Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_D11

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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33

Warning! 408745 characters in sequence are not A, C, G, or T


File 193 of 226

Found at i:58281231 original size:24 final size:24

Alignment explanation

Indices: 58281202--58281248 Score: 62 Period size: 24 Copynumber: 2.0 Consensus size: 24 58281192 TATATATACC 58281202 AATTCAATCA-ATA-TAAATTCAATA 1 AATTC-ATCACATATTAAA-TCAATA 58281226 AATTCATCACATATTAAATCAAT 1 AATTCATCACATATTAAATCAAT 58281249 CCATTTCAAT Statistics Matches: 21, Mismatches: 0, Indels: 4 0.84 0.00 0.16 Matches are distributed among these distances: 23 4 0.19 24 13 0.62 25 4 0.19 ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34 Consensus pattern (24 bp): AATTCATCACATATTAAATCAATA Found at i:58281935 original size:16 final size:15 Alignment explanation

Indices: 58281914--58281945 Score: 55 Period size: 16 Copynumber: 2.1 Consensus size: 15 58281904 ACTTTTCTCC 58281914 TTCTTTCTTCCTCTTT 1 TTCTTTCTTCCT-TTT 58281930 TTCTTTCTTCCTTTT 1 TTCTTTCTTCCTTTT 58281945 T 1 T 58281946 CCCCCTGTTT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 4 0.25 16 12 0.75 ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72 Consensus pattern (15 bp): TTCTTTCTTCCTTTT Found at i:58282068 original size:19 final size:20 Alignment explanation

Indices: 58282044--58282082 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 58282034 ATTAATAAGT 58282044 AATACATAT-TTTATTATTA 1 AATACATATATTTATTATTA 58282063 AATACATATATTTATTATTA 1 AATACATATATTTATTATTA 58282083 TTACACATGT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 19 9 0.47 20 10 0.53 ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51 Consensus pattern (20 bp): AATACATATATTTATTATTA Found at i:58282090 original size:21 final size:20 Alignment explanation

Indices: 58282047--58282097 Score: 59 Period size: 21 Copynumber: 2.5 Consensus size: 20 58282037 AATAAGTAAT * 58282047 ACATAT-TTTATTATTAAAT 1 ACATATATTTATTATTAAAC * 58282066 ACATATATTTATTATTATTAC 1 ACATATATTTATTATTA-AAC * 58282087 ACATGTATTTA 1 ACATATATTTA 58282098 CCAACACCAC Statistics Matches: 27, Mismatches: 3, Indels: 2 0.84 0.09 0.06 Matches are distributed among these distances: 19 6 0.22 20 10 0.37 21 11 0.41 ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51 Consensus pattern (20 bp): ACATATATTTATTATTAAAC Found at i:58282446 original size:21 final size:21 Alignment explanation

Indices: 58282406--58282446 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 58282396 TTTAACATCT * 58282406 AATTTTTTAAATTTATCTTTC 1 AATTTTTTAAATTTACCTTTC * * 58282427 AATTTTTTTAATTTGCCTTT 1 AATTTTTTAAATTTACCTTT 58282447 ATTTTTATAA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.24, C:0.10, G:0.02, T:0.63 Consensus pattern (21 bp): AATTTTTTAAATTTACCTTTC Found at i:58283114 original size:23 final size:22 Alignment explanation

Indices: 58283088--58283154 Score: 73 Period size: 23 Copynumber: 3.0 Consensus size: 22 58283078 TATGATTTTG * 58283088 ATTTATTTAATTTTATATTATT 1 ATTTATTTTATTTTATATTATT * 58283110 AATTT-TTTTATTTTCATAATATT 1 -ATTTATTTTATTTT-ATATTATT * * 58283133 ATTAATTTTATTGTATATTATT 1 ATTTATTTTATTTTATATTATT 58283155 TATAATTTTA Statistics Matches: 37, Mismatches: 5, Indels: 5 0.79 0.11 0.11 Matches are distributed among these distances: 22 18 0.49 23 19 0.51 ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66 Consensus pattern (22 bp): ATTTATTTTATTTTATATTATT Found at i:58283157 original size:23 final size:23 Alignment explanation

Indices: 58283092--58283165 Score: 73 Period size: 22 Copynumber: 3.3 Consensus size: 23 58283082 ATTTTGATTT * * 58283092 ATTTAATTTTATATTATTAATT- 1 ATTTTATTTTATATTATTTATTA * * 58283114 TTTTTATTTTCATAATA-TTATTA 1 ATTTTATTTT-ATATTATTTATTA * 58283137 ATTTTATTGTATATTATTTA-TA 1 ATTTTATTTTATATTATTTATTA 58283159 ATTTTAT 1 ATTTTAT 58283166 AAATTTTAAA Statistics Matches: 42, Mismatches: 7, Indels: 6 0.76 0.13 0.11 Matches are distributed among these distances: 22 26 0.62 23 16 0.38 ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65 Consensus pattern (23 bp): ATTTTATTTTATATTATTTATTA Found at i:58290897 original size:11 final size:11 Alignment explanation

Indices: 58290881--58290915 Score: 54 Period size: 11 Copynumber: 3.2 Consensus size: 11 58290871 CCCTTCCCCC 58290881 CTCCCTTCTCT 1 CTCCCTTCTCT 58290892 CTCCCTTCTCT 1 CTCCCTTCTCT 58290903 CTTCCC-TCTCT 1 C-TCCCTTCTCT 58290914 CT 1 CT 58290916 TCTTTTTTTT Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 10 1 0.04 11 18 0.78 12 4 0.17 ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46 Consensus pattern (11 bp): CTCCCTTCTCT Found at i:58291402 original size:3 final size:3 Alignment explanation

Indices: 58291394--58291418 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 58291384 TGTATTTCAA 58291394 TAT TAT TAT TAT TAT TAT TAT TAT T 1 TAT TAT TAT TAT TAT TAT TAT TAT T 58291419 GTACATTAGT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TAT Found at i:58291518 original size:123 final size:123 Alignment explanation

Indices: 58291381--58291622 Score: 314 Period size: 123 Copynumber: 2.0 Consensus size: 123 58291371 AATATTACAT * * * * 58291381 TTTTGTATTTCAATATTATTATTATTATTATTATTATTGTACATTAGTGTATA-TCTTCATGT-A 1 TTTTGTATTTCAATATTATTATT-TT-TTATTATCATT-AACATTACTATATATTCTT-AT-TAA * * * 58291444 TGTATATATA-ATGTAGTAATGTTTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGC 61 TGTATATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGC 58291504 TTTTGTATTTCAATATTATTATTTTTTATTATCATTAACATTACTATATATTCTTATTAGATGTA 1 TTTTGTATTTCAATATTATTATTTTTTATTATCATTAACATTACTATATATTCTTATTA-ATGTA * * 58291569 TATATACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA 65 TATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA 58291623 TTTACTTTTT Statistics Matches: 104, Mismatches: 9, Indels: 11 0.84 0.07 0.09 Matches are distributed among these distances: 119 1 0.01 120 13 0.12 121 25 0.24 122 15 0.14 123 40 0.38 124 10 0.10 ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57 Consensus pattern (123 bp): TTTTGTATTTCAATATTATTATTTTTTATTATCATTAACATTACTATATATTCTTATTAATGTAT ATATACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGC Found at i:58302127 original size:71 final size:69 Alignment explanation

Indices: 58302005--58302179 Score: 192 Period size: 71 Copynumber: 2.5 Consensus size: 69 58301995 CTTTCCAAGG * ** * 58302005 AAAATCAACTTATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT 1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTT-AGTTT * * 58302069 TTTTTT 64 ATGTTT ** * 58302075 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA 1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTA 58302140 TGTTT 65 TGTTT ** * * 58302145 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT 1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT 58302180 TTTAATTTTT Statistics Matches: 90, Mismatches: 13, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 68 31 0.34 70 8 0.09 71 49 0.54 72 2 0.02 ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34 Consensus pattern (69 bp): AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAGTTTAT GTTT Found at i:58302555 original size:76 final size:75 Alignment explanation

Indices: 58302196--58302535 Score: 429 Period size: 76 Copynumber: 4.5 Consensus size: 75 58302186 TTTTGTTTTC * * 58302196 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT 58302261 GTTGTTAAAAA 66 GTT-TTAAAAA * ** * 58302272 AAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT * 58302337 GTTTT---CA 66 GTTTTAAAAA * * * ** * * 58302344 AAATTCAAATTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT 58302409 GTTTTCAAAAAA 66 GTTTT--AAAAA * * 58302421 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT 58302485 TCTGTTTT-AAAA 63 TCTGTTTTAAAAA * * 58302497 AAGATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG 58302536 ATTACACACT Statistics Matches: 232, Mismatches: 23, Indels: 17 0.85 0.08 0.06 Matches are distributed among these distances: 72 64 0.28 75 2 0.01 76 103 0.44 77 35 0.15 79 28 0.12 ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32 Consensus pattern (75 bp): AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT GTTTTAAAAA Found at i:58303085 original size:73 final size:72 Alignment explanation

Indices: 58302842--58303174 Score: 384 Period size: 73 Copynumber: 4.5 Consensus size: 72 58302832 GTTTTTCAAA * * ** * * * * * 58302842 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTC 1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC * 58302907 TGTTTTC 66 TCTTTTC * * 58302914 ATTATTATGTCAACTCATATTGCGAGAAATGAGTTGAGTCCTCAAGACACATTGAGGTAATTTCA 1 A--A-AAT-TCAACTCATATTGCGAGAAATGAGTTGAG-CCTCAAGACACACTGAGGTAATTTCA 58302979 A-TT-TCTTTTC 61 ATTTCTCTTTTC ** * 58302989 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC 1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC 58303054 TACTTTTC 66 T-CTTTTC * * 58303062 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC 1 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC * * 58303127 TGTTGTC 66 TCTTTTC * 58303134 AAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA 1 --AAAATTCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA 58303175 GTTCACATGT Statistics Matches: 229, Mismatches: 21, Indels: 20 0.85 0.08 0.07 Matches are distributed among these distances: 70 25 0.11 71 31 0.14 72 8 0.03 73 73 0.32 74 35 0.15 75 8 0.03 76 28 0.12 77 21 0.09 ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32 Consensus pattern (72 bp): AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACTGAGGTAATTTCAATTTC TCTTTTC Found at i:58303145 original size:147 final size:149 Alignment explanation

Indices: 58302826--58303174 Score: 444 Period size: 147 Copynumber: 2.3 Consensus size: 149 58302816 AAGCCTTTTG * ** * * 58302826 ATTTCTGTTTTTCAAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACACCG 1 ATTTCTG--TTTC-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACCG * * * 58302891 AGGTATTTTCCATTTCTGTTTTCATTATTATGTCAACTCATATTGCGAGAAATGAGTTGAGTCCT 63 AGGTATTTTCAATTTCTCTTTTCA-TATAATGTCAACTCATATTGCGAGAAATGAGTTGAGTCCT * 58302956 CAAGACACATTGAGGTAATTTCA 127 CAAGACACACTGAGGTAATTTCA * *** 58302979 ATTTCT-TTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG 1 ATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACCGAGG * 58303041 TATTTTCAATTTCTACTTTTCA-A-AAT-TCAACTCATATTGCGAGAAATGAGTTGAG-CCTCAG 66 TATTTTCAATTTCT-CTTTTCATATAATGTCAACTCATATTGCGAGAAATGAGTTGAGTCCTCAA * 58303102 GACACGCTGAGGTAATTTCA 130 GACACACTGAGGTAATTTCA 58303122 ATTTCTGTTGTCAAAAAAATCAACTCATATTGCGA-AAAGTGAGTTGAGCCTCA 1 ATTTCTGTT-TCAAAAAAATCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA 58303175 GTTCACATGT Statistics Matches: 174, Mismatches: 16, Indels: 18 0.84 0.08 0.09 Matches are distributed among these distances: 143 29 0.17 144 31 0.18 145 4 0.02 146 4 0.02 147 90 0.52 148 6 0.03 150 4 0.02 153 6 0.03 ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33 Consensus pattern (149 bp): ATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACCGAGG TATTTTCAATTTCTCTTTTCATATAATGTCAACTCATATTGCGAGAAATGAGTTGAGTCCTCAAG ACACACTGAGGTAATTTCA Found at i:58304305 original size:10 final size:9 Alignment explanation

Indices: 58304278--58304320 Score: 50 Period size: 10 Copynumber: 4.4 Consensus size: 9 58304268 TACATATATT * 58304278 AAAACATAA 1 AAAAAATAA 58304287 AAGAAAATACA 1 AA-AAAATA-A 58304298 AAAAAATAA 1 AAAAAATAA 58304307 AAAAAATATA 1 AAAAAATA-A 58304317 AAAA 1 AAAA 58304321 TATAGCGCCG Statistics Matches: 30, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 9 11 0.37 10 16 0.53 11 3 0.10 ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12 Consensus pattern (9 bp): AAAAAATAA Found at i:58304312 original size:19 final size:20 Alignment explanation

Indices: 58304278--58304320 Score: 61 Period size: 19 Copynumber: 2.2 Consensus size: 20 58304268 TACATATATT * 58304278 AAAACATAAAAGAAAATACA 1 AAAAAATAAAAGAAAATACA * 58304298 AAAAAATAAAA-AAAATATA 1 AAAAAATAAAAGAAAATACA 58304317 AAAA 1 AAAA 58304321 TATAGCGCCG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 11 0.52 20 10 0.48 ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12 Consensus pattern (20 bp): AAAAAATAAAAGAAAATACA Found at i:58304409 original size:11 final size:11 Alignment explanation

Indices: 58304393--58304427 Score: 61 Period size: 11 Copynumber: 3.2 Consensus size: 11 58304383 CCCTTCCCCC 58304393 CTCCCTTCTCT 1 CTCCCTTCTCT 58304404 CTCCCTTCTCT 1 CTCCCTTCTCT * 58304415 CTTCCTTCTCT 1 CTCCCTTCTCT 58304426 CT 1 CT 58304428 TCTTTTTTTT Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 23 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (11 bp): CTCCCTTCTCT Found at i:58305446 original size:11 final size:11 Alignment explanation

Indices: 58305430--58305456 Score: 54 Period size: 11 Copynumber: 2.5 Consensus size: 11 58305420 GTACGTATTG 58305430 TATATGTTCTA 1 TATATGTTCTA 58305441 TATATGTTCTA 1 TATATGTTCTA 58305452 TATAT 1 TATAT 58305457 TTTTAATATT Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 16 1.00 ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56 Consensus pattern (11 bp): TATATGTTCTA Found at i:58307204 original size:47 final size:47 Alignment explanation

Indices: 58307141--58307486 Score: 455 Period size: 47 Copynumber: 7.3 Consensus size: 47 58307131 CCCTTCGGGA * * * * 58307141 CTTATCACATTTATACACT-TCCACATCCGTCACATTGGCCATTCGGC 1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC 58307188 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC * * 58307235 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC 1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC * * * 58307282 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGAC 1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC * * * 58307329 CTTATCACACATACACATGTTCACATTCATCACATTGGCCATTCGAC 1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC * * * * 58307376 CTTATCACACATACACATGTTCACCTTTATCACATTGGCCATTCGGC 1 CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC * * 58307423 CTTATCACGCATATATATACT-TTCACATTCATCACATTGGCCACTCGGC 1 CTTATCA--CATATATACA-TGTTCACATTCATCACATTGGCCATTCGGC * 58307472 CCTATCACATATATA 1 CTTATCACATATATA 58307487 TACTTGTACA Statistics Matches: 274, Mismatches: 21, Indels: 8 0.90 0.07 0.03 Matches are distributed among these distances: 46 1 0.00 47 234 0.85 49 38 0.14 50 1 0.00 ACGTcount: A:0.27, C:0.31, G:0.10, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGC Found at i:58311565 original size:30 final size:32 Alignment explanation

Indices: 58311497--58311565 Score: 79 Period size: 32 Copynumber: 2.2 Consensus size: 32 58311487 TATATATTGT * * 58311497 AATATTATAATATTATATCTTAATTATTAAGTA 1 AATA-TATAATATTATATATTAATTAATAAGTA * * 58311530 TATATATTATATTATATATT-A-TAATAAGTA 1 AATATATAATATTATATATTAATTAATAAGTA 58311560 AATATA 1 AATATA 58311566 ATAAAAGAAA Statistics Matches: 31, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 30 13 0.42 31 1 0.03 32 14 0.45 33 3 0.10 ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48 Consensus pattern (32 bp): AATATATAATATTATATATTAATTAATAAGTA Found at i:58311632 original size:11 final size:11 Alignment explanation

Indices: 58311569--58311642 Score: 53 Period size: 11 Copynumber: 6.7 Consensus size: 11 58311559 AAATATAATA 58311569 AAAG-AAAAAG 1 AAAGAAAAAAG * 58311579 AAATAGAAAAAG 1 AAAGA-AAAAAG * * 58311591 AAAGAAAGAAC 1 AAAGAAAAAAG * 58311602 AAATG-AAATAG 1 AAA-GAAAAAAG * * 58311613 AAGGGAAAAAG 1 AAAGAAAAAAG * 58311624 AAAGAAAAAGG 1 AAAGAAAAAAG 58311635 AAAGAAAA 1 AAAGAAAA 58311643 GGAGAAAGAC Statistics Matches: 48, Mismatches: 12, Indels: 7 0.72 0.18 0.10 Matches are distributed among these distances: 10 4 0.08 11 33 0.69 12 11 0.23 ACGTcount: A:0.73, C:0.01, G:0.22, T:0.04 Consensus pattern (11 bp): AAAGAAAAAAG Found at i:58311649 original size:29 final size:29 Alignment explanation

Indices: 58311591--58311649 Score: 75 Period size: 29 Copynumber: 2.0 Consensus size: 29 58311581 ATAGAAAAAG * * * 58311591 AAAGAAAGAACAAATGAAATAGAAGGGAA 1 AAAGAAAGAACAAAGGAAAGAAAAGGGAA 58311620 AAAGAAAGAA-AAAGGAAAGAAAAGGAGAA 1 AAAGAAAGAACAAAGGAAAGAAAAGG-GAA 58311649 A 1 A 58311650 GACCAAAGCT Statistics Matches: 26, Mismatches: 3, Indels: 2 0.84 0.10 0.06 Matches are distributed among these distances: 28 12 0.46 29 14 0.54 ACGTcount: A:0.69, C:0.02, G:0.25, T:0.03 Consensus pattern (29 bp): AAAGAAAGAACAAAGGAAAGAAAAGGGAA Found at i:58312596 original size:40 final size:39 Alignment explanation

Indices: 58312473--58312613 Score: 110 Period size: 40 Copynumber: 3.6 Consensus size: 39 58312463 CAACTTCGAG * * * 58312473 TCGATGAGACACT-GGATGTCAACTTACTACTTCGTATTAA 1 TCGATGAGACACTAGG-TGTCAAATTATTACTTCGAATT-A * * * * 58312513 TTCGATGAGGCACTATGTGT-GAA-T-TTACTTCGATTTA 1 -TCGATGAGACACTAGGTGTCAAATTATTACTTCGAATTA * * 58312550 GTCGATGAGACACTGGGTGTCAAATTATTACTTTGAATTA 1 -TCGATGAGACACTAGGTGTCAAATTATTACTTCGAATTA * * 58312590 TCCGATGAGGCACTAGGTGCCAAA 1 T-CGATGAGACACTAGGTGTCAAA 58312614 CTAGTGTGTT Statistics Matches: 78, Mismatches: 17, Indels: 11 0.74 0.16 0.10 Matches are distributed among these distances: 37 17 0.22 38 11 0.14 39 3 0.04 40 31 0.40 41 15 0.19 42 1 0.01 ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33 Consensus pattern (39 bp): TCGATGAGACACTAGGTGTCAAATTATTACTTCGAATTA Found at i:58316133 original size:13 final size:15 Alignment explanation

Indices: 58316105--58316148 Score: 51 Period size: 14 Copynumber: 3.1 Consensus size: 15 58316095 AAAATATGTT 58316105 TATGAAAAAATAAAA 1 TATGAAAAAATAAAA 58316120 TATG-AAAAAT-AAA 1 TATGAAAAAATAAAA 58316133 TA--AAAAAATGAAAA 1 TATGAAAAAAT-AAAA 58316147 TA 1 TA 58316149 ATAAATTTAC Statistics Matches: 26, Mismatches: 0, Indels: 7 0.79 0.00 0.21 Matches are distributed among these distances: 12 6 0.23 13 5 0.19 14 11 0.42 15 4 0.15 ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20 Consensus pattern (15 bp): TATGAAAAAATAAAA Found at i:58316426 original size:157 final size:156 Alignment explanation

Indices: 58316125--58316534 Score: 587 Period size: 157 Copynumber: 2.6 Consensus size: 156 58316115 TAAAATATGA * * ** * * 58316125 AAAAT-AAATAAAAAAATGAAAATAATAAATTTACTGAAAGTAATAAAATCCGAAAAAAAGAAAA 1 AAAATAAAATAAAAAAACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAA 58316189 ATACGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATAAT 66 ATACGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATAAT * 58316254 ATATTTCAAACATTATGTACTAAAAT 131 ACATTTCAAACATTATGTACTAAAAT * 58316280 AATATAAAATAATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAA 1 AAAATAAAATAA-AAAA-ACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAA * 58316345 AAATACGAACAAA-GGCAAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATA 64 AAATACGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATA 58316409 ATACATTTCGAAA-ATTATGTACTAAAAT 129 ATACATTTC-AAACATTATGTACTAAAAT * * * 58316437 AAAATAAAATAAATAGACAC-AAAGATAGTATATATTTTGAAAGTAATAAAATCCT-AAAATAAG 1 AAAATAAAATAAA-A-AAACGAAA-ATAATATATTTTTTGAAAGTAATAAAAT-CTGAAAATAAG * * * 58316500 AGAAATACGAACAAATGGCCAAAATGAGGGTTTTT 62 AAAAATACGAACAAAGGGCCAAAATAAGGGTTTTT 58316535 ACATAAAGTT Statistics Matches: 230, Mismatches: 16, Indels: 15 0.88 0.06 0.06 Matches are distributed among these distances: 155 4 0.02 156 10 0.04 157 139 0.60 158 77 0.33 ACGTcount: A:0.56, C:0.09, G:0.10, T:0.26 Consensus pattern (156 bp): AAAATAAAATAAAAAAACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAA ATACGAACAAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACACACTAAAATAAT ACATTTCAAACATTATGTACTAAAAT Found at i:58316635 original size:16 final size:16 Alignment explanation

Indices: 58316614--58316647 Score: 50 Period size: 16 Copynumber: 2.1 Consensus size: 16 58316604 ATTTGTTCGT * * 58316614 AATTTTCTTATTTTCA 1 AATTTTATTACTTTCA 58316630 AATTTTATTACTTTCA 1 AATTTTATTACTTTCA 58316646 AA 1 AA 58316648 AAATATACTA Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56 Consensus pattern (16 bp): AATTTTATTACTTTCA Found at i:58319734 original size:43 final size:44 Alignment explanation

Indices: 58319670--58319760 Score: 166 Period size: 43 Copynumber: 2.1 Consensus size: 44 58319660 CATTACCCAA 58319670 ACACATAAAAAAAAATCTACTAACTAAGATTGGTTTTATCAAAC 1 ACACATAAAAAAAAATCTACTAACTAAGATTGGTTTTATCAAAC * 58319714 ACACAT-AAAAAAAATCTACTAACTATGATTGGTTTTATCAAAC 1 ACACATAAAAAAAAATCTACTAACTAAGATTGGTTTTATCAAAC 58319757 ACAC 1 ACAC 58319761 GTAACATAAC Statistics Matches: 46, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 43 40 0.87 44 6 0.13 ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27 Consensus pattern (44 bp): ACACATAAAAAAAAATCTACTAACTAAGATTGGTTTTATCAAAC Found at i:58323244 original size:73 final size:74 Alignment explanation

Indices: 58323157--58323329 Score: 214 Period size: 73 Copynumber: 2.4 Consensus size: 74 58323147 TTTGGAAGAT * 58323157 GTAAAAGTTTTGGGGAGAAAGTAAAAGGAATAAAA-TTTGGGGGG-TTGGGAGGAAGTAAAATTC 1 GTAAAAGTTTTGGGGAGAAAGTAAAAGGAA-AAAAGTTTGGGGGGTTTGGGAGGAAATAAAATT- 58323220 TCTAGGGG-AA 64 TCTAGGGGAAA * * 58323230 GTAAAAGTTTTGGGGAGAAAATAAAA--AAAAAAGTTTTGGGGGGTTTGGGGGGAAATAAAATTT 1 GTAAAAGTTTTGGGGAGAAAGTAAAAGGAAAAAAG-TTTGGGGGGTTTGGGAGGAAATAAAATTT * * 58323293 TTTGGGGAAA 65 CTAGGGGAAA * * 58323303 GTAAAATTTTTAGGG-GAAAGTAAAAGG 1 GTAAAAGTTTTGGGGAGAAAGTAAAAGG 58323330 GTTTAAAGAG Statistics Matches: 86, Mismatches: 8, Indels: 11 0.82 0.08 0.10 Matches are distributed among these distances: 70 4 0.05 71 2 0.02 72 24 0.28 73 56 0.65 ACGTcount: A:0.40, C:0.01, G:0.34, T:0.25 Consensus pattern (74 bp): GTAAAAGTTTTGGGGAGAAAGTAAAAGGAAAAAAGTTTGGGGGGTTTGGGAGGAAATAAAATTTC TAGGGGAAA Found at i:58323307 original size:19 final size:19 Alignment explanation

Indices: 58323278--58323327 Score: 84 Period size: 19 Copynumber: 2.7 Consensus size: 19 58323268 GGGGGTTTGG * 58323278 GGGGAAA-TAAAATTTTTT 1 GGGGAAAGTAAAATTTTTA 58323296 GGGGAAAGTAAAATTTTTA 1 GGGGAAAGTAAAATTTTTA 58323315 GGGGAAAGTAAAA 1 GGGGAAAGTAAAA 58323328 GGGTTTAAAG Statistics Matches: 30, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 18 7 0.23 19 23 0.77 ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28 Consensus pattern (19 bp): GGGGAAAGTAAAATTTTTA Found at i:58327017 original size:20 final size:20 Alignment explanation

Indices: 58326994--58327061 Score: 75 Period size: 20 Copynumber: 3.4 Consensus size: 20 58326984 CATGGTATCA * * 58326994 ATACTTTGAGGAAGGTATTG 1 ATACTTTGAGGAAAGTATAG 58327014 ATACTTTG-GGTAAAGTATAG 1 ATACTTTGAGG-AAAGTATAG * * * 58327034 ATACTCTGAGTAAAGTATCG 1 ATACTTTGAGGAAAGTATAG 58327054 ATACTTTG 1 ATACTTTG 58327062 TTAAGGGTAT Statistics Matches: 40, Mismatches: 6, Indels: 4 0.80 0.12 0.08 Matches are distributed among these distances: 19 2 0.05 20 37 0.93 21 1 0.03 ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35 Consensus pattern (20 bp): ATACTTTGAGGAAAGTATAG Found at i:58327078 original size:40 final size:40 Alignment explanation

Indices: 58326987--58327078 Score: 98 Period size: 40 Copynumber: 2.3 Consensus size: 40 58326977 GGTGGGACAT * * * 58326987 GGTATCAATACTTTGAGGAAGGTATTGATACTTTGGGTAA 1 GGTATCAATACTCTGAGGAAAGTATCGATACTTTGGGTAA * * * 58327027 AGTAT-AGATACTCTGAGTAAAGTATCGATACTTT-GTTAA 1 GGTATCA-ATACTCTGAGGAAAGTATCGATACTTTGGGTAA 58327066 GGGTATCAATACT 1 -GGTATCAATACT 58327079 TTTTTATTTT Statistics Matches: 42, Mismatches: 7, Indels: 6 0.76 0.13 0.11 Matches are distributed among these distances: 39 5 0.12 40 36 0.86 41 1 0.02 ACGTcount: A:0.33, C:0.10, G:0.23, T:0.35 Consensus pattern (40 bp): GGTATCAATACTCTGAGGAAAGTATCGATACTTTGGGTAA Found at i:58328316 original size:20 final size:21 Alignment explanation

Indices: 58328291--58328332 Score: 68 Period size: 21 Copynumber: 2.0 Consensus size: 21 58328281 CCTCACGTTC 58328291 CATTTTT-CTTTTCTTTCTTT 1 CATTTTTCCTTTTCTTTCTTT * 58328311 CATTTTTCCTTTTGTTTCTTT 1 CATTTTTCCTTTTCTTTCTTT 58328332 C 1 C 58328333 TCTTTCTTCA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 20 7 0.35 21 13 0.65 ACGTcount: A:0.05, C:0.21, G:0.02, T:0.71 Consensus pattern (21 bp): CATTTTTCCTTTTCTTTCTTT Found at i:58332577 original size:18 final size:17 Alignment explanation

Indices: 58332551--58332586 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 58332541 TTTGGTTATA 58332551 TTTAATTTTCGATATGTT 1 TTTAATTTT-GATATGTT * 58332569 TTTATTTTTGATATGTT 1 TTTAATTTTGATATGTT 58332586 T 1 T 58332587 CATTTAAAAC Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 17 9 0.53 18 8 0.47 ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67 Consensus pattern (17 bp): TTTAATTTTGATATGTT Found at i:58336641 original size:21 final size:21 Alignment explanation

Indices: 58336600--58336642 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 21 58336590 AATAAAGTAG * 58336600 ATTATATATTATTTTTATAGT 1 ATTATATATTATATTTATAGT 58336621 ATTATATATTATGATTT-TAGT 1 ATTATATATTAT-ATTTATAGT 58336642 A 1 A 58336643 AATTTATATA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 21 17 0.85 22 3 0.15 ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58 Consensus pattern (21 bp): ATTATATATTATATTTATAGT Found at i:58338172 original size:20 final size:21 Alignment explanation

Indices: 58338149--58338192 Score: 65 Period size: 20 Copynumber: 2.2 Consensus size: 21 58338139 TATTATTATA * 58338149 TTTAAAATTTT-AAAATGTTT 1 TTTAAAATTTTAAAAATATTT 58338169 TTT-AAATTTTAAAAATATTT 1 TTTAAAATTTTAAAAATATTT 58338189 TTTA 1 TTTA 58338193 TTAATTACGT Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 19 7 0.33 20 14 0.67 ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57 Consensus pattern (21 bp): TTTAAAATTTTAAAAATATTT Found at i:58339718 original size:20 final size:19 Alignment explanation

Indices: 58339682--58339720 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 58339672 AAAATATTTT * 58339682 TATTTTTTTATTTTTAAAA 1 TATTTTTGTATTTTTAAAA * 58339701 TATTTTTGTGTTTATTAAAA 1 TATTTTTGTATTT-TTAAAA 58339721 ATCGGGCTGG Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 19 11 0.65 20 6 0.35 ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64 Consensus pattern (19 bp): TATTTTTGTATTTTTAAAA Found at i:58350881 original size:16 final size:17 Alignment explanation

Indices: 58350852--58350884 Score: 59 Period size: 16 Copynumber: 2.0 Consensus size: 17 58350842 CCAAATACAA 58350852 AAAATAACTATTAAAAT 1 AAAATAACTATTAAAAT 58350869 AAAATAA-TATTAAAAT 1 AAAATAACTATTAAAAT 58350885 CTAAAAGTCT Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 9 0.56 17 7 0.44 ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30 Consensus pattern (17 bp): AAAATAACTATTAAAAT Found at i:58351466 original size:23 final size:23 Alignment explanation

Indices: 58351439--58351484 Score: 67 Period size: 23 Copynumber: 2.0 Consensus size: 23 58351429 AACAAATACC 58351439 CATATTTATATAAT-TAAAACATT 1 CATATTT-TATAATATAAAACATT * 58351462 CATATTTTATACTATAAAACATT 1 CATATTTTATAATATAAAACATT 58351485 TATTATTAAA Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 22 5 0.24 23 16 0.76 ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43 Consensus pattern (23 bp): CATATTTTATAATATAAAACATT Found at i:58351541 original size:24 final size:22 Alignment explanation

Indices: 58351484--58351543 Score: 72 Period size: 20 Copynumber: 2.8 Consensus size: 22 58351474 TATAAAACAT 58351484 TTATTAT-TAAATATTTATAAA 1 TTATTATATAAATATTTATAAA * 58351505 TT-TTA-ATATATATTTATTAAA 1 TTATTATATAAATATTTA-TAAA 58351526 TTATTGATATAAATATTT 1 TTATT-ATATAAATATTT 58351544 TTCAATAATA Statistics Matches: 32, Mismatches: 2, Indels: 7 0.78 0.05 0.17 Matches are distributed among these distances: 20 12 0.38 21 8 0.25 22 2 0.06 23 1 0.03 24 9 0.28 ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55 Consensus pattern (22 bp): TTATTATATAAATATTTATAAA Found at i:58352565 original size:16 final size:15 Alignment explanation

Indices: 58352539--58352597 Score: 73 Period size: 16 Copynumber: 3.7 Consensus size: 15 58352529 AGAAAGTAAA * 58352539 AGAGCTGTAATGAAAT 1 AGAGTTGTAATG-AAT * 58352555 AGGGTTGTAATTGAAT 1 AGAGTTGTAA-TGAAT 58352571 AGAGTTGTAATGGAAT 1 AGAGTTGTAAT-GAAT 58352587 AGAGTTGTAAT 1 AGAGTTGTAAT 58352598 CAGTAATTCA Statistics Matches: 38, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 15 1 0.03 16 35 0.92 17 2 0.05 ACGTcount: A:0.37, C:0.02, G:0.29, T:0.32 Consensus pattern (15 bp): AGAGTTGTAATGAAT Found at i:58354891 original size:52 final size:51 Alignment explanation

Indices: 58354813--58354933 Score: 172 Period size: 52 Copynumber: 2.4 Consensus size: 51 58354803 GTAATGGGCC * * 58354813 TAAATTACTGAAATACCCTCGATGGGTAAATTACCAAAATACCCTCGAT-GG 1 TAAATTACTGAAATACCCTCAATGGGTAAATTACCAAAATACCC-CCATAGG * * * 58354864 TTAAATTACTCAAATACCCTCAATGGGTAAATTATCGAAATACCCCCATAGG 1 -TAAATTACTGAAATACCCTCAATGGGTAAATTACCAAAATACCCCCATAGG 58354916 TAAATTACTGAAATACCC 1 TAAATTACTGAAATACCC 58354934 CGTAGGAAAA Statistics Matches: 62, Mismatches: 6, Indels: 3 0.87 0.08 0.04 Matches are distributed among these distances: 51 20 0.32 52 42 0.68 ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26 Consensus pattern (51 bp): TAAATTACTGAAATACCCTCAATGGGTAAATTACCAAAATACCCCCATAGG Found at i:58354934 original size:25 final size:26 Alignment explanation

Indices: 58354813--58354933 Score: 156 Period size: 26 Copynumber: 4.7 Consensus size: 26 58354803 GTAATGGGCC 58354813 TAAATTACTGAAATACCCTCGATGGG 1 TAAATTACTGAAATACCCTCGATGGG ** * 58354839 TAAATTACCAAAATACCCTCGATGGT 1 TAAATTACTGAAATACCCTCGATGGG * * 58354865 TAAATTACTCAAATACCCTCAATGGG 1 TAAATTACTGAAATACCCTCGATGGG * * 58354891 TAAATTA-TCGAAATACCC-CCATAGG 1 TAAATTACT-GAAATACCCTCGATGGG 58354916 TAAATTACTGAAATACCC 1 TAAATTACTGAAATACCC 58354934 CGTAGGAAAA Statistics Matches: 83, Mismatches: 10, Indels: 5 0.85 0.10 0.05 Matches are distributed among these distances: 25 22 0.27 26 61 0.73 ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26 Consensus pattern (26 bp): TAAATTACTGAAATACCCTCGATGGG Found at i:58355366 original size:28 final size:28 Alignment explanation

Indices: 58355311--58355368 Score: 71 Period size: 28 Copynumber: 2.1 Consensus size: 28 58355301 GATACTGTAA * 58355311 TGGGCTTAAGCCCACACTATTATTATAT 1 TGGGCTTAAGCCCACACTATTATGATAT * * * * 58355339 TGGGCTTAGGCCCGCACTGTTCTGATAT 1 TGGGCTTAAGCCCACACTATTATGATAT 58355367 TG 1 TG 58355369 TATTGGGCTA Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 28 25 1.00 ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34 Consensus pattern (28 bp): TGGGCTTAAGCCCACACTATTATGATAT Found at i:58355709 original size:23 final size:24 Alignment explanation

Indices: 58355682--58355727 Score: 69 Period size: 23 Copynumber: 2.0 Consensus size: 24 58355672 TACAAATAAG 58355682 TTTTCACA-ACAAACAC-TATTTTT 1 TTTTCA-AGACAAACACGTATTTTT 58355705 TTTTCAAGACAAACACGTATTTT 1 TTTTCAAGACAAACACGTATTTT 58355728 CAATTTCAAA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 22 1 0.05 23 14 0.67 24 6 0.29 ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41 Consensus pattern (24 bp): TTTTCAAGACAAACACGTATTTTT Found at i:58358994 original size:22 final size:21 Alignment explanation

Indices: 58358944--58358994 Score: 52 Period size: 22 Copynumber: 2.4 Consensus size: 21 58358934 CAAACATTAT 58358944 AAAAA-TAAAATAAGATAACA 1 AAAAATTAAAATAAGATAACA * 58358964 ATAATATTAAAATGAAG-TAATCA 1 A-AAAATTAAAAT-AAGATAA-CA 58358987 AAAAATTA 1 AAAAATTA 58358995 TATAAAGGCT Statistics Matches: 25, Mismatches: 2, Indels: 6 0.76 0.06 0.18 Matches are distributed among these distances: 20 1 0.04 21 3 0.12 22 15 0.60 23 6 0.24 ACGTcount: A:0.67, C:0.04, G:0.06, T:0.24 Consensus pattern (21 bp): AAAAATTAAAATAAGATAACA Found at i:58359779 original size:17 final size:17 Alignment explanation

Indices: 58359759--58359807 Score: 62 Period size: 17 Copynumber: 2.8 Consensus size: 17 58359749 AATTTAATTT * 58359759 TTTTTTTTATTTTTTTA 1 TTTTTTTTATTTTTATA 58359776 TTTTTTTATATTTTTATA 1 TTTTTTT-TATTTTTATA * * 58359794 TGTTTTCTATTTTT 1 TTTTTTTTATTTTT 58359808 GCACTATATA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 17 14 0.50 18 14 0.50 ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82 Consensus pattern (17 bp): TTTTTTTTATTTTTATA Found at i:58359799 original size:10 final size:8 Alignment explanation

Indices: 58359756--58359807 Score: 61 Period size: 8 Copynumber: 6.2 Consensus size: 8 58359746 AAAAATTTAA 58359756 TTTT-TTT 1 TTTTATTT 58359763 TTTTATTT 1 TTTTATTT 58359771 TTTTATTT 1 TTTTATTT 58359779 TTTTATATT 1 TTTTAT-TT 58359788 TTTATATGTT 1 TTT-TAT-TT * 58359798 TTCTATTT 1 TTTTATTT 58359806 TT 1 TT 58359808 GCACTATATA Statistics Matches: 40, Mismatches: 2, Indels: 5 0.85 0.04 0.11 Matches are distributed among these distances: 7 4 0.10 8 21 0.52 9 8 0.20 10 7 0.17 ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83 Consensus pattern (8 bp): TTTTATTT Found at i:58361286 original size:72 final size:72 Alignment explanation

Indices: 58361053--58361302 Score: 385 Period size: 72 Copynumber: 3.4 Consensus size: 72 58361043 GTGAACTGAT * * * * 58361053 GCTCAACTCACTTT-TCGCAATATGAGTTGATTTTTTTTGACAACAGAAATTGAAATTACTTCAG 1 GCTCAACTCA-TTTCTCGCAATATGAGTTGA---ATTTTGAAAACAGAAATTGAAATTACCTCAA * 58361117 CGTGTCCTGAG 62 CGTGTCTTGAG * 58361128 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTGAAAATACCTCAACGT 1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAATTACCTCAACGT 58361193 GTCTTGAG 65 GTCTTGAG * 58361201 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAATGTG 1 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG 58361266 TCTTGAG 66 TCTTGAG 58361273 GCTCAACTCATTTCTCGCAATATGAGTTGA 1 GCTCAACTCATTTCTCGCAATATGAGTTGA 58361303 TTCTTTCAAA Statistics Matches: 165, Mismatches: 8, Indels: 7 0.92 0.04 0.04 Matches are distributed among these distances: 72 68 0.41 73 68 0.41 74 3 0.02 75 26 0.16 ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33 Consensus pattern (72 bp): GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACGTG TCTTGAG Found at i:58361384 original size:88 final size:87 Alignment explanation

Indices: 58361235--58361481 Score: 291 Period size: 88 Copynumber: 2.8 Consensus size: 87 58361225 AGTTGAATTT * ** * ** 58361235 TGAAAACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT 1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT 58361300 TGA-TTCTTTCAAAAACATAATAA 66 TGATTTCTTTCAAAAACA-AA-AA * * 58361323 TGAAAACAGAAATAGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT 1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT * * * 58361388 TGATTTTTTTTTAAAAACAGAAA 66 TGA-TTTCTTTCAAAAACAAAAA * ** 58361411 TCAAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT 1 TGAAAA--CAGAAATTGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT 58361475 GAGTTGA 62 GAGTTGA 58361482 AATTAAAACA Statistics Matches: 137, Mismatches: 16, Indels: 9 0.85 0.10 0.06 Matches are distributed among these distances: 88 67 0.49 89 15 0.11 90 14 0.10 91 41 0.30 ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29 Consensus pattern (87 bp): TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT TGATTTCTTTCAAAAACAAAAA Found at i:58361812 original size:76 final size:73 Alignment explanation

Indices: 58361703--58362060 Score: 391 Period size: 76 Copynumber: 4.8 Consensus size: 73 58361693 AGTGTGTAAT * * * 58361703 CTGAAGCTCAACTCACCTCTCGTAAGATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATACCT 1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTTTAAAAACAGAAATTGAAAATACCT * 58361768 CAGCATGTGAAC 65 CAGC--GTG-TC * * * 58361780 C-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAAAAATTGAAAATA 1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTAAAAACAGAAATTGAAAATA * 58361844 CCTCAACGTGTC 62 CCTCAGCGTGTC * ** * * * * 58361856 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTC 1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTC 58361920 AGCGTGTC 66 AGCGTGTC ** * * 58361928 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAGAAATTGAAATTAC 1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTAAAAACAGAAATTGAAAATAC 58361993 CTCAGCGTGTC 63 CTCAGCGTGTC * * * 58362004 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT-AAAA 1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATTGAAAA 58362061 GGCTTAACTC Statistics Matches: 245, Mismatches: 27, Indels: 24 0.83 0.09 0.08 Matches are distributed among these distances: 71 3 0.01 72 81 0.33 76 96 0.39 77 35 0.14 79 29 0.12 80 1 0.00 ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31 Consensus pattern (73 bp): CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTAAAAACAGAAATTGAAAATACCTC AGCGTGTC Found at i:58362012 original size:148 final size:149 Alignment explanation

Indices: 58361703--58362060 Score: 429 Period size: 148 Copynumber: 2.4 Consensus size: 149 58361693 AGTGTGTAAT * * * * * * 58361703 CTGAAGCTCAACTCACCTCTCGTAAGATGAGTTGATCTTTTTAAAAACAGAAATTGAAAATACCT 1 CTGAGGCTCAACTCACCTCTAGCAATATAAGTTGA---TTTTGAAAACAGAAATTGAAAATACCT 58361768 CAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAAA 63 CAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAAA 58361833 AATTGAAAATACCTCAACGTGTC 127 AATTGAAAATACCTCAACGTGTC * ** * * 58361856 TTGAGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCA 1 CTGAGGCTCAACTCACCTCTAGCAATATAAGTTG-ATTTTGAAAACAGAAATTGAAAATACCTCA * ** * * 58361921 GC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTTTT-AACAACAGAA 65 GCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAA-AACAAAA * * 58361982 ATTGAAATTACCTCAGCGTGTC 128 ATTGAAAATACCTCAACGTGTC * * 58362004 CTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT-AAAA 1 CTGAGGCTCAACTCACCTCTAGCAATATAAGTTGATTTTG-AAAACAGAAATTGAAAA 58362061 GGCTTAACTC Statistics Matches: 178, Mismatches: 23, Indels: 14 0.83 0.11 0.07 Matches are distributed among these distances: 147 11 0.06 148 77 0.43 149 33 0.19 151 29 0.16 153 27 0.15 154 1 0.01 ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31 Consensus pattern (149 bp): CTGAGGCTCAACTCACCTCTAGCAATATAAGTTGATTTTGAAAACAGAAATTGAAAATACCTCAG CAGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAAAAATT GAAAATACCTCAACGTGTC Found at i:58362208 original size:71 final size:70 Alignment explanation

Indices: 58362060--58362235 Score: 212 Period size: 71 Copynumber: 2.5 Consensus size: 70 58362050 AAAAATTAAA * * * * * * ** 58362060 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG 1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG 58362124 CCCCG 66 CCCCG * 58362129 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAAAAAAATTAAAAATACCTCAACGT 1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAAAAAAAACTAAAAATACCTCAACGT * ** 58362194 GTCTTG 65 GCCCCG 58362200 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT 1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT 58362236 CCTTGGAAAG Statistics Matches: 92, Mismatches: 12, Indels: 4 0.85 0.11 0.04 Matches are distributed among these distances: 69 26 0.28 70 6 0.07 71 60 0.65 ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28 Consensus pattern (70 bp): AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACTAAAAATACCTCAACGTG CCCCG Found at i:58369157 original size:8 final size:8 Alignment explanation

Indices: 58369146--58369175 Score: 51 Period size: 8 Copynumber: 3.6 Consensus size: 8 58369136 TTTTTATTTT 58369146 TTTTTATA 1 TTTTTATA 58369154 TTTTTATA 1 TTTTTATA 58369162 TGTTTTATA 1 T-TTTTATA 58369171 TTTTT 1 TTTTT 58369176 GCACTATATA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 8 13 0.62 9 8 0.38 ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77 Consensus pattern (8 bp): TTTTTATA Found at i:58370602 original size:140 final size:140 Alignment explanation

Indices: 58370421--58370700 Score: 499 Period size: 140 Copynumber: 2.0 Consensus size: 140 58370411 ACTTGAAAAC * * * 58370421 AAACTCATAAAAAATAGAGATTTCAATATTCTCTAGTTGATGCATAAAATAGAGTGAAATTT-GG 1 AAACTCATAAAAAACAGAGATTTCAATATTCTCCAGCTGATGCATAAAATAGAGTGAAATTTCGG 58370485 ATAAAAAAAAGAAAAACATTTTACCTGAATTAACTCTGTTAACATGATGAGGCTGTCCAACTGAG 66 -TAAAAAAAAGAAAAACATTTTACCTGAATTAACTCTGTTAACATGATGAGGCTGTCCAACTGAG 58370550 CTGTCTTTAGT 130 CTGTCTTTAGT 58370561 AAACTCATAAAAAACAGAGATTTCAATATTCTCCAGCTGATGCATAAAATAGAGTGAAATTTCGG 1 AAACTCATAAAAAACAGAGATTTCAATATTCTCCAGCTGATGCATAAAATAGAGTGAAATTTCGG * * 58370626 TAAGAAAAAGAAAAACATTTTACCTTAATTAACTCTGTTAACATGATGAGGCTGTCCAACTGAGC 66 TAAAAAAAAGAAAAACATTTTACCTGAATTAACTCTGTTAACATGATGAGGCTGTCCAACTGAGC 58370691 TGTCTTTAGT 131 TGTCTTTAGT 58370701 TGAATCCTTT Statistics Matches: 134, Mismatches: 5, Indels: 2 0.95 0.04 0.01 Matches are distributed among these distances: 140 132 0.99 141 2 0.01 ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30 Consensus pattern (140 bp): AAACTCATAAAAAACAGAGATTTCAATATTCTCCAGCTGATGCATAAAATAGAGTGAAATTTCGG TAAAAAAAAGAAAAACATTTTACCTGAATTAACTCTGTTAACATGATGAGGCTGTCCAACTGAGC TGTCTTTAGT Found at i:58371494 original size:15 final size:15 Alignment explanation

Indices: 58371474--58371503 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 58371464 TTAAATACCT * 58371474 TTTTAGAATTTTATA 1 TTTTAGAATTCTATA 58371489 TTTTAGAATTCTATA 1 TTTTAGAATTCTATA 58371504 AAAAATTGTT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57 Consensus pattern (15 bp): TTTTAGAATTCTATA Found at i:58374298 original size:13 final size:13 Alignment explanation

Indices: 58374280--58374306 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 58374270 AAACCCAACA 58374280 TCTGAATTCACTG 1 TCTGAATTCACTG 58374293 TCTGAATTCACTG 1 TCTGAATTCACTG 58374306 T 1 T 58374307 ATTTTACATG 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:0.15, T:0.41 Consensus pattern (13 bp): TCTGAATTCACTG Found at i:58377791 original size:19 final size:19 Alignment explanation

Indices: 58377767--58377805 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 58377757 TTCCAAACAG 58377767 TATGCTGCTTACCTGATAT 1 TATGCTGCTTACCTGATAT 58377786 TATGCTGCTTACCTGATAT 1 TATGCTGCTTACCTGATAT 58377805 T 1 T 58377806 TTCATACATT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44 Consensus pattern (19 bp): TATGCTGCTTACCTGATAT Found at i:58380899 original size:16 final size:16 Alignment explanation

Indices: 58380878--58380917 Score: 62 Period size: 16 Copynumber: 2.5 Consensus size: 16 58380868 TGAATTACTG * 58380878 ATTACAGCTCTATTCC 1 ATTACAACTCTATTCC * 58380894 ATTACAACTTTATTCC 1 ATTACAACTCTATTCC 58380910 ATTACAAC 1 ATTACAAC 58380918 GAACCAAACA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 16 22 1.00 ACGTcount: A:0.33, C:0.28, G:0.03, T:0.38 Consensus pattern (16 bp): ATTACAACTCTATTCC Found at i:58385864 original size:18 final size:18 Alignment explanation

Indices: 58385838--58385875 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 58385828 TGAATATTAC 58385838 AATTCGAATAACTCGAAT 1 AATTCGAATAACTCGAAT * * 58385856 AATTTGAATAATTCGAAT 1 AATTCGAATAACTCGAAT 58385874 AA 1 AA 58385876 CAGATTGGTG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32 Consensus pattern (18 bp): AATTCGAATAACTCGAAT Found at i:58386055 original size:9 final size:9 Alignment explanation

Indices: 58385954--58386058 Score: 50 Period size: 9 Copynumber: 11.0 Consensus size: 9 58385944 CAAAAATTAA * 58385954 AAAAAATTC 1 AAAAAATTT * 58385963 AAAATATTT 1 AAAAAATTT 58385972 ATAAAAATTT 1 A-AAAAATTT * 58385982 -TAAAATTT 1 AAAAAATTT * *** 58385990 ATATTTTTT 1 AAAAAATTT * 58385999 AGAAAATTCT 1 AAAAAATT-T 58386009 AAAAAATTCT 1 AAAAAATT-T * 58386019 AAAAAACATAT 1 -AAAAA-ATTT * 58386030 AAAGAAAGTTA 1 AAA-AAA-TTT 58386041 AAAAAATTT 1 AAAAAATTT 58386050 AAAAAATTT 1 AAAAAATTT 58386059 CTAGAATAAT Statistics Matches: 73, Mismatches: 16, Indels: 14 0.71 0.16 0.14 Matches are distributed among these distances: 8 7 0.10 9 28 0.38 10 24 0.33 11 12 0.16 12 2 0.03 ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35 Consensus pattern (9 bp): AAAAAATTT Found at i:58394962 original size:15 final size:15 Alignment explanation

Indices: 58394942--58394970 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 58394932 AACATCACTT 58394942 ATAGCAACTTTATTC 1 ATAGCAACTTTATTC 58394957 ATAGCAACTTTATT 1 ATAGCAACTTTATT 58394971 TAACTTGAAA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41 Consensus pattern (15 bp): ATAGCAACTTTATTC Found at i:58395901 original size:63 final size:63 Alignment explanation

Indices: 58395830--58395966 Score: 168 Period size: 63 Copynumber: 2.2 Consensus size: 63 58395820 ATGGGGCCCT * * * * ** * 58395830 CCACCATTCGGGCCAA-GAGTTTGTGGCTTATACTCATGGCTTTCAACATTCGGCCTGGGCCAA 1 CCACCATTCGGCCCAATG-GTTTGTGGCCTATACGCATGACACTCAACATTCAGCCTGGGCCAA * * 58395893 CCACCATTCGGCCCAATGGTTTGTGGCCTATACGCATGACACTCAACATTCAGCTTGGGCCCA 1 CCACCATTCGGCCCAATGGTTTGTGGCCTATACGCATGACACTCAACATTCAGCCTGGGCCAA * 58395956 CCACCAATCGG 1 CCACCATTCGG 58395967 TCCTGCATAT Statistics Matches: 63, Mismatches: 10, Indels: 2 0.84 0.13 0.03 Matches are distributed among these distances: 63 62 0.98 64 1 0.02 ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24 Consensus pattern (63 bp): CCACCATTCGGCCCAATGGTTTGTGGCCTATACGCATGACACTCAACATTCAGCCTGGGCCAA Found at i:58397592 original size:19 final size:19 Alignment explanation

Indices: 58397554--58397591 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 19 58397544 TTCTCCATTT * 58397554 TTAATGAAAATATTAAAAA 1 TTAATGAAAATAATAAAAA 58397573 TTAATGAAAAATAATAAAA 1 TTAATG-AAAATAATAAAA 58397592 TAATTATAAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 6 0.35 20 11 0.65 ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29 Consensus pattern (19 bp): TTAATGAAAATAATAAAAA Found at i:58400632 original size:4 final size:4 Alignment explanation

Indices: 58400623--58400649 Score: 54 Period size: 4 Copynumber: 6.8 Consensus size: 4 58400613 TAGGAATGGT 58400623 ATGC ATGC ATGC ATGC ATGC ATGC ATG 1 ATGC ATGC ATGC ATGC ATGC ATGC ATG 58400650 TATATTGGAG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 23 1.00 ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26 Consensus pattern (4 bp): ATGC Found at i:58408166 original size:86 final size:84 Alignment explanation

Indices: 58408033--58408236 Score: 218 Period size: 86 Copynumber: 2.4 Consensus size: 84 58408023 TGTGATTTTG * ** * * * 58408033 TGTAAGACCACATTTGGGATGTTGGCATC-AATTTGAGATTTCGTGTAAGACCAC-GTTTGGGAC 1 TGTAAGACCACATCTGGGACATTGGCATCGTATAT--GATTTCGTGTAAGACC-CTGTCTGGGAC * 58408096 -GTTGGCATCGAT-TTGAGATTTACG 63 AG-TGGCATCGATATT--GA-TTACA ** 58408120 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCGTGTAAGACCCTGTCTGGGACAGT 1 TGTAAGACCACATCTGGGACATTGGCATCGTATATGATTTCGTGTAAGACCCTGTCTGGGACAGT 58408185 GGCATCGATAGTTGATTACA 66 GGCATCGATA-TTGATTACA * 58408205 TGTAAGACCACATCTGGGACGTTGGCATCGTA 1 TGTAAGACCACATCTGGGACATTGGCATCGTA 58408237 CAAGCTTTTC Statistics Matches: 100, Mismatches: 12, Indels: 12 0.81 0.10 0.10 Matches are distributed among these distances: 85 34 0.34 86 36 0.36 87 25 0.25 88 5 0.05 ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31 Consensus pattern (84 bp): TGTAAGACCACATCTGGGACATTGGCATCGTATATGATTTCGTGTAAGACCCTGTCTGGGACAGT GGCATCGATATTGATTACA Found at i:58408234 original size:43 final size:43 Alignment explanation

Indices: 58408032--58408234 Score: 195 Period size: 43 Copynumber: 4.7 Consensus size: 43 58408022 TTGTGATTTT * * * * * 58408032 GTGTAAGACCACATTTGGGATGTTGGCATCAAT-TTGAGATTTC 1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-AGATTAC * 58408075 GTGTAAGACCACGTTTGGGACGTTGGCATCGAT-TTGAGATTTAC 1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATT-AGA-TTAC * * * 58408119 GTGTAAGACCATGTCTGGGACATTGGCATCG-TA-TATGATTTC 1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTA-GATTAC 58408161 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATAGTT-GATTAC 1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATA-TTAGATTAC * * 58408204 ATGTAAGACCACATCTGGGACGTTGGCATCG 1 GTGTAAGACCACGTCTGGGACGTTGGCATCG 58408235 TACAAGCTTT Statistics Matches: 137, Mismatches: 13, Indels: 20 0.81 0.08 0.12 Matches are distributed among these distances: 42 32 0.23 43 72 0.53 44 32 0.23 45 1 0.01 ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31 Consensus pattern (43 bp): GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTAGATTAC Found at i:58408247 original size:86 final size:85 Alignment explanation

Indices: 58408068--58408240 Score: 210 Period size: 85 Copynumber: 2.0 Consensus size: 85 58408058 CATCAATTTG * * ** 58408068 AGATTTCGTGTAAGACCACGTTTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATGT 1 AGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATTT-AGATTTACATGTAAGACCACAT * 58408133 CTGGGACATTGGCATCGTATA 65 CTGGGACATTGGCATCGTACA * 58408154 TGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATAGTT-GA-TTACATGTAAGACCA 1 AGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT--TTAGATTTACATGTAAGACCA * 58408215 CATCTGGGACGTTGGCATCGTACA 62 CATCTGGGACATTGGCATCGTACA 58408239 AG 1 AG 58408241 CTTTTCGAGC Statistics Matches: 75, Mismatches: 8, Indels: 9 0.82 0.09 0.10 Matches are distributed among these distances: 85 36 0.48 86 36 0.48 87 1 0.01 88 2 0.03 ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29 Consensus pattern (85 bp): AGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATTTAGATTTACATGTAAGACCACATC TGGGACATTGGCATCGTACA Found at i:58412492 original size:16 final size:17 Alignment explanation

Indices: 58412471--58412507 Score: 58 Period size: 17 Copynumber: 2.2 Consensus size: 17 58412461 ATTTAATTAG 58412471 AAAATACA-TATTTTTA 1 AAAATACATTATTTTTA * 58412487 AAAATATATTATTTTTA 1 AAAATACATTATTTTTA 58412504 AAAA 1 AAAA 58412508 ATATATTCAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 16 7 0.37 17 12 0.63 ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43 Consensus pattern (17 bp): AAAATACATTATTTTTA Found at i:58412501 original size:17 final size:18 Alignment explanation

Indices: 58412479--58412514 Score: 65 Period size: 18 Copynumber: 2.1 Consensus size: 18 58412469 AGAAAATACA 58412479 TATTTTT-AAAAATATAT 1 TATTTTTAAAAAATATAT 58412496 TATTTTTAAAAAATATAT 1 TATTTTTAAAAAATATAT 58412514 T 1 T 58412515 CAATCCAATT Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 17 7 0.39 18 11 0.61 ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53 Consensus pattern (18 bp): TATTTTTAAAAAATATAT Found at i:58415800 original size:3 final size:3 Alignment explanation

Indices: 58415792--58415835 Score: 79 Period size: 3 Copynumber: 14.7 Consensus size: 3 58415782 GGAGAAACAG * 58415792 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CCT CAT CA 1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA 58415836 ACCGCAGCAA Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 3 39 1.00 ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32 Consensus pattern (3 bp): CAT Found at i:58418799 original size:29 final size:29 Alignment explanation

Indices: 58418756--58418811 Score: 94 Period size: 29 Copynumber: 1.9 Consensus size: 29 58418746 CTACCAATTA 58418756 GCTAGGTTGGCTTTGTTTTAAATTGGGAT 1 GCTAGGTTGGCTTTGTTTTAAATTGGGAT * * 58418785 GCTAGGTTGGGTTTGTTTTAGATTGGG 1 GCTAGGTTGGCTTTGTTTTAAATTGGG 58418812 CGAATATGGG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 29 25 1.00 ACGTcount: A:0.14, C:0.05, G:0.36, T:0.45 Consensus pattern (29 bp): GCTAGGTTGGCTTTGTTTTAAATTGGGAT Found at i:58425968 original size:24 final size:23 Alignment explanation

Indices: 58425924--58425968 Score: 56 Period size: 24 Copynumber: 1.9 Consensus size: 23 58425914 ATTTTTACAC * 58425924 TTTAATAGTTTGTTTTATGTGAT 1 TTTAATAGTTTGTATTATGTGAT 58425947 TTTAATAAGTTTGATATT-TGTG 1 TTTAAT-AGTTTG-TATTATGTG 58425969 TCACGAACAT Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 23 6 0.32 24 10 0.53 25 3 0.16 ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58 Consensus pattern (23 bp): TTTAATAGTTTGTATTATGTGAT Found at i:58426042 original size:20 final size:19 Alignment explanation

Indices: 58426000--58426042 Score: 52 Period size: 20 Copynumber: 2.2 Consensus size: 19 58425990 CGTTATCATA * 58426000 TATTTTAATTATTTTACAT 1 TATTTTAATTATTTTAAAT 58426019 TATTTT-ATTATATCTTAAAT 1 TATTTTAATTAT-T-TTAAAT 58426039 TATT 1 TATT 58426043 CTGAAGTTCA Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 18 5 0.24 19 7 0.33 20 9 0.43 ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63 Consensus pattern (19 bp): TATTTTAATTATTTTAAAT Found at i:58433185 original size:21 final size:19 Alignment explanation

Indices: 58433156--58433196 Score: 55 Period size: 21 Copynumber: 2.1 Consensus size: 19 58433146 AATTTGACTA 58433156 TTTTATATTTAGTGATTTAAT 1 TTTTATATTTA--GATTTAAT * 58433177 TTTTTTATTTAGATTTAAT 1 TTTTATATTTAGATTTAAT 58433196 T 1 T 58433197 AATTGTATTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 19 9 0.47 21 10 0.53 ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66 Consensus pattern (19 bp): TTTTATATTTAGATTTAAT Found at i:58436842 original size:22 final size:20 Alignment explanation

Indices: 58436795--58436843 Score: 53 Period size: 22 Copynumber: 2.3 Consensus size: 20 58436785 TTTATTATTT * * 58436795 TATTTTTCATTATTTTACTA 1 TATTTTACATTATATTACTA 58436815 TCATTTTACTATTATATTACTA 1 T-ATTTTAC-ATTATATTACTA 58436837 CTATTTT 1 -TATTTT 58436844 GTTGTTATTG Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 20 1 0.04 21 6 0.25 22 16 0.67 23 1 0.04 ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61 Consensus pattern (20 bp): TATTTTACATTATATTACTA Found at i:58444024 original size:24 final size:26 Alignment explanation

Indices: 58443966--58444024 Score: 70 Period size: 26 Copynumber: 2.3 Consensus size: 26 58443956 ATTCGAAAAA * 58443966 GACTTTGGTTAAATGCATTAGCTTAT 1 GACTTTGGTTAAATGCATTAGCTTAG * 58443992 GACTGTGGTTAAATG-A-TATG-TTAG 1 GACTTTGGTTAAATGCATTA-GCTTAG 58444016 GACTTTGGT 1 GACTTTGGT 58444025 GTCACGCATA Statistics Matches: 29, Mismatches: 3, Indels: 4 0.81 0.08 0.11 Matches are distributed among these distances: 24 13 0.45 25 2 0.07 26 14 0.48 ACGTcount: A:0.25, C:0.08, G:0.25, T:0.41 Consensus pattern (26 bp): GACTTTGGTTAAATGCATTAGCTTAG Found at i:58447795 original size:51 final size:49 Alignment explanation

Indices: 58447736--58447910 Score: 179 Period size: 51 Copynumber: 3.4 Consensus size: 49 58447726 GTCATGTGTC * * * 58447736 TAGTACTATGGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATATG 1 TAGTACTAT-GTGCAGGCTACTACGTGTACTGG-ATGATAGGTCACATGTG * * * * * * * * 58447787 TAGTACTATGTGCAGACCACTATGCGTACTGGATAGCTTCGATCACGTGTG 1 TAGTACTATGTGCAGGCTACTACGTGTACTGGAT-G-ATAGGTCACATGTG * * 58447838 TAGTACTATGTGCAGGCTACTACGTGTATTGGATGGTAATGGTCACATGTG 1 TAGTACTATGTGCAGGCTACTACGTGTACTGGATGAT-A-GGTCACATGTG 58447889 TAGTACTATGTGCAGGCTACTA 1 TAGTACTATGTGCAGGCTACTA 58447911 TGTGAACCAA Statistics Matches: 100, Mismatches: 20, Indels: 8 0.78 0.16 0.06 Matches are distributed among these distances: 49 3 0.03 50 20 0.20 51 77 0.77 ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30 Consensus pattern (49 bp): TAGTACTATGTGCAGGCTACTACGTGTACTGGATGATAGGTCACATGTG Found at i:58447914 original size:26 final size:26 Alignment explanation

Indices: 58447834--58447914 Score: 62 Period size: 26 Copynumber: 3.2 Consensus size: 26 58447824 TTCGATCACG 58447834 TGTGTAGTACTATGTGCAGGCTACTA 1 TGTGTAGTACTATGTGCAGGCTACTA * *** * 58447860 CGTGTA-TTGGATG-GTAATGG-TCAC-A 1 TGTGTAGTACTATGTG-CA-GGCT-ACTA 58447885 TGTGTAGTACTATGTGCAGGCTACTA 1 TGTGTAGTACTATGTGCAGGCTACTA 58447911 TGTG 1 TGTG 58447915 AACCAAACAT Statistics Matches: 38, Mismatches: 10, Indels: 14 0.61 0.16 0.23 Matches are distributed among these distances: 24 1 0.03 25 16 0.42 26 20 0.53 27 1 0.03 ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35 Consensus pattern (26 bp): TGTGTAGTACTATGTGCAGGCTACTA Found at i:58447972 original size:45 final size:45 Alignment explanation

Indices: 58447916--58448008 Score: 141 Period size: 45 Copynumber: 2.1 Consensus size: 45 58447906 TACTATGTGA * * * 58447916 ACCAAACATCATTGATTAGTAACGTGGTTGCTATGTGCTGATTCC 1 ACCAAACATCATTGATTAATAACGTGGTTGCTATGTGCTAAATCC * * 58447961 ACCAGACATCATTGATTAATAAGGTGGTTGCTATGTGCTAAATCC 1 ACCAAACATCATTGATTAATAACGTGGTTGCTATGTGCTAAATCC 58448006 ACC 1 ACC 58448009 GAGTATCTGT Statistics Matches: 43, Mismatches: 5, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 45 43 1.00 ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31 Consensus pattern (45 bp): ACCAAACATCATTGATTAATAACGTGGTTGCTATGTGCTAAATCC Found at i:58451114 original size:4 final size:4 Alignment explanation

Indices: 58451105--58451137 Score: 50 Period size: 4 Copynumber: 8.2 Consensus size: 4 58451095 TTGCTTGTAC 58451105 ATAA ATAA ATAAA ATAA A-AA ATAA ATAA ATAA A 1 ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA A 58451138 GGCTCAAGTT Statistics Matches: 27, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 3 3 0.11 4 20 0.74 5 4 0.15 ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21 Consensus pattern (4 bp): ATAA Found at i:58455181 original size:11 final size:11 Alignment explanation

Indices: 58455165--58455257 Score: 86 Period size: 11 Copynumber: 8.8 Consensus size: 11 58455155 AAATAAATCA 58455165 TTCCTCTCAAT 1 TTCCTCTCAAT 58455176 TTCCTCTCAAT 1 TTCCTCTCAAT * 58455187 TTGCTCTCAAT 1 TTCCTCTCAAT 58455198 TTCCTCTCAAT 1 TTCCTCTCAAT ** 58455209 TTTATCTCAA- 1 TTCCTCTCAAT * 58455219 ATCC-CT--AT 1 TTCCTCTCAAT ** 58455227 TTAATCTCAAT 1 TTCCTCTCAAT * * 58455238 TTGCTCTGAAT 1 TTCCTCTCAAT 58455249 TTCCTCTCA 1 TTCCTCTCA 58455258 GATCCCTATT Statistics Matches: 63, Mismatches: 15, Indels: 8 0.73 0.17 0.09 Matches are distributed among these distances: 7 1 0.02 8 1 0.02 9 4 0.06 10 1 0.02 11 56 0.89 ACGTcount: A:0.22, C:0.30, G:0.03, T:0.45 Consensus pattern (11 bp): TTCCTCTCAAT Found at i:58455236 original size:40 final size:40 Alignment explanation

Indices: 58455191--58455270 Score: 115 Period size: 40 Copynumber: 2.0 Consensus size: 40 58455181 CTCAATTTGC * 58455191 TCTCAATTTCCTCTCAATTTTATCTCAAATCCCTATTTAA 1 TCTCAATTTCCTCTCAATTTCATCTCAAATCCCTATTTAA * * * * 58455231 TCTCAATTTGCTCTGAATTTCCTCTCAGATCCCTATTTAA 1 TCTCAATTTCCTCTCAATTTCATCTCAAATCCCTATTTAA 58455271 AAGAGCTTTA Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 40 35 1.00 ACGTcount: A:0.25, C:0.28, G:0.04, T:0.44 Consensus pattern (40 bp): TCTCAATTTCCTCTCAATTTCATCTCAAATCCCTATTTAA Found at i:58460347 original size:26 final size:25 Alignment explanation

Indices: 58460292--58460349 Score: 64 Period size: 25 Copynumber: 2.3 Consensus size: 25 58460282 TAATATCTTA * * * 58460292 AATATATTAAAATAATATTTTATTT 1 AATAAATTAAAAAAATATTTAATTT 58460317 AATAAATTAAAAAAATAATTTAAATTT 1 AATAAATTAAAAAAAT-ATTT-AATTT 58460344 -ATAAAT 1 AATAAAT 58460350 AAATTAATAC Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 25 14 0.50 26 10 0.36 27 4 0.14 ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43 Consensus pattern (25 bp): AATAAATTAAAAAAATATTTAATTT Found at i:58461570 original size:13 final size:13 Alignment explanation

Indices: 58461552--58461578 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 58461542 CAATAAAGTC 58461552 CAATTACAATGGG 1 CAATTACAATGGG 58461565 CAATTACAATGGG 1 CAATTACAATGGG 58461578 C 1 C 58461579 CAAATTCATA 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:0.37, C:0.19, G:0.22, T:0.22 Consensus pattern (13 bp): CAATTACAATGGG Found at i:58464243 original size:15 final size:15 Alignment explanation

Indices: 58464200--58464248 Score: 55 Period size: 15 Copynumber: 3.3 Consensus size: 15 58464190 AAAAAATATC * 58464200 ATAAATAACTAAAAT 1 ATAAATGACTAAAAT ** * 58464215 AT-AATGTTTTAAAT 1 ATAAATGACTAAAAT 58464229 ATAAATGACTAAAAT 1 ATAAATGACTAAAAT 58464244 ATAAA 1 ATAAA 58464249 CTAAACTAAA Statistics Matches: 26, Mismatches: 7, Indels: 2 0.74 0.20 0.06 Matches are distributed among these distances: 14 10 0.38 15 16 0.62 ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33 Consensus pattern (15 bp): ATAAATGACTAAAAT Found at i:58469153 original size:19 final size:21 Alignment explanation

Indices: 58469120--58469159 Score: 57 Period size: 19 Copynumber: 2.0 Consensus size: 21 58469110 TCAACCTCCA * 58469120 AAACTTTTTATTTTTC-CCCT 1 AAACTTTTTACTTTTCACCCT 58469140 AAAC-TTTTACTTTTCACCCT 1 AAACTTTTTACTTTTCACCCT 58469160 TTACCCCCAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 19 10 0.56 20 8 0.44 ACGTcount: A:0.23, C:0.28, G:0.00, T:0.50 Consensus pattern (21 bp): AAACTTTTTACTTTTCACCCT Found at i:58472861 original size:38 final size:38 Alignment explanation

Indices: 58472810--58472886 Score: 95 Period size: 38 Copynumber: 2.0 Consensus size: 38 58472800 GCATGGTGGG * * 58472810 GGAGTGTTGGAGTGATTTTCA-GAGGAAAATATGGGATT 1 GGAGTGTTGGAGTGACTTT-AGGAGGAAAATATGAGATT * 58472848 GGAGTGTAT-GAGTGACTTTAGGAGGAGAATATGAGATT 1 GGAGTGT-TGGAGTGACTTTAGGAGGAAAATATGAGATT 58472886 G 1 G 58472887 TGGAGTTATC Statistics Matches: 34, Mismatches: 3, Indels: 4 0.83 0.07 0.10 Matches are distributed among these distances: 37 1 0.03 38 32 0.94 39 1 0.03 ACGTcount: A:0.30, C:0.03, G:0.38, T:0.30 Consensus pattern (38 bp): GGAGTGTTGGAGTGACTTTAGGAGGAAAATATGAGATT Found at i:58478897 original size:39 final size:37 Alignment explanation

Indices: 58478831--58478922 Score: 96 Period size: 39 Copynumber: 2.4 Consensus size: 37 58478821 CCAGTATGGA * * 58478831 ACCCAGTGCCTCATCAGATAGTTCGAAGCAATAGTTGAC 1 ACCCAGTGCCTCATCAGAAAGTCCGAAG-AA-AGTTGAC * ** 58478870 ACCCAGTGTCTCATCAGCAAAG-CCGAAGAAAGTTGGT 1 ACCCAGTGCCTCATCAG-AAAGTCCGAAGAAAGTTGAC * 58478907 ACCCAGTACCTCATCA 1 ACCCAGTGCCTCATCA 58478923 AATCTATCCG Statistics Matches: 45, Mismatches: 7, Indels: 4 0.80 0.12 0.07 Matches are distributed among these distances: 37 19 0.42 38 2 0.04 39 21 0.47 40 3 0.07 ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21 Consensus pattern (37 bp): ACCCAGTGCCTCATCAGAAAGTCCGAAGAAAGTTGAC Found at i:58482621 original size:38 final size:38 Alignment explanation

Indices: 58482579--58482653 Score: 114 Period size: 38 Copynumber: 2.0 Consensus size: 38 58482569 ATGGTGGGGG * * * 58482579 AGTGTTGGAGTGATTTTAGGAGGAAAATATGAGATTGA 1 AGTGTTAGAGTGACTTGAGGAGGAAAATATGAGATTGA * 58482617 AGTGTTAGAGTGACTTGAGGAGGAAAATATGGGATTG 1 AGTGTTAGAGTGACTTGAGGAGGAAAATATGAGATTG 58482654 TGGAGTCATC Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 38 33 1.00 ACGTcount: A:0.33, C:0.01, G:0.36, T:0.29 Consensus pattern (38 bp): AGTGTTAGAGTGACTTGAGGAGGAAAATATGAGATTGA Found at i:58483624 original size:11 final size:11 Alignment explanation

Indices: 58483605--58483648 Score: 65 Period size: 11 Copynumber: 4.2 Consensus size: 11 58483595 AACATCGAAC * 58483605 TTTTTGGGTAA 1 TTTTCGGGTAA 58483616 TTTTCGGGTAA 1 TTTTCGGGTAA 58483627 --TTCGGGTAA 1 TTTTCGGGTAA 58483636 TTTTCGGGTAA 1 TTTTCGGGTAA 58483647 TT 1 TT 58483649 CGGTTAATTC Statistics Matches: 30, Mismatches: 1, Indels: 4 0.86 0.03 0.11 Matches are distributed among these distances: 9 9 0.30 11 21 0.70 ACGTcount: A:0.18, C:0.07, G:0.27, T:0.48 Consensus pattern (11 bp): TTTTCGGGTAA Found at i:58483632 original size:9 final size:9 Alignment explanation

Indices: 58483618--58483692 Score: 98 Period size: 9 Copynumber: 8.2 Consensus size: 9 58483608 TTGGGTAATT 58483618 TTCGGGTAA 1 TTCGGGTAA 58483627 TTCGGGTAA 1 TTCGGGTAA 58483636 TTTTCGGGTAA 1 --TTCGGGTAA * 58483647 TTCGGTTAA 1 TTCGGGTAA * 58483656 TTCGGTTAA 1 TTCGGGTAA * 58483665 TTCGGTTAA 1 TTCGGGTAA 58483674 TT-GGGTAA 1 TTCGGGTAA 58483682 TTCGGGTAA 1 TTCGGGTAA 58483691 TT 1 TT 58483693 TTTAACCAAA Statistics Matches: 61, Mismatches: 2, Indels: 6 0.88 0.03 0.09 Matches are distributed among these distances: 8 7 0.11 9 45 0.74 11 9 0.15 ACGTcount: A:0.21, C:0.09, G:0.28, T:0.41 Consensus pattern (9 bp): TTCGGGTAA Found at i:58483635 original size:20 final size:20 Alignment explanation

Indices: 58483610--58483694 Score: 108 Period size: 20 Copynumber: 4.5 Consensus size: 20 58483600 CGAACTTTTT 58483610 GGGTAATTTTCGGGTAATTC 1 GGGTAATTTTCGGGTAATTC 58483630 GGGTAATTTTCGGGTAATTC 1 GGGTAATTTTCGGGTAATTC * * 58483650 GGTTAA--TTCGGTTAATTC 1 GGGTAATTTTCGGGTAATTC * 58483668 GGTTAA--TT-GGGTAATTC 1 GGGTAATTTTCGGGTAATTC 58483685 GGGTAATTTT 1 GGGTAATTTT 58483695 TAACCAAAAA Statistics Matches: 59, Mismatches: 4, Indels: 5 0.87 0.06 0.07 Matches are distributed among these distances: 17 13 0.22 18 19 0.32 19 2 0.03 20 25 0.42 ACGTcount: A:0.21, C:0.08, G:0.28, T:0.42 Consensus pattern (20 bp): GGGTAATTTTCGGGTAATTC Found at i:58493220 original size:22 final size:22 Alignment explanation

Indices: 58493192--58493246 Score: 92 Period size: 22 Copynumber: 2.5 Consensus size: 22 58493182 GTCTAAACAG 58493192 AGAAGAAGATTGCAGAGCAAAC 1 AGAAGAAGATTGCAGAGCAAAC 58493214 AGAAGAAGATTGCAGAGCAAAC 1 AGAAGAAGATTGCAGAGCAAAC * * 58493236 AAAAGCAGATT 1 AGAAGAAGATT 58493247 CAGCATTATC Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 22 31 1.00 ACGTcount: A:0.51, C:0.13, G:0.25, T:0.11 Consensus pattern (22 bp): AGAAGAAGATTGCAGAGCAAAC Found at i:58497354 original size:19 final size:19 Alignment explanation

Indices: 58497330--58497368 Score: 53 Period size: 19 Copynumber: 2.1 Consensus size: 19 58497320 GTTTAAAAAT 58497330 AATATAT-AATAAATAATTA 1 AATATATGAATAAA-AATTA * 58497349 AATATATGATTAAAAATTA 1 AATATATGAATAAAAATTA 58497368 A 1 A 58497369 TTAATTATAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 19 13 0.72 20 5 0.28 ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36 Consensus pattern (19 bp): AATATATGAATAAAAATTA Found at i:58497408 original size:43 final size:40 Alignment explanation

Indices: 58497325--58497426 Score: 107 Period size: 43 Copynumber: 2.5 Consensus size: 40 58497315 TGTATGTTTA * 58497325 AAAATAATATATAATAAATAATTAAATATATGATTAAAAAT 1 AAAATAAT-TATAATAAATAATAAAATATATGATTAAAAAT * * * 58497366 TAATTAATTATAAT-AATATATAAAATATGTATGATATTAAAAT 1 AAAATAATTATAATAAATA-ATAAAATA--TATGAT-TAAAAAT * 58497409 AAAATAATTAAAATAAAT 1 AAAATAATTATAATAAAT 58497427 TAGGAGTAAA Statistics Matches: 49, Mismatches: 7, Indels: 7 0.78 0.11 0.11 Matches are distributed among these distances: 39 4 0.08 40 13 0.27 41 6 0.12 42 6 0.12 43 17 0.35 44 3 0.06 ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36 Consensus pattern (40 bp): AAAATAATTATAATAAATAATAAAATATATGATTAAAAAT Found at i:58498011 original size:11 final size:11 Alignment explanation

Indices: 58497995--58498184 Score: 65 Period size: 11 Copynumber: 18.2 Consensus size: 11 58497985 TTTTTATTTT 58497995 AAAAATTTTAA 1 AAAAATTTTAA * 58498006 AAAAA-TTAAA 1 AAAAATTTTAA * 58498016 AAAAGTATTTTTA 1 AAAA--ATTTTAA * * 58498029 AAATATTTTTA 1 AAAAATTTTAA * 58498040 AAATATTTT-- 1 AAAAATTTTAA 58498049 -AAAA--TTAA 1 AAAAATTTTAA * 58498057 AAAAATTTAAA 1 AAAAATTTTAA 58498068 AAAAGTATTTTAA 1 AAAA--ATTTTAA * 58498081 AAATATTTT-- 1 AAAAATTTTAA 58498090 -AAAA--TTAA 1 AAAAATTTTAA * 58498098 AAAAA-TTAAA 1 AAAAATTTTAA 58498108 AAAAGTATTTTAA 1 AAAA--ATTTTAA * 58498121 AAATATTTT-- 1 AAAAATTTTAA 58498130 -AAAA-TTTAA 1 AAAAATTTTAA * 58498139 AAAAA-ATTAA 1 AAAAATTTTAA * * 58498149 AAAAGTATGTAA 1 AAAAAT-TTTAA 58498161 AAAATATTTT-A 1 AAAA-ATTTTAA * 58498172 AAATATTTTAA 1 AAAAATTTTAA 58498183 AA 1 AA 58498185 TTAAAAAAAT Statistics Matches: 135, Mismatches: 20, Indels: 48 0.67 0.10 0.24 Matches are distributed among these distances: 6 4 0.03 7 3 0.02 8 9 0.07 9 8 0.06 10 32 0.24 11 45 0.33 12 11 0.08 13 23 0.17 ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37 Consensus pattern (11 bp): AAAAATTTTAA Found at i:58498079 original size:40 final size:40 Alignment explanation

Indices: 58498028--58498193 Score: 228 Period size: 41 Copynumber: 4.1 Consensus size: 40 58498018 AAGTATTTTT * 58498028 AAAA-TATTTTTAAAATATTTTAAAATTAAAAAAATTTAAA 1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAA-TTAAA 58498068 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA 1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA 58498108 AAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAATT-AA 1 AAAAGTATTTTAAAAATATTTTAAAA-TT-AAAAAAATTAAA * * *** 58498149 AAAAGTATGTAAAAAATATTTTAAAATATTTTAAAATTAAA 1 AAAAGTATTTTAAAAATATTTTAAAAT-TAAAAAAATTAAA 58498190 AAAA 1 AAAA 58498194 TAAATATAAT Statistics Matches: 115, Mismatches: 6, Indels: 9 0.88 0.05 0.07 Matches are distributed among these distances: 40 42 0.37 41 64 0.56 42 9 0.08 ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36 Consensus pattern (40 bp): AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAA Found at i:58498082 original size:12 final size:11 Alignment explanation

Indices: 58498053--58498184 Score: 68 Period size: 11 Copynumber: 12.5 Consensus size: 11 58498043 TATTTTAAAA * 58498053 TTAAAAAAATT 1 TTAAAAATATT * 58498064 TAAAAAAAGTATT 1 T-TAAAAA-TATT 58498077 TTAAAAATATT 1 TTAAAAATATT 58498088 TT--AAA-A-- 1 TTAAAAATATT * 58498094 TTAAAAAAATT 1 TTAAAAATATT ** 58498105 AAAAAAAGTATT 1 TTAAAAA-TATT 58498117 TTAAAAATATT 1 TTAAAAATATT 58498128 TT--AAA-A-T 1 TTAAAAATATT * * 58498135 TTAAAAAAAAT 1 TTAAAAATATT * * 58498146 TAAAAAAGTATG 1 TTAAAAA-TATT * 58498158 TAAAAAATATT 1 TTAAAAATATT 58498169 TT-AAAATATT 1 TTAAAAATATT 58498179 TTAAAA 1 TTAAAA 58498185 TTAAAAAAAT Statistics Matches: 93, Mismatches: 14, Indels: 28 0.69 0.10 0.21 Matches are distributed among these distances: 6 2 0.02 7 3 0.03 8 5 0.05 9 10 0.11 10 11 0.12 11 32 0.34 12 26 0.28 13 4 0.04 ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36 Consensus pattern (11 bp): TTAAAAATATT Found at i:58498127 original size:81 final size:81 Alignment explanation

Indices: 58498028--58498195 Score: 241 Period size: 81 Copynumber: 2.1 Consensus size: 81 58498018 AAGTATTTTT * * * * 58498028 AAAATATTTTTAAAATATTTTAAAA-TTAAAAAAATTTAAAAAAAGTATTTTAAAAATATTTTAA 1 AAAATATTTTAAAAATATTTTAAAATTTAAAAAAAATT-AAAAAAGTATGTAAAAAATATTTTAA 58498092 AAT-TAAAAAAATTAAA 65 AATATAAAAAAATTAAA 58498108 AAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAA 1 AAAA-TATTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAA *** 58498173 AATATTTTAAAATTAAA 65 AATATAAAAAAATTAAA 58498190 AAAATA 1 AAAATA 58498196 AATATAATTA Statistics Matches: 78, Mismatches: 7, Indels: 5 0.87 0.08 0.06 Matches are distributed among these distances: 80 4 0.05 81 49 0.63 82 25 0.32 ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36 Consensus pattern (81 bp): AAAATATTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAA ATATAAAAAAATTAAA Found at i:58498185 original size:51 final size:50 Alignment explanation

Indices: 58498090--58498193 Score: 151 Period size: 51 Copynumber: 2.1 Consensus size: 50 58498080 AAAATATTTT 58498090 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAA 1 AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA-TTAAAA 58498141 AAAATTAAAAAAGTATGT-AAAAAA-TATTTT-AAAATATTTTAAAATTAAAA 1 AAAATTAAAAAA--AT-TAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA 58498191 AAA 1 AAA 58498194 TAAATATAAT Statistics Matches: 50, Mismatches: 0, Indels: 7 0.88 0.00 0.12 Matches are distributed among these distances: 50 9 0.18 51 26 0.52 52 6 0.12 53 8 0.16 54 1 0.02 ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33 Consensus pattern (50 bp): AAAATTAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA Found at i:58507182 original size:22 final size:23 Alignment explanation

Indices: 58507148--58507205 Score: 66 Period size: 23 Copynumber: 2.6 Consensus size: 23 58507138 TGGTCTTCAT 58507148 ATTTTTTCGTTTTAAGCT-ATTTA 1 ATTTTTTC-TTTTAAGCTCATTTA * * 58507171 ATTTTTTCTTTTATGTTCATTTA 1 ATTTTTTCTTTTAAGCTCATTTA * 58507194 ACTTTTT-TTTTA 1 ATTTTTTCTTTTA 58507206 TTATTTTCCA Statistics Matches: 31, Mismatches: 3, Indels: 3 0.84 0.08 0.08 Matches are distributed among these distances: 22 12 0.39 23 19 0.61 ACGTcount: A:0.19, C:0.09, G:0.05, T:0.67 Consensus pattern (23 bp): ATTTTTTCTTTTAAGCTCATTTA Found at i:58511787 original size:11 final size:11 Alignment explanation

Indices: 58511771--58511816 Score: 55 Period size: 11 Copynumber: 4.5 Consensus size: 11 58511761 GCGGTGCCGA 58511771 AAAAAGAGAAG 1 AAAAAGAGAAG 58511782 AAAAAGAG-AG 1 AAAAAGAGAAG 58511792 AAAGAAGA-AAG 1 AAA-AAGAGAAG 58511803 --AAAGAGAAG 1 AAAAAGAGAAG 58511812 AAAAA 1 AAAAA 58511817 AATAGAAAAA Statistics Matches: 30, Mismatches: 0, Indels: 10 0.75 0.00 0.25 Matches are distributed among these distances: 8 4 0.13 9 4 0.13 10 5 0.17 11 17 0.57 ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00 Consensus pattern (11 bp): AAAAAGAGAAG Found at i:58511791 original size:13 final size:13 Alignment explanation

Indices: 58511769--58511816 Score: 53 Period size: 15 Copynumber: 3.5 Consensus size: 13 58511759 GGGCGGTGCC 58511769 GAAAAA-AGAGAA 1 GAAAAAGAGAGAA 58511781 GAAAAAGAGAGAAA 1 GAAAAAGAGAG-AA 58511795 GAAGAAAGAAAGAGAA 1 GAA-AAAG--AGAGAA 58511811 GAAAAA 1 GAAAAA 58511817 AATAGAAAAA Statistics Matches: 31, Mismatches: 0, Indels: 7 0.82 0.00 0.18 Matches are distributed among these distances: 12 6 0.19 13 4 0.13 14 5 0.16 15 7 0.23 16 5 0.16 17 4 0.13 ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00 Consensus pattern (13 bp): GAAAAAGAGAGAA Found at i:58511823 original size:13 final size:13 Alignment explanation

Indices: 58511770--58511827 Score: 55 Period size: 13 Copynumber: 4.2 Consensus size: 13 58511760 GGCGGTGCCG 58511770 AAAAAAGAGAAGA 1 AAAAAAGAGAAGA 58511783 AAAAGAGAGAAAGAAGA 1 AAAA-A-AG--AGAAGA * 58511800 AAGAAAGAGAAGA 1 AAAAAAGAGAAGA * 58511813 AAAAAATAGAA-A 1 AAAAAAGAGAAGA 58511825 AAA 1 AAA 58511828 TAAGGTATTT Statistics Matches: 38, Mismatches: 3, Indels: 9 0.76 0.06 0.18 Matches are distributed among these distances: 12 4 0.11 13 19 0.50 14 1 0.03 15 4 0.11 16 1 0.03 17 9 0.24 ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02 Consensus pattern (13 bp): AAAAAAGAGAAGA Found at i:58512141 original size:40 final size:38 Alignment explanation

Indices: 58512074--58512171 Score: 121 Period size: 40 Copynumber: 2.6 Consensus size: 38 58512064 TTTTACATTA ** 58512074 TATTATTGTTAG-T-TATTATTTTTAGTAAAACCCTAAT 1 TATTATTGTTAGTTATATTATTTTTAGTAAAAAACT-AT 58512111 TATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTAT 1 TATTATTGTTAGTTA-TATTATTTTTAGTAAAAAACTAT * 58512150 TATTATTATTA-TTATTATTATT 1 TATTATTGTTAGTTA-TATTATT 58512172 ATTATTGTGT Statistics Matches: 54, Mismatches: 4, Indels: 5 0.86 0.06 0.08 Matches are distributed among these distances: 37 12 0.22 38 11 0.20 39 12 0.22 40 19 0.35 ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55 Consensus pattern (38 bp): TATTATTGTTAGTTATATTATTTTTAGTAAAAAACTAT Found at i:58512155 original size:3 final size:3 Alignment explanation

Indices: 58512147--58512177 Score: 62 Period size: 3 Copynumber: 10.3 Consensus size: 3 58512137 AGTAAAAAAC 58512147 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T 58512178 GTGTTAGTTA Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 28 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TAT Found at i:58515083 original size:8 final size:8 Alignment explanation

Indices: 58515055--58515096 Score: 59 Period size: 8 Copynumber: 5.4 Consensus size: 8 58515045 GAGCTTAGGC * 58515055 TGTAAAGT 1 TGTAATGT * 58515063 TGTTATG- 1 TGTAATGT 58515070 TGTAATGT 1 TGTAATGT 58515078 TGTAATGT 1 TGTAATGT 58515086 TGTAATGT 1 TGTAATGT 58515094 TGT 1 TGT 58515097 TGTAACACCC Statistics Matches: 30, Mismatches: 3, Indels: 2 0.86 0.09 0.06 Matches are distributed among these distances: 7 6 0.20 8 24 0.80 ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50 Consensus pattern (8 bp): TGTAATGT Found at i:58517670 original size:16 final size:15 Alignment explanation

Indices: 58517649--58517678 Score: 51 Period size: 16 Copynumber: 1.9 Consensus size: 15 58517639 TAAAAAAATA 58517649 TATTATTTTCGTATTT 1 TATTATTTT-GTATTT 58517665 TATTATTTTGTATT 1 TATTATTTTGTATT 58517679 ATTTTAATAC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 5 0.36 16 9 0.64 ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70 Consensus pattern (15 bp): TATTATTTTGTATTT Found at i:58517708 original size:160 final size:159 Alignment explanation

Indices: 58517414--58517827 Score: 618 Period size: 160 Copynumber: 2.6 Consensus size: 159 58517404 TCAAAACAAT * * 58517414 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTC-TTTTTTCCTGGATTTTGTTAC 1 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTTCC-GAATTTTATTAC * * * 58517478 TTTCAAAAAATATACTATTTTGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTAAAAT 65 TATAAAAAAATATACTATTTTGTATTTTATTATTTTATATTATTTTAATACATAATGTTTAAAAT * 58517543 GTATTAATTTAGTGTG-TTTTTTATATAAA 130 GTATTAATTTAGTGTGAGTTTTTATATAAA 58517572 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTTTCCGAATTTTATTAC 1 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTC-TTTTTTTCCGAATTTTATTAC * * * 58517637 TATAAAAAAATATATTATTTTCGTATTTTATTATTTTGTATTATTTTAATACATAATGTTTGAAA 65 TATAAAAAAATATACTATTTT-GTATTTTATTATTTTATATTATTTTAATACATAATGTTTAAAA * 58517702 TGTATTATTTTAGTGTGAGTTTTTATATAAA 129 TGTATTAATTTAGTGTGAGTTTTTATATAAA * * 58517733 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTAATTTTCTTATTTT-CGAATTTTATTACT 1 TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTTCCGAATTTTATTACT * * ** * 58517797 TTCAGTAAATATACTATTTTTGTTTTTTATT 66 ATAAAAAAATATACTA-TTTTGTATTTTATT 58517828 TCTTTTCGTA Statistics Matches: 233, Mismatches: 18, Indels: 9 0.90 0.07 0.03 Matches are distributed among these distances: 158 43 0.18 159 62 0.27 160 74 0.32 161 54 0.23 ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54 Consensus pattern (159 bp): TTTAGTAAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTTTTTTCCGAATTTTATTACT ATAAAAAAATATACTATTTTGTATTTTATTATTTTATATTATTTTAATACATAATGTTTAAAATG TATTAATTTAGTGTGAGTTTTTATATAAA Found at i:58517876 original size:16 final size:16 Alignment explanation

Indices: 58517830--58517879 Score: 50 Period size: 16 Copynumber: 3.2 Consensus size: 16 58517820 TTTTTATTTC 58517830 TTTTC-GTATTTTATT 1 TTTTCAGTATTTTATT *** 58517845 TTTTCA-TAAACATATT 1 TTTTCAGT-ATTTTATT 58517861 TTTTCAGTATTTTATT 1 TTTTCAGTATTTTATT 58517877 TTT 1 TTT 58517880 AATGCTATTT Statistics Matches: 26, Mismatches: 6, Indels: 5 0.70 0.16 0.14 Matches are distributed among these distances: 15 6 0.23 16 19 0.73 17 1 0.04 ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66 Consensus pattern (16 bp): TTTTCAGTATTTTATT Found at i:58518212 original size:10 final size:10 Alignment explanation

Indices: 58518194--58518238 Score: 54 Period size: 10 Copynumber: 4.5 Consensus size: 10 58518184 CTTCTTCTCA * 58518194 TTTCCTTTTC 1 TTTCTTTTTC 58518204 TTTCTTTTTC 1 TTTCTTTTTC * * 58518214 TTTCTTCTCC 1 TTTCTTTTTC * 58518224 TTTCCTTTTC 1 TTTCTTTTTC 58518234 TTTCT 1 TTTCT 58518239 CCTCCTTCTG Statistics Matches: 28, Mismatches: 7, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 10 28 1.00 ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71 Consensus pattern (10 bp): TTTCTTTTTC Found at i:58518224 original size:45 final size:43 Alignment explanation

Indices: 58518109--58518224 Score: 110 Period size: 45 Copynumber: 2.6 Consensus size: 43 58518099 TTTCCTTTTT 58518109 TTTTCTTTCTTTTTCCTTCATTC-CCTCCCTCTTCTTCTTCTCC 1 TTTTCTTTCTTTTTCCTTC-TTCTCCTCCCTCTTCTTCTTCTCC * * ** * 58518152 TTCTCTTTCTCTTTTTCCTGCGCCTCCT-CCTCCTTCTTCTCATTTCC 1 TTTTC-TT-TCTTTTTCCTTCTTCTCCTCCCT-CTTCTTCT--TCTCC * 58518199 TTTTCTTTCTTTTTCTTTCTTCTCCT 1 TTTTCTTTCTTTTTCCTTCTTCTCCT 58518225 TTCCTTTTCT Statistics Matches: 57, Mismatches: 10, Indels: 10 0.74 0.13 0.13 Matches are distributed among these distances: 43 4 0.07 44 6 0.11 45 37 0.65 46 2 0.04 47 8 0.14 ACGTcount: A:0.02, C:0.38, G:0.02, T:0.59 Consensus pattern (43 bp): TTTTCTTTCTTTTTCCTTCTTCTCCTCCCTCTTCTTCTTCTCC Found at i:58518243 original size:20 final size:20 Alignment explanation

Indices: 58518203--58518245 Score: 68 Period size: 20 Copynumber: 2.1 Consensus size: 20 58518193 ATTTCCTTTT * * 58518203 CTTTCTTTTTCTTTCTTCTC 1 CTTTCCTTTTCTTTCTCCTC 58518223 CTTTCCTTTTCTTTCTCCTC 1 CTTTCCTTTTCTTTCTCCTC 58518243 CTT 1 CTT 58518246 CTGCCGAAGT Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65 Consensus pattern (20 bp): CTTTCCTTTTCTTTCTCCTC Found at i:58518338 original size:27 final size:27 Alignment explanation

Indices: 58518290--58518354 Score: 76 Period size: 27 Copynumber: 2.4 Consensus size: 27 58518280 TCCCCCAAGG * * * * 58518290 TGGTGCCGCCTGTGGCAGTGGCACATT 1 TGGTGCCGCCTCTGCCACTGGCACATC * 58518317 TGGTGCCGCCTCTGCCACTGGCACCTC 1 TGGTGCCGCCTCTGCCACTGGCACATC * 58518344 TAGTGCCGCCT 1 TGGTGCCGCCT 58518355 GTGGCAGGCC Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 27 32 1.00 ACGTcount: A:0.09, C:0.35, G:0.31, T:0.25 Consensus pattern (27 bp): TGGTGCCGCCTCTGCCACTGGCACATC Found at i:58518583 original size:18 final size:18 Alignment explanation

Indices: 58518547--58518588 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 18 58518537 AAATAATGTT 58518547 AATTTTGAGTAGAATTTAA 1 AATTTTGAGTAGAATTT-A 58518566 AATTTTGATGT-G-ATTTA 1 AATTTTGA-GTAGAATTTA 58518583 AATTTT 1 AATTTT 58518589 AATTTACTAA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 17 7 0.32 18 4 0.18 19 9 0.41 20 2 0.09 ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50 Consensus pattern (18 bp): AATTTTGAGTAGAATTTA Found at i:58523243 original size:31 final size:31 Alignment explanation

Indices: 58523205--58523274 Score: 113 Period size: 31 Copynumber: 2.3 Consensus size: 31 58523195 TATAAAATGA * * 58523205 TCACTAAACTATTTGAAAGTTTTTATTCAAG 1 TCACTAAACTATTCGAAAATTTTTATTCAAG * 58523236 TCACTAAACTATTCGAAAATTTTTATTTAAG 1 TCACTAAACTATTCGAAAATTTTTATTCAAG 58523267 TCACTAAA 1 TCACTAAA 58523275 TTGTTAAGTT Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 31 36 1.00 ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40 Consensus pattern (31 bp): TCACTAAACTATTCGAAAATTTTTATTCAAG Found at i:58525230 original size:2 final size:2 Alignment explanation

Indices: 58525223--58525255 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 58525213 GATACAATGA 58525223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A 58525256 GTTGAAAGGA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 31 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:58528934 original size:26 final size:24 Alignment explanation

Indices: 58528902--58528951 Score: 64 Period size: 24 Copynumber: 2.0 Consensus size: 24 58528892 CAATTCAGTT * 58528902 AATAAAATTATAAAAATATTTTTTAA 1 AATAAAA-TA-AAAAATATTATTTAA * 58528928 AATAAAATAAAATATATTATTTAA 1 AATAAAATAAAAAATATTATTTAA 58528952 GGATATTTTA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 24 13 0.59 25 2 0.09 26 7 0.32 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (24 bp): AATAAAATAAAAAATATTATTTAA Found at i:58530951 original size:19 final size:21 Alignment explanation

Indices: 58530928--58530974 Score: 55 Period size: 19 Copynumber: 2.4 Consensus size: 21 58530918 GAATTTTTTT * * 58530928 TTATTTGTT-TATTTTTTGAA 1 TTATTTGTTATAATTTTTAAA 58530948 -TATTT-TTATAATTTTTAAA 1 TTATTTGTTATAATTTTTAAA 58530967 TTATTTGT 1 TTATTTGT 58530975 AGACTTGGTA Statistics Matches: 22, Mismatches: 2, Indels: 5 0.76 0.07 0.17 Matches are distributed among these distances: 18 2 0.09 19 14 0.64 20 5 0.23 21 1 0.05 ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68 Consensus pattern (21 bp): TTATTTGTTATAATTTTTAAA Found at i:58531739 original size:37 final size:39 Alignment explanation

Indices: 58531692--58531765 Score: 98 Period size: 37 Copynumber: 1.9 Consensus size: 39 58531682 ACAAAATAAA * 58531692 TTTTAAATTTTCAAAATATT-TA-TAAAAAATATATATT 1 TTTTAAATTTTCAAAAAATTATACTAAAAAATATATATT * * * 58531729 TTTTATATTTTTAAAAAATTATACTAAAGAATATATA 1 TTTTAAATTTTCAAAAAATTATACTAAAAAATATATA 58531766 AAGAAAATTT Statistics Matches: 31, Mismatches: 4, Indels: 2 0.84 0.11 0.05 Matches are distributed among these distances: 37 17 0.55 38 2 0.06 39 12 0.39 ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47 Consensus pattern (39 bp): TTTTAAATTTTCAAAAAATTATACTAAAAAATATATATT Done.