ATAAGAAAATGTATGTAAGATGACTATAAAAGCAAAACCAAAAGTCCATTGTAAAAAAAAAAGGA 36502573 AAGAATTGTATTTTTTAAAAGTTTTTTTGATACAAAAAAAGAGAAGAATGTAAAAGCAAAAGGTT 196 AAGAATTGTATTTTTTAAAAGTTTTTTTGATACAAAAAAAGAGAAGAATGTAAAAGCAAAAGGTT 36502638 TGCAAGCAAATCTGAAATAAAAAAAGCGAGTATTGAAAAAGAAAAGATTCAAACGCGTTAAGGTT 261 TGCAAGCAAATCTGAAATAAAAAAAGCGAGTATTGAAAAAGAAAAGATTCAAACGCGTTAAGGTT 36502703 TTTATTTCTTTTTTCTTTTTATTTTCACTTTTTTTATACATATAAACATTTTTTCTTTTTTTCTT 326 TTTATTTCTTTTTTCTTTTTATTTTCACTTTTTTTATACATATAAACATTTTTTCTTTTTTTCTT 36502768 TTCTTTCAAAAATAGTATACATATATTTAGATATAAAAATAAAAAAGAAAACAAAAAATAATACA 391 TTCTTTCAAAAATAGTATACATATATTTAGATATAAAAATAAAAAAGAAAACAAAAAATAATACA 36502833 TTTTTTAAATTTCTGGCCACCGCGCACGGTGGCCGGCGACGGCGGCAAAGAAGGCGGACGGCGCC 456 TTTTTTAAATTTCTGGCCACCGCGCACGGTGGCCGGCGACGGCGGCAAAGAAGGCGGACGGCGCC 36502898 GGTCCGGCGTCTGGGTACTGACCGGACCATGGTCGGAATGGGGAAAGAGGGAGAGAGTTGAGAGC 521 GGTCCGGCGTCTGGGTACTGACCGGACCATGGTCGGAATGGGGAAAGAGGGAGAGAGTTGAGAGC 36502963 TTTGTTTTATTTTTTTTATTATTTTTACTATTATTTATATTATTATTATTATTTCTCATGTATAT 586 TTTGTTTTATTTTTTTTATTATTTTTACTATTATTTATATTATTATTATTATTTCTCATGTATAT 36503028 ATTATTATTTATATTATTATATTGTATATACACTCTCTATATTTATTTATATTATTACTATCATT 651 ATTATTATTTATATTATTATATTGTATATACACTCTCTATATTTATTTATATTATTACTATCATT 36503093 ATTGTTACTTCTATTATTTTTTATC 716 ATTGTTACTTCTATTATTTTTTATC 36503118 TCTGACTACT Statistics Matches: 740, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 740 740 1.00 ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35 Consensus pattern (740 bp): AAGACAAAACCCTAGCCACCTTGCCTCCCAATTGCACCTACTCCACCACCTTGCCTCCCACTTGC ATCTACTCCACCACCTTATCTCCCACTTGCACCTACACCATCAAATGGAGAAGAGACATAGAATG ATAAGAAAATGTATGTAAGATGACTATAAAAGCAAAACCAAAAGTCCATTGTAAAAAAAAAAGGA AAGAATTGTATTTTTTAAAAGTTTTTTTGATACAAAAAAAGAGAAGAATGTAAAAGCAAAAGGTT TGCAAGCAAATCTGAAATAAAAAAAGCGAGTATTGAAAAAGAAAAGATTCAAACGCGTTAAGGTT TTTATTTCTTTTTTCTTTTTATTTTCACTTTTTTTATACATATAAACATTTTTTCTTTTTTTCTT TTCTTTCAAAAATAGTATACATATATTTAGATATAAAAATAAAAAAGAAAACAAAAAATAATACA TTTTTTAAATTTCTGGCCACCGCGCACGGTGGCCGGCGACGGCGGCAAAGAAGGCGGACGGCGCC GGTCCGGCGTCTGGGTACTGACCGGACCATGGTCGGAATGGGGAAAGAGGGAGAGAGTTGAGAGC TTTGTTTTATTTTTTTTATTATTTTTACTATTATTTATATTATTATTATTATTTCTCATGTATAT ATTATTATTTATATTATTATATTGTATATACACTCTCTATATTTATTTATATTATTACTATCATT ATTGTTACTTCTATTATTTTTTATC Found at i:36503174 original size:12 final size:13 Alignment explanation

Indices: 36503127--36503179 Score: 53 Period size: 12 Copynumber: 4.5 Consensus size: 13 36503117 CTCTGACTAC * 36503127 TATTATTATATA- 1 TATTATTATGTAT 36503139 TA-TA-TATGTAT 1 TATTATTATGTAT * 36503150 TATTGTT-TGTAT 1 TATTATTATGTAT 36503162 TATTATTAT-TAT 1 TATTATTATGTAT 36503174 TATTAT 1 TATTAT 36503180 CACCCCTATT Statistics Matches: 34, Mismatches: 3, Indels: 8 0.76 0.07 0.18 Matches are distributed among these distances: 10 5 0.15 11 4 0.12 12 23 0.68 13 2 0.06 ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62 Consensus pattern (13 bp): TATTATTATGTAT Found at i:36505470 original size:19 final size:19 Alignment explanation

Indices: 36505446--36505491 Score: 58 Period size: 19 Copynumber: 2.4 Consensus size: 19 36505436 CTTCCTCTCT * 36505446 TTTGCATT-CATTTCATGCA 1 TTTGCATTGCATTGCAT-CA * 36505465 TTTGCATTGCATTGCATTA 1 TTTGCATTGCATTGCATCA 36505484 TTTGCATT 1 TTTGCATT 36505492 AGGCTTTCCC Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 19 17 0.71 20 7 0.29 ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50 Consensus pattern (19 bp): TTTGCATTGCATTGCATCA Found at i:36513943 original size:88 final size:87 Alignment explanation

Indices: 36513828--36514059 Score: 349 Period size: 88 Copynumber: 2.6 Consensus size: 87 36513818 TGACCTTCGC 36513828 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGAGGAGCAGATCGAAGACATAGCTG 1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCG-GGAGCAGATCGAAGACATAGCTG * * 36513893 ATTTGGTTTTCACGTGTTTACGT 65 ATTTGGCTTTCACGTGTTTACAT * 36513916 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCGAAGACATAGTTG 1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGC-GGGAGCAGATCGAAGACATAGCTG 36513981 ATTTGGCTTTCACGTGTTTACAT 65 ATTTGGCTTTCACGTGTTTACAT * * ** * * 36514004 TGAAACAAATCCAAGATGATTTGGTGTCTCTGTAGC-GGCGGAGAACAGATCGAAGA 1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGG-GAGCAGATCGAAGA 36514060 TTGCAGATTT Statistics Matches: 133, Mismatches: 9, Indels: 5 0.90 0.06 0.03 Matches are distributed among these distances: 86 2 0.02 87 16 0.12 88 114 0.86 89 1 0.01 ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28 Consensus pattern (87 bp): TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGAGCAGATCGAAGACATAGCTGA TTTGGCTTTCACGTGTTTACAT Found at i:36514197 original size:88 final size:88 Alignment explanation

Indices: 36514047--36515024 Score: 463 Period size: 88 Copynumber: 11.1 Consensus size: 88 36514037 AGCGGCGGAG * * * * * 36514047 AACAGATCGAAGATTGCAGATTTGGCATCCCTATGTTTATAGGGAA-AAGATCAAAGATAGCAGA 1 AACAGATCGAAGATTACAGA-TTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAA-ATAGCAGA * 36514111 TCTGACATTCTC-GTGCTTACAGTAA 64 TCTGACATTCTCTGTGCTTACAG-GA * * 36514136 AACAGATCGAAGATTTCAGCA-TGGCATCCCTATGCTTATAGGGAACAAGTTGAAAATAGCAGAT 1 AACAGATCGAAGATTACAG-ATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGAT * * * * * 36514200 TTGGCATCCT-TGTGCTTATAGGG 65 CTGACATTCTCTGTGCTTACAGGA * * * * * * * * ** 36514223 AATAGATCGAAGATAACAGATCTGACATTCCTGTGCTTACAGTGAAGC-AGATCGAAGATTTCAG 1 AACAGATCGAAGATTACAGAT-TGGCATCCCTGTGCTTATAGGGAA-CAAG-TTGAAAATAGCAG * * * * 36514287 --CATGGCA-TCCCTGTGCTTATAGGG 63 ATC-TGACATTCTCTGTGCTTACAGGA * * * * * * 36514311 AACA-AGTTGAAAATAACAGATTTGGCATCCCTGTGCTTATAGGGAAC-AGATCGAAGATAACAG 1 AACAGA-TCGAAGATTACAGA-TTGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAATAGCAG 36514374 ATCTGACATTC-CTGTGCTTACAGTGA 63 ATCTGACATTCTCTGTGCTTACAG-GA * * * * * 36514400 AGCAGATCGAAGATTTCAGCA-TGGTATCCCTGGGCTTATAGGGAACAAGTTAAAAATAGCAGAT 1 AACAGATCGAAGATTACAG-ATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGAT * * * * * 36514464 TTGGCA-TCCCTGTGCTTATAGGG 65 CTGACATTCTCTGTGCTTACAGGA * * * * * * * ** 36514487 AACAGATCGAAGATAACAGATCTGACATTCCTGTGCTTACAGTGAAGC-AGATCGAAGATTTCAG 1 AACAGATCGAAGATTACAGAT-TGGCATCCCTGTGCTTATAGGGAA-CAAG-TTGAAAATAGCAG ** * * * * 36514551 --CATGGTA-TCCCTGGGCTTATAGGG 63 ATC-TGACATTCTCTGTGCTTACAGGA * * * * * * ** 36514575 AACA-AGT-TAAAAATAGCAGATTTGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAATA 1 AACAGA-TCGAAGATTA-CAGA-TTGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAATAGCA 36514637 GATCTGACATTC-CTGTGCTTACAGTGA 62 GATCTGACATTCTCTGTGCTTACAG-GA * * * * * 36514664 AACAGATCGAAGATTTCA-ACATGGCATCCCTATGCTTATAGGGAACAAGTTGAAAATGGAAGAT 1 AACAGATCGAAGATTACAGA-TTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGAT * * * * * 36514728 TTGGCA-TCCCTGTGCTTATAGGG 65 CTGACATTCTCTGTGCTTACAGGA * * * * * * * * ** 36514751 AACAGATCGAAGATAACAGATCTGACATTCATGTGCTTACAGTGAAGC-AGATCGAAGATTTCAG 1 AACAGATCGAAGATTACAGAT-TGGCATCCCTGTGCTTATAGGGAA-CAAG-TTGAAAATAGCAG * * * * * 36514815 --CATGGCA-TCCCTGTACTTATAGGG 63 ATC-TGACATTCTCTGTGCTTACAGGA * * * * * * * 36514839 AACA-AGTTGAAAATAACAGATTTGGCATCCCTGTGCTTATAGGGGAC-AGATCGAAGATAACAG 1 AACAGA-TCGAAGATTACAGA-TTGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAAATAGCAG * 36514902 ATCTGACATTC-ATGTGCTTACAGTGA 63 ATCTGACATTCTCTGTGCTTACAG-GA * * * * 36514928 AGCAGATCGAAGATTTCAGCA-TGGCATCCCTGTACTTATAGGGAACAAGTTGAAAATAACAGAT 1 AACAGATCGAAGATTACAG-ATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGAT * * * * * * 36514992 TTGGCA-TCCCTGTGTTTATAGGG 65 CTGACATTCTCTGTGCTTACAGGA 36515015 AACAGATCGA 1 AACAGATCGA 36515025 CGATAGTAGA Statistics Matches: 689, Mismatches: 150, Indels: 102 0.73 0.16 0.11 Matches are distributed among these distances: 86 2 0.00 87 118 0.17 88 454 0.66 89 105 0.15 90 10 0.01 ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26 Consensus pattern (88 bp): AACAGATCGAAGATTACAGATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATC TGACATTCTCTGTGCTTACAGGA Found at i:36514236 original size:132 final size:132 Alignment explanation

Indices: 36514062--36515904 Score: 3050 Period size: 132 Copynumber: 14.1 Consensus size: 132 36514052 ATCGAAGATT * * * * * 36514062 GCAGATTTGGCATCCCTATGTTTATAGGGAAAAGATCAAAGATAGCAGATCTGACATT-CTCGTG 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCT-GTG * * * 36514126 CTTACAGTAAAACAGATCGAAGATTTCAGCATGGCATCCCTATGCTTATAGGGAACAAGTTGAAA 65 CTTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAA 36514191 ATA 130 ATA * * 36514194 GCAGATTTGGCATCCTTGTGCTTATAGGGAATAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 36514259 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36514324 TA 131 TA * 36514326 ACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * * 36514391 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGGGCTTATAGGGAACAAGTTAAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36514456 TA 131 TA 36514458 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * * 36514523 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGGGCTTATAGGGAACAAGTTAAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36514588 TA 131 TA * * 36514590 GCAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAATAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * * 36514655 TTACAGTGAAACAGATCGAAGATTTCAACATGGCATCCCTATGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA * 36514720 TG 131 TA * * 36514722 GAAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCATGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * 36514787 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTACTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36514852 TA 131 TA * * * 36514854 ACAGATTTGGCATCCCTGTGCTTATAGGGGACAGATCGAAGATAACAGATCTGACATTCATGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * 36514919 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTACTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36514984 TA 131 TA * * * ** * 36514986 ACAGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGACGATAGTAGATCTAACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * * 36515051 TTACAGTGAAACAGATCGAAAATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTAAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515116 TA 131 TA * 36515118 GCAGATTTGGCATCCCTGTGCTTAT---G----G---G--G--AACAGATTTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * 36515169 TTACAGTGAAGTAGATCAAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515234 TA 131 TA * 36515236 ACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 36515301 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515366 TA 131 TA * * * * * * 36515368 ACAGATTTGACATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCTTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * * * * 36515433 TTACAGTGAAACAGATCGAAGATTTCAGTATGACATCCCTGTGCTTTTAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515498 TA 131 TA 36515500 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * 36515565 TTACAGTGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515630 TA 131 TA * 36515632 ACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC 36515697 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515762 TA 131 TA * 36515764 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATTGAAGATAACAGATCTGACATTCCTGTGC 1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC * 36515829 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAA 66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA 36515894 TA 131 TA * 36515896 ACAGATTTG 1 GCAGATTTG 36515905 ACCCCCTAAG Statistics Matches: 1607, Mismatches: 89, Indels: 30 0.93 0.05 0.02 Matches are distributed among these distances: 118 104 0.06 120 1 0.00 121 1 0.00 122 1 0.00 125 2 0.00 128 1 0.00 129 1 0.00 130 1 0.00 132 1493 0.93 133 2 0.00 ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27 Consensus pattern (132 bp): GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA TA Found at i:36515247 original size:44 final size:44 Alignment explanation

Indices: 36515147--36515904 Score: 632 Period size: 44 Copynumber: 17.2 Consensus size: 44 36515137 GCTTATGGGG * * * * * * 36515147 AACAGATTTGACATTCCTGTGCTTACAGTGAAGTAGATCAAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGAT ** * * 36515192 TTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAAT 1 AACAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT 36515235 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT * * * * * 36515279 AACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGAT ** * * 36515324 TTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAAT 1 AACAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT * * 36515367 AACAGATTTGACATCCCTGTGTTTATAGGGAACAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT * * ** * * * * 36515411 AGCAGATCTAACATTCTTGTGCTTACAGTGAAACAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAG-GGAACAGATCGAAGAT ** * * * * * 36515456 TTCAG-TATGACATCCCTGTGCTTTTAGGGAACA-AGTTGAAAAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT * 36515499 AGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT * * * * * * 36515543 AACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCAAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGAT ** * * 36515588 TTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAAT 1 AACAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT 36515631 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT * * * * * 36515675 AACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGAT ** * * 36515720 TTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAAT 1 AACAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT * * 36515763 AGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATTGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT * * * * * 36515807 AACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGAT 1 AACAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGAT ** * * * 36515852 TTCAGCA--TGGCATCCATGTGCTTATAGGGAACA-AGTTGAAAAT 1 AACAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGAT 36515895 AACAGATTTG 1 AACAGATTTG 36515905 ACCCCCTAAG Statistics Matches: 568, Mismatches: 113, Indels: 65 0.76 0.15 0.09 Matches are distributed among these distances: 42 11 0.02 43 66 0.12 44 402 0.71 45 84 0.15 46 5 0.01 ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27 Consensus pattern (44 bp): AACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGAT Found at i:36516007 original size:87 final size:87 Alignment explanation

Indices: 36515896--36516321 Score: 534 Period size: 87 Copynumber: 4.9 Consensus size: 87 36515886 GTTGAAAATA * ** ** 36515896 ACAGAT-TTGACCCCCTAAGCAGTAGGGAAACAGATTAAAAGCGACGGGCCTT-AACTCCCTAAG 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAAC-CCCTAAG * 36515959 TAGTAGGGTAACAGGTTAAATTT 65 CAGTAGGGTAACAGGTTAAATTT ** * * 36515982 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGACGGCGATGAACCTTAAACCCTTAAGC 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAACCCCTAAGC * * 36516047 AGTAGGGTAATAGGTTGAATTT 66 AGTAGGGTAACAGGTTAAATTT * * 36516069 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAGCCTT-AACTCCTTAAG 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAAC-CCCTAAG * * * 36516133 TAGTAGGGTAACAAGCTAAATTT 65 CAGTAGGGTAACAGGTTAAATTT * * * 36516156 ACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAACCTTAAACCCCTAAGC 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAACCCCTAAGC * * 36516221 AGTAGGGTAATAGGTTGAATTT 66 AGTAGGGTAACAGGTTAAATTT * * * * ** * * 36516243 ACAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGTGATGGGCTTTAAACCCCAAAGC 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAACCCCTAAGC * 36516308 AATAGGGTAACAGG 66 AGTAGGGTAACAGG 36516322 CTGAAAATTA Statistics Matches: 296, Mismatches: 40, Indels: 7 0.86 0.12 0.02 Matches are distributed among these distances: 86 9 0.03 87 281 0.95 88 6 0.02 ACGTcount: A:0.36, C:0.21, G:0.23, T:0.21 Consensus pattern (87 bp): ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAACCTTAAACCCCTAAGC AGTAGGGTAACAGGTTAAATTT Found at i:36516276 original size:43 final size:43 Alignment explanation

Indices: 36515896--36516273 Score: 228 Period size: 43 Copynumber: 8.7 Consensus size: 43 36515886 GTTGAAAATA * * * *** 36515896 ACAGAT-TTGACCCCCTAAGCAGTAGGGAAACAGATTAAAAGCG 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTT-GAATTT * ** * * * * 36515939 ACGGGCCTTAACTCCCTAAGTAGTAGGGTAACAGGTTAAATTT 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT * * ** 36515982 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCG-A-CG 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT * * * * * * 36516023 GCGATGAACCTTAAACCCTTAAGCAGTAGGGTAATAGGTTGAATTT 1 AC-A-G-ATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT * * *** 36516069 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCG 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTG-AATTT * * * * * * * * 36516113 AC-GAGCCTTAACTCCTTAAGTAGTAGGGTAACAAGCTAAATTT 1 ACAGA-TCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT * * * * 36516156 ACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAA--G 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT * * * * * 36516197 GCGATGAACCTTAAACCCCTAAGCAGTAGGGTAATAGGTTGAATTT 1 AC-A-G-ATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT 36516243 ACAGATCTTAACCCCCTAAGCAGTAGGGAAA 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAA 36516274 TAGATCGAAG Statistics Matches: 240, Mismatches: 81, Indels: 28 0.69 0.23 0.08 Matches are distributed among these distances: 41 2 0.01 42 3 0.01 43 118 0.49 44 112 0.47 45 3 0.01 46 2 0.01 ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21 Consensus pattern (43 bp): ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGGTTGAATTT Found at i:36516319 original size:174 final size:174 Alignment explanation

Indices: 36515896--36516282 Score: 668 Period size: 174 Copynumber: 2.2 Consensus size: 174 36515886 GTTGAAAATA * ** 36515896 ACAGAT-TTGACCCCCTAAGCAGTAGGGAAACAGATTAAAAGCGACGGGCCTTAACTCCCTAAGT 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGGGCCTTAACTCCCTAAGT * * * * 36515960 AGTAGGGTAACAGGTTAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGACGGC 66 AGTAGGGTAACAAGCTAAATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGC * 36516025 GATGAACCTTAAACCCTTAAGCAGTAGGGTAATAGGTTGAATTT 131 GATGAACCTTAAACCCCTAAGCAGTAGGGTAATAGGTTGAATTT * * 36516069 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGAGCCTTAACTCCTTAAGT 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGGGCCTTAACTCCCTAAGT 36516134 AGTAGGGTAACAAGCTAAATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGC 66 AGTAGGGTAACAAGCTAAATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGC 36516199 GATGAACCTTAAACCCCTAAGCAGTAGGGTAATAGGTTGAATTT 131 GATGAACCTTAAACCCCTAAGCAGTAGGGTAATAGGTTGAATTT * 36516243 ACAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAA 1 ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAA 36516283 GGTGATGGGC Statistics Matches: 202, Mismatches: 11, Indels: 1 0.94 0.05 0.00 Matches are distributed among these distances: 173 6 0.03 174 196 0.97 ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21 Consensus pattern (174 bp): ACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAAGCGACGGGCCTTAACTCCCTAAGT AGTAGGGTAACAAGCTAAATTTACAAATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGC GATGAACCTTAAACCCCTAAGCAGTAGGGTAATAGGTTGAATTT Found at i:36516524 original size:87 final size:85 Alignment explanation

Indices: 36516378--36516799 Score: 433 Period size: 79 Copynumber: 5.0 Consensus size: 85 36516368 CGAAGCCACA * ** 36516378 TGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGGCCTTAAACC 1 TGAATTTACA-ATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACC 36516443 CCTAAGCAGTAGGGTAACATGC 65 CCTAAGCAGTAGGGTAACA-GC * * * 36516465 TGAATTTACATATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGACGATAAGCCTTAAACC 1 TGAATTTACA-ATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACC * 36516530 CCTAAGCAGTAGAGTAACAG- 65 CCTAAGCAGTAGGGTAACAGC * * * * 36516550 -G---TTA-AAT-TTATAGACCCTAAACAGTAGGGAAACAGATCGAAGGTGACAAGCCTTAAACC 1 TGAATTTACAATCTTA-ACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACC * 36516609 CCTAAGCAGTAGAGTAACAG- 65 CCTAAGCAGTAGGGTAACAGC * * * * 36516629 -G---TTA-AAT-TTATAGACCCTAAACAGTAGGGAAACAGATCGAAGGTGACAAGCCTT-AACC 1 TGAATTTACAATCTTA-ACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACC ** 36516687 CCTAAATAGTAGGGTAACAGGC 65 CCTAAGCAGTAGGGTAACA-GC * * ** ** * 36516709 TAAATTAACAGATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAATACGATGGGCCTTAAATC 1 TGAATTTACA-ATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACC * 36516774 CCTAAGCAGTAGGGTACCAAGC 65 CCTAAGCAGTAGGGTAAC-AGC 36516796 TGAA 1 TGAA 36516800 AATTACAACT Statistics Matches: 292, Mismatches: 31, Indels: 24 0.84 0.09 0.07 Matches are distributed among these distances: 78 23 0.08 79 118 0.40 80 1 0.00 81 3 0.01 84 3 0.01 85 1 0.00 86 38 0.13 87 104 0.36 88 1 0.00 ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20 Consensus pattern (85 bp): TGAATTTACAATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAAGGCGATAAGCCTTAAACCC CTAAGCAGTAGGGTAACAGC Found at i:36516549 original size:44 final size:43 Alignment explanation

Indices: 36516391--36516541 Score: 153 Period size: 44 Copynumber: 3.5 Consensus size: 43 36516381 ATTTACAGAT * * * * 36516391 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGGC 1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGAT-AGC * * * ** * 36516435 CTTAAACCCCTAAGCAGTAGGGTAACATGCTGAATTTAC-ATA-T 1 CTTAAACCCCTAAGCAGTAGGGAAACA-GATCAA-AGACGATAGC * 36516478 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAGACGATAAGC 1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGAT-AGC 36516522 CTTAAACCCCTAAGCAGTAG 1 CTTAAACCCCTAAGCAGTAG 36516542 AGTAACAGGT Statistics Matches: 84, Mismatches: 18, Indels: 10 0.75 0.16 0.09 Matches are distributed among these distances: 41 2 0.02 42 6 0.07 43 26 0.31 44 44 0.52 45 5 0.06 46 1 0.01 ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19 Consensus pattern (43 bp): CTTAAACCCCTAAGCAGTAGGGAAACAGATCAAAGACGATAGC Found at i:36516575 original size:35 final size:35 Alignment explanation

Indices: 36516529--36516655 Score: 87 Period size: 35 Copynumber: 3.4 Consensus size: 35 36516519 AGCCTTAAAC * 36516529 CCCTAAGCAGTAGAGTAACAGGTTAAATTTATAGA 1 CCCTAAACAGTAGAGTAACAGGTTAAATTTATAGA ** * * 36516564 CCCTAAACAGTAGGGAAACAGATCGAAGGTGACAAGCCTTA-A-A 1 CCCTAAACAGTA--G-AGTA-A-C--AGGTTA-AA--TTTATAGA * 36516607 CCCCTAAGCAGTAGAGTAACAGGTTAAATTTATAGA 1 C-CCTAAACAGTAGAGTAACAGGTTAAATTTATAGA 36516643 CCCTAAACAGTAG 1 CCCTAAACAGTAG 36516656 GGAAACAGAT Statistics Matches: 68, Mismatches: 11, Indels: 26 0.65 0.10 0.25 Matches are distributed among these distances: 34 3 0.04 35 23 0.34 36 4 0.06 37 6 0.09 38 2 0.03 39 2 0.03 40 2 0.03 41 2 0.03 42 6 0.09 43 4 0.06 44 11 0.16 45 3 0.04 ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20 Consensus pattern (35 bp): CCCTAAACAGTAGAGTAACAGGTTAAATTTATAGA Found at i:36516691 original size:43 final size:44 Alignment explanation

Indices: 36516642--36516755 Score: 117 Period size: 43 Copynumber: 2.6 Consensus size: 44 36516632 AAATTTATAG * * 36516642 ACCCTAAACAGTAGGGAAACAGATCGAAGGTGACA-AGCCTTAAC 1 ACCCTAAACAGTAGGGAAACAGATCGAAAGTAACAGA-CCTTAAC * * * * * * 36516686 -CCCTAAATAGTAGGGTAACAG-GCTAAATTAACAGATCTTAAC 1 ACCCTAAACAGTAGGGAAACAGATCGAAAGTAACAGACCTTAAC * 36516728 ACCCTAAGCAGTAGGGAAACAGATCGAA 1 ACCCTAAACAGTAGGGAAACAGATCGAA 36516756 TACGATGGGC Statistics Matches: 54, Mismatches: 13, Indels: 6 0.74 0.18 0.08 Matches are distributed among these distances: 42 13 0.24 43 38 0.70 44 3 0.06 ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17 Consensus pattern (44 bp): ACCCTAAACAGTAGGGAAACAGATCGAAAGTAACAGACCTTAAC Found at i:36518905 original size:31 final size:31 Alignment explanation

Indices: 36518870--36518961 Score: 72 Period size: 31 Copynumber: 3.2 Consensus size: 31 36518860 AATAATTTAT 36518870 TTAAAGTAAAAAAATAATATTTTAAATTTTC 1 TTAAAGTAAAAAAATAATATTTTAAATTTTC **** * * 36518901 TTAAAAGTTCTCACAT-ATAATTT--A--TT- 1 TT-AAAGTAAAAAAATAATATTTTAAATTTTC 36518927 -TAAAGTAAAAAAATAATATTTTAAATTTTC 1 TTAAAGTAAAAAAATAATATTTTAAATTTTC 36518957 TTAAA 1 TTAAA 36518962 AGTTCTCACA Statistics Matches: 41, Mismatches: 12, Indels: 16 0.59 0.17 0.23 Matches are distributed among these distances: 24 8 0.20 25 7 0.17 27 3 0.07 29 3 0.07 31 12 0.29 32 8 0.20 ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42 Consensus pattern (31 bp): TTAAAGTAAAAAAATAATATTTTAAATTTTC Found at i:36518922 original size:56 final size:56 Alignment explanation

Indices: 36518861--36518973 Score: 226 Period size: 56 Copynumber: 2.0 Consensus size: 56 36518851 TTTGCTGAGA 36518861 ATAATTTATTTAAAGTAAAAAAATAATATTTTAAATTTTCTTAAAAGTTCTCACAT 1 ATAATTTATTTAAAGTAAAAAAATAATATTTTAAATTTTCTTAAAAGTTCTCACAT 36518917 ATAATTTATTTAAAGTAAAAAAATAATATTTTAAATTTTCTTAAAAGTTCTCACAT 1 ATAATTTATTTAAAGTAAAAAAATAATATTTTAAATTTTCTTAAAAGTTCTCACAT 36518973 A 1 A 36518974 CATAACACTC Statistics Matches: 57, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 56 57 1.00 ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42 Consensus pattern (56 bp): ATAATTTATTTAAAGTAAAAAAATAATATTTTAAATTTTCTTAAAAGTTCTCACAT Found at i:36519655 original size:13 final size:13 Alignment explanation

Indices: 36519639--36519670 Score: 55 Period size: 13 Copynumber: 2.5 Consensus size: 13 36519629 AAAATAAGTC 36519639 TAAAAAATTAAAA 1 TAAAAAATTAAAA * 36519652 TAAAAAATTAATA 1 TAAAAAATTAAAA 36519665 TAAAAA 1 TAAAAA 36519671 CTAAAACGAA Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 13 18 1.00 ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25 Consensus pattern (13 bp): TAAAAAATTAAAA Found at i:36527666 original size:12 final size:13 Alignment explanation

Indices: 36527651--36527683 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 36527641 TTAGATTAAA 36527651 ATTTAAAT-ATGT 1 ATTTAAATAATGT * 36527663 ATTTAAATAATTT 1 ATTTAAATAATGT 36527676 ATTTAAAT 1 ATTTAAAT 36527684 TTAAAATTAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 8 0.42 13 11 0.58 ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52 Consensus pattern (13 bp): ATTTAAATAATGT Found at i:36527725 original size:18 final size:20 Alignment explanation

Indices: 36527702--36527746 Score: 58 Period size: 18 Copynumber: 2.4 Consensus size: 20 36527692 AATTAAACAT 36527702 TTTATTAAAATA-TA-TTAA 1 TTTATTAAAATATTAGTTAA * 36527720 TTTATTCAAATATTAGTTAA 1 TTTATTAAAATATTAGTTAA * 36527740 TTAATTA 1 TTTATTA 36527747 TATAAAAAAT Statistics Matches: 22, Mismatches: 3, Indels: 2 0.81 0.11 0.07 Matches are distributed among these distances: 18 11 0.50 19 2 0.09 20 9 0.41 ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51 Consensus pattern (20 bp): TTTATTAAAATATTAGTTAA Found at i:36527819 original size:16 final size:16 Alignment explanation

Indices: 36527798--36527829 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 36527788 AAGCTAAAAG 36527798 TGTAAGAACTAAATTT 1 TGTAAGAACTAAATTT * 36527814 TGTAAGTACTAAATTT 1 TGTAAGAACTAAATTT 36527830 ATATTATAAA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41 Consensus pattern (16 bp): TGTAAGAACTAAATTT Found at i:36531287 original size:22 final size:22 Alignment explanation

Indices: 36531229--36531287 Score: 64 Period size: 22 Copynumber: 2.7 Consensus size: 22 36531219 CATTTCACTG * * 36531229 CTATTTTGTTGTTGTTTTGCTA 1 CTATTTTGTTGTTATATTGCTA * * * 36531251 CCATTTCGTTATTATATTGCTA 1 CTATTTTGTTGTTATATTGCTA * 36531273 CTATTTTGTCGTTAT 1 CTATTTTGTTGTTAT 36531288 TGTTTTATTG Statistics Matches: 28, Mismatches: 9, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 22 28 1.00 ACGTcount: A:0.15, C:0.14, G:0.14, T:0.58 Consensus pattern (22 bp): CTATTTTGTTGTTATATTGCTA Found at i:36532907 original size:17 final size:19 Alignment explanation

Indices: 36532885--36532925 Score: 54 Period size: 17 Copynumber: 2.4 Consensus size: 19 36532875 AGCTCGCAGT 36532885 TGAGCTCTCAA-G-CTTGG 1 TGAGCTCTCAAGGTCTTGG 36532902 TGAG--CTCAAGGTCTTGG 1 TGAGCTCTCAAGGTCTTGG 36532919 TGAGCTC 1 TGAGCTC 36532926 ATAGTTTTAT Statistics Matches: 20, Mismatches: 0, Indels: 6 0.77 0.00 0.23 Matches are distributed among these distances: 15 5 0.25 16 1 0.05 17 13 0.65 19 1 0.05 ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29 Consensus pattern (19 bp): TGAGCTCTCAAGGTCTTGG Found at i:36532972 original size:17 final size:16 Alignment explanation

Indices: 36532918--36532976 Score: 50 Period size: 17 Copynumber: 3.5 Consensus size: 16 36532908 CAAGGTCTTG 36532918 GTGAGCTCATAGTTTTA 1 GTGAGCTCATAG-TTTA * 36532935 -TAGAGCTCGTATA-TTTG 1 GT-GAGCTC--ATAGTTTA 36532952 GTGAGCTCATAGTTCTA 1 GTGAGCTCATAGTT-TA 36532969 GTGAGCTC 1 GTGAGCTC 36532977 GCAGTTCGCT Statistics Matches: 34, Mismatches: 2, Indels: 12 0.71 0.04 0.25 Matches are distributed among these distances: 15 3 0.09 16 3 0.09 17 24 0.71 18 1 0.03 19 3 0.09 ACGTcount: A:0.22, C:0.15, G:0.25, T:0.37 Consensus pattern (16 bp): GTGAGCTCATAGTTTA Found at i:36533919 original size:17 final size:17 Alignment explanation

Indices: 36533899--36533950 Score: 61 Period size: 17 Copynumber: 3.1 Consensus size: 17 36533889 ATTAACAAAT * 36533899 TAAAATAATTAT-GTTAA 1 TAAAATAATAATAG-TAA * 36533916 TAAAACAATAATAGTAA 1 TAAAATAATAATAGTAA * 36533933 TAAAATAATAATATTAA 1 TAAAATAATAATAGTAA 36533950 T 1 T 36533951 GATATACTAA Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 17 29 0.97 18 1 0.03 ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35 Consensus pattern (17 bp): TAAAATAATAATAGTAA Found at i:36535198 original size:19 final size:19 Alignment explanation

Indices: 36535170--36535209 Score: 55 Period size: 19 Copynumber: 2.1 Consensus size: 19 36535160 TATGTTATTA 36535170 TATTACTTT-AATAAAATAT 1 TATTACTTTAAATAAAA-AT * 36535189 TATTATTTTAAATAAAAAT 1 TATTACTTTAAATAAAAAT 36535208 TA 1 TA 36535210 AATAAAAAAT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 19 12 0.63 20 7 0.37 ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47 Consensus pattern (19 bp): TATTACTTTAAATAAAAAT Found at i:36535219 original size:12 final size:11 Alignment explanation

Indices: 36535196--36535233 Score: 51 Period size: 11 Copynumber: 3.5 Consensus size: 11 36535186 TATTATTATT 36535196 TTAAATAAAAA 1 TTAAATAAAAA 36535207 TTAAATAAAAA 1 TTAAATAAAAA * * 36535218 AT-AATTAAAA 1 TTAAATAAAAA 36535228 TTAAAT 1 TTAAAT 36535234 GTAATGACCC Statistics Matches: 23, Mismatches: 3, Indels: 2 0.82 0.11 0.07 Matches are distributed among these distances: 10 8 0.35 11 15 0.65 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (11 bp): TTAAATAAAAA Found at i:36535715 original size:27 final size:26 Alignment explanation

Indices: 36535683--36535759 Score: 66 Period size: 27 Copynumber: 2.8 Consensus size: 26 36535673 ATTTCTTAAA 36535683 TAATAAGTAAAAGATATTTATATATAT- 1 TAATAAGTAAAAGATA-TTATAT-TATG * 36535710 TAATAATTAATAATTGATATTATATTATG 1 TAATAAGTAA-AA--GATATTATATTATG * * 36535739 AAATAAGTAAATGATAATTAT 1 TAATAAGTAAAAGAT-ATTAT 36535760 TATTGGTACA Statistics Matches: 41, Mismatches: 4, Indels: 10 0.75 0.07 0.18 Matches are distributed among these distances: 26 3 0.07 27 14 0.34 28 6 0.15 29 14 0.34 30 4 0.10 ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42 Consensus pattern (26 bp): TAATAAGTAAAAGATATTATATTATG Found at i:36536015 original size:18 final size:18 Alignment explanation

Indices: 36535971--36536006 Score: 56 Period size: 18 Copynumber: 2.1 Consensus size: 18 36535961 AAAGAAAATG * 36535971 AAAGAAAGA-AGAACAAA 1 AAAGAAACAGAGAACAAA 36535988 AAAGAAACAGAGAACAAA 1 AAAGAAACAGAGAACAAA 36536006 A 1 A 36536007 CGGAAACAGG Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 8 0.47 18 9 0.53 ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00 Consensus pattern (18 bp): AAAGAAACAGAGAACAAA Found at i:36536980 original size:27 final size:27 Alignment explanation

Indices: 36536917--36537016 Score: 96 Period size: 27 Copynumber: 3.6 Consensus size: 27 36536907 TTTAATGCCT 36536917 TATTGGTGTGTTTGGGAGGATATGA-TA 1 TATTGGTGTGTTTGGGAGGATAT-ATTA ** * * 36536944 TACCGATGTGTTTGGGAGGCTATATTA 1 TATTGGTGTGTTTGGGAGGATATATTA * 36536971 TATTGGTGTGTTAGGGAGGATTTATATTA 1 TATTGGTGTGTTTGGGAGGA--TATATTA 36537000 T-TCTGGGTGTGTTTGGG 1 TAT-T-GGTGTGTTTGGG 36537017 TTGGATATTC Statistics Matches: 58, Mismatches: 10, Indels: 7 0.77 0.13 0.09 Matches are distributed among these distances: 26 1 0.02 27 36 0.62 28 1 0.02 29 9 0.16 30 11 0.19 ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42 Consensus pattern (27 bp): TATTGGTGTGTTTGGGAGGATATATTA Found at i:36538899 original size:69 final size:69 Alignment explanation

Indices: 36538788--36538925 Score: 249 Period size: 69 Copynumber: 2.0 Consensus size: 69 36538778 TTCCTCTAAC 36538788 TTTTCCAGATTCTTTATTTGATCACAAGTCACTTGATTCATTGTCCAATGGCACTAAAGATATGA 1 TTTTCCAGATTCTTTATTTGATCACAAGTCACTTGATTCATTGTCCAATGGCACTAAAGATATGA 36538853 ATTA 66 ATTA * * * 36538857 TTTTCTAGATTCTTTATTTGATCACAAGTCACTTGATTCATTGTCCAATTGCACTAAAGATATGG 1 TTTTCCAGATTCTTTATTTGATCACAAGTCACTTGATTCATTGTCCAATGGCACTAAAGATATGA 36538922 ATTA 66 ATTA 36538926 GTTAGAATCA Statistics Matches: 66, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 69 66 1.00 ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41 Consensus pattern (69 bp): TTTTCCAGATTCTTTATTTGATCACAAGTCACTTGATTCATTGTCCAATGGCACTAAAGATATGA ATTA Found at i:36542439 original size:43 final size:43 Alignment explanation

Indices: 36542377--36542666 Score: 282 Period size: 43 Copynumber: 6.8 Consensus size: 43 36542367 TTACATTACC * * 36542377 TTTAGCGGCGCTTTTCCCACAAACGCTGCTATAGAACATGACT 1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT * * * 36542420 TTTAGCGACGCTTTACCCACAAACACCGCTAAAGAACATGACT 1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT * * * * * * 36542463 TTTAGCGGTGCTTTCCCCATAAATGCCGCTAAAGAACATAACC 1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT * ** * * * * 36542506 TTTAACGATGC-TTTCTCTACAAATGCCGCTAGAGAACATGACC 1 TTTAGCGGCGCTTTTC-CCACAAACGCCGCTAAAGAACATGACT * * * 36542549 TTTAGCGGCGCTTTTCCCA-AAAAGCCGCTAAAAAACATAACT 1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT * * * 36542591 TTTAGCGGCGCTTTTCCCAAAAATGCTGCTAAAGAA-ATGACT 1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT ** * * 36542633 TTTAGCAACAG-TTTTCCCAAAAACGCTGCTAAAG 1 TTTAGCGGC-GCTTTTCCCACAAACGCCGCTAAAG 36542667 GTCATGAAAA Statistics Matches: 207, Mismatches: 36, Indels: 9 0.82 0.14 0.04 Matches are distributed among these distances: 42 74 0.36 43 129 0.62 44 4 0.02 ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26 Consensus pattern (43 bp): TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACT Found at i:36544148 original size:183 final size:183 Alignment explanation

Indices: 36543421--36544368 Score: 797 Period size: 183 Copynumber: 5.2 Consensus size: 183 36543411 TTCTAGCAAC * * * * * 36543421 TAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTT-AAA 1 TAAACACTTCAATTTGCAACACTTAAACAATTCAATTTACAACATTTAAACACATCAATTTGCAG ** * * * * * * * 36543485 CA-TTTAAACA-CTTCAATTTGCAGCACTTTA-ACATCTTAATTAACAAC-ATTTATACACCTCA 66 CACTTT-AACATC-TCAATTAACAACA-TTTATACACCTCAATT-ACAGCGA-TAAAACATCTCA * * * * * 36543546 A-TTACAGCGA-TAAAACATTTCAATTTCCAGCAAC-TAAACACTTCAATTTACAGCATT 126 ATTTCCAGCAACT-AAACACTTCAATTTGCAGC-ACTTAAACACTTCAATTTACAACATT * * * * * * * 36543603 TAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTTT-AACACTTCAATTTACA 1 TAAACACTTCAATTTGCAACACTTAAACAATTCAATTTACAACA-TTTAAACACATCAATTTGCA * * * * ** 36543667 GCA-TTTAAACA-CTTCAATTTACAACATTTAAACACTTCAATTTGCAGC-ACTTTAACA-CTTC 65 GCACTTT-AACATC-TCAATTAACAACATTTATACACCTCAA-TTACAGCGA-TAAAACATC-TC * ** * * * * * 36543728 AATTTACAGCATTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTGCAGCACTT 125 AATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACA-TT ** * * * ** * * * 36543788 T-AACA-TCTCAATTAACAATATTTATACACCTCAA-TTACAGCGA-TAAAACATC-TCAATTTC 1 TAAACACT-TCAATTTGCAACACTTAAACAATTCAATTTACAAC-ATTTAAACA-CATCAATTTG ** * * * * 36543848 CAGCAACTAATTAAACA-CTTCAATTTGCAACACTTA-ATCACTTCAACTTACAAC-ATTTAAAC 63 CAGC-ACT--TT-AACATC-TCAATTAACAACATTTATA-CACCTCAA-TTACAGCGA-TAAAAC * ** * ** * * * * 36543910 A-CTTTAATTTAAAACATTTGAACACTTCAATTTGCAACACTTTAACACTTCAATTTACAGCATT 120 ATC-TCAATTTCCAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATT * * 36543974 TAAACACTTCAATTTGCAGCGCTTAAACAATTCAATTTACAACATTTAAACACATCAATTTGCAG 1 TAAACACTTCAATTTGCAACACTTAAACAATTCAATTTACAACATTTAAACACATCAATTTGCAG * * 36544039 CACTTTAACATCTCAATTAACAATATTTATACACCTCAATTACAGCGATAAAACATCTTAATTTC 66 CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC * * 36544104 CAGCAACTAAACACTTCAATTTGCAGCGCTTAAACAATTCAATTTACAACATT 131 CAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATT * * 36544157 TAAACACTTCAATTTGCAACACTTTAACACTTCAATTTACAACATTTAAACACATCAATTTGCAG 1 TAAACACTTCAATTTGCAACACTTAAACAATTCAATTTACAACATTTAAACACATCAATTTGCAG * 36544222 CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTG 66 CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC * 36544287 CATCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATT 131 CAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATT * * * 36544340 TAAACACTTAAATTTACAACATTTAAACA 1 TAAACACTTCAATTTGCAACACTTAAACA 36544369 CTTAATAAAT Statistics Matches: 649, Mismatches: 90, Indels: 53 0.82 0.11 0.07 Matches are distributed among these distances: 182 58 0.09 183 329 0.51 184 101 0.16 185 9 0.01 186 4 0.01 187 124 0.19 188 24 0.04 ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32 Consensus pattern (183 bp): TAAACACTTCAATTTGCAACACTTAAACAATTCAATTTACAACATTTAAACACATCAATTTGCAG CACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTC CAGCAACTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATT Found at i:36544373 original size:23 final size:23 Alignment explanation

Indices: 36543421--36544371 Score: 807 Period size: 23 Copynumber: 41.4 Consensus size: 23 36543411 TTCTAGCAAC * * * 36543421 TAAACACTTCAATTTGCAGCACT 1 TAAACACTTCAATTTACAACATT 36543444 TAAACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT 36543467 TAAACACTTCAATTTA-AACATT 1 TAAACACTTCAATTTACAACATT * * 36543489 TAAACACTTCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * 36543513 T-AACATCTT-AATTAACAACATT 1 TAAACA-CTTCAATTTACAACATT * * * 36543535 TATACACCTCAA-TTACAGCGA-T 1 TAAACACTTCAATTTACAAC-ATT * * * * ** 36543557 AAAACATTTCAATTTCCAGCAAC 1 TAAACACTTCAATTTACAACATT * 36543580 TAAACACTTCAATTTACAGCATT 1 TAAACACTTCAATTTACAACATT 36543603 TAAACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * * 36543626 TAAACACTTCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * 36543650 T-AACACTTCAATTTACAGCATT 1 TAAACACTTCAATTTACAACATT 36543672 TAAACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * * 36543695 TAAACACTTCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * 36543719 T-AACACTTCAATTTACAGCATT 1 TAAACACTTCAATTTACAACATT 36543741 TAAACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * * 36543764 TAAACACTTCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * * 36543788 T-AACA-TCTCAATTAACAATATT 1 TAAACACT-TCAATTTACAACATT * * * 36543810 TATACACCTCAA-TTACAGCGA-T 1 TAAACACTTCAATTTACAAC-ATT * * 36543832 AAAACA-TCTCAATTTCCAGCAACTAAT 1 TAAACACT-TCAATTT--A-CAAC-ATT * * 36543859 TAAACACTTCAATTTGCAACACT 1 TAAACACTTCAATTTACAACATT * * 36543882 TAATCACTTCAACTTACAACATT 1 TAAACACTTCAATTTACAACATT * * 36543905 TAAACACTTTAATTTAAAACATT 1 TAAACACTTCAATTTACAACATT * * 36543928 TGAACACTTCAATTTGCAACACTT 1 TAAACACTTCAATTTACAACA-TT * 36543952 T-AACACTTCAATTTACAGCATT 1 TAAACACTTCAATTTACAACATT * * ** 36543974 TAAACACTTCAATTTGCAGCGCT 1 TAAACACTTCAATTTACAACATT * 36543997 TAAACAATTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * * * 36544020 TAAACACATCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * * 36544044 T-AACA-TCTCAATTAACAATATT 1 TAAACACT-TCAATTTACAACATT * * * 36544066 TATACACCTCAA-TTACAGCGA-T 1 TAAACACTTCAATTTACAAC-ATT * * * ** 36544088 AAAACATCTT-AATTTCCAGCAAC 1 TAAACA-CTTCAATTTACAACATT * * ** 36544111 TAAACACTTCAATTTGCAGCGCT 1 TAAACACTTCAATTTACAACATT * 36544134 TAAACAATTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * 36544157 TAAACACTTCAATTTGCAACACTT 1 TAAACACTTCAATTTACAACA-TT 36544181 T-AACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * * * 36544203 TAAACACATCAATTTGCAGCACTT 1 TAAACACTTCAATTTACAACA-TT * 36544227 T-AACA-TCTCAATTAACAACATT 1 TAAACACT-TCAATTTACAACATT * * * 36544249 TATACACCTCAA-TTACAGCGA-T 1 TAAACACTTCAATTTACAAC-ATT * * * ** 36544271 AAAACA-TCTCAATTTGCATCAAC 1 TAAACACT-TCAATTTACAACATT * * * 36544294 TAAACACTTCAATTTGCAGCACT 1 TAAACACTTCAATTTACAACATT 36544317 TAAACACTTCAATTTACAACATT 1 TAAACACTTCAATTTACAACATT * 36544340 TAAACACTTAAATTTACAACATT 1 TAAACACTTCAATTTACAACATT 36544363 TAAACACTT 1 TAAACACTT 36544372 AATAAATTAA Statistics Matches: 752, Mismatches: 130, Indels: 92 0.77 0.13 0.09 Matches are distributed among these distances: 22 106 0.14 23 595 0.79 24 32 0.04 25 1 0.00 26 4 0.01 27 13 0.02 28 1 0.00 ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32 Consensus pattern (23 bp): TAAACACTTCAATTTACAACATT Found at i:36545875 original size:6 final size:6 Alignment explanation

Indices: 36545840--36545874 Score: 54 Period size: 6 Copynumber: 6.0 Consensus size: 6 36545830 TGTAAGAAAT * 36545840 CAAAAA CAAAAA CAAAAA CAAAAG CAAAAA -AAAAA 1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA 36545875 AGCTTTAAAA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 5 5 0.19 6 22 0.81 ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00 Consensus pattern (6 bp): CAAAAA Found at i:36546122 original size:14 final size:14 Alignment explanation

Indices: 36546099--36546194 Score: 97 Period size: 14 Copynumber: 6.8 Consensus size: 14 36546089 GTTTTTATCA * 36546099 AAACCTTAAACACT 1 AAACCCTAAACACT 36546113 AAACCCTAAACACT 1 AAACCCTAAACACT * 36546127 AAACCCAAAAC-CT 1 AAACCCTAAACACT * 36546140 AAAACCTTAAACTA-T 1 -AAACCCTAAAC-ACT * * 36546155 AAATCCTAAACCCT 1 AAACCCTAAACACT * 36546169 AAACTCTAAACACT 1 AAACCCTAAACACT 36546183 AAAACCCTAAAC 1 -AAACCCTAAAC 36546195 TAAAAAATCA Statistics Matches: 66, Mismatches: 11, Indels: 9 0.77 0.13 0.10 Matches are distributed among these distances: 13 2 0.03 14 53 0.80 15 11 0.17 ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18 Consensus pattern (14 bp): AAACCCTAAACACT Found at i:36546194 original size:7 final size:7 Alignment explanation

Indices: 36546099--36546194 Score: 77 Period size: 7 Copynumber: 13.6 Consensus size: 7 36546089 GTTTTTATCA * 36546099 AAACCTT 1 AAACCCT * 36546106 AAACACT 1 AAACCCT 36546113 AAACCCT 1 AAACCCT * 36546120 AAACACT 1 AAACCCT 36546127 AAACCC- 1 AAACCCT * 36546133 AAAACCT 1 AAACCCT * 36546140 AAAACCTT 1 -AAACCCT ** 36546148 AAACTAT 1 AAACCCT * 36546155 AAATCCT 1 AAACCCT 36546162 AAACCCT 1 AAACCCT * 36546169 AAACTCT 1 AAACCCT * 36546176 AAACACT 1 AAACCCT 36546183 AAAACCCT 1 -AAACCCT 36546191 AAAC 1 AAAC 36546195 TAAAAAATCA Statistics Matches: 69, Mismatches: 17, Indels: 6 0.75 0.18 0.07 Matches are distributed among these distances: 6 5 0.07 7 53 0.77 8 11 0.16 ACGTcount: A:0.51, C:0.31, G:0.00, T:0.18 Consensus pattern (7 bp): AAACCCT Found at i:36547018 original size:41 final size:41 Alignment explanation

Indices: 36546967--36547062 Score: 111 Period size: 41 Copynumber: 2.3 Consensus size: 41 36546957 TGATTTTTTG * ** * * 36546967 CAAACACCGCTAATAATTGACCTTTTGAGGCATTTTTCTCA 1 CAAACGCCGCTAATAACAGACATTTTGAGACATTTTTCTCA * * * 36547008 CAAACGCCGCTAATACCAGACATTTTGCGACGTTTTTCTCA 1 CAAACGCCGCTAATAACAGACATTTTGAGACATTTTTCTCA * 36547049 CAAACGCCACTAAT 1 CAAACGCCGCTAAT 36547063 GCCAGACCTT Statistics Matches: 46, Mismatches: 9, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 41 46 1.00 ACGTcount: A:0.30, C:0.28, G:0.12, T:0.29 Consensus pattern (41 bp): CAAACGCCGCTAATAACAGACATTTTGAGACATTTTTCTCA Found at i:36547068 original size:41 final size:41 Alignment explanation

Indices: 36546999--36547103 Score: 133 Period size: 41 Copynumber: 2.6 Consensus size: 41 36546989 TTTTGAGGCA * * 36546999 TTTTTCTCACAAACGCCGCTAATACCAGACATTTTGC-GACG 1 TTTTTCTCACAAACGCCACTAATGCCAGACATTTTGCAG-CG * 36547040 TTTTTCTCACAAACGCCACTAATGCCAGACCTTTTGCAGCG 1 TTTTTCTCACAAACGCCACTAATGCCAGACATTTTGCAGCG * ** 36547081 -TTTTCTAATTAACGCCACTAATG 1 TTTTTCTCACAAACGCCACTAATG 36547104 TTTAACTTTT Statistics Matches: 57, Mismatches: 6, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 40 20 0.35 41 36 0.63 42 1 0.02 ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31 Consensus pattern (41 bp): TTTTTCTCACAAACGCCACTAATGCCAGACATTTTGCAGCG Found at i:36552156 original size:18 final size:18 Alignment explanation

Indices: 36552119--36552157 Score: 51 Period size: 18 Copynumber: 2.2 Consensus size: 18 36552109 TAATTAATCT * * 36552119 AATAACAAAATAGTAATA 1 AATAACAAAAAAGGAATA * 36552137 AATAACAAAAAAGGACTA 1 AATAACAAAAAAGGAATA 36552155 AAT 1 AAT 36552158 CAAACCTTAA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.67, C:0.08, G:0.08, T:0.18 Consensus pattern (18 bp): AATAACAAAAAAGGAATA Found at i:36556206 original size:5 final size:5 Alignment explanation

Indices: 36556198--36556223 Score: 52 Period size: 5 Copynumber: 5.2 Consensus size: 5 36556188 AACTTCACTT 36556198 TATTA TATTA TATTA TATTA TATTA T 1 TATTA TATTA TATTA TATTA TATTA T 36556224 CATGTAAAAA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 21 1.00 ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62 Consensus pattern (5 bp): TATTA Found at i:36557923 original size:26 final size:25 Alignment explanation

Indices: 36557887--36557937 Score: 75 Period size: 26 Copynumber: 2.0 Consensus size: 25 36557877 AGGATTTTGA * 36557887 ATATCTGAATCTAATTCTGTAATCTG 1 ATATCTGAATCTAAATCTGT-ATCTG * 36557913 ATATTTGAATCTAAATCTGTATCTG 1 ATATCTGAATCTAAATCTGTATCTG 36557938 TTACTGTCTG Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 25 5 0.22 26 18 0.78 ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43 Consensus pattern (25 bp): ATATCTGAATCTAAATCTGTATCTG Found at i:36558253 original size:17 final size:17 Alignment explanation

Indices: 36558227--36558259 Score: 50 Period size: 17 Copynumber: 1.9 Consensus size: 17 36558217 GCTTTGGTAA 36558227 AACATTTTAT-TAAAAC 1 AACATTTTATGTAAAAC 36558243 AACAGTTTTATGTAAAA 1 AACA-TTTTATGTAAAA 36558260 AATGGTTTTC Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 4 0.27 17 6 0.40 18 5 0.33 ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36 Consensus pattern (17 bp): AACATTTTATGTAAAAC Found at i:36569300 original size:17 final size:18 Alignment explanation

Indices: 36569278--36569312 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 36569268 AATCTAGGTG 36569278 TGTGGGCC-ACACGGGTA 1 TGTGGGCCTACACGGGTA 36569295 TGTGGGCCTACACGGGTA 1 TGTGGGCCTACACGGGTA 36569313 AGCCACACGG Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 17 8 0.47 18 9 0.53 ACGTcount: A:0.17, C:0.23, G:0.40, T:0.20 Consensus pattern (18 bp): TGTGGGCCTACACGGGTA Done.