Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr05 97880472 

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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 192 characters in sequence are not A, C, G, or T


File 299 of 335

Found at i:89046215 original size:2 final size:2

Alignment explanation

Indices: 89046210--89046246 Score: 67 Period size: 2 Copynumber: 19.0 Consensus size: 2 89046200 AAAAAAAAAA 89046210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 89046247 GACAGGATTA Statistics Matches: 34, Mismatches: 0, Indels: 2 0.94 0.00 0.06 Matches are distributed among these distances: 1 1 0.03 2 33 0.97 ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49 Consensus pattern (2 bp): AT Found at i:89047896 original size:30 final size:30 Alignment explanation

Indices: 89047860--89047922 Score: 90 Period size: 30 Copynumber: 2.1 Consensus size: 30 89047850 ACTTATTTTA 89047860 TTGTTAACTTTGTTATTATTTTAAAGACAT 1 TTGTTAACTTTGTTATTATTTTAAAGACAT * * * * 89047890 TTGTTAATTTTTTTATTATTTTAGAGGCAT 1 TTGTTAACTTTGTTATTATTTTAAAGACAT 89047920 TTG 1 TTG 89047923 CTTGTTAAAT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57 Consensus pattern (30 bp): TTGTTAACTTTGTTATTATTTTAAAGACAT Found at i:89048027 original size:19 final size:20 Alignment explanation

Indices: 89047998--89048045 Score: 57 Period size: 18 Copynumber: 2.5 Consensus size: 20 89047988 TTGTTGGAAA * 89047998 ATATTTA-TTTTGATGT-TT 1 ATATTTATTTTTTATGTATT * 89048016 TTA-TTATTTTTTATGTATT 1 ATATTTATTTTTTATGTATT 89048035 ATATTTATTTT 1 ATATTTATTTT 89048046 AAATTTATAA Statistics Matches: 24, Mismatches: 3, Indels: 4 0.77 0.10 0.13 Matches are distributed among these distances: 17 3 0.12 18 10 0.42 19 4 0.17 20 7 0.29 ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71 Consensus pattern (20 bp): ATATTTATTTTTTATGTATT Found at i:89050417 original size:52 final size:52 Alignment explanation

Indices: 89050355--89050458 Score: 190 Period size: 52 Copynumber: 2.0 Consensus size: 52 89050345 TATAGTTTAA 89050355 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT 1 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT * * 89050407 CCTATTTTTAAATAGTAAAACAAGTCCTGCGAAGTCAATCCAAATTTAAACT 1 CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT 89050459 ATCTAAACCC Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 52 50 1.00 ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30 Consensus pattern (52 bp): CCTATTTTTAAATAGTAAAACAAGTCCTGCAAAGTCAAGCCAAATTTAAACT Found at i:89050681 original size:21 final size:21 Alignment explanation

Indices: 89050657--89050720 Score: 60 Period size: 21 Copynumber: 3.1 Consensus size: 21 89050647 ACCATAATCT 89050657 ATTTTTATAAAAATATTTAAA 1 ATTTTTATAAAAATATTTAAA * * * 89050678 A-TTTAAAAGAAAATATATAAA 1 ATTTTTATA-AAAATATTTAAA ** 89050699 AAATTTATAAAAAT-TTTAAA 1 ATTTTTATAAAAATATTTAAA 89050719 AT 1 AT 89050721 ATAAAAGAAA Statistics Matches: 33, Mismatches: 8, Indels: 5 0.72 0.17 0.11 Matches are distributed among these distances: 20 11 0.33 21 18 0.55 22 4 0.12 ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39 Consensus pattern (21 bp): ATTTTTATAAAAATATTTAAA Found at i:89050738 original size:26 final size:27 Alignment explanation

Indices: 89050687--89050753 Score: 75 Period size: 26 Copynumber: 2.4 Consensus size: 27 89050677 AATTTAAAAG * 89050687 AAAATATATAAAAAATTTATAAAAATTTT 1 AAAATATA-AAAAAATTTAT-AAAATTAT 89050716 AAAATATAAAAGAAA-TTAT-AAATTAT 1 AAAATATAAAA-AAATTTATAAAATTAT * 89050742 AAATTATAAAAA 1 AAAATATAAAAA 89050754 TATGTGTATC Statistics Matches: 35, Mismatches: 2, Indels: 6 0.81 0.05 0.14 Matches are distributed among these distances: 25 1 0.03 26 16 0.46 28 7 0.20 29 11 0.31 ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33 Consensus pattern (27 bp): AAAATATAAAAAAATTTATAAAATTAT Found at i:89050749 original size:42 final size:42 Alignment explanation

Indices: 89050661--89050756 Score: 126 Period size: 42 Copynumber: 2.3 Consensus size: 42 89050651 TAATCTATTT * * 89050661 TTATAAAAATATTTAAAATTTAAAAGAAAATATATAAAAAAT 1 TTATAAAAATATTTAAAATATAAAAGAAAATATATAAAAAAA 89050703 TTATAAAAAT-TTTAAAATATAAAAG-AAAT-TATAAATTATAAA 1 TTATAAAAATATTTAAAATATAAAAGAAAATATATAAA--A-AAA 89050745 TTATAAAAATAT 1 TTATAAAAATAT 89050757 GTGTATCTAA Statistics Matches: 48, Mismatches: 2, Indels: 7 0.84 0.04 0.12 Matches are distributed among these distances: 39 6 0.12 40 4 0.08 41 15 0.31 42 22 0.46 43 1 0.02 ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35 Consensus pattern (42 bp): TTATAAAAATATTTAAAATATAAAAGAAAATATATAAAAAAA Found at i:89051539 original size:66 final size:66 Alignment explanation

Indices: 89051433--89051556 Score: 248 Period size: 66 Copynumber: 1.9 Consensus size: 66 89051423 TAACTTGTTC 89051433 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA 1 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA 89051498 T 66 T 89051499 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAA 1 TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAA 89051557 GGGTTTAATG Statistics Matches: 58, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 66 58 1.00 ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31 Consensus pattern (66 bp): TAAAAGCATGAGATGTCTTCCAAATGCAATGCATGCTGACATGTATGATATTTAAAAATGGCTTA T Found at i:89056380 original size:20 final size:22 Alignment explanation

Indices: 89056354--89056397 Score: 63 Period size: 22 Copynumber: 2.0 Consensus size: 22 89056344 CATAATCTAT * * 89056354 TTTTTAAA-AAAATATTTAAAA 1 TTTTAAAAGAAAATATATAAAA 89056375 TTTTAAAAGAAAATATATAAAA 1 TTTTAAAAGAAAATATATAAAA 89056397 T 1 T 89056398 ATATAAAATT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 21 7 0.35 22 13 0.65 ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39 Consensus pattern (22 bp): TTTTAAAAGAAAATATATAAAA Found at i:89056398 original size:9 final size:9 Alignment explanation

Indices: 89056384--89056418 Score: 52 Period size: 9 Copynumber: 3.9 Consensus size: 9 89056374 ATTTTAAAAG 89056384 AAAATATAT 1 AAAATATAT 89056393 AAAATATAT 1 AAAATATAT * * 89056402 AAAATTTTT 1 AAAATATAT 89056411 AAAATATA 1 AAAATATA 89056419 AAAGAAATTA Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 9 22 1.00 ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37 Consensus pattern (9 bp): AAAATATAT Found at i:89060275 original size:2 final size:2 Alignment explanation

Indices: 89060268--89060293 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 89060258 TATGCCCATA 89060268 AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT 89060294 TGTAGCACCC Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:89061247 original size:27 final size:26 Alignment explanation

Indices: 89061210--89061324 Score: 140 Period size: 27 Copynumber: 4.3 Consensus size: 26 89061200 AGCATGGCTG * * 89061210 CCAGAACAGATAATGTGACAGAGTCA 1 CCAGAACAGATAATGTGGCAGAGCCA 89061236 CCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGA-ACAGATAAT-GTGGCAGAGCCA 89061264 CCAGAACAGATATATGTGGCAGAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA * * * 89061291 CCAGATCAGATATTTGTGGCATAGCCA 1 CCAGAACAGATA-ATGTGGCAGAGCCA * 89061318 TCAGAAC 1 CCAGAAC 89061325 GCTTCCTCCA Statistics Matches: 79, Mismatches: 7, Indels: 5 0.87 0.08 0.05 Matches are distributed among these distances: 26 5 0.06 27 57 0.72 28 17 0.22 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17 Consensus pattern (26 bp): CCAGAACAGATAATGTGGCAGAGCCA Found at i:89061274 original size:54 final size:54 Alignment explanation

Indices: 89061210--89061324 Score: 160 Period size: 54 Copynumber: 2.1 Consensus size: 54 89061200 AGCATGGCTG * 89061210 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA * * * * 89061264 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA 1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA * 89061318 TCAGAAC 1 CCAGAAC 89061325 GCTTCCTCCA Statistics Matches: 54, Mismatches: 6, Indels: 2 0.87 0.10 0.03 Matches are distributed among these distances: 54 36 0.67 55 18 0.33 ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17 Consensus pattern (54 bp): CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA Found at i:89062975 original size:26 final size:26 Alignment explanation

Indices: 89062938--89063046 Score: 175 Period size: 26 Copynumber: 4.2 Consensus size: 26 89062928 CATGAAATTC * 89062938 TTAT-ATGAAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCCA 89062963 TTATCATGGAACATTTACCTAACCCA 1 TTATCATGGAACATTTACCTAACCCA * 89062989 TTATCATGGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCCA * * 89063015 TTATCATTGAACATTTACCTAACCTA 1 TTATCATGGAACATTTACCTAACCCA 89063041 TTATCA 1 TTATCA 89063047 ATTTGTACCA Statistics Matches: 80, Mismatches: 3, Indels: 1 0.95 0.04 0.01 Matches are distributed among these distances: 25 4 0.05 26 76 0.95 ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35 Consensus pattern (26 bp): TTATCATGGAACATTTACCTAACCCA Found at i:89065821 original size:3 final size:3 Alignment explanation

Indices: 89065813--89065841 Score: 58 Period size: 3 Copynumber: 9.7 Consensus size: 3 89065803 AGGTGAACCA 89065813 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT 89065842 TTTTCTTAAT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69 Consensus pattern (3 bp): TTC Found at i:89071947 original size:21 final size:21 Alignment explanation

Indices: 89071921--89071961 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 89071911 ATCTGCTCAA * * 89071921 ACTCCACCTGTTTTGGAGTAC 1 ACTCCACCTGCTGTGGAGTAC 89071942 ACTCCACCTGCTGTGGAGTA 1 ACTCCACCTGCTGTGGAGTA 89071962 TCGCTTGTCT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29 Consensus pattern (21 bp): ACTCCACCTGCTGTGGAGTAC Found at i:89082314 original size:2 final size:2 Alignment explanation

Indices: 89082307--89082339 Score: 66 Period size: 2 Copynumber: 16.5 Consensus size: 2 89082297 ATCTATGCAC 89082307 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 89082340 AGGTATCTTA 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:89083959 original size:2 final size:2 Alignment explanation

Indices: 89083952--89083994 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 89083942 ATTGAAAGGG * 89083952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 89083994 A 1 A 89083995 AAAGTATGTG Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49 Consensus pattern (2 bp): AT Found at i:89085470 original size:26 final size:26 Alignment explanation

Indices: 89085434--89085543 Score: 184 Period size: 26 Copynumber: 4.2 Consensus size: 26 89085424 TGATACAAAT 89085434 TGATAATAGGTTAGGTAAATGTTCCA 1 TGATAATAGGTTAGGTAAATGTTCCA 89085460 TGATAATAGGTTAGGTAAATGTTCCA 1 TGATAATAGGTTAGGTAAATGTTCCA * * 89085486 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATAGGTTAGGTAAATGTTCCA * * 89085512 TGATAATGGGTTAGGTAAATGTTTCA 1 TGATAATAGGTTAGGTAAATGTTCCA 89085538 TGATAA 1 TGATAA 89085544 GAATTTCATG Statistics Matches: 82, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 26 82 1.00 ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36 Consensus pattern (26 bp): TGATAATAGGTTAGGTAAATGTTCCA Found at i:89087056 original size:26 final size:26 Alignment explanation

Indices: 89087026--89087078 Score: 72 Period size: 26 Copynumber: 2.0 Consensus size: 26 89087016 TTTATAGTTT 89087026 TACCCCTAGGAGATAAATT-ACCGAAA 1 TACCCCTAGG-GATAAATTGACCGAAA * * 89087052 TACCCCTAGGGTTAAATTGACCTAAA 1 TACCCCTAGGGATAAATTGACCGAAA 89087078 T 1 T 89087079 GCATGTTTGA Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 25 7 0.29 26 17 0.71 ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25 Consensus pattern (26 bp): TACCCCTAGGGATAAATTGACCGAAA Found at i:89088988 original size:24 final size:24 Alignment explanation

Indices: 89088956--89089008 Score: 63 Period size: 24 Copynumber: 2.2 Consensus size: 24 89088946 TAATTTGTGC * * 89088956 ATATTAAAATAAAAACATATG-GAA 1 ATATCAAAAT-AAAACATATGAAAA * 89088980 ATATCAAAATGAAACATATGAAAA 1 ATATCAAAATAAAACATATGAAAA 89089004 ATATC 1 ATATC 89089009 CAATTGGTGT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 23 9 0.36 24 16 0.64 ACGTcount: A:0.60, C:0.08, G:0.08, T:0.25 Consensus pattern (24 bp): ATATCAAAATAAAACATATGAAAA Found at i:89089611 original size:10 final size:10 Alignment explanation

Indices: 89089596--89089621 Score: 52 Period size: 10 Copynumber: 2.6 Consensus size: 10 89089586 TATTTTTATT 89089596 TTTAAAAATA 1 TTTAAAAATA 89089606 TTTAAAAATA 1 TTTAAAAATA 89089616 TTTAAA 1 TTTAAA 89089622 TATTAGTATA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 16 1.00 ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42 Consensus pattern (10 bp): TTTAAAAATA Found at i:89089642 original size:26 final size:25 Alignment explanation

Indices: 89089613--89089697 Score: 68 Period size: 26 Copynumber: 3.3 Consensus size: 25 89089603 ATATTTAAAA 89089613 ATATTTAAATATTAGTATAAAATATT 1 ATATTTAAATATTA-TATAAAATATT * 89089639 ATATTTTTTAATATTAT-TAAACATA-T 1 ATA--TTTAAATATTATATAAA-ATATT * ** 89089665 ATATTTAATTATTAATATAATTTATT 1 ATATTTAAATATT-ATATAAAATATT 89089691 AT-TTTAA 1 ATATTTAA 89089698 TAAATTATTT Statistics Matches: 48, Mismatches: 5, Indels: 13 0.73 0.08 0.20 Matches are distributed among these distances: 24 8 0.17 25 9 0.19 26 17 0.35 27 4 0.08 28 10 0.21 ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53 Consensus pattern (25 bp): ATATTTAAATATTATATAAAATATT Found at i:89092665 original size:47 final size:47 Alignment explanation

Indices: 89092600--89092893 Score: 482 Period size: 47 Copynumber: 6.3 Consensus size: 47 89092590 ATAAGATATG * * 89092600 TATATGTGGTAAAGCCGAATGGCCAATGTGACGAATGTGAATGTGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA * 89092647 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATATGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA * 89092694 TATATGTGATAAGGCCAAATGGCCAATGTGACGAATGTG-ATGTGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA 89092740 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA * * 89092787 TATATGTGATACGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA * * * * 89092834 TATATGTGATAAGGCCAAATGGCCAATGTGATGGATGTGAAAGTGTA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA * 89092881 TAAATGTGATAAG 1 TATATGTGATAAG 89092894 TCCCGAAGGG Statistics Matches: 233, Mismatches: 13, Indels: 2 0.94 0.05 0.01 Matches are distributed among these distances: 46 44 0.19 47 189 0.81 ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28 Consensus pattern (47 bp): TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTA Found at i:89092770 original size:22 final size:22 Alignment explanation

Indices: 89092743--89092865 Score: 61 Period size: 22 Copynumber: 5.3 Consensus size: 22 89092733 ATGTGTATAT 89092743 ATGTGATAAGGCCGAATGGCCA 1 ATGTGATAAGGCCGAATGGCCA * * * ** 89092765 ATGTGACGAATG-TGAATGTGTATA 1 ATGTGA-TAAGGCCGAATG-G-CCA * 89092789 TATGTGATACGGCCGAATGGCCA 1 -ATGTGATAAGGCCGAATGGCCA * * ** 89092812 ATGTGATGAATG-TGAATGTGTATA 1 ATGTGAT-AAGGCCGAATG-G-CCA * 89092836 TATGTGATAAGGCCAAATGGCCA 1 -ATGTGATAAGGCCGAATGGCCA 89092859 ATGTGAT 1 ATGTGAT 89092866 GGATGTGAAA Statistics Matches: 70, Mismatches: 21, Indels: 20 0.63 0.19 0.18 Matches are distributed among these distances: 22 30 0.43 23 9 0.13 24 9 0.13 25 22 0.31 ACGTcount: A:0.32, C:0.11, G:0.29, T:0.28 Consensus pattern (22 bp): ATGTGATAAGGCCGAATGGCCA Found at i:89092852 original size:140 final size:141 Alignment explanation

Indices: 89092600--89092893 Score: 500 Period size: 140 Copynumber: 2.1 Consensus size: 141 89092590 ATAAGATATG * * 89092600 TATATGTGGTAAAGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA 89092665 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT 66 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT * 89092730 GTG-ATGTGTA 131 GTGAAAGTGTA * 89092740 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATACGGCCGA 1 TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA * * * * 89092805 ATGGCCAATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCAAATGGCCAATGTGATGGAT 66 ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT 89092870 GTGAAAGTGTA 131 GTGAAAGTGTA * 89092881 TAAATGTGATAAG 1 TATATGTGATAAG 89092894 TCCCGAAGGG Statistics Matches: 144, Mismatches: 9, Indels: 1 0.94 0.06 0.01 Matches are distributed among these distances: 140 126 0.88 141 18 0.12 ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28 Consensus pattern (141 bp): TATATGTGATAAGGCCGAATGGCCAATGTGACGAATGTGAATGTGTATATATGTGATAAGGCCGA ATGGCCAATGTGACGAATGTGAATATGTATATATGTGATAAGGCCAAATGGCCAATGTGACGAAT GTGAAAGTGTA Found at i:89096159 original size:92 final size:93 Alignment explanation

Indices: 89096035--89096287 Score: 292 Period size: 92 Copynumber: 2.8 Consensus size: 93 89096025 TTAAAAAAAG * 89096035 AAAAGCAATTAAG--TCTCCTTTTTTTTTTTTGCACTCAATTGGATAGC-TGAACTTTCAAGGTG 1 AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATA-CTTGAACTTTCAAAGTG * 89096097 TATCAAAAAGG-CTCTCAAACTTTTT-AAA 65 CATCAAAAAGGTC-CTCAAACTTTTTCAAA * * * * 89096125 AAAAGTAATTAAGCCTCTGCTTTTTTTTTTTTGCACTCAATTGGGTACTTGAA-TATTCAAAATG 1 AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACT-TTCAAAGTG * * 89096189 CATTAAAAAGGTCCTCAAATTTTTTCAAA 65 CATCAAAAAGGTCCTCAAACTTTTTCAAA ** * * 89096218 AAAATGCAATTAA-CC-C-CCTACTTTTTTTTTGCACT-AACTGGATACTTGAACTGTCAAAGTG 1 AAAA-GCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAGTG 89096279 CATCAAAAA 65 CATCAAAAA 89096288 AGCCCTGTGA Statistics Matches: 138, Mismatches: 17, Indels: 16 0.81 0.10 0.09 Matches are distributed among these distances: 90 40 0.29 91 19 0.14 92 62 0.45 93 10 0.07 94 7 0.05 ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37 Consensus pattern (93 bp): AAAAGCAATTAAGCCTCTCCTTTTTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAGTGC ATCAAAAAGGTCCTCAAACTTTTTCAAA Found at i:89096418 original size:19 final size:19 Alignment explanation

Indices: 89096396--89096451 Score: 60 Period size: 19 Copynumber: 2.9 Consensus size: 19 89096386 TAAAATCAAT 89096396 AAAATATATAAAAATTAGA 1 AAAATATATAAAAATTAGA * * 89096415 AAAAT-TATAAAATTTTATA 1 AAAATATATAAAA-ATTAGA * 89096434 AAAATCATAAAAAAATTA 1 AAAAT-ATATAAAAATTA 89096452 TAAATTGCAT Statistics Matches: 30, Mismatches: 4, Indels: 5 0.77 0.10 0.13 Matches are distributed among these distances: 18 7 0.23 19 14 0.47 20 3 0.10 21 6 0.20 ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30 Consensus pattern (19 bp): AAAATATATAAAAATTAGA Found at i:89096443 original size:9 final size:9 Alignment explanation

Indices: 89096396--89096446 Score: 57 Period size: 9 Copynumber: 5.4 Consensus size: 9 89096386 TAAAATCAAT 89096396 AAAATATATA 1 AAAAT-TATA * 89096406 AAAATTAGA 1 AAAATTATA 89096415 AAAATTATA 1 AAAATTATA * 89096424 AAATTTTATA 1 AAA-ATTATA * 89096434 AAAATCATA 1 AAAATTATA 89096443 AAAA 1 AAAA 89096447 AATTATAAAT Statistics Matches: 35, Mismatches: 5, Indels: 3 0.81 0.12 0.07 Matches are distributed among these distances: 9 22 0.63 10 13 0.37 ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29 Consensus pattern (9 bp): AAAATTATA Found at i:89096656 original size:21 final size:18 Alignment explanation

Indices: 89096635--89096707 Score: 74 Period size: 20 Copynumber: 3.8 Consensus size: 18 89096625 GTACTATAAT 89096635 TTTTATATATTTTTTACGAA 1 TTTTATAT-TTTTTTAC-AA * * 89096655 TTTTATATTTCTTTACATTT 1 TTTTATATTTTTTTACA--A * 89096675 TTTTATAATTTTCTTACAA 1 TTTTAT-ATTTTTTTACAA 89096694 TTTTATATTTTTTT 1 TTTTATATTTTTTT 89096708 CTATTTTTAT Statistics Matches: 44, Mismatches: 6, Indels: 8 0.76 0.10 0.14 Matches are distributed among these distances: 18 8 0.18 19 13 0.30 20 14 0.32 21 9 0.20 ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67 Consensus pattern (18 bp): TTTTATATTTTTTTACAA Found at i:89096686 original size:39 final size:39 Alignment explanation

Indices: 89096634--89096725 Score: 116 Period size: 39 Copynumber: 2.3 Consensus size: 39 89096624 GGTACTATAA 89096634 TTTTTATATATTTT-TTACGAATTTTATATTTCTTTAC-ATT 1 TTTTTATA-ATTTTCTTAC-AATTTTATATTT-TTTACTATT * 89096674 TTTTTATAATTTTCTTACAATTTTATATTTTTTTCTATT 1 TTTTTATAATTTTCTTACAATTTTATATTTTTTACTATT * 89096713 TTTATTAAAATTT 1 TTT-TTATAATTT 89096726 AATAATTTAA Statistics Matches: 47, Mismatches: 2, Indels: 6 0.85 0.04 0.11 Matches are distributed among these distances: 38 4 0.09 39 23 0.49 40 20 0.43 ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66 Consensus pattern (39 bp): TTTTTATAATTTTCTTACAATTTTATATTTTTTACTATT Found at i:89096698 original size:29 final size:29 Alignment explanation

Indices: 89096666--89096725 Score: 75 Period size: 29 Copynumber: 2.1 Consensus size: 29 89096656 TTTATATTTC * * 89096666 TTTACATTTTTTTATAATTTTCTTACAAT 1 TTTACATTTTTTTATAATTTTATTAAAAT * * * 89096695 TTTATATTTTTTTCTATTTTTATTAAAAT 1 TTTACATTTTTTTATAATTTTATTAAAAT 89096724 TT 1 TT 89096726 AATAATTTAA Statistics Matches: 26, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 29 26 1.00 ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67 Consensus pattern (29 bp): TTTACATTTTTTTATAATTTTATTAAAAT Found at i:89097068 original size:85 final size:86 Alignment explanation

Indices: 89096856--89097101 Score: 302 Period size: 86 Copynumber: 2.9 Consensus size: 86 89096846 GTCAAAAAGC * * * * * ** * * * 89096856 CTTTTTGAAGCATTTTGATAGTTCAAGTATCCAACTGAGTG-AAAATTGGAGGGGTTTAATTGC- 1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT * 89096919 TTTTTTAAAAAAGTTAAGGGT 66 TTTTTTGAAAAAGTTAAGGGT * * 89096940 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAA-AATGGGCTTAATTACT 1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT * 89097004 TTTTTTGAAAAAGTTTGAGGGT 66 TTTTTTGAAAAAG-TTAAGGGT * * * 89097026 CTTTTTGATGTATTTTGAAAGTT-AAGTACCCAATTTAATGCAAAAAAGAAGGGGCTTAATTAAT 1 CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT 89097090 TTTTTTGAAAAA 66 TTTTTTGAAAAA 89097102 AAATTGAGGA Statistics Matches: 141, Mismatches: 17, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 84 48 0.34 85 38 0.27 86 55 0.39 ACGTcount: A:0.34, C:0.09, G:0.20, T:0.38 Consensus pattern (86 bp): CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAATGCAAAAAAGAAGGGGCTTAATTACT TTTTTTGAAAAAGTTAAGGGT Found at i:89099829 original size:47 final size:44 Alignment explanation

Indices: 89099760--89099877 Score: 130 Period size: 46 Copynumber: 2.6 Consensus size: 44 89099750 GAGTTCTGAA * * 89099760 CTCGTTGAGTTGAGCCCGAGTTCGTGA-GATGTAACTAGGCATCCGAG 1 CTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGTAA--ACGC--CCGAG * * * 89099807 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACGCGCGAG 1 CTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGTAAACGCCCGAG 89099853 CTCGTTGAGTTGAGTCCGAGTTCGT 1 CTCGTTGAGTTGAGTCCGAGTTCGT 89099878 TTATGGGCGG Statistics Matches: 62, Mismatches: 6, Indels: 8 0.82 0.08 0.11 Matches are distributed among these distances: 45 1 0.02 46 27 0.44 47 22 0.35 48 5 0.08 50 7 0.11 ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29 Consensus pattern (44 bp): CTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGTAAACGCCCGAG Found at i:89104843 original size:93 final size:93 Alignment explanation

Indices: 89104731--89104902 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 89104721 GCCCATAAGT * * 89104731 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 89104796 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 89104824 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 89104889 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 89104903 CAAATATCCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:89104898 original size:46 final size:46 Alignment explanation

Indices: 89104723--89104898 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 89104713 TGTAACCCGC * * * 89104723 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 89104769 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 89104819 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 89104862 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 89104899 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:89112027 original size:19 final size:18 Alignment explanation

Indices: 89112005--89112044 Score: 71 Period size: 19 Copynumber: 2.2 Consensus size: 18 89111995 AGAATAAAAC 89112005 TTATCTACCTAAATAAGAT 1 TTATCTACCTAAATAA-AT 89112024 TTATCTACCTAAATAAAT 1 TTATCTACCTAAATAAAT 89112042 TTA 1 TTA 89112045 AAATGTATGC Statistics Matches: 21, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 5 0.24 19 16 0.76 ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40 Consensus pattern (18 bp): TTATCTACCTAAATAAAT Found at i:89112993 original size:40 final size:40 Alignment explanation

Indices: 89112919--89112994 Score: 98 Period size: 40 Copynumber: 1.9 Consensus size: 40 89112909 TCACACCATG * ** 89112919 TGGGAATAAAATCGACCCACCCATCCCTGTACACCAAATA 1 TGGGAATAAAATCGACCCACCCAACCCTAAACACCAAATA * * * 89112959 TGGGGATAATATCGACCCATCCAACCCTAAACACCA 1 TGGGAATAAAATCGACCCACCCAACCCTAAACACCA 89112995 TAAGGTATCA Statistics Matches: 30, Mismatches: 6, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 40 30 1.00 ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17 Consensus pattern (40 bp): TGGGAATAAAATCGACCCACCCAACCCTAAACACCAAATA Found at i:89123144 original size:46 final size:46 Alignment explanation

Indices: 89123092--89123498 Score: 582 Period size: 46 Copynumber: 8.8 Consensus size: 46 89123082 GAGTGTGCTC * 89123092 CCTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 89123138 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA * * 89123184 CGTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 89123230 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA * * 89123276 CGTGATATGAAATGTATAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA * ** 89123322 CGTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA * * * 89123368 CCTAACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA * *** ** 89123414 CATGACGGGAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA 1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA ** * * * * 89123461 AATGATA-GAAAACGAGTAAAACCATAGTTGAAAGATAC 1 CCTGATATG-AAATGTGTAAGACCATGGTTGAAAGATAC 89123499 TATGACATCA Statistics Matches: 336, Mismatches: 24, Indels: 2 0.93 0.07 0.01 Matches are distributed among these distances: 46 296 0.88 47 40 0.12 ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22 Consensus pattern (46 bp): CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA Found at i:89130237 original size:43 final size:44 Alignment explanation

Indices: 89130157--89130273 Score: 116 Period size: 43 Copynumber: 2.7 Consensus size: 44 89130147 TCGATGCCAC * 89130157 TGTCCTAGACAA-GGTCTTATACG-AAATCAC-ATAACAATACCGA 1 TGTCCTAGA-AATGGTCTTATATGTAAA-CACAATAACAATACCGA * * 89130200 TGTCCTAGAAATGGTCTTATATGTAAACACAAT-ACAATGCCTA 1 TGTCCTAGAAATGGTCTTATATGTAAACACAATAACAATACCGA * * * * * 89130243 TGTCCCAGACATGATCTTACATGTAATCACA 1 TGTCCTAGAAATGGTCTTATATGTAAACACA 89130274 TCCCGGTAAT Statistics Matches: 63, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 42 2 0.03 43 56 0.89 44 5 0.08 ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27 Consensus pattern (44 bp): TGTCCTAGAAATGGTCTTATATGTAAACACAATAACAATACCGA Found at i:89131182 original size:11 final size:11 Alignment explanation

Indices: 89131164--89131203 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 89131154 ACAATAACAA 89131164 CAAAATAATAG 1 CAAAATAATAG * 89131175 CAACATAATAG 1 CAAAATAATAG * * 89131186 TAAAATAGTAG 1 CAAAATAATAG 89131197 CAAAATA 1 CAAAATA 89131204 TGGAAAAAAC Statistics Matches: 24, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 11 24 1.00 ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20 Consensus pattern (11 bp): CAAAATAATAG Found at i:89135297 original size:129 final size:129 Alignment explanation

Indices: 89135064--89135320 Score: 455 Period size: 129 Copynumber: 2.0 Consensus size: 129 89135054 AACTTTGGCC 89135064 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC 1 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC * * 89135129 CACTCGTTTTTCTTCCATTTGTTAGTTTCTTATAGAGCTTCCAACACGTTTCTCGAGTGTGCCG 66 CACTCGTTTTTCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCCG * 89135193 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCTCTAATTGT-AAGCCACAACCATTG 1 CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAA-CCACAACCATTG 89135257 CCACTC-TTTTTCCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCC 65 CCACTCGTTTTT-CTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCC 89135321 AATATTTTTT Statistics Matches: 123, Mismatches: 3, Indels: 4 0.95 0.02 0.03 Matches are distributed among these distances: 128 7 0.06 129 116 0.94 ACGTcount: A:0.21, C:0.26, G:0.14, T:0.38 Consensus pattern (129 bp): CTCATAATTTCCATTAGTTGTTTGGAAAGCTCTGCTATCCCCTAATTGTGAACCACAACCATTGC CACTCGTTTTTCTTCCATTTGTCAGTTTCTTATAAAGCTTCCAACACGTTTCTCGAGTGTGCCG Found at i:89135492 original size:16 final size:16 Alignment explanation

Indices: 89135471--89135504 Score: 68 Period size: 16 Copynumber: 2.1 Consensus size: 16 89135461 TTCTAACATC 89135471 AGAAAAAATCTCACGA 1 AGAAAAAATCTCACGA 89135487 AGAAAAAATCTCACGA 1 AGAAAAAATCTCACGA 89135503 AG 1 AG 89135505 TTTTGGAAGC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.56, C:0.18, G:0.15, T:0.12 Consensus pattern (16 bp): AGAAAAAATCTCACGA Found at i:89136394 original size:19 final size:19 Alignment explanation

Indices: 89136370--89136413 Score: 70 Period size: 19 Copynumber: 2.3 Consensus size: 19 89136360 TTAGAATATG * 89136370 AATAAAACTTATTTATCTA 1 AATAAAACTTATTTACCTA * 89136389 AATAAAATTTATTTACCTA 1 AATAAAACTTATTTACCTA 89136408 AATAAA 1 AATAAA 89136414 TTTAAAATAT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 19 23 1.00 ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39 Consensus pattern (19 bp): AATAAAACTTATTTACCTA Found at i:89145156 original size:16 final size:16 Alignment explanation

Indices: 89145145--89145176 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 89145135 ATTGTAATTG 89145145 AATAGAGCTGTAATAA 1 AATAGAGCTGTAATAA * 89145161 AATAGAGTTGTAATAA 1 AATAGAGCTGTAATAA 89145177 GTAATTTAAC 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:0.50, C:0.03, G:0.19, T:0.28 Consensus pattern (16 bp): AATAGAGCTGTAATAA Found at i:89145271 original size:16 final size:16 Alignment explanation

Indices: 89145236--89145291 Score: 62 Period size: 16 Copynumber: 3.6 Consensus size: 16 89145226 GTTTGGTTCA * 89145236 CTGTAATGAAATAG-G 1 CTGTAATTAAATAGAG * * 89145251 ACTGTAATTGAATTGAG 1 -CTGTAATTAAATAGAG 89145268 CTGTAA-TAAATAGAG 1 CTGTAATTAAATAGAG 89145283 CTGTAATTA 1 CTGTAATTA 89145292 GTAATTTAAC Statistics Matches: 33, Mismatches: 5, Indels: 4 0.79 0.12 0.10 Matches are distributed among these distances: 15 13 0.39 16 19 0.58 17 1 0.03 ACGTcount: A:0.39, C:0.07, G:0.21, T:0.32 Consensus pattern (16 bp): CTGTAATTAAATAGAG Found at i:89145333 original size:115 final size:116 Alignment explanation

Indices: 89145107--89145334 Score: 368 Period size: 115 Copynumber: 2.0 Consensus size: 116 89145097 TTACTTACGT ** * * 89145107 TACGTTTGGTTGGCTGTAATGAAATAGGATTGTAATTGAATAGAGCTGTAATAAAATAGAGTTGT 1 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT 89145172 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG 66 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG * 89145223 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATTGAGCTGTAAT-AAATAGAGCTGT 1 TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT * * * * 89145287 AATTAGTAATTTAACTGTTTGGTTGAATGGAATGGAATAGAGCTGTAA 66 AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAA 89145335 TAGAATTCTT Statistics Matches: 103, Mismatches: 9, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 115 55 0.53 116 48 0.47 ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34 Consensus pattern (116 bp): TACGTTTGGTTCACTGTAATGAAATAGGACTGTAATTGAATAGAGCTGTAATAAAATAGAGCTGT AATAAGTAATTTAACTGTTTGGTTGAATAGAATGGAATAAAACTGTAACGG Found at i:89145359 original size:44 final size:46 Alignment explanation

Indices: 89145276--89145364 Score: 139 Period size: 44 Copynumber: 2.0 Consensus size: 46 89145266 AGCTGTAATA 89145276 AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG 1 AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG * 89145322 AATAGAGCTGTAA-TAG-AATTCTTA-TGTTTGGTTGAATGGAATG 1 AATAGAGCTGTAATTAGTAATT-TAACTGTTTGGTTGAATGGAATG 89145365 ATGTTGTAAT Statistics Matches: 41, Mismatches: 1, Indels: 4 0.89 0.02 0.09 Matches are distributed among these distances: 44 23 0.56 45 5 0.12 46 13 0.32 ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37 Consensus pattern (46 bp): AATAGAGCTGTAATTAGTAATTTAACTGTTTGGTTGAATGGAATGG Found at i:89145527 original size:61 final size:55 Alignment explanation

Indices: 89145445--89145593 Score: 140 Period size: 61 Copynumber: 2.5 Consensus size: 55 89145435 GATTATTATT * 89145445 ATTAAATTTTAATA-AGATTATTGATACATATATTTTAATAAAAATAAAAATAAATAATTTA 1 ATTAAATTTTAATATA-ATTATT-ATA-ATATAATTTAAT-AAAAT---AATAAATAATTTA * * * 89145506 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATATATATTTTA 1 ATTAAATTTTAATATAATTATTA-T-AATATAATTTAATAAAATAATAAATAATTTA 89145563 A-TAACATTATTAATATAATTATTAATAATAT 1 ATTAA-ATT-TTAATATAATTATT-ATAATAT 89145594 TTAATAATAA Statistics Matches: 77, Mismatches: 5, Indels: 16 0.79 0.05 0.16 Matches are distributed among these distances: 56 2 0.03 57 20 0.26 58 15 0.19 59 1 0.01 60 6 0.08 61 31 0.40 62 2 0.03 ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46 Consensus pattern (55 bp): ATTAAATTTTAATATAATTATTATAATATAATTTAATAAAATAATAAATAATTTA Found at i:89145575 original size:12 final size:11 Alignment explanation

Indices: 89145514--89145611 Score: 51 Period size: 12 Copynumber: 8.5 Consensus size: 11 89145504 TAATTATATT 89145514 TTAATATAATTA 1 TTAATA-AATTA * 89145526 TTATTAAATATAA 1 TTAATAAAT-T-A * 89145539 TTTAATAAAATA 1 -TTAATAAATTA * * 89145551 AT-ATATATT- 1 TTAATAAATTA 89145560 TTAATAACATTA 1 TTAATAA-ATTA 89145572 TTAATATAATTA 1 TTAATA-AATTA 89145584 TTAATAATATTTA 1 TTAATAA-A-TTA * 89145597 ATAAT-AATT- 1 TTAATAAATTA 89145606 TTAATA 1 TTAATA 89145612 TAAAATTATT Statistics Matches: 66, Mismatches: 10, Indels: 22 0.67 0.10 0.22 Matches are distributed among these distances: 9 5 0.08 10 10 0.15 11 9 0.14 12 25 0.38 13 10 0.15 14 7 0.11 ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48 Consensus pattern (11 bp): TTAATAAATTA Found at i:89145599 original size:46 final size:47 Alignment explanation

Indices: 89145500--89145614 Score: 127 Period size: 46 Copynumber: 2.5 Consensus size: 47 89145490 AAAAATAAAT * 89145500 AATTTAAT-TATATTTTAATATAATTATTATTAAATATAATTTAATA 1 AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA * 89145546 AA-ATAATATATATTTTAATA-ACATTATTAATATAAT-T-A-TTAATA 1 AATTTAATATATATTTTAATATA-ATTATTAATA-AATATAATTTAATA 89145590 ATATTTAATA-ATAATTTTAATATAA 1 A-ATTTAATATAT-ATTTTAATATAA 89145615 AATTATTATT Statistics Matches: 59, Mismatches: 3, Indels: 14 0.78 0.04 0.18 Matches are distributed among these distances: 44 7 0.12 45 9 0.15 46 39 0.66 47 4 0.07 ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49 Consensus pattern (47 bp): AATTTAATATATATTTTAATATAATTATTAATAAATATAATTTAATA Found at i:89156959 original size:5 final size:5 Alignment explanation

Indices: 89156949--89156979 Score: 62 Period size: 5 Copynumber: 6.2 Consensus size: 5 89156939 ATTTACCTCC 89156949 TTATA TTATA TTATA TTATA TTATA TTATA T 1 TTATA TTATA TTATA TTATA TTATA TTATA T 89156980 ATTTTTAATT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 26 1.00 ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61 Consensus pattern (5 bp): TTATA Found at i:89159946 original size:17 final size:17 Alignment explanation

Indices: 89159926--89159959 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 89159916 AAATAGATTT 89159926 TTAATTAAAAATTTTAA 1 TTAATTAAAAATTTTAA * 89159943 TTAATTAAAATTTTTAA 1 TTAATTAAAAATTTTAA 89159960 ACCTAAACCT Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (17 bp): TTAATTAAAAATTTTAA Found at i:89160720 original size:94 final size:92 Alignment explanation

Indices: 89160584--89160774 Score: 235 Period size: 94 Copynumber: 2.1 Consensus size: 92 89160574 AAACTTTTTT * * * 89160584 AAAAAAAATAATTAAGTCCCTCTCCTTTTTTTTGCACTCAATT-GAGCAATTTAACTTTCAAAAT 1 AAAAAAAAAAATTAAGTCCCTCTCCTTTTTTTTCCACTCAATTAG-GCAATTAAACTTTCAAAAT * * 89160648 GCATCAAAAAGGCCCCCAAACTTCTTTAA 65 GCATCAAAAAGACCCCCAAAATT-TTTAA * * 89160677 AAAAAAAAGAAATTAAG-CCCT-TGCCTGTTTTTTTCCACTCAATTAGGTACTTAAACTTTCAAA 1 AAAAAAAA-AAATTAAGTCCCTCT-CCT-TTTTTTTCCACTCAATTAGGCAATTAAACTTTCAAA * * 89160740 ATGCATCAAAAAGACCCTCAAAATTTTTCA 63 ATGCATCAAAAAGACCCCCAAAATTTTTAA 89160770 AAAAA 1 AAAAA 89160775 GCAATTAAGC Statistics Matches: 85, Mismatches: 9, Indels: 8 0.83 0.09 0.08 Matches are distributed among these distances: 92 1 0.01 93 24 0.28 94 59 0.69 95 1 0.01 ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31 Consensus pattern (92 bp): AAAAAAAAAAATTAAGTCCCTCTCCTTTTTTTTCCACTCAATTAGGCAATTAAACTTTCAAAATG CATCAAAAAGACCCCCAAAATTTTTAA Found at i:89161108 original size:10 final size:10 Alignment explanation

Indices: 89161095--89161174 Score: 55 Period size: 10 Copynumber: 8.5 Consensus size: 10 89161085 CTTTATAAAA 89161095 TTTTATAATT 1 TTTTATAATT 89161105 TTTT-T-ATAT 1 TTTTATAAT-T * * 89161114 TTCTAT-ATA 1 TTTTATAATT 89161123 TTTTATAATT 1 TTTTATAATT * 89161133 TTTTATGA-T 1 TTTTATAATT 89161142 TTTTAT-A-T 1 TTTTATAATT * 89161150 TTTTCTAATT 1 TTTTATAATT * * 89161160 TTTAATAAAT 1 TTTTATAATT 89161170 TTTTA 1 TTTTA 89161175 ATATTTTAAA Statistics Matches: 55, Mismatches: 10, Indels: 10 0.73 0.13 0.13 Matches are distributed among these distances: 8 9 0.16 9 18 0.33 10 28 0.51 ACGTcount: A:0.29, C:0.03, G:0.01, T:0.68 Consensus pattern (10 bp): TTTTATAATT Found at i:89161128 original size:17 final size:18 Alignment explanation

Indices: 89161105--89161152 Score: 55 Period size: 17 Copynumber: 2.7 Consensus size: 18 89161095 TTTTATAATT 89161105 TTTTTATATTTCTATAT-A 1 TTTTTATATTT-TATATGA * 89161123 -TTTTATAATTTTTTATGA 1 TTTTTAT-ATTTTATATGA 89161141 TTTTTATATTTT 1 TTTTTATATTTT 89161153 TCTAATTTTT Statistics Matches: 26, Mismatches: 1, Indels: 6 0.79 0.03 0.18 Matches are distributed among these distances: 17 10 0.38 18 10 0.38 19 6 0.23 ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71 Consensus pattern (18 bp): TTTTTATATTTTATATGA Found at i:89161130 original size:28 final size:28 Alignment explanation

Indices: 89161094--89161188 Score: 108 Period size: 28 Copynumber: 3.5 Consensus size: 28 89161084 ACTTTATAAA * 89161094 ATTTTATAATTTTTTTATATTTCTATAT 1 ATTTTATAATTTTTTTATATTTTTATAT 89161122 ATTTTATAA-TTTTTTATGATTTTTATAT 1 ATTTTATAATTTTTTTAT-ATTTTTATAT * * * 89161150 -TTTTCTAATTTTTAATAAATTTTTA-AT 1 ATTTTATAATTTTT-TTATATTTTTATAT 89161177 ATTTTA-AATTTT 1 ATTTTATAATTTT 89161189 ATTAAGTTTA Statistics Matches: 58, Mismatches: 5, Indels: 9 0.81 0.07 0.12 Matches are distributed among these distances: 27 23 0.40 28 33 0.57 29 2 0.03 ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66 Consensus pattern (28 bp): ATTTTATAATTTTTTTATATTTTTATAT Found at i:89161135 original size:9 final size:9 Alignment explanation

Indices: 89161095--89161254 Score: 73 Period size: 9 Copynumber: 17.6 Consensus size: 9 89161085 CTTTATAAAA 89161095 TTTTATAAT 1 TTTTATAAT * 89161104 TTTTTTATAT 1 TTTTATA-AT * 89161114 TTCTAT-AT 1 TTTTATAAT 89161122 ATTTTATAATT 1 -TTTTATAA-T * 89161133 TTTTATGAT 1 TTTTATAAT 89161142 TTTTAT-AT 1 TTTTATAAT * 89161150 TTTTCTAAT 1 TTTTATAAT * 89161159 TTTTAATAAA 1 TTTT-ATAAT 89161169 TTTT-TAAT 1 TTTTATAAT 89161177 ATTTTA-AA- 1 -TTTTATAAT * 89161185 TTTTATTAAG 1 TTTTA-TAAT * 89161195 TTTAATAAT 1 TTTTATAAT * ** 89161204 ATTTATAGC 1 TTTTATAAT * * 89161213 TTTAAT-TT 1 TTTTATAAT 89161221 ATTTTA-AATT 1 -TTTTATAA-T 89161231 TTTTATAATT 1 TTTTATAA-T * 89161241 TTTTCTAAT 1 TTTTATAAT 89161250 TTTTA 1 TTTTA 89161255 ATAAAAAAAG Statistics Matches: 113, Mismatches: 23, Indels: 30 0.68 0.14 0.18 Matches are distributed among these distances: 7 5 0.04 8 12 0.11 9 58 0.51 10 37 0.33 11 1 0.01 ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64 Consensus pattern (9 bp): TTTTATAAT Found at i:89161153 original size:19 final size:18 Alignment explanation

Indices: 89161095--89161163 Score: 59 Period size: 19 Copynumber: 3.7 Consensus size: 18 89161085 CTTTATAAAA * * 89161095 TTTTATAATTTTTTTATAT 1 TTTTAT-ATTTTTATATTT * * 89161114 TTCTATATATTTTATAATT 1 TTTTATAT-TTTTATATTT 89161133 TTTTATGATTTTTATATTT 1 TTTTAT-ATTTTTATATTT * 89161152 TTCTA-ATTTTTA 1 TTTTATATTTTTA 89161164 ATAAATTTTT Statistics Matches: 41, Mismatches: 7, Indels: 6 0.76 0.13 0.11 Matches are distributed among these distances: 17 7 0.17 18 2 0.05 19 30 0.73 20 2 0.05 ACGTcount: A:0.26, C:0.03, G:0.01, T:0.70 Consensus pattern (18 bp): TTTTATATTTTTATATTT Found at i:89161160 original size:17 final size:18 Alignment explanation

Indices: 89161102--89161163 Score: 65 Period size: 19 Copynumber: 3.4 Consensus size: 18 89161092 AAATTTTATA * * 89161102 ATTTTTTTATATTTCTAT 1 ATTTTTATATTTTTCTAT 89161120 ATATTTTATAATTTTT-TAT 1 AT-TTTTAT-ATTTTTCTAT 89161139 GATTTTTATATTTTTCTA- 1 -ATTTTTATATTTTTCTAT 89161157 ATTTTTA 1 ATTTTTA 89161164 ATAAATTTTT Statistics Matches: 38, Mismatches: 2, Indels: 9 0.78 0.04 0.18 Matches are distributed among these distances: 17 7 0.18 18 8 0.21 19 16 0.42 20 7 0.18 ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69 Consensus pattern (18 bp): ATTTTTATATTTTTCTAT Found at i:89161182 original size:36 final size:37 Alignment explanation

Indices: 89161086--89161188 Score: 97 Period size: 38 Copynumber: 2.8 Consensus size: 37 89161076 TTCTTACGAC * * 89161086 TTTATAAAATTTTATAAT-TTTTTTATATTTCTATATAT 1 TTTAT-AAATTTT-TAATATTTTATATTTTTCTATATAT * 89161124 TTTAT-AATTTTTTATGATTTTTATATTTTTCTA-AT-T 1 TTTATAAATTTTTAAT-A-TTTTATATTTTTCTATATAT * 89161160 TTTAATAAATTTTTAATATTTTAAATTTT 1 TTT-ATAAATTTTTAATATTTTATATTTT 89161189 ATTAAGTTTA Statistics Matches: 55, Mismatches: 5, Indels: 12 0.76 0.07 0.17 Matches are distributed among these distances: 35 3 0.05 36 20 0.36 37 5 0.09 38 27 0.49 ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65 Consensus pattern (37 bp): TTTATAAATTTTTAATATTTTATATTTTTCTATATAT Found at i:89161251 original size:27 final size:26 Alignment explanation

Indices: 89161095--89161252 Score: 79 Period size: 28 Copynumber: 5.8 Consensus size: 26 89161085 CTTTATAAAA * * 89161095 TTTTATAATTTTTTTATATTTCTATATA 1 TTTTATAATTTTTTTA-ATTT-TAAATT * * 89161123 TTTTATAATTTTTTATGATTTT-TATAT 1 TTTTATAATTTTTT-TAATTTTAAAT-T * * * * 89161150 TTTTCTAATTTTTAATAAATTTTTAATA 1 TTTTATAATTTTT--TTAATTTTAAATT * * * 89161178 TTTTA-AATTTTATTAAGTTTAATAAT 1 TTTTATAATTTTTTTAATTTTAA-ATT * * * 89161204 ATTTATAGCTTTAATTT-ATTTTAAATT 1 TTTTATA-ATTT-TTTTAATTTTAAATT 89161231 TTTTATAATTTTTTCTAATTTT 1 TTTTATAATTTTTT-TAATTTT 89161253 TAATAAAAAA Statistics Matches: 96, Mismatches: 23, Indels: 23 0.68 0.16 0.16 Matches are distributed among these distances: 25 9 0.09 26 12 0.12 27 33 0.34 28 36 0.38 29 6 0.06 ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65 Consensus pattern (26 bp): TTTTATAATTTTTTTAATTTTAAATT Found at i:89162982 original size:11 final size:11 Alignment explanation

Indices: 89162961--89162994 Score: 50 Period size: 11 Copynumber: 3.0 Consensus size: 11 89162951 TTGTAGTTCA 89162961 AAAACAAAAAAG 1 AAAA-AAAAAAG 89162973 AAAAAAAAAAG 1 AAAAAAAAAAG * 89162984 AAAAAGAAAAG 1 AAAAAAAAAAG 89162995 GCATGGCAAT Statistics Matches: 21, Mismatches: 1, Indels: 1 0.91 0.04 0.04 Matches are distributed among these distances: 11 17 0.81 12 4 0.19 ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAG Found at i:89163170 original size:130 final size:132 Alignment explanation

Indices: 89162917--89163170 Score: 352 Period size: 133 Copynumber: 1.9 Consensus size: 132 89162907 AGATTTGCGT * * * 89162917 GCACTAGTGATGTTTATTGATTGGGTTTTACTTTTTGTAGTTCAAAAACAAAAAAGAAAAAAAAA 1 GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA * 89162982 AGAAAAAGAAAAGGCATGGCAATGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGC 66 AG-AAAAGAAAAGGCATGGCAAAGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGC 89163047 TAA 130 TAA * * * * * * 89163050 GCACTAATGATGTTTATTGTTTGGATTTTACTTTTTATATTTTAAAAA-TAAATA-AAAAAGAAA 1 GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA * * * 89163113 AG-AAAGAAAAGGCATGGCAAAGATGCTTCTATTTTTAACCCACCTATTAACACCAAGC 66 AGAAAAGAAAAGGCATGGCAAAGAT-CTTCTAATTTTAACCCACCTAATAACAACAAGC 89163171 TCATAACAAT Statistics Matches: 107, Mismatches: 13, Indels: 5 0.86 0.10 0.04 Matches are distributed among these distances: 129 21 0.20 130 30 0.28 131 10 0.09 132 4 0.04 133 42 0.39 ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30 Consensus pattern (132 bp): GCACTAATGATGTTTATTGATTGGATTTTACTTTTTATAGTTCAAAAACAAAAAAGAAAAAAAAA AGAAAAGAAAAGGCATGGCAAAGATCTTCTAATTTTAACCCACCTAATAACAACAAGCACATGCT AA Found at i:89163360 original size:40 final size:39 Alignment explanation

Indices: 89163312--89163390 Score: 113 Period size: 40 Copynumber: 2.0 Consensus size: 39 89163302 CTAATTGGTA * * * 89163312 GGTTAAAATTATAAATATATAAAAAGTGTTAAGGAGATTT 1 GGTTAAAATTAGAAACATATAAAAAGAG-TAAGGAGATTT * 89163352 GGTTAAAATTAGATACATATAAAAAGAGTAAGGAGATTT 1 GGTTAAAATTAGAAACATATAAAAAGAGTAAGGAGATTT 89163391 AATTAACACC Statistics Matches: 35, Mismatches: 4, Indels: 1 0.88 0.10 0.03 Matches are distributed among these distances: 39 11 0.31 40 24 0.69 ACGTcount: A:0.48, C:0.01, G:0.19, T:0.32 Consensus pattern (39 bp): GGTTAAAATTAGAAACATATAAAAAGAGTAAGGAGATTT Found at i:89165058 original size:28 final size:28 Alignment explanation

Indices: 89165017--89165085 Score: 122 Period size: 28 Copynumber: 2.5 Consensus size: 28 89165007 TTTAAAACCC * 89165017 TAGGGGT-ATATCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 89165044 TAGGGGTAATTTCGGTAATTTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTCTT 89165072 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 89165086 TGATCTACGC Statistics Matches: 40, Mismatches: 1, Indels: 1 0.95 0.02 0.02 Matches are distributed among these distances: 27 7 0.17 28 33 0.82 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43 Consensus pattern (28 bp): TAGGGGTAATTTCGGTAATTTTGCTCTT Found at i:89166917 original size:19 final size:18 Alignment explanation

Indices: 89166880--89166923 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 89166870 ATACATATAG 89166880 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 89166897 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 89166916 TACTAATT 1 TAATAATT 89166924 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:89167675 original size:59 final size:59 Alignment explanation

Indices: 89167583--89167700 Score: 218 Period size: 59 Copynumber: 2.0 Consensus size: 59 89167573 GTAGATGAAT * 89167583 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGGGGAGAAGCTAAAATTTTGAGC 1 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC * 89167642 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGTTAAAATTTTGAGC 1 GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC 89167701 TTTTGAAAAA Statistics Matches: 57, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 59 57 1.00 ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35 Consensus pattern (59 bp): GCCTAGTTTAGGTATGCTTATCACAAAAATATTTTTGAGGAGAAGCTAAAATTTTGAGC Found at i:89168327 original size:14 final size:14 Alignment explanation

Indices: 89168290--89168327 Score: 51 Period size: 14 Copynumber: 2.7 Consensus size: 14 89168280 TTTCCATTTC 89168290 TATTTCATTTAATT 1 TATTTCATTTAATT * 89168304 TTTTTCATTTAAATT 1 TATTTCATTT-AATT 89168319 TATTT-ATTT 1 TATTTCATTT 89168328 CTCATTTCAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 14 13 0.62 15 8 0.38 ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68 Consensus pattern (14 bp): TATTTCATTTAATT Found at i:89168348 original size:52 final size:55 Alignment explanation

Indices: 89168268--89168439 Score: 147 Period size: 58 Copynumber: 3.1 Consensus size: 55 89168258 TTTTCCTTTC * 89168268 ATTTCATTTTCATTTCCATTTCTATTTCATTT-A-ATTT-TTTTCATTTAAATTT 1 ATTTCATTTTCATTTCAATTTCTATTTCATTTCAGATTTGTTTTCATTTAAATTT * * * 89168320 ATTT-ATTTCTCATTTCAATTTTTTTTTCATTTCAGTTTTTGTTTTCATTTAAATTT 1 ATTTCATTT-TCATTTCAATTTCTATTTCATTTCAG-ATTTGTTTTCATTTAAATTT * * * * ** 89168376 ATAATTTATTTCCATTTAAACTTTC-ATTTCATTTCATATTCATATTTCATTTAACATTT 1 AT--TTCATTTTCATTTCAA-TTTCTATTTCATTTCAGATTTGT-TTTCATTTAA-ATTT 89168435 CATTT 1 -ATTT 89168440 TATTAATTTT Statistics Matches: 96, Mismatches: 12, Indels: 18 0.76 0.10 0.14 Matches are distributed among these distances: 51 4 0.04 52 24 0.25 53 1 0.01 55 3 0.03 56 17 0.18 57 3 0.03 58 31 0.32 59 11 0.11 60 2 0.02 ACGTcount: A:0.24, C:0.13, G:0.01, T:0.61 Consensus pattern (55 bp): ATTTCATTTTCATTTCAATTTCTATTTCATTTCAGATTTGTTTTCATTTAAATTT Found at i:89168364 original size:18 final size:17 Alignment explanation

Indices: 89168245--89168375 Score: 90 Period size: 17 Copynumber: 7.5 Consensus size: 17 89168235 AGGCCTATCC * 89168245 TTTCAACTTTTATTTTTCC 1 TTTCAA-TTTT-TTTTTCA ** 89168264 TTTC-ATTTCATTTTCA 1 TTTCAATTTTTTTTTCA * * * 89168280 TTTCCATTTCTATTTCA 1 TTTCAATTTTTTTTTCA 89168297 TTT-AA--TTTTTTTCA 1 TTTCAATTTTTTTTTCA * 89168311 TTTAAATTTATTTATTTCTCA 1 TTTCAA-TT-TTT-TTT-TCA 89168332 TTTCAATTTTTTTTTCA 1 TTTCAATTTTTTTTTCA * 89168349 TTTCAGTTTTTGTTTTCA 1 TTTCAATTTTT-TTTTCA * 89168367 TTTAAATTT 1 TTTCAATTT 89168376 ATAATTTATT Statistics Matches: 91, Mismatches: 12, Indels: 19 0.75 0.10 0.16 Matches are distributed among these distances: 14 10 0.11 15 2 0.02 16 10 0.11 17 29 0.32 18 17 0.19 19 10 0.11 20 5 0.05 21 8 0.09 ACGTcount: A:0.20, C:0.14, G:0.02, T:0.65 Consensus pattern (17 bp): TTTCAATTTTTTTTTCA Found at i:89168408 original size:17 final size:18 Alignment explanation

Indices: 89168362--89168439 Score: 51 Period size: 17 Copynumber: 4.4 Consensus size: 18 89168352 CAGTTTTTGT * 89168362 TTTCATTTAAATTTATAA 1 TTTCATTTACATTTATAA * 89168380 TTT-ATTTCCATTTA-AA 1 TTTCATTTACATTTATAA 89168396 CTTTCATTT-CATTTCAT-A 1 -TTTCATTTACATTT-ATAA * 89168414 -TTCATATTTCATTTA-ACA 1 TTTCAT-TTACATTTATA-A 89168432 TTTCATTT 1 TTTCATTT 89168440 TATTAATTTT Statistics Matches: 49, Mismatches: 2, Indels: 18 0.71 0.03 0.26 Matches are distributed among these distances: 16 7 0.14 17 20 0.41 18 17 0.35 19 5 0.10 ACGTcount: A:0.29, C:0.14, G:0.00, T:0.56 Consensus pattern (18 bp): TTTCATTTACATTTATAA Found at i:89168442 original size:58 final size:57 Alignment explanation

Indices: 89168305--89168443 Score: 149 Period size: 58 Copynumber: 2.4 Consensus size: 57 89168295 CATTTAATTT * * ** * ** 89168305 TTTTCATTTAAATTTA-TTTATTTCTCATTTCAATTTTTTTTTCATTTCAGTTTTTG 1 TTTTCATTTAAATTTATTTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA 89168361 TTTTCATTTAAATTTATAATTTATTTC-CATTTAAACTTTCATTTCATTTCA-TATTCA 1 TTTTCATTTAAATTTAT--TTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA 89168418 TATTTCATTTAACATTTCATTTTATT 1 T-TTTCATTTAA-ATTT-ATTTTATT 89168444 AATTTTTTCA Statistics Matches: 70, Mismatches: 7, Indels: 10 0.80 0.08 0.11 Matches are distributed among these distances: 56 16 0.23 57 4 0.06 58 36 0.51 59 12 0.17 60 2 0.03 ACGTcount: A:0.25, C:0.12, G:0.01, T:0.61 Consensus pattern (57 bp): TTTTCATTTAAATTTATTTTATTTCTCATTTAAACTTTCATTTCATTTCAGTATTCA Found at i:89168556 original size:14 final size:14 Alignment explanation

Indices: 89168521--89168556 Score: 54 Period size: 15 Copynumber: 2.4 Consensus size: 14 89168511 TCGTTTTAAG 89168521 TTATCTTTTTTCAAT 1 TTAT-TTTTTTCAAT 89168536 TTAATTTTTTTCAAT 1 TT-ATTTTTTTCAAT 89168551 TTATTT 1 TTATTT 89168557 CATATTTTTT Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 14 4 0.20 15 14 0.70 16 2 0.10 ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69 Consensus pattern (14 bp): TTATTTTTTTCAAT Found at i:89168568 original size:11 final size:11 Alignment explanation

Indices: 89168539--89168573 Score: 54 Period size: 11 Copynumber: 3.3 Consensus size: 11 89168529 TTTCAATTTA 89168539 ATTTTTTTCA- 1 ATTTTTTTCAT * 89168549 ATTTATTTCAT 1 ATTTTTTTCAT 89168560 ATTTTTTTCAT 1 ATTTTTTTCAT 89168571 ATT 1 ATT 89168574 AATTAAAAAT Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 10 9 0.41 11 13 0.59 ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69 Consensus pattern (11 bp): ATTTTTTTCAT Found at i:89168878 original size:23 final size:20 Alignment explanation

Indices: 89168847--89168901 Score: 65 Period size: 22 Copynumber: 2.5 Consensus size: 20 89168837 TGTAATTCCA 89168847 TTTTCATTTCATTTAAATTATT 1 TTTTCATTTCATTT-AATTA-T * 89168869 TTTTCTATTTAAATTTAATTAT 1 TTTTC-ATTT-CATTTAATTAT 89168891 TTTTCATTTCA 1 TTTTCATTTCA 89168902 AAATTTTTAT Statistics Matches: 29, Mismatches: 2, Indels: 6 0.78 0.05 0.16 Matches are distributed among these distances: 20 1 0.03 21 4 0.14 22 11 0.38 23 9 0.31 24 4 0.14 ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64 Consensus pattern (20 bp): TTTTCATTTCATTTAATTAT Found at i:89168905 original size:23 final size:23 Alignment explanation

Indices: 89168857--89168921 Score: 68 Period size: 20 Copynumber: 2.9 Consensus size: 23 89168847 TTTTCATTTC 89168857 ATTTAAATTATTTTTTCTATTT--AA 1 ATTT-AATTA-TTTTTC-ATTTCAAA 89168881 ATTTAATTATTTTTCATTTCAAA 1 ATTTAATTATTTTTCATTTCAAA 89168904 ATTT--TTA-TTTTCATTTCA 1 ATTTAATTATTTTTCATTTCA 89168922 GTTTTTGTTT Statistics Matches: 39, Mismatches: 0, Indels: 8 0.83 0.00 0.17 Matches are distributed among these distances: 20 11 0.28 21 7 0.18 22 6 0.15 23 11 0.28 24 4 0.10 ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62 Consensus pattern (23 bp): ATTTAATTATTTTTCATTTCAAA Found at i:89169055 original size:30 final size:29 Alignment explanation

Indices: 89168987--89169079 Score: 95 Period size: 28 Copynumber: 3.2 Consensus size: 29 89168977 TCATAATCAT ** 89168987 CATTTTATTTCATATTCATTTAACATTT-- 1 CATTTTATTTCATATTC-TTTTTCATTTAA * 89169015 CATTTCATTTCATATTCTTGTTTCATTTAA 1 CATTTTATTTCATATTCTT-TTTCATTTAA 89169045 CATTTTATTTCAATAATT-TTTTTCATTTAA 1 CATTTTATTTC-AT-ATTCTTTTTCATTTAA 89169075 -ATTTT 1 CATTTT 89169080 TTTTTCAATA Statistics Matches: 56, Mismatches: 4, Indels: 9 0.81 0.06 0.13 Matches are distributed among these distances: 27 2 0.04 28 22 0.39 29 5 0.09 30 20 0.36 31 4 0.07 32 3 0.05 ACGTcount: A:0.27, C:0.13, G:0.01, T:0.59 Consensus pattern (29 bp): CATTTTATTTCATATTCTTTTTCATTTAA Found at i:89169096 original size:19 final size:17 Alignment explanation

Indices: 89169061--89169109 Score: 62 Period size: 20 Copynumber: 2.7 Consensus size: 17 89169051 ATTTCAATAA * 89169061 TTTTTTTCATTTAAATT 1 TTTTTTTCATATAAATT 89169078 TTTTTTTCAATATACAATTT 1 TTTTTTTC-ATATA-AA-TT 89169098 TTTTTTTCATAT 1 TTTTTTTCATAT 89169110 TAATCACAAA Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 17 8 0.29 18 4 0.14 19 6 0.21 20 10 0.36 ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67 Consensus pattern (17 bp): TTTTTTTCATATAAATT Found at i:89169257 original size:21 final size:21 Alignment explanation

Indices: 89169215--89169257 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 21 89169205 TATTAAGGAC * 89169215 ATTTAAATTTTTTCATATTTT 1 ATTTAAATTTTTTCATAATTT 89169236 ATTTAAATTTTTTC-TCAATTT 1 ATTTAAATTTTTTCAT-AATTT 89169257 A 1 A 89169258 AATATCATTC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 20 1 0.05 21 19 0.95 ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63 Consensus pattern (21 bp): ATTTAAATTTTTTCATAATTT Found at i:89169535 original size:49 final size:47 Alignment explanation

Indices: 89169479--89169748 Score: 305 Period size: 47 Copynumber: 5.6 Consensus size: 47 89169469 CTTCGATTTC * 89169479 ATTTAATTTGTATTTC-CATTTCATTTAAATTATCTTTATTCCCATTTTA 1 ATTTAATTT-T-TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA * * * 89169528 ATTTAATTTTTTTTGTCATTTCATTTAAATTAT-TATTTTTTCATTTAA 1 ATTTAA-TTTTTTTCTCATTTCATTTAAATTATCT-TTTTTCCATTTTA * * * * * 89169576 ATCTAATTTTGTTCTCAGTTCATTTAAATTATCTTTCTTCCCATCTTA 1 ATTTAATTTTTTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA * * * 89169624 ATTTAAATTTTTTTCTTATTTCATTTAAATTAT-TTTTTTCAATTTAA 1 ATTT-AATTTTTTTCTCATTTCATTTAAATTATCTTTTTTCCATTTTA * * 89169671 ATTTAATTTTTATCCTCATTTCATTCAAATTATCTTTCTTTCCATTTTA 1 ATTTAATTTTT-TTCTCATTTCATTTAAATTATCTTT-TTTCCATTTTA 89169720 ATTT-ATTTTTTTCTCATTTCATTTAAATT 1 ATTTAATTTTTTTCTCATTTCATTTAAATT 89169749 TAATTTTTTC Statistics Matches: 185, Mismatches: 27, Indels: 20 0.80 0.12 0.09 Matches are distributed among these distances: 46 7 0.04 47 71 0.38 48 40 0.22 49 64 0.35 50 3 0.02 ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60 Consensus pattern (47 bp): ATTTAATTTTTTTCTCATTTCATTTAAATTATCTTTTTTCCATTTTA Found at i:89169554 original size:22 final size:22 Alignment explanation

Indices: 89169451--89169771 Score: 123 Period size: 24 Copynumber: 13.5 Consensus size: 22 89169441 CATCTTTTTT * ** 89169451 TTTCATTTTATTTCATTTCTTCGA 1 TTTCATTTAATTTTTTTTC-TC-A * 89169475 TTTCATTTAATTTGTATTTC-CA 1 TTTCATTTAATTT-TTTTTCTCA * 89169497 TTTCATTTAAATTATCTTTATTCCCA 1 TTTCATTT-AATT-T-TTT-TTCTCA * * 89169523 TTTTAATTTAATTTTTTTTGTCA 1 -TTTCATTTAATTTTTTTTCTCA * 89169546 TTTCATTTAAATTATTATTTTTTCA 1 TTTCATTT-AATT-TT-TTTTCTCA * * * 89169571 TTTAAATCTAA-TTTTGTTCTCA 1 TTT-CATTTAATTTTTTTTCTCA * * 89169593 GTTCATTTAAATTATCTTTCTTCCCA 1 TTTCATTT-AATT-T-TTT-TTCTCA * * * 89169619 TCTTAATTTAAATTTTTTTCTTA 1 T-TTCATTTAATTTTTTTTCTCA 89169642 TTTCATTTAAATTATTTTTT-TCAA 1 TTTCATTT-AATT-TTTTTTCTC-A * * * 89169666 TTTAAATTTAATTTTTATCCTCA 1 TTT-CATTTAATTTTTTTTCTCA * 89169689 TTTCATTCAAATTATCTTTCTT-TCCA 1 TTTCATT-TAATT-T-TTT-TTCT-CA * 89169715 TTTTAATTT-A-TTTTTTTCTCA 1 -TTTCATTTAATTTTTTTTCTCA * 89169736 TTTCATTTAAATTTAATTTTTTCTCT 1 TTTCATTT-AA-TT--TTTTTTCTCA 89169762 TTTCATTTAA 1 TTTCATTTAA 89169772 ATTACCTTTC Statistics Matches: 226, Mismatches: 37, Indels: 67 0.68 0.11 0.20 Matches are distributed among these distances: 20 7 0.03 21 7 0.03 22 40 0.18 23 38 0.17 24 44 0.19 25 34 0.15 26 37 0.16 27 19 0.08 ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60 Consensus pattern (22 bp): TTTCATTTAATTTTTTTTCTCA Found at i:89169554 original size:27 final size:25 Alignment explanation

Indices: 89169537--89169775 Score: 68 Period size: 26 Copynumber: 9.9 Consensus size: 25 89169527 AATTTAATTT 89169537 TTTTTGTCATTTCATTTAAATTATTA 1 TTTTT-TCATTTCATTTAAATTATTA * * 89169563 TTTTTTCATTTAAATCT-AA-T-TT- 1 TTTTTTCATTT-CATTTAAATTATTA * * * 89169585 TGTTCTCAGTTCATTTAAATTATCT- 1 TTTTTTCATTTCATTTAAATTAT-TA ** * 89169610 TTCTTCCCATCTTAATTTAAATT-TT- 1 TT-TTTTCAT-TTCATTTAAATTATTA * 89169635 TTTCTT-ATTTCATTTAAATTA-T- 1 TTTTTTCATTTCATTTAAATTATTA * 89169657 TTTTTTCAATTTAAATTT-AATT-TT- 1 TTTTTTC-ATTT-CATTTAAATTATTA * ** * 89169681 TATCCTCATTTCA-TTCAA--ATTA 1 TTTTTTCATTTCATTTAAATTATTA * * 89169703 -TCTTTC-TTTCCATTTTAATTTATT- 1 TTTTTTCATTT-CA-TTTAAATTATTA 89169727 TTTTTCTCATTTCATTTAAATTTAATT- 1 TTTTT-TCATTTCATTTAAA-TT-ATTA * * 89169754 TTTTCTCTTTTCATTTAAATTA 1 TTTTTTCATTTCATTTAAATTA 89169776 CCTTTCTTTC Statistics Matches: 157, Mismatches: 31, Indels: 52 0.65 0.13 0.22 Matches are distributed among these distances: 20 3 0.02 21 11 0.07 22 30 0.19 23 12 0.08 24 17 0.11 25 30 0.19 26 33 0.21 27 21 0.13 ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60 Consensus pattern (25 bp): TTTTTTCATTTCATTTAAATTATTA Found at i:89169609 original size:96 final size:97 Alignment explanation

Indices: 89169498--89169758 Score: 365 Period size: 96 Copynumber: 2.7 Consensus size: 97 89169488 GTATTTCCAT * * 89169498 TTCATTTAAATTATCTTTATTCCCATTTTAATTTAATTTTTTTTGTCATTTCATTTAAATTATTA 1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAA-TTTTTTTCTCATTTCATTTAAATTATTA 89169563 TTTTTTC-ATTTAAATCTAATTTTGT-T-CTCAG 65 TTTTTTCAATTTAAATCTAATTTT-TATCCTCAG * * 89169594 TTCATTTAAATTATCTTTCTTCCCATCTTAATTTAAATTTTTTTCTTATTTCATTTAAATTA-T- 1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTT-AATTTTTTTCTCATTTCATTTAAATTATTA * * 89169657 TTTTTTCAATTTAAATTTAATTTTTATCCTCAT 65 TTTTTTCAATTTAAATCTAATTTTTATCCTCAG * * * 89169690 TTCATTCAAATTATCTTTCTTTCCATTTTAATTT-ATTTTTTTCTCATTTCATTTAAATT-TAAT 1 TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTATTAT 89169753 TTTTTC 66 TTTTTC 89169759 TCTTTTCATT Statistics Matches: 148, Mismatches: 11, Indels: 13 0.86 0.06 0.08 Matches are distributed among these distances: 94 32 0.22 95 24 0.16 96 90 0.61 97 2 0.01 ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60 Consensus pattern (97 bp): TTCATTTAAATTATCTTTCTTCCCATTTTAATTTAATTTTTTTCTCATTTCATTTAAATTATTAT TTTTTCAATTTAAATCTAATTTTTATCCTCAG Found at i:89169789 original size:73 final size:77 Alignment explanation

Indices: 89169660--89169807 Score: 232 Period size: 73 Copynumber: 2.0 Consensus size: 77 89169650 AAATTATTTT * 89169660 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTATCTTTCTTTCCATTTTAATTTA 1 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA 89169725 -TTTTTTTCTCA 66 CTTTTTTTCTCA * * 89169736 TTTC-ATTTAAATTTAATTTTT-T-CTCTTTTCATTTAAATTACCTTTCTTTCCATTTTAATTTA 1 TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA 89169798 CGTTTTTTTC 66 C-TTTTTTTC 89169808 ATATTAATTT Statistics Matches: 67, Mismatches: 3, Indels: 5 0.89 0.04 0.07 Matches are distributed among these distances: 73 37 0.55 74 1 0.01 75 25 0.37 76 4 0.06 ACGTcount: A:0.23, C:0.16, G:0.01, T:0.61 Consensus pattern (77 bp): TTTCAATTTAAATTTAATTTTTATCCTCATTTCATTCAAATTACCTTTCTTTCCATTTTAATTTA CTTTTTTTCTCA Found at i:89169798 original size:22 final size:22 Alignment explanation

Indices: 89169759--89169817 Score: 68 Period size: 21 Copynumber: 2.8 Consensus size: 22 89169749 TAATTTTTTC * 89169759 TCTTTTCA-TTTAAATTACCTT 1 TCTTTTCATTTTAATTTACCTT * * 89169780 TCTTTCCATTTTAATTTACGTT 1 TCTTTTCATTTTAATTTACCTT * 89169802 T-TTTTCATATTAATTT 1 TCTTTTCATTTTAATTT 89169818 TTCTCTTATT Statistics Matches: 32, Mismatches: 5, Indels: 2 0.82 0.13 0.05 Matches are distributed among these distances: 21 20 0.62 22 12 0.38 ACGTcount: A:0.22, C:0.15, G:0.02, T:0.61 Consensus pattern (22 bp): TCTTTTCATTTTAATTTACCTT Found at i:89173636 original size:25 final size:25 Alignment explanation

Indices: 89173566--89173636 Score: 72 Period size: 25 Copynumber: 2.8 Consensus size: 25 89173556 CAGCTCTCTT * * 89173566 GAGCTTCTCGATATTTGGCTCACAA 1 GAGCTTCCCGATATATGGCTCACAA ** * * 89173591 GAGCTTCCCGATATACAGCTCATAT 1 GAGCTTCCCGATATATGGCTCACAA 89173616 GAGCTTCCC-ATTATATGGCTC 1 GAGCTTCCCGA-TATATGGCTC 89173637 GAAAAAGCTT Statistics Matches: 37, Mismatches: 8, Indels: 2 0.79 0.17 0.04 Matches are distributed among these distances: 24 1 0.03 25 36 0.97 ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31 Consensus pattern (25 bp): GAGCTTCCCGATATATGGCTCACAA Found at i:89174849 original size:3 final size:3 Alignment explanation

Indices: 89174843--89174992 Score: 58 Period size: 3 Copynumber: 48.0 Consensus size: 3 89174833 ATAACATGAC * * * * * 89174843 AAT AAT AAT AAC AGT AGT AAT AAAT AAAT AAAT AAAT AAT GAT AAT AAA 1 AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT -AAT AAT AAT AAT AAT * * * * 89174892 AAT AAT AGT AAAT AA- AAT AA- AGAT AA- AATT AAT AAT GAT AGT AACG 1 AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AA-T AAT AAT AAT AAT AA-T * * * 89174938 AAT -AT AAAT AAT AAT AGT AAA AAT AAT AAT AAT GAT AAT ACA- AATT 1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T 89174984 AAT AAT AAT 1 AAT AAT AAT 89174993 GATGATATAA Statistics Matches: 112, Mismatches: 22, Indels: 26 0.70 0.14 0.16 Matches are distributed among these distances: 2 8 0.07 3 77 0.69 4 27 0.24 ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28 Consensus pattern (3 bp): AAT Found at i:89174887 original size:22 final size:22 Alignment explanation

Indices: 89174862--89174995 Score: 57 Period size: 22 Copynumber: 6.1 Consensus size: 22 89174852 AACAGTAGTA 89174862 ATAAATAAATAAATAAATAATG 1 ATAAATAAATAAATAAATAATG * * 89174884 ATAATAAAAATAATAGTAAATAA-A 1 ATAA-ATAAATAA-A-TAAATAATG * * * 89174908 ATAAAGATA-AAATTAATAATG 1 ATAAATAAATAAATAAATAATG * ** * 89174929 AT-AGTAACGAATATAAATAATA 1 ATAAATAAATAA-ATAAATAATG 89174951 ATAGTAA-AAAT-AAT-AATAATG 1 ATA--AATAAATAAATAAATAATG * * 89174972 ATAATACAAATTAAT-AATAATG 1 ATAA-ATAAATAAATAAATAATG 89174994 AT 1 AT 89174996 GATATAAGTA Statistics Matches: 84, Mismatches: 16, Indels: 24 0.68 0.13 0.19 Matches are distributed among these distances: 19 1 0.01 20 9 0.11 21 18 0.21 22 30 0.36 23 11 0.13 24 7 0.08 25 8 0.10 ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28 Consensus pattern (22 bp): ATAAATAAATAAATAAATAATG Found at i:89175133 original size:3 final size:3 Alignment explanation

Indices: 89175125--89175314 Score: 72 Period size: 3 Copynumber: 62.7 Consensus size: 3 89175115 GGTAGAAAAG * * * 89175125 ATA ATA ATA ACGTA CTA ATA AGA ATA AAA AT- ATA ATA ATA ATA ATA 1 ATA ATA ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA * * * * * 89175171 ATA ATA AT- ATT TTAA ATA A-G ATA ATA ATA ATA GAT- AGA AT- GTA 1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA * * * * * * 89175214 GTA GTA ATA ATA CGTTA ATA A-A AGTA AGA GTA ATA ATA ATA AAA ATA 1 ATA ATA ATA ATA --ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA * * * 89175261 AAA ATA ATA GTA A-A TATA ATA A-A TATA ATA ATA AAA GATA ATA ATA 1 ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA -ATA ATA ATA * 89175307 AAA ATA AT 1 ATA ATA AT 89175315 TAATTGGAAA Statistics Matches: 138, Mismatches: 31, Indels: 36 0.67 0.15 0.18 Matches are distributed among these distances: 2 11 0.08 3 114 0.83 4 9 0.07 5 4 0.03 ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29 Consensus pattern (3 bp): ATA Found at i:89175272 original size:27 final size:27 Alignment explanation

Indices: 89175230--89175313 Score: 93 Period size: 27 Copynumber: 3.2 Consensus size: 27 89175220 ATAATACGTT * * 89175230 AATAAAAGTAAGAGTAATAATAATAAA 1 AATAAAAATAAAAGTAATAATAATAAA * 89175257 AATAAAAATAATAGTAA-ATATAATAAA 1 AATAAAAATAAAAGTAATA-ATAATAAA * * 89175284 TATAATAATAAAAG--ATAATAATAAA 1 AATAAAAATAAAAGTAATAATAATAAA 89175309 AATAA 1 AATAA 89175314 TTAATTGGAA Statistics Matches: 49, Mismatches: 6, Indels: 6 0.80 0.10 0.10 Matches are distributed among these distances: 25 13 0.27 26 2 0.04 27 34 0.69 ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25 Consensus pattern (27 bp): AATAAAAATAAAAGTAATAATAATAAA Found at i:89175330 original size:34 final size:32 Alignment explanation

Indices: 89175245--89175314 Score: 90 Period size: 34 Copynumber: 2.2 Consensus size: 32 89175235 AAGTAAGAGT * 89175245 AATAAT-AATA-AAAATAAAAATAATAGTAAA 1 AATAATAAATATAAAATAAAAATAATAATAAA * 89175275 TATAATAAATATAATAATAAAAGATAATAATAAA 1 AATAATAAATATAA-AATAAAA-ATAATAATAAA 89175309 AATAAT 1 AATAAT 89175315 TAATTGGAAA Statistics Matches: 33, Mismatches: 3, Indels: 4 0.82 0.08 0.10 Matches are distributed among these distances: 30 5 0.15 31 4 0.12 32 2 0.06 33 7 0.21 34 15 0.45 ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27 Consensus pattern (32 bp): AATAATAAATATAAAATAAAAATAATAATAAA Found at i:89184979 original size:49 final size:49 Alignment explanation

Indices: 89184922--89185020 Score: 171 Period size: 49 Copynumber: 2.0 Consensus size: 49 89184912 AATTTAAAGT * * 89184922 TAGGAAAATTATCTTTAAAAAGACGAAAATGAGTTCATAAGATATGTAG 1 TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG * 89184971 TAGGAAAATTATCTTTAGAAAGACGAAAAGGAGTTAATAAGATATGTAG 1 TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG 89185020 T 1 T 89185021 TGTTAATAAG Statistics Matches: 47, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 49 47 1.00 ACGTcount: A:0.46, C:0.05, G:0.20, T:0.28 Consensus pattern (49 bp): TAGGAAAATTATCTTTAAAAAGACGAAAAGGAGTTAATAAGATATGTAG Found at i:89186997 original size:19 final size:19 Alignment explanation

Indices: 89186973--89187018 Score: 74 Period size: 19 Copynumber: 2.4 Consensus size: 19 89186963 TCCTAGAAAA 89186973 TAAATAAAACTTATCTATC 1 TAAATAAAACTTATCTATC * * 89186992 TAAATAAGATTTATCTATC 1 TAAATAAAACTTATCTATC 89187011 TAAATAAA 1 TAAATAAA 89187019 TATATAAGTA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 19 24 1.00 ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37 Consensus pattern (19 bp): TAAATAAAACTTATCTATC Found at i:89191614 original size:61 final size:61 Alignment explanation

Indices: 89191504--89191688 Score: 275 Period size: 61 Copynumber: 3.0 Consensus size: 61 89191494 GTGATGTAGT * * ** * 89191504 AATTTTAAAATTATTTTTTGAAAAA-AATTTGAGGTTACTTACTACTGAAGTGCCTAATTA 1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA 89191564 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA 1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA * * * 89191625 AATTTTAAAATTATATTTTAAAAAAGAAATTGAGGTTACTTCA-GATTGAAGTACCTAATTA 1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATG-TTGAAGTACCTAATTA 89191686 AAT 1 AAT 89191689 ATTTGTTTTT Statistics Matches: 115, Mismatches: 8, Indels: 3 0.91 0.06 0.02 Matches are distributed among these distances: 60 26 0.23 61 89 0.77 ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40 Consensus pattern (61 bp): AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATGTTGAAGTACCTAATTA Found at i:89192003 original size:22 final size:22 Alignment explanation

Indices: 89191975--89192021 Score: 94 Period size: 22 Copynumber: 2.1 Consensus size: 22 89191965 TAAAAGATAC 89191975 TTTGATATCCATACGTTAAGAA 1 TTTGATATCCATACGTTAAGAA 89191997 TTTGATATCCATACGTTAAGAA 1 TTTGATATCCATACGTTAAGAA 89192019 TTT 1 TTT 89192022 TCTTTCATAA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 25 1.00 ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40 Consensus pattern (22 bp): TTTGATATCCATACGTTAAGAA Found at i:89208292 original size:60 final size:61 Alignment explanation

Indices: 89208155--89208283 Score: 224 Period size: 60 Copynumber: 2.1 Consensus size: 61 89208145 GTGATGTAGT * 89208155 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATCTTGAAGTACCTAATTA 1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA * 89208216 AATTTTAAAATTATTTTTT-AAAAAGAAATTGAGGTTACTTCATATTGAAGTACCTAATTA 1 AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA 89208276 AATATTTA 1 AAT-TTTA 89208284 TTTTATTTTA Statistics Matches: 65, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 60 42 0.65 61 23 0.35 ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42 Consensus pattern (61 bp): AATTTTAAAATTATTTTTTGAAAAAGAAATTGAGGTTACTTAATATTGAAGTACCTAATTA Found at i:89209028 original size:15 final size:16 Alignment explanation

Indices: 89209008--89209037 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 89208998 GATTAAATTG 89209008 TATATT-TTTATAATC 1 TATATTATTTATAATC 89209023 TATATTATTTATAAT 1 TATATTATTTATAAT 89209038 TTTTAAATAA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 6 0.43 16 8 0.57 ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60 Consensus pattern (16 bp): TATATTATTTATAATC Found at i:89209254 original size:278 final size:272 Alignment explanation

Indices: 89208750--89209429 Score: 761 Period size: 278 Copynumber: 2.5 Consensus size: 272 89208740 TTTAATAGTT * * 89208750 TATATATTTATAATTTTTAAAAAATTAAATTAATTTTTTATCATTTTCTAGAGTTAAAGTGTAAT 1 TATATATTTATAATTTTT-AAAAATTAAATTAA-TTTTTATCATTTT-TAGAATTAAAGTATAAT * * *** 89208815 TTCATTATTATTAACTTAAAATTTTATAAATTATAAAAT-ATTTAAA--AAAAAATT-ATTTTAG 63 TT-ATTATTATTAATTTAAAATTTTATAAATTAT-AAATGACTTAAATGAAATTTTTCATTTTAG * * * * 89208876 GAGGTCGAGACATTTGCCAGTCACCTCTTGCTCCACCACTAGCTAATGAATCTATTTCTAGTACC 126 GAGGTCAAGACATCTGCCAGTCACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGTACC * * 89208941 AAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCTAAGAAAATTTT-TGTGAG-TAGG-ATTA 191 AAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCCAA-AAAATTTTATGAG-GCT-GGAATTA 89209003 AATTGTATATTTTTATAATC 253 AATTGTATATTTTTATAATC * * * 89209023 TATATTATTTATAATTTTTAAATAATTAAATCAGATTTTTATCATTTTTAGAATTAATGTACAAT 1 TATA-TATTTATAATTTTTAAA-AATTAAATTA-ATTTTTATCATTTTTAGAATTAAAGTATAAT * * 89209088 CTTATCATTATTAATTTAAAATTTTATAAATTATAAATGGCTTAAATGATAATTTTTCATTTTAG 63 -TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATGA-AATTTTTCATTTTAG * * * ** * * 89209153 AGAGGTTAAGGC-TCCTGCCAG-CAACCTCTAGCTCCATCGTTGGCTAATGAATCTATTTATATT 126 -GAGGTCAAGACAT-CTGCCAGTC-ACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGT * * 89209216 ACCAAAATTTACTTTTTACTTATTAGGAAGGTTAAGAGCCAATAAATTTTATGAGGCTGGAATTA 188 ACCAAAATTTACTTTTTACTTATTAGGAAGGCTAAGAGCCAAAAAATTTTATGAGGCTGGAATTA * * * 89209281 AATTGTATGTTTTTATAGTT 253 AATTGTATATTTTTATAATC * * * * * ** 89209301 TATATCTTTATAATTTTT--AGATGAAATTATTTTTTATTATTTTTTTAATGTCAAAGTATAATT 1 TATATATTTATAATTTTTAAAAATTAAATTAATTTTTATCATTTTTAGAAT-T-AAAGTATAA-T 89209364 TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATAGAAAATTTTTCATTTTAG 63 TTATTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAAT-G-AAATTTTTCATTTTAG 89209429 G 126 G 89209430 CTTACCAGCC Statistics Matches: 345, Mismatches: 42, Indels: 38 0.81 0.10 0.09 Matches are distributed among these distances: 272 4 0.01 273 70 0.20 274 46 0.13 275 55 0.16 276 21 0.06 277 33 0.10 278 116 0.34 ACGTcount: A:0.36, C:0.09, G:0.10, T:0.44 Consensus pattern (272 bp): TATATATTTATAATTTTTAAAAATTAAATTAATTTTTATCATTTTTAGAATTAAAGTATAATTTA TTATTATTAATTTAAAATTTTATAAATTATAAATGACTTAAATGAAATTTTTCATTTTAGGAGGT CAAGACATCTGCCAGTCACCTCTAGCTCCACCACTAGCTAATGAATCTATTTATAGTACCAAAAT TTACTTTTTACTTATTAGGAAGGCTAAGAGCCAAAAAATTTTATGAGGCTGGAATTAAATTGTAT ATTTTTATAATC Found at i:89209904 original size:34 final size:34 Alignment explanation

Indices: 89209862--89209932 Score: 133 Period size: 34 Copynumber: 2.1 Consensus size: 34 89209852 AAAAGATACG * 89209862 TTTAATTAATTCATATTTTTTATATATATAATAT 1 TTTAATTAATTCATATTTTCTATATATATAATAT 89209896 TTTAATTAATTCATATTTTCTATATATATAATAT 1 TTTAATTAATTCATATTTTCTATATATATAATAT 89209930 TTT 1 TTT 89209933 GACTTTAAGT Statistics Matches: 36, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 34 36 1.00 ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59 Consensus pattern (34 bp): TTTAATTAATTCATATTTTCTATATATATAATAT Found at i:89209911 original size:16 final size:16 Alignment explanation

Indices: 89209862--89209914 Score: 54 Period size: 16 Copynumber: 3.2 Consensus size: 16 89209852 AAAAGATACG 89209862 TTTAATTAATTCATAT 1 TTTAATTAATTCATAT * * 89209878 TTT-TTATATATATAATAT 1 TTTAAT-TA-AT-TCATAT 89209896 TTTAATTAATTCATAT 1 TTTAATTAATTCATAT 89209912 TTT 1 TTT 89209915 CTATATATAT Statistics Matches: 29, Mismatches: 4, Indels: 8 0.71 0.10 0.20 Matches are distributed among these distances: 15 1 0.03 16 13 0.45 17 4 0.14 18 10 0.34 19 1 0.03 ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60 Consensus pattern (16 bp): TTTAATTAATTCATAT Found at i:89209931 original size:18 final size:17 Alignment explanation

Indices: 89209878--89209932 Score: 60 Period size: 16 Copynumber: 3.2 Consensus size: 17 89209868 TAATTCATAT 89209878 TTTTTATATATATAATA 1 TTTTTATATATATAATA * * 89209895 TTTTAAT-TA-ATTCATA 1 TTTTTATATATA-TAATA 89209911 TTTTCTATATATATAATA 1 TTTT-TATATATATAATA 89209929 TTTT 1 TTTT 89209933 GACTTTAAGT Statistics Matches: 30, Mismatches: 4, Indels: 7 0.73 0.10 0.17 Matches are distributed among these distances: 15 1 0.03 16 10 0.33 17 8 0.27 18 10 0.33 19 1 0.03 ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60 Consensus pattern (17 bp): TTTTTATATATATAATA Found at i:89210093 original size:23 final size:23 Alignment explanation

Indices: 89210067--89210113 Score: 94 Period size: 23 Copynumber: 2.0 Consensus size: 23 89210057 CTGAACCCGA 89210067 ACTCTTTTTCTATCAACAAAATT 1 ACTCTTTTTCTATCAACAAAATT 89210090 ACTCTTTTTCTATCAACAAAATT 1 ACTCTTTTTCTATCAACAAAATT 89210113 A 1 A 89210114 GTAGAGCGAC Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43 Consensus pattern (23 bp): ACTCTTTTTCTATCAACAAAATT Found at i:89210810 original size:21 final size:21 Alignment explanation

Indices: 89210786--89210828 Score: 86 Period size: 21 Copynumber: 2.0 Consensus size: 21 89210776 ATCCTAGGGG 89210786 TGGCCTGAGTTCTAGTCGCCC 1 TGGCCTGAGTTCTAGTCGCCC 89210807 TGGCCTGAGTTCTAGTCGCCC 1 TGGCCTGAGTTCTAGTCGCCC 89210828 T 1 T 89210829 AATCGTGCTT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 22 1.00 ACGTcount: A:0.09, C:0.33, G:0.28, T:0.30 Consensus pattern (21 bp): TGGCCTGAGTTCTAGTCGCCC Found at i:89213575 original size:3 final size:3 Alignment explanation

Indices: 89213567--89213660 Score: 72 Period size: 3 Copynumber: 31.3 Consensus size: 3 89213557 TCCATTTCGG * 89213567 GAA GAA GAA -AA GAAA GAA GGA GAA GAA GAA -AA GGAA GAA TG-A GAA 1 GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA -GAA GAA -GAA GAA * * * 89213612 GAA GGAA GGA GAA TAA GAA -AA GGAA GAA G-A GAA GAA GAA GAA GGA 1 GAA -GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA 89213657 GAA G 1 GAA G 89213661 GAGTCGGCTG Statistics Matches: 73, Mismatches: 8, Indels: 20 0.72 0.08 0.20 Matches are distributed among these distances: 2 9 0.12 3 53 0.73 4 11 0.15 ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02 Consensus pattern (3 bp): GAA Found at i:89213593 original size:21 final size:21 Alignment explanation

Indices: 89213567--89213615 Score: 80 Period size: 21 Copynumber: 2.3 Consensus size: 21 89213557 TCCATTTCGG 89213567 GAAGAAGAAAAGAAAGAAGGA 1 GAAGAAGAAAAGAAAGAAGGA * * 89213588 GAAGAAGAAAAGGAAGAATGA 1 GAAGAAGAAAAGAAAGAAGGA 89213609 GAAGAAG 1 GAAGAAG 89213616 GAAGGAGAAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02 Consensus pattern (21 bp): GAAGAAGAAAAGAAAGAAGGA Found at i:89213655 original size:21 final size:22 Alignment explanation

Indices: 89213608--89213656 Score: 54 Period size: 20 Copynumber: 2.5 Consensus size: 22 89213598 AGGAAGAATG * 89213608 AGAAGAAGGAAG---GAGAATA 1 AGAAGAAGGAAGAATGAGAAGA 89213627 AGAA-AAGGAAGAA-GAGAAGA 1 AGAAGAAGGAAGAATGAGAAGA 89213647 AGAAGAAGGA 1 AGAAGAAGGA 89213657 GAAGGAGTCG Statistics Matches: 26, Mismatches: 1, Indels: 4 0.84 0.03 0.13 Matches are distributed among these distances: 18 7 0.27 19 4 0.15 20 10 0.38 21 5 0.19 ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02 Consensus pattern (22 bp): AGAAGAAGGAAGAATGAGAAGA Found at i:89214125 original size:9 final size:9 Alignment explanation

Indices: 89214102--89214181 Score: 56 Period size: 9 Copynumber: 8.7 Consensus size: 9 89214092 CTACTCTTAT 89214102 TAAACATTTA 1 TAAA-ATTTA * 89214112 AAAAATTTA 1 TAAAATTTA * * 89214121 TAAAAATTG 1 TAAAATTTA 89214130 TAAAATTTTA 1 TAAAA-TTTA 89214140 TAAAATTGTA 1 TAAAATT-TA * 89214150 -AAATTTTA 1 TAAAATTTA * 89214158 TAATAA-TCA 1 TAA-AATTTA * 89214167 TAAAAATTA 1 TAAAATTTA 89214176 TAAAAT 1 TAAAAT 89214182 ACATTAAAAA Statistics Matches: 54, Mismatches: 11, Indels: 11 0.71 0.14 0.14 Matches are distributed among these distances: 8 4 0.07 9 37 0.69 10 13 0.24 ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39 Consensus pattern (9 bp): TAAAATTTA Found at i:89214134 original size:19 final size:19 Alignment explanation

Indices: 89214112--89214180 Score: 79 Period size: 18 Copynumber: 3.7 Consensus size: 19 89214102 TAAACATTTA 89214112 AAAAATTTATAAAAATTGT 1 AAAAATTTATAAAAATTGT * 89214131 AAAATTTTAT-AAAATTGT 1 AAAAATTTATAAAAATTGT * * ** 89214149 AAAATTTTATAATAATCAT 1 AAAAATTTATAAAAATTGT 89214168 AAAAA-TTATAAAA 1 AAAAATTTATAAAA 89214181 TACATTAAAA Statistics Matches: 43, Mismatches: 6, Indels: 3 0.83 0.12 0.06 Matches are distributed among these distances: 18 25 0.58 19 18 0.42 ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38 Consensus pattern (19 bp): AAAAATTTATAAAAATTGT Found at i:89214465 original size:18 final size:18 Alignment explanation

Indices: 89214444--89214490 Score: 53 Period size: 17 Copynumber: 2.7 Consensus size: 18 89214434 ATTGTATAAT * 89214444 TTTTTATATTTCTATA-TA 1 TTTTTATATTT-TATACGA * 89214462 -TTTTATATTTTTTACGA 1 TTTTTATATTTTATACGA 89214479 TTTTTATATTTT 1 TTTTTATATTTT 89214491 TTTCTAAATT Statistics Matches: 25, Mismatches: 2, Indels: 4 0.81 0.06 0.13 Matches are distributed among these distances: 16 3 0.12 17 11 0.44 18 11 0.44 ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70 Consensus pattern (18 bp): TTTTTATATTTTATACGA Found at i:89214491 original size:9 final size:9 Alignment explanation

Indices: 89214442--89214492 Score: 52 Period size: 9 Copynumber: 5.8 Consensus size: 9 89214432 AAATTGTATA 89214442 ATTTTTTAT 1 ATTTTTTAT * 89214451 A-TTTCTAT 1 ATTTTTTAT * 89214459 ATATTTTAT 1 ATTTTTTAT * 89214468 ATTTTTTACG 1 ATTTTTTA-T 89214478 A-TTTTTAT 1 ATTTTTTAT 89214486 ATTTTTT 1 ATTTTTT 89214493 TCTAAATTTT Statistics Matches: 33, Mismatches: 6, Indels: 6 0.73 0.13 0.13 Matches are distributed among these distances: 8 8 0.24 9 24 0.73 10 1 0.03 ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71 Consensus pattern (9 bp): ATTTTTTAT Found at i:89214501 original size:20 final size:20 Alignment explanation

Indices: 89214452--89214513 Score: 56 Period size: 18 Copynumber: 3.1 Consensus size: 20 89214442 ATTTTTTATA * 89214452 TTTCTATATATTTTATATTTT 1 TTTCTAAAT-TTTTATATTTT * * 89214473 TTAC--GATTTTTATATTTT 1 TTTCTAAATTTTTATATTTT * 89214491 TTTCTAAATTTTAATAATTTT 1 TTTCTAAATTTTTAT-ATTTT 89214512 TT 1 TT 89214514 AAATATTTAA Statistics Matches: 33, Mismatches: 5, Indels: 6 0.75 0.11 0.14 Matches are distributed among these distances: 18 14 0.42 19 2 0.06 20 7 0.21 21 10 0.30 ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68 Consensus pattern (20 bp): TTTCTAAATTTTTATATTTT Found at i:89214522 original size:19 final size:19 Alignment explanation

Indices: 89214489--89214544 Score: 64 Period size: 18 Copynumber: 3.1 Consensus size: 19 89214479 TTTTTATATT 89214489 TTTTTCTAAAT-TTTAATAA 1 TTTTT-TAAATATTTAATAA 89214508 TTTTTTAAATATTTAAT-A 1 TTTTTTAAATATTTAATAA * * 89214526 TTTATTAAA-ATCTAATAA 1 TTTTTTAAATATTTAATAA 89214544 T 1 T 89214545 ATTTATAGCT Statistics Matches: 33, Mismatches: 2, Indels: 5 0.82 0.05 0.12 Matches are distributed among these distances: 17 6 0.18 18 16 0.48 19 11 0.33 ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55 Consensus pattern (19 bp): TTTTTTAAATATTTAATAA Found at i:89214528 original size:18 final size:18 Alignment explanation

Indices: 89214459--89214534 Score: 64 Period size: 19 Copynumber: 4.1 Consensus size: 18 89214449 ATATTTCTAT * * 89214459 ATATTTTATATTTTTTACG 1 ATATTTAATATTTTTTA-A * * 89214478 ATTTTTATATTTTTTTCTAA 1 ATATTTA-ATATTTTT-TAA 89214498 AT-TTTAATAATTTTTTAA 1 ATATTTAAT-ATTTTTTAA * 89214516 ATATTTAATATTTATTAA 1 ATATTTAATATTTTTTAA 89214534 A 1 A 89214535 ATCTAATAAT Statistics Matches: 47, Mismatches: 6, Indels: 9 0.76 0.10 0.15 Matches are distributed among these distances: 18 16 0.34 19 20 0.43 20 9 0.19 21 2 0.04 ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62 Consensus pattern (18 bp): ATATTTAATATTTTTTAA Found at i:89214581 original size:10 final size:10 Alignment explanation

Indices: 89214566--89214598 Score: 57 Period size: 10 Copynumber: 3.3 Consensus size: 10 89214556 TTATTGATTT * 89214566 TAATTTTTAA 1 TAATTTTTTA 89214576 TAATTTTTTA 1 TAATTTTTTA 89214586 TAATTTTTTA 1 TAATTTTTTA 89214596 TAA 1 TAA 89214599 AAGCAGGGGC Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64 Consensus pattern (10 bp): TAATTTTTTA Found at i:89217696 original size:50 final size:50 Alignment explanation

Indices: 89217630--89217806 Score: 273 Period size: 50 Copynumber: 3.5 Consensus size: 50 89217620 CCATGGCAAC * 89217630 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGGCAAATGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA * * * * 89217680 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTAATCAATGACAAGTGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA * 89217730 AAGTGATAAGTGATAGCTTCGGCTGCACTTATCTGATCAAGGACAAATGA 1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA * * 89217780 CAAGTGAAAAGTGGTAGCTTCGGCTAC 1 -AAGTGATAAGTGATAGCTTCGGCTAC 89217807 CTGATCGGTG Statistics Matches: 113, Mismatches: 13, Indels: 1 0.89 0.10 0.01 Matches are distributed among these distances: 50 90 0.80 51 23 0.20 ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26 Consensus pattern (50 bp): AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA Found at i:89217821 original size:31 final size:31 Alignment explanation

Indices: 89217782--89217930 Score: 226 Period size: 31 Copynumber: 4.8 Consensus size: 31 89217772 ACAAATGACA 89217782 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * * 89217813 GGTGAAAAGTGGTAGCTTCTGCTACCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * * 89217844 AGTGAAAAGTGGTAGCTCCGGCTACCTAATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * * * 89217875 AGTGAAAAATGGTAGCTCCGGCTATCTGATC 1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC * 89217906 AGTGAATAGTGGTAGCTTCGGCTAC 1 AGTGAAAAGTGGTAGCTTCGGCTAC 89217931 AAGTGACAAG Statistics Matches: 105, Mismatches: 13, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 31 105 1.00 ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26 Consensus pattern (31 bp): AGTGAAAAGTGGTAGCTTCGGCTACCTGATC Found at i:89218018 original size:47 final size:46 Alignment explanation

Indices: 89217948--89218162 Score: 152 Period size: 47 Copynumber: 4.7 Consensus size: 46 89217938 AAGTAATTTC * * * * 89217948 CGTATAAGATCAGATCTGGGATATGGCATCAGTGTGATATATGCTA 1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA * * * * 89217994 CTGTATAAGACCATATCTGAGATATAGCATCAGTGAGATATGTGATT 1 C-GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA * * * * * * 89218041 CGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTA 1 CGTATAAGACCATATCTGGGATATGGCATC-A-GTGAGATATATGA-TA * * * * 89218090 CGTGTAAGACCATAGCTAGGCTATGGCATC-----GATATATGAATA 1 CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATG-ATA * * * * 89218132 TGTGTAAGACCATAGCTGGGCTATGGCATCA 1 CGTATAAGACCATATCTGGGATATGGCATCA 89218163 TTATATGAAG Statistics Matches: 143, Mismatches: 20, Indels: 15 0.80 0.11 0.08 Matches are distributed among these distances: 42 37 0.26 43 1 0.01 46 25 0.17 47 39 0.27 48 11 0.08 49 30 0.21 ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29 Consensus pattern (46 bp): CGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATA Found at i:89218100 original size:49 final size:48 Alignment explanation

Indices: 89218030--89218205 Score: 198 Period size: 42 Copynumber: 3.9 Consensus size: 48 89218020 GCATCAGTGA * 89218030 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGT 1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT * 89218078 GATATGTGATTACGTGTAAGACCATAGCTAGGCTATGGCATCGATATAT 1 GATATGTGATT-CGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT 89218127 GA-A--T-A-T-GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATAT 1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA-TATAT * ** 89218169 GA-A---GA-T-GTGTAAGACCATAGTTGAACTATGGCATCGA 1 GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGA 89218206 GAAAACGAAG Statistics Matches: 118, Mismatches: 6, Indels: 13 0.86 0.04 0.09 Matches are distributed among these distances: 41 1 0.01 42 64 0.54 43 1 0.01 44 1 0.01 45 1 0.01 46 1 0.01 48 12 0.10 49 37 0.31 ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30 Consensus pattern (48 bp): GATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCGATATAT Found at i:89221680 original size:2 final size:2 Alignment explanation

Indices: 89221673--89221697 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 89221663 CCAAAGTGAG 89221673 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 A 89221698 AAAGTTTTGA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Done.