Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence

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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 139000 characters in sequence are not A, C, G, or T


File 134 of 190

Found at i:21583956 original size:22 final size:22

Alignment explanation

Indices: 21583926--21583980 Score: 67 Period size: 22 Copynumber: 2.5 Consensus size: 22 21583916 CTTTAATATT * * 21583926 AATA-ATATTTGAATTTATTTA 1 AATATATATTTAAATTTATTAA * * 21583947 AATATTTATTTAAATTTGTTAA 1 AATATATATTTAAATTTATTAA 21583969 AATATATATTTA 1 AATATATATTTA 21583981 TTTAAATTTT Statistics Matches: 28, Mismatches: 5, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 21 4 0.14 22 24 0.86 ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53 Consensus pattern (22 bp): AATATATATTTAAATTTATTAA Found at i:21585620 original size:19 final size:20 Alignment explanation

Indices: 21585572--21585620 Score: 57 Period size: 20 Copynumber: 2.5 Consensus size: 20 21585562 AACATGTTAG * 21585572 AAAATATTTTTTTCTATCCA 1 AAAATATTATTTTCTATCCA * 21585592 AAAA-ATTTATTTTCTAT-TA 1 AAAATA-TTATTTTCTATCCA 21585611 AAAATATTAT 1 AAAATATTAT 21585621 ATATCTTTTT Statistics Matches: 25, Mismatches: 2, Indels: 5 0.78 0.06 0.16 Matches are distributed among these distances: 19 10 0.40 20 15 0.60 ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49 Consensus pattern (20 bp): AAAATATTATTTTCTATCCA Found at i:21585698 original size:21 final size:21 Alignment explanation

Indices: 21585664--21585704 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 21585654 TTATAAAGAA * 21585664 AAAAATGAAAAAAGTAAAAAT 1 AAAAATGAAAAAAGGAAAAAT ** 21585685 AAAAATGATGAAAGGAAAAA 1 AAAAATGAAAAAAGGAAAAA 21585705 GACCTTTTAC 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:0.73, C:0.00, G:0.15, T:0.12 Consensus pattern (21 bp): AAAAATGAAAAAAGGAAAAAT Found at i:21585826 original size:17 final size:17 Alignment explanation

Indices: 21585804--21585837 Score: 59 Period size: 17 Copynumber: 2.0 Consensus size: 17 21585794 TCCTTTGAAT 21585804 ATAAAATATAATTAAAA 1 ATAAAATATAATTAAAA * 21585821 ATAAAATATAGTTAAAA 1 ATAAAATATAATTAAAA 21585838 TTTTGAAAAT 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:0.68, C:0.00, G:0.03, T:0.29 Consensus pattern (17 bp): ATAAAATATAATTAAAA Found at i:21585887 original size:22 final size:22 Alignment explanation

Indices: 21585873--21585917 Score: 90 Period size: 22 Copynumber: 2.0 Consensus size: 22 21585863 AATTTTTTAT 21585873 ATAAGTTTAAAAAATTAAATAA 1 ATAAGTTTAAAAAATTAAATAA 21585895 ATAAGTTTAAAAAATTAAATAA 1 ATAAGTTTAAAAAATTAAATAA 21585917 A 1 A 21585918 AAACTCCATA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 23 1.00 ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31 Consensus pattern (22 bp): ATAAGTTTAAAAAATTAAATAA Found at i:21585942 original size:30 final size:30 Alignment explanation

Indices: 21585908--21585966 Score: 75 Period size: 30 Copynumber: 2.0 Consensus size: 30 21585898 AGTTTAAAAA 21585908 ATTAAATAAAAAAC-TCCATATCATTTTAAT 1 ATTAAAT-AAAAACTTCCATATCATTTTAAT * ** 21585938 ATTAACTAAAAACTTTTATATCATTTTAA 1 ATTAAATAAAAACTTCCATATCATTTTAA 21585967 AAAATAGATT Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 29 6 0.24 30 19 0.76 ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41 Consensus pattern (30 bp): ATTAAATAAAAACTTCCATATCATTTTAAT Found at i:21595169 original size:3 final size:3 Alignment explanation

Indices: 21595161--21595210 Score: 100 Period size: 3 Copynumber: 16.7 Consensus size: 3 21595151 CCCAAAATTT 21595161 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA 21595209 AT 1 AT 21595211 TCCCATCCAA Statistics Matches: 47, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 47 1.00 ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:21597933 original size:41 final size:42 Alignment explanation

Indices: 21597855--21597978 Score: 153 Period size: 42 Copynumber: 3.0 Consensus size: 42 21597845 TTTTTTATTA * 21597855 CAATGATGACATTTTTCATGAACAAAACATTGTAATTGCTAC 1 CAATGATGACGTTTTTCATGAACAAAACATTGTAATTGCTAC ** * 21597897 CAATGATGACGTTTTTCATG-ACAAAATGTTGTAATTGCTAT 1 CAATGATGACGTTTTTCATGAACAAAACATTGTAATTGCTAC * * * * 21597938 CAACT-ACGATGTTTTTCATGAACAAAACATCGTAGTTGCTA 1 CAA-TGATGACGTTTTTCATGAACAAAACATTGTAATTGCTA 21597979 TAGTACAATT Statistics Matches: 70, Mismatches: 10, Indels: 4 0.83 0.12 0.05 Matches are distributed among these distances: 41 34 0.49 42 36 0.51 ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35 Consensus pattern (42 bp): CAATGATGACGTTTTTCATGAACAAAACATTGTAATTGCTAC Found at i:21601565 original size:14 final size:14 Alignment explanation

Indices: 21601546--21601573 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 21601536 CCACTTTAAA 21601546 CAATTGAATAAGGG 1 CAATTGAATAAGGG 21601560 CAATTGAATAAGGG 1 CAATTGAATAAGGG 21601574 TAAGAAAAAG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21 Consensus pattern (14 bp): CAATTGAATAAGGG Found at i:21605731 original size:22 final size:22 Alignment explanation

Indices: 21605701--21605784 Score: 136 Period size: 22 Copynumber: 3.9 Consensus size: 22 21605691 AGTTGTTTGG 21605701 TTTC-ATTTTCTTAGCATTTCC 1 TTTCAATTTTCTTAGCATTTCC * 21605722 TTTCAATTTTCTTAGCGTTTCC 1 TTTCAATTTTCTTAGCATTTCC * 21605744 TTTCAATTTTCTTAGCGTTTCC 1 TTTCAATTTTCTTAGCATTTCC 21605766 TTTCAATTTTC-TAGCATTT 1 TTTCAATTTTCTTAGCATTT 21605785 ATTGTTCTTT Statistics Matches: 60, Mismatches: 2, Indels: 2 0.94 0.03 0.03 Matches are distributed among these distances: 21 11 0.18 22 49 0.82 ACGTcount: A:0.15, C:0.21, G:0.07, T:0.56 Consensus pattern (22 bp): TTTCAATTTTCTTAGCATTTCC Found at i:21607416 original size:18 final size:18 Alignment explanation

Indices: 21607393--21607427 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 21607383 CCTGATCCAC 21607393 CACAATA-TCATCATTCAT 1 CACAATACT-ATCATTCAT 21607411 CACAATACTATCATTCA 1 CACAATACTATCATTCA 21607428 CCATAGTATT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 18 15 0.94 19 1 0.06 ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31 Consensus pattern (18 bp): CACAATACTATCATTCAT Found at i:21608796 original size:20 final size:19 Alignment explanation

Indices: 21608751--21608800 Score: 55 Period size: 20 Copynumber: 2.5 Consensus size: 19 21608741 GGGTATTGAG * 21608751 AAATTTTATGCCAAAATTTTC 1 AAATTTT-T-CCAAAATTTTA * 21608772 CAATTTTTCCAAAATTTTTA 1 AAATTTTTCCAAAA-TTTTA 21608792 AAATTTTTC 1 AAATTTTTC 21608801 ATGGAATTAT Statistics Matches: 25, Mismatches: 3, Indels: 3 0.81 0.10 0.10 Matches are distributed among these distances: 19 6 0.24 20 13 0.52 21 6 0.24 ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48 Consensus pattern (19 bp): AAATTTTTCCAAAATTTTA Found at i:21614606 original size:12 final size:12 Alignment explanation

Indices: 21614589--21614617 Score: 51 Period size: 11 Copynumber: 2.5 Consensus size: 12 21614579 AAAGGAGAAG 21614589 AAATCAAAAGTT 1 AAATCAAAAGTT 21614601 AAATC-AAAGTT 1 AAATCAAAAGTT 21614612 AAATCA 1 AAATCA 21614618 TTATTTGAAT Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 11 11 0.69 12 5 0.31 ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24 Consensus pattern (12 bp): AAATCAAAAGTT Found at i:21615088 original size:15 final size:16 Alignment explanation

Indices: 21615062--21615091 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 21615052 ATTGGATCTT 21615062 TATAATATTATTGTTA 1 TATAATATTATTGTTA 21615078 TATAA-ATTATTGTT 1 TATAATATTATTGTT 21615092 TTTATGAATT Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 9 0.64 16 5 0.36 ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57 Consensus pattern (16 bp): TATAATATTATTGTTA Found at i:21619518 original size:46 final size:45 Alignment explanation

Indices: 21619379--21619526 Score: 135 Period size: 41 Copynumber: 3.4 Consensus size: 45 21619369 AAGCATCGAG * ** * 21619379 TATAAGTAATGAAATATAACCAAGACATAAGTGATAAAACAAGGC 1 TATAAGTAATGAAATATAGCCAAGACATAAGCAATAAAATAAGGC * * * * * 21619424 TATAAGTAATGAAATATAGTC-A-A-A-AA-CTATAAAGCTACGAC 1 TATAAGTAATGAAATATAGCCAAGACATAAGCAATAAA-ATAAGGC * ** 21619465 TACAAGTAATGAAATATAGCCAAGACATAAGCAATAAAATTGTGGC 1 TATAAGTAATGAAATATAGCCAAGACATAAGCAATAAAA-TAAGGC 21619511 TATAAGTAATGAAATA 1 TATAAGTAATGAAATA 21619527 CAACCAAAAT Statistics Matches: 80, Mismatches: 16, Indels: 13 0.73 0.15 0.12 Matches are distributed among these distances: 40 5 0.06 41 24 0.30 42 2 0.03 43 2 0.03 44 2 0.03 45 21 0.26 46 24 0.30 ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23 Consensus pattern (45 bp): TATAAGTAATGAAATATAGCCAAGACATAAGCAATAAAATAAGGC Found at i:21625783 original size:5 final size:5 Alignment explanation

Indices: 21625774--21625806 Score: 52 Period size: 5 Copynumber: 7.0 Consensus size: 5 21625764 TCCAATTCCT 21625774 TAAAA -AAAA -AAAA TAAAA TAAAA TAAAA TAAAA 1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA 21625807 AAACCTGCTC Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 4 8 0.30 5 19 0.70 ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15 Consensus pattern (5 bp): TAAAA Found at i:21626740 original size:18 final size:18 Alignment explanation

Indices: 21626717--21626752 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 21626707 CGAAATAAGT 21626717 AATTTTTAAATTTAATTA 1 AATTTTTAAATTTAATTA * 21626735 AATTTTTATATTTAATTA 1 AATTTTTAAATTTAATTA 21626753 TTTTAATTAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58 Consensus pattern (18 bp): AATTTTTAAATTTAATTA Found at i:21631317 original size:9 final size:9 Alignment explanation

Indices: 21631303--21631336 Score: 50 Period size: 9 Copynumber: 3.6 Consensus size: 9 21631293 AATTTTTGCT 21631303 TAAAATATA 1 TAAAATATA 21631312 TAAAATATA 1 TAAAATATA 21631321 TTAATAATATA 1 -TAA-AATATA 21631332 TAAAA 1 TAAAA 21631337 AAGATTTTTA Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 9 11 0.48 10 6 0.26 11 6 0.26 ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35 Consensus pattern (9 bp): TAAAATATA Found at i:21631635 original size:255 final size:249 Alignment explanation

Indices: 21630954--21631642 Score: 997 Period size: 255 Copynumber: 2.7 Consensus size: 249 21630944 CAAAATTCAC * * 21630954 AATTATAATAACAAAAAATGTTATAATAAAAGCATGTAACATATAATAAGCAAATACTCACATAA 1 AATTATAATAAGAACAAATGTTAT-A-AAAA-CATGTAACATATAATAAGCAAATACTCACATAA 21631019 AATAATTATTTATAATAATAATTTTTTCTTAAAATATATAAAATAT-TTAATAATATATATAAAA 63 AATAATTATTTATAATAATAATTTTTTCTTAAAATATATAAAATATATTAAT-A-ATATAT--AA * * 21631083 AAAAGATTTTTAGGTGCAATATATAAAAACAAAATTTAAAATTATAATAAGAAAAAAATGTTATA 124 AAAAGATTTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATA * 21631148 ATAAGAACATGTAACATATAATAAAAAAAATTGGTTGAAAAAAATGTTATTTATAATTGTG 189 ATAAGAACATGTAACATATAATAAAAAAAATTGGCTGAAAAAAATGTTATTTATAATTGTG 21631209 AATTATAATAAGAACAAATGTTATAATTACAACATGTAACATATAATAAGCAAATACTCACATAA 1 AATTATAATAAGAACAAATGTTATAA--A-AACATGTAACATATAATAAGCAAATACTCACATAA * 21631274 AATAATTATTTATAATAATAATTTTTGCTTAAAATATATAAAATATATTAATAATATATAAAAAA 63 AATAATTATTTATAATAATAATTTTTTCTTAAAATATATAAAATATATTAATAATATATAAAAAA * * * 21631339 GATTTTTAGGTGAAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAACTATTATAATAG 128 GATTTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATAATAA 21631404 GAACATGTAACATATAATAAGAAAAAATATTTGGCTGAAAAAAATGTTATTTATAATTGTG 193 GAACATGTAACATATAAT-A-AAAAAA-A-TTGGCTGAAAAAAATGTTATTTATAATTGTG * ** * * * * * 21631465 AATTTTTTTTA-TA-TATTGCATCTATAAAAACATGTAACATATAATAAGCAAATGCTCACATAA 1 AATTATAATAAGAACAAATG--T-TATAAAAACATGTAACATATAATAAGCAAATACTCACATAA * * 21631528 AATAATTATTTATAATAATAATTTTTTTCTTAAAATATATAAATTATATTAATAGTATATAAAAA 63 AATAATTATTTATAATAATAA-TTTTTTCTTAAAATATATAAAATATATTAATAATATATAAAAA * * * 21631593 AGATTTTTAAGTGCAATATACAAAAATAAAATTCAAAATTATAATAAGAA 127 AGATTTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAA 21631643 CATGTAACAT Statistics Matches: 398, Mismatches: 24, Indels: 24 0.89 0.05 0.05 Matches are distributed among these distances: 252 84 0.21 253 2 0.01 254 71 0.18 255 191 0.48 256 45 0.11 257 5 0.01 ACGTcount: A:0.53, C:0.06, G:0.07, T:0.35 Consensus pattern (249 bp): AATTATAATAAGAACAAATGTTATAAAAACATGTAACATATAATAAGCAAATACTCACATAAAAT AATTATTTATAATAATAATTTTTTCTTAAAATATATAAAATATATTAATAATATATAAAAAAGAT TTTTAGGTGCAATATATAAAAACAAAATTCAAAATTATAATAAGAAAAAAATATTATAATAAGAA CATGTAACATATAATAAAAAAAATTGGCTGAAAAAAATGTTATTTATAATTGTG Found at i:21631760 original size:9 final size:9 Alignment explanation

Indices: 21631733--21631766 Score: 50 Period size: 9 Copynumber: 3.6 Consensus size: 9 21631723 TAAAAATCTT 21631733 TTTTATATA 1 TTTTATATA 21631742 TTATTAATATA 1 TT-TT-ATATA 21631753 TTTTATATA 1 TTTTATATA 21631762 TTTTA 1 TTTTA 21631767 AGAAAAAATT Statistics Matches: 23, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 9 12 0.52 10 4 0.17 11 7 0.30 ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65 Consensus pattern (9 bp): TTTTATATA Found at i:21636682 original size:25 final size:26 Alignment explanation

Indices: 21636649--21636697 Score: 66 Period size: 25 Copynumber: 1.9 Consensus size: 26 21636639 CTCTTTTAGG * 21636649 TAGCTTTA-TCTCTTTCTCCCTTTCGA 1 TAGCTTTATTC-CCTTCTCCCTTTCGA 21636675 TAGC-TTATTCCCTTCTCCCTTTC 1 TAGCTTTATTCCCTTCTCCCTTTC 21636698 AACAATTTCC Statistics Matches: 21, Mismatches: 1, Indels: 3 0.84 0.04 0.12 Matches are distributed among these distances: 25 15 0.71 26 6 0.29 ACGTcount: A:0.10, C:0.35, G:0.06, T:0.49 Consensus pattern (26 bp): TAGCTTTATTCCCTTCTCCCTTTCGA Found at i:21637476 original size:136 final size:136 Alignment explanation

Indices: 21637224--21637488 Score: 343 Period size: 136 Copynumber: 1.9 Consensus size: 136 21637214 TGAAAAGGTC * * * * * * 21637224 AAATTATGAAAATACCCTTATAGGGGTATTTTGGTAATTTCACACTTCTCAAGGTACTGCTGTGA 1 AAATTATAAAAATACCCTTATAAGGATATTTTAGTAATTTCACAATTCTCAAGGTACTACTGTGA * * 21637289 TTTTAAATGCATCAAAAAGCAAGAAATATTATGAAATTAAGATCTAGAAAGTTTCATCAAAATTT 66 TTTCAAATGCATCAAAAAGCAAGAAATATTATGAAATTAAGATATAGAAAGTTTCATCAAAATTT 21637354 AAGGCT 131 AAGGCT * * * * * * 21637360 AAATTATAAAAATACCTTTATAAGGATATTTTAGTAATTTCATAATTTTTACGGTACTATTGTGA 1 AAATTATAAAAATACCCTTATAAGGATATTTTAGTAATTTCACAATTCTCAAGGTACTACTGTGA * * * * * 21637425 TTTCAAATGCATTAAAAATCATGAAATATTATGAAATTCAGATAT-GAAAAGTTTCATGAAAATT 66 TTTCAAATGCATCAAAAAGCAAGAAATATTATGAAATTAAGATATAG-AAAGTTTCATCAAAATT 21637489 CCAACTCAGG Statistics Matches: 109, Mismatches: 19, Indels: 2 0.84 0.15 0.02 Matches are distributed among these distances: 135 1 0.01 136 108 0.99 ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36 Consensus pattern (136 bp): AAATTATAAAAATACCCTTATAAGGATATTTTAGTAATTTCACAATTCTCAAGGTACTACTGTGA TTTCAAATGCATCAAAAAGCAAGAAATATTATGAAATTAAGATATAGAAAGTTTCATCAAAATTT AAGGCT Found at i:21638255 original size:74 final size:74 Alignment explanation

Indices: 21638119--21638270 Score: 191 Period size: 74 Copynumber: 2.1 Consensus size: 74 21638109 AAAGGCTATG * * * ** 21638119 AAAATGGCTCCCCCTCAACAAAGGCTTTGAAACTTCAAAGATGGCTCTCCTTAAACTGAGGCTTT 1 AAAATAGCTCCCCCTAAACAAAGGCTTTGAAACTTCAAAGATGGCTCTACTTAAACAAAGGCTTT 21638184 GAAACTTTT 66 GAAACTTTT * * * * 21638193 AAAATAGCTCCCCCTAAATAGAGGCTTTGAAACTTTGAAA-ATGGCTCCTAC-TATACAAAGGCT 1 AAAATAGCTCCCCCTAAACAAAGGCTTTGAAAC-TTCAAAGATGGCT-CTACTTAAACAAAGGCT 21638256 TTGAAACTTTT 64 TTGAAACTTTT 21638267 AAAA 1 AAAA 21638271 ATAAAATCTT Statistics Matches: 67, Mismatches: 9, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 74 59 0.88 75 8 0.12 ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28 Consensus pattern (74 bp): AAAATAGCTCCCCCTAAACAAAGGCTTTGAAACTTCAAAGATGGCTCTACTTAAACAAAGGCTTT GAAACTTTT Found at i:21638265 original size:37 final size:37 Alignment explanation

Indices: 21638117--21638270 Score: 166 Period size: 37 Copynumber: 4.2 Consensus size: 37 21638107 ACAAAGGCTA * 21638117 TGAAAATGGCTCCCCCTCAACAAAGGCTTTGAAAC-T 1 TGAAAATGGCTCCCCCTAAACAAAGGCTTTGAAACTT * * * ** 21638153 TCAAAGATGGCTCTCCTTAAACTGAGGCTTTGAAACTT 1 TGAAA-ATGGCTCCCCCTAAACAAAGGCTTTGAAACTT * * * * 21638191 TTAAAATAGCTCCCCCTAAATAGAGGCTTTGAAACTT 1 TGAAAATGGCTCCCCCTAAACAAAGGCTTTGAAACTT ** * 21638228 TGAAAATGGCTCCTACTATACAAAGGCTTTGAAACTT 1 TGAAAATGGCTCCCCCTAAACAAAGGCTTTGAAACTT * 21638265 TTAAAA 1 TGAAAA 21638271 ATAAAATCTT Statistics Matches: 96, Mismatches: 20, Indels: 3 0.81 0.17 0.03 Matches are distributed among these distances: 36 4 0.04 37 87 0.91 38 5 0.05 ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29 Consensus pattern (37 bp): TGAAAATGGCTCCCCCTAAACAAAGGCTTTGAAACTT Found at i:21639462 original size:33 final size:33 Alignment explanation

Indices: 21639395--21639603 Score: 158 Period size: 33 Copynumber: 6.3 Consensus size: 33 21639385 AGTTAAGTTG * * * 21639395 GGCTTAAAAATTCATTGAGG-ACCAGATAAACTA 1 GGCTTAAAATTTCATT-AGGTGCTAGATAAACTA * * 21639428 GGCTTAAAATTTCATTAGGTGCTAGCTAAGCTA 1 GGCTTAAAATTTCATTAGGTGCTAGATAAACTA * ** * 21639461 GGCTTAAACTTTCA-CCGGTGCTAGGTAAACTA 1 GGCTTAAAATTTCATTAGGTGCTAGATAAACTA * 21639493 GGCTTAAAATTTTCATCAAGG-G-TCAGATAAACT- 1 GGCTTAAAA-TTTCAT-TAGGTGCT-AGATAAACTA * * * * * * 21639526 GGACTTAAATTTTCATTGGGAGCCAGTTAAGCTA 1 GG-CTTAAAATTTCATTAGGTGCTAGATAAACTA * * 21639560 GGCTTTAAAATCTTCATTAGGTGCTTGGTAAACTA 1 GGC-TTAAAAT-TTCATTAGGTGCTAGATAAACTA 21639595 GGCTTAAAA 1 GGCTTAAAA 21639604 ATCTTTCTTT Statistics Matches: 138, Mismatches: 27, Indels: 21 0.74 0.15 0.11 Matches are distributed among these distances: 32 27 0.20 33 60 0.43 34 29 0.21 35 22 0.16 ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31 Consensus pattern (33 bp): GGCTTAAAATTTCATTAGGTGCTAGATAAACTA Found at i:21639468 original size:66 final size:65 Alignment explanation

Indices: 21639395--21639605 Score: 178 Period size: 66 Copynumber: 3.2 Consensus size: 65 21639385 AGTTAAGTTG * * 21639395 GGCTTAAAAATTCATTGAGGACCAGATAAACTAGGCTTAAAATTTCATTAGGTGCTAGCTAAGCT 1 GGCTTAAAAATTCATTG-GGACCAGATAAACTAGGCTTAAAATTTCATTAGGTGCTAGATAAACT 21639460 A 65 A ** ** * * * 21639461 GGCTTAAACTTTCACCGGTG-CTAGGTAAACTAGGCTTAAAATTTTCATCAAGG-G-TCAGATAA 1 GGCTTAAAAATTCATTGG-GACCAGATAAACTAGGCTTAAAA-TTTCAT-TAGGTGCT-AGATAA 21639523 ACT- 62 ACTA ** * * * * 21639526 GGACTTAAATTTTCATTGGGAGCCAGTTAAGCTAGGCTTTAAAATCTTCATTAGGTGCTTGGTAA 1 GG-CTTAAAAATTCATTGGGA-CCAGATAAACTAGGC-TTAAAAT-TTCATTAGGTGCTAGATAA 21639591 ACTA 62 ACTA 21639595 GGCTTAAAAAT 1 GGCTTAAAAAT 21639606 CTTTCTTTAG Statistics Matches: 113, Mismatches: 20, Indels: 22 0.73 0.13 0.14 Matches are distributed among these distances: 65 24 0.21 66 41 0.36 67 19 0.17 68 26 0.23 69 3 0.03 ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31 Consensus pattern (65 bp): GGCTTAAAAATTCATTGGGACCAGATAAACTAGGCTTAAAATTTCATTAGGTGCTAGATAAACTA Found at i:21639521 original size:99 final size:102 Alignment explanation

Indices: 21639417--21639603 Score: 256 Period size: 99 Copynumber: 1.9 Consensus size: 102 21639407 CATTGAGGAC * * * * 21639417 CAGATAAACTAGG-CTTAAAATTTCATTAGGTGCTAGCTAAGCTAGGC-TTAAACT-TTCA-CCG 1 CAGATAAACT-GGACTTAAAATTTCATTAGGAGCCAGCTAAGCTAGGCTTTAAAATCTTCATCAG 21639478 GTGCTAGGTAAACTAGGCTTAAAATTTTCATCAAGGGT 65 GTGCTAGGTAAACTAGGCTTAAAATTTTCATCAAGGGT * * * * 21639516 CAGATAAACTGGACTTAAATTTTCATTGGGAGCCAGTTAAGCTAGGCTTTAAAATCTTCATTAGG 1 CAGATAAACTGGACTTAAAATTTCATTAGGAGCCAGCTAAGCTAGGCTTTAAAATCTTCATCAGG * 21639581 TGCTTGGTAAACTAGGCTTAAAA 66 TGCTAGGTAAACTAGGCTTAAAA 21639604 ATCTTTCTTT Statistics Matches: 75, Mismatches: 9, Indels: 5 0.84 0.10 0.06 Matches are distributed among these distances: 98 2 0.03 99 39 0.52 100 6 0.08 101 4 0.05 102 24 0.32 ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31 Consensus pattern (102 bp): CAGATAAACTGGACTTAAAATTTCATTAGGAGCCAGCTAAGCTAGGCTTTAAAATCTTCATCAGG TGCTAGGTAAACTAGGCTTAAAATTTTCATCAAGGGT Found at i:21639690 original size:179 final size:178 Alignment explanation

Indices: 21639485--21639819 Score: 442 Period size: 179 Copynumber: 1.9 Consensus size: 178 21639475 CCGGTGCTAG * * * 21639485 GTAAACTAGGCTTAAAATTTTCATC-AAGGGTCAGATAAACTG-GACTTAAATTTTCATTGGGAG 1 GTAAACTAGGCTTAAAATTTTCATCAAAGGCT-AAATAAACTGTG-CTTAAATTTTCACTGGGAG ** ** *** * 21639548 CCAGTTAAGCTAGGCTTTAAAATCTTCATTAGGTGCTTGGTAAACTAGGCTTAAAAATCTTTCTT 64 CCAACTAAGCTAGGCTTTAAAATCTTCATTAGACGCCAAGTAAACTAAGCTT-AAAATCTTTCTT * * * 21639613 TAGTGTAAGATAAATTGGGCTTGAAATTTCATTGGGTTTCATTAGTGCCAA 128 TAGTGTAAGATAAACTAGGCTTAAAATTTCATTGGGTTTCATTAGTGCCAA * 21639664 GTAAACT-GAGCTTAAAATTTTCATCAAAGGCTAAATAAATTGTGCTTAAATTTTCACTGGGAGC 1 GTAAACTAG-GCTTAAAATTTTCATCAAAGGCTAAATAAACTGTGCTTAAATTTTCACTGGGAGC * * * 21639728 TAACTAAGCTGGGCTTTAAAATCTTCATTAGACGCCAAGTAAACTAAGCTTAAAATCTTTCTTTG 65 CAACTAAGCTAGGCTTTAAAATCTTCATTAGACGCCAAGTAAACTAAGCTTAAAATCTTTCTTTA * 21639793 GTGTTAGATAAACTAGGCTTAAAATTT 130 GTGTAAGATAAACTAGGCTTAAAATTT 21639820 TTATTAGTAC Statistics Matches: 134, Mismatches: 19, Indels: 7 0.84 0.12 0.04 Matches are distributed among these distances: 178 37 0.28 179 91 0.68 180 6 0.04 ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35 Consensus pattern (178 bp): GTAAACTAGGCTTAAAATTTTCATCAAAGGCTAAATAAACTGTGCTTAAATTTTCACTGGGAGCC AACTAAGCTAGGCTTTAAAATCTTCATTAGACGCCAAGTAAACTAAGCTTAAAATCTTTCTTTAG TGTAAGATAAACTAGGCTTAAAATTTCATTGGGTTTCATTAGTGCCAA Found at i:21640295 original size:22 final size:22 Alignment explanation

Indices: 21640270--21640311 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 21640260 ATGCTTTTTT 21640270 AACTAATCCGGGCTTATGTGCC 1 AACTAATCCGGGCTTATGTGCC ** 21640292 AACTAATTTGGGCTTATGTG 1 AACTAATCCGGGCTTATGTG 21640312 TCAGTTAAAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 22 18 1.00 ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33 Consensus pattern (22 bp): AACTAATCCGGGCTTATGTGCC Found at i:21640350 original size:22 final size:22 Alignment explanation

Indices: 21640280--21640351 Score: 58 Period size: 22 Copynumber: 3.3 Consensus size: 22 21640270 AACTAATCCG * * * * 21640280 GGCTTATGTGCCAACTAATTTG 1 GGCTTATGTGCTAGCTAATCTA * * 21640302 GGCTTATGTG-TCAGTTAAATCGA 1 GGCTTATGTGCT-AGCT-AATCTA 21640325 -GCTTATGTGCTAGCTAATCTA 1 GGCTTATGTGCTAGCTAATCTA 21640346 GGCTTA 1 GGCTTA 21640352 AGACTTCATT Statistics Matches: 38, Mismatches: 8, Indels: 8 0.70 0.15 0.15 Matches are distributed among these distances: 21 5 0.13 22 29 0.76 23 4 0.11 ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36 Consensus pattern (22 bp): GGCTTATGTGCTAGCTAATCTA Found at i:21645882 original size:30 final size:30 Alignment explanation

Indices: 21645843--21645912 Score: 113 Period size: 30 Copynumber: 2.3 Consensus size: 30 21645833 TGTGCATAAA * 21645843 ATAGGATGCATGTACTATCCATTGATGTGG 1 ATAGGATGCATGTACTATCCATTGATATGG * * 21645873 ATGGGATGCATGTACTATTCATTGATATGG 1 ATAGGATGCATGTACTATCCATTGATATGG 21645903 ATAGGATGCA 1 ATAGGATGCA 21645913 ATGCATGTAT Statistics Matches: 36, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 30 36 1.00 ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33 Consensus pattern (30 bp): ATAGGATGCATGTACTATCCATTGATATGG Found at i:21650451 original size:145 final size:145 Alignment explanation

Indices: 21650183--21650523 Score: 400 Period size: 145 Copynumber: 2.3 Consensus size: 145 21650173 TTAAAACACC * * * * * * ** 21650183 AAAAATCATGAAATATTATAAGATTGAGATTTGAAAAGTTTCATAAAAATTCGAACTCGGTAAGA 1 AAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAACTCGAAAAGA * * * * 21650248 TCAAATTATAAAAATACCCTTTATGGGATATTTTGGTAATTCTACACTTTTCAAGGTACTGCTAT 66 TCAAATTACAAAAATACCCTTTATGGGACATTTTGATAATTCTACACTTTTCAAGGTACTACTAT 21650313 GATTTAAAATCCATA 131 GATTTAAAATCCATA * 21650328 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCGAAAATG 1 AAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAACTCGAAAA-G * * * *** 21650393 A-CAAATTACAAAAATA-TCTTTATAGGGGCATTTTGATAATT-TCATACTTTTTGGGGTACTAC 65 ATCAAATTACAAAAATACCCTTTAT-GGGACATTTTGATAATTCT-ACACTTTTCAAGGTACTAC * * * * 21650455 TGTGATTTCAAATGCATC 128 TATGATTTAAAATCCATA * * 21650473 AAAAATCATGAAATATTTATGAAATTAAGATCTGAAAAGTTTTATGAAAAT 1 AAAAATCATGAAATA-TTATAAAATTAAGATCTGAAAAGTTTCATGAAAAT 21650524 TTGAGCTCAA Statistics Matches: 166, Mismatches: 26, Indels: 7 0.83 0.13 0.04 Matches are distributed among these distances: 144 7 0.04 145 125 0.75 146 34 0.20 ACGTcount: A:0.43, C:0.11, G:0.13, T:0.34 Consensus pattern (145 bp): AAAAATCATGAAATATTATAAAATTAAGATCTGAAAAGTTTCATGAAAATCCAAACTCGAAAAGA TCAAATTACAAAAATACCCTTTATGGGACATTTTGATAATTCTACACTTTTCAAGGTACTACTAT GATTTAAAATCCATA Found at i:21650587 original size:145 final size:145 Alignment explanation

Indices: 21650183--21650579 Score: 354 Period size: 145 Copynumber: 2.7 Consensus size: 145 21650173 TTAAAACACC * * * * * * * *** 21650183 AAAAATCATGAAATATTATAAGATTGAGATTTGAAAAGTTTCATAAAAATTCGAACTCGGTAA-G 1 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCAAAAAGG * * * * * * * *** * 21650247 ATCAAATTATAAAAATACC-CTTTATGGGATATTTTGGTAA-TTCTACACTTTTCAAGGTACTGC 66 A-CAAATTACAAAAATACCTCTATAAGAG-CATTTTGATAATTTC-ATACTTTTTGGGGTACTAC 21650310 TATGATTTAAAATCCATA 128 TATGATTTAAAATCCATA * * 21650328 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCGAAAATG 1 AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCAAAAAGG * * * * * 21650393 ACAAATTACAAAAATATCTTTATAGGGGCATTTTGATAATTTCATACTTTTTGGGGTACTACTGT 66 ACAAATTACAAAAATACCTCTATAAGAGCATTTTGATAATTTCATACTTTTTGGGGTACTACTAT * * * 21650458 GATTTCAAATGCATC 131 GATTTAAAATCCATA * * * *** * 21650473 AAAAATCATGAAATATTTATGAAATTAAGATCTGAAAAGTTTTATGAAAATTTGAGCTCAAAAAG 1 AAAAATCATGAAATA-TTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCAAAAAG * * 21650538 GCCAAATTACGAAAATACCTCTA-AAGAGCATTTT-AGTAATTT 65 GACAAATTACAAAAATACCTCTATAAGAGCATTTTGA-TAATTT 21650580 TGTACTTTCC Statistics Matches: 207, Mismatches: 40, Indels: 10 0.81 0.16 0.04 Matches are distributed among these distances: 144 1 0.00 145 136 0.66 146 70 0.34 ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33 Consensus pattern (145 bp): AAAAATCATGAAATATTATAAAATTAAGATCTAAAAAGTTTCATGAAAATCCAAACTCAAAAAGG ACAAATTACAAAAATACCTCTATAAGAGCATTTTGATAATTTCATACTTTTTGGGGTACTACTAT GATTTAAAATCCATA Found at i:21651699 original size:128 final size:130 Alignment explanation

Indices: 21651514--21651750 Score: 352 Period size: 128 Copynumber: 1.8 Consensus size: 130 21651504 GCAATTTTGA * 21651514 TACCAATTATTAGTTATTTTGTTCACAACTTTCAAGGATAACAATATATTTCAAGCATCTAAAAA 1 TACCAATTATTAGTTATTTTGTTCACAA---T-AAGGATAACAATATATTTCAAGCATATAAAAA * 21651579 GTACAATCAATACATGCATAATAGCATTCTTTCATAAGCATATCTTTTAGCAATTTTGATATCAA 62 GTACAAACAATACATGCATAATAGCATTCTTTCATAAGCATATCTTTTAGCAATTTTGATATCAA 21651644 TTGT 127 TTGT * * * * * 21651648 TACCAATTGTTAGTTATTTTGTTCAC-A-AAGGATCATAATATATTTCAAGCATATGAAAAGTTC 1 TACCAATTATTAGTTATTTTGTTCACAATAAGGATAACAATATATTTCAAGCATATAAAAAGTAC * 21651711 AAACAATACATGCATAATAGCATTCTTTCATCAGCATATC 66 AAACAATACATGCATAATAGCATTCTTTCATAAGCATATC 21651751 CTATCCAAAA Statistics Matches: 95, Mismatches: 8, Indels: 6 0.87 0.07 0.06 Matches are distributed among these distances: 128 69 0.73 133 1 0.01 134 25 0.26 ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37 Consensus pattern (130 bp): TACCAATTATTAGTTATTTTGTTCACAATAAGGATAACAATATATTTCAAGCATATAAAAAGTAC AAACAATACATGCATAATAGCATTCTTTCATAAGCATATCTTTTAGCAATTTTGATATCAATTGT Found at i:21659242 original size:11 final size:12 Alignment explanation

Indices: 21659221--21659260 Score: 55 Period size: 12 Copynumber: 3.3 Consensus size: 12 21659211 TTATTTATAT 21659221 TTTAATTTTTTAG 1 TTTAA-TTTTTAG * 21659234 TTTAATTTTTGG 1 TTTAATTTTTAG 21659246 TTTAATTTTT-G 1 TTTAATTTTTAG 21659257 TTTA 1 TTTA 21659261 TTTAGTCAAA Statistics Matches: 26, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 11 5 0.19 12 16 0.62 13 5 0.19 ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70 Consensus pattern (12 bp): TTTAATTTTTAG Found at i:21659881 original size:20 final size:19 Alignment explanation

Indices: 21659853--21659935 Score: 88 Period size: 20 Copynumber: 4.6 Consensus size: 19 21659843 TTTTGCATGA * 21659853 ATTTTCATGACTAATATTAT 1 ATTTGCATGA-TAATATTAT 21659873 ATTTGCATGATTAATATTAT 1 ATTTGCATGA-TAATATTAT 21659893 ATTTGCATGAT-A-ATT-T 1 ATTTGCATGATAATATTAT * 21659909 ATTTGC-T--TAATATTTT 1 ATTTGCATGATAATATTAT 21659925 ATTTGCATGAT 1 ATTTGCATGAT 21659936 TAGTATATTT Statistics Matches: 55, Mismatches: 2, Indels: 13 0.79 0.03 0.19 Matches are distributed among these distances: 13 1 0.02 14 1 0.02 15 4 0.07 16 14 0.25 17 4 0.07 18 1 0.02 19 2 0.04 20 28 0.51 ACGTcount: A:0.31, C:0.07, G:0.10, T:0.52 Consensus pattern (19 bp): ATTTGCATGATAATATTAT Found at i:21659913 original size:16 final size:16 Alignment explanation

Indices: 21659872--21659935 Score: 65 Period size: 16 Copynumber: 3.8 Consensus size: 16 21659862 ACTAATATTA 21659872 TATTTGCATGATTAATATT 1 TATTTGCATGA-T-A-ATT 21659891 ATATTTGCATGATAATT 1 -TATTTGCATGATAATT * * * 21659908 TATTTGCTTAATATTT 1 TATTTGCATGATAATT 21659924 TATTTGCATGAT 1 TATTTGCATGAT 21659936 TAGTATATTT Statistics Matches: 39, Mismatches: 5, Indels: 4 0.81 0.10 0.08 Matches are distributed among these distances: 16 23 0.59 17 3 0.08 18 1 0.03 19 1 0.03 20 11 0.28 ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53 Consensus pattern (16 bp): TATTTGCATGATAATT Found at i:21659998 original size:20 final size:20 Alignment explanation

Indices: 21659955--21660012 Score: 62 Period size: 20 Copynumber: 2.9 Consensus size: 20 21659945 TGTGTGATTT * ** 21659955 ATTAATATATTTGCATTACT 1 ATTAATATATTTGCATGAAA * 21659975 ATTAATATGTTTGCATGAAA 1 ATTAATATATTTGCATGAAA * * 21659995 ATTAATTTATTTCCATGA 1 ATTAATATATTTGCATGA 21660013 TTGGCAATTT Statistics Matches: 31, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 20 31 1.00 ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47 Consensus pattern (20 bp): ATTAATATATTTGCATGAAA Found at i:21660129 original size:41 final size:43 Alignment explanation

Indices: 21660067--21660157 Score: 105 Period size: 43 Copynumber: 2.2 Consensus size: 43 21660057 ATTTAATTGC * * * 21660067 ATATTTATTTGTATGA-CT-TATATTGCTATTTGCATGATTAT 1 ATATTTATTTGCATGATCTATATATTGCTATTTGAATGAATAT * * ** 21660108 ATATTTATTTGCATGGTTTATATATTTTTATTTGAATGAATAT 1 ATATTTATTTGCATGATCTATATATTGCTATTTGAATGAATAT 21660151 ATATTTA 1 ATATTTA 21660158 ATTACATGTT Statistics Matches: 41, Mismatches: 7, Indels: 2 0.82 0.14 0.04 Matches are distributed among these distances: 41 14 0.34 42 1 0.02 43 26 0.63 ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55 Consensus pattern (43 bp): ATATTTATTTGCATGATCTATATATTGCTATTTGAATGAATAT Found at i:21660137 original size:23 final size:20 Alignment explanation

Indices: 21660067--21660157 Score: 85 Period size: 21 Copynumber: 4.3 Consensus size: 20 21660057 ATTTAATTGC * 21660067 ATATTTATTTGTATGACTTAT 1 ATATTTATTTGCATGA-TTAT * 21660088 AT-TGCTATTTGCATGATTAT 1 ATAT-TTATTTGCATGATTAT * 21660108 ATATTTATTTGCATGGTTTAT 1 ATATTTATTTGCAT-GATTAT * * 21660129 ATATTTTTATTTGAATGAATAT 1 ATA--TTTATTTGCATGATTAT 21660151 ATATTTA 1 ATATTTA 21660158 ATTACATGTT Statistics Matches: 58, Mismatches: 7, Indels: 11 0.76 0.09 0.14 Matches are distributed among these distances: 20 20 0.34 21 21 0.36 22 7 0.12 23 10 0.17 ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55 Consensus pattern (20 bp): ATATTTATTTGCATGATTAT Found at i:21660487 original size:20 final size:20 Alignment explanation

Indices: 21660464--21660506 Score: 50 Period size: 20 Copynumber: 2.1 Consensus size: 20 21660454 GATTATATAT * 21660464 TTGCACAGTATTTTATATTA 1 TTGCACAGCATTTTATATTA *** 21660484 TTGCTTGGCATTTTATATTA 1 TTGCACAGCATTTTATATTA 21660504 TTG 1 TTG 21660507 GATGATAATT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53 Consensus pattern (20 bp): TTGCACAGCATTTTATATTA Found at i:21660550 original size:38 final size:37 Alignment explanation

Indices: 21660508--21660580 Score: 87 Period size: 37 Copynumber: 1.9 Consensus size: 37 21660498 ATATTATTGG 21660508 ATGATAATTAATATATTTGCATAAT-ATT-ATATATTTAA 1 ATGATAATT-AT-TA-TTGCATAATAATTAATATATTTAA ** 21660546 ATGATTGTTATTATTGCATAATAATTAATATATTT 1 ATGATAATTATTATTGCATAATAATTAATATATTT 21660581 GCATGACATT Statistics Matches: 31, Mismatches: 2, Indels: 5 0.82 0.05 0.13 Matches are distributed among these distances: 35 9 0.29 36 5 0.16 37 10 0.32 38 7 0.23 ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49 Consensus pattern (37 bp): ATGATAATTATTATTGCATAATAATTAATATATTTAA Found at i:21660584 original size:20 final size:20 Alignment explanation

Indices: 21660511--21660584 Score: 70 Period size: 20 Copynumber: 4.0 Consensus size: 20 21660501 TTATTGGATG 21660511 ATAATTAATATATTTGCATA 1 ATAATTAATATATTTGCATA 21660531 AT-ATT-ATATATTT--A-A 1 ATAATTAATATATTTGCATA * ** 21660546 ATGATTGTTAT-TATTGCATA 1 ATAATTAATATAT-TTGCATA 21660566 ATAATTAATATATTTGCAT 1 ATAATTAATATATTTGCAT 21660585 GACATTCTTC Statistics Matches: 43, Mismatches: 4, Indels: 14 0.70 0.07 0.23 Matches are distributed among these distances: 15 3 0.07 16 5 0.12 17 5 0.12 18 8 0.19 19 4 0.09 20 17 0.40 21 1 0.02 ACGTcount: A:0.41, C:0.04, G:0.07, T:0.49 Consensus pattern (20 bp): ATAATTAATATATTTGCATA Found at i:21660807 original size:39 final size:39 Alignment explanation

Indices: 21660758--21660837 Score: 160 Period size: 39 Copynumber: 2.1 Consensus size: 39 21660748 TTGTAAATAA 21660758 ATAAAAAATTTAGAATTGATTTATTTGCATAATAAAACT 1 ATAAAAAATTTAGAATTGATTTATTTGCATAATAAAACT 21660797 ATAAAAAATTTAGAATTGATTTATTTGCATAATAAAACT 1 ATAAAAAATTTAGAATTGATTTATTTGCATAATAAAACT 21660836 AT 1 AT 21660838 CTTTGATAAG Statistics Matches: 41, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 39 41 1.00 ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39 Consensus pattern (39 bp): ATAAAAAATTTAGAATTGATTTATTTGCATAATAAAACT Found at i:21662108 original size:22 final size:22 Alignment explanation

Indices: 21662083--21662124 Score: 57 Period size: 22 Copynumber: 1.9 Consensus size: 22 21662073 AAGTTTGAGG 21662083 ACCTTGCACTACTTCTTTCAAA 1 ACCTTGCACTACTTCTTTCAAA ** * 21662105 ACCTTTTATTACTTCTTTCA 1 ACCTTGCACTACTTCTTTCA 21662125 GTTCTTGTTG Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 22 17 1.00 ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45 Consensus pattern (22 bp): ACCTTGCACTACTTCTTTCAAA Found at i:21666309 original size:24 final size:25 Alignment explanation

Indices: 21666273--21666327 Score: 62 Period size: 24 Copynumber: 2.3 Consensus size: 25 21666263 GATCTTTCCT * * 21666273 AAAAA-ATGATGAA-AAATGTAAATA 1 AAAAAGATGATGAAGAAAAG-AAAAA 21666297 AAAAAGATG-TGAAGAAAAGAAAAA 1 AAAAAGATGATGAAGAAAAGAAAAA 21666321 AAAAAGA 1 AAAAAGA 21666328 AAAAAAGAGA Statistics Matches: 27, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 24 20 0.74 25 7 0.26 ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13 Consensus pattern (25 bp): AAAAAGATGATGAAGAAAAGAAAAA Found at i:21668177 original size:43 final size:43 Alignment explanation

Indices: 21668107--21668218 Score: 163 Period size: 43 Copynumber: 2.6 Consensus size: 43 21668097 ATGATCTCAC * * * * * 21668107 TTTATTTTCCAAAACTTTCAAAACCTCAATTGTTGGGGAGCATT 1 TTTATTTTTCAAAAGTTTCAAAGCCTCAATTATAGGGGAGCA-T 21668151 TTTATTTTTC-AAAGTTTCAAAGCCTCAATTATAGGGGAGCAT 1 TTTATTTTTCAAAAGTTTCAAAGCCTCAATTATAGGGGAGCAT 21668193 TTTATTTTTCAAAAGTTTCAAAGCCT 1 TTTATTTTTCAAAAGTTTCAAAGCCT 21668219 TGTGGAAAAG Statistics Matches: 62, Mismatches: 5, Indels: 3 0.89 0.07 0.04 Matches are distributed among these distances: 42 11 0.18 43 42 0.68 44 9 0.15 ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40 Consensus pattern (43 bp): TTTATTTTTCAAAAGTTTCAAAGCCTCAATTATAGGGGAGCAT Found at i:21668564 original size:14 final size:14 Alignment explanation

Indices: 21668545--21668585 Score: 59 Period size: 13 Copynumber: 3.1 Consensus size: 14 21668535 TTATTTATAT 21668545 TTTAATTTTTTTAG 1 TTTAATTTTTTTAG * 21668559 TTTAA-TTTTTCA- 1 TTTAATTTTTTTAG 21668571 TTTAATTTTTTTAG 1 TTTAATTTTTTTAG 21668585 T 1 T 21668586 AAAAAAAGTC Statistics Matches: 23, Mismatches: 2, Indels: 4 0.79 0.07 0.14 Matches are distributed among these distances: 12 5 0.22 13 12 0.52 14 6 0.26 ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71 Consensus pattern (14 bp): TTTAATTTTTTTAG Found at i:21669385 original size:20 final size:20 Alignment explanation

Indices: 21669194--21669387 Score: 108 Period size: 20 Copynumber: 10.2 Consensus size: 20 21669184 TTTTACATGA * * 21669194 ATTTGCATGACTAAT-ATTAT 1 ATTTGCATGATTATTAATT-T * 21669214 ATTTGCATGATTAAT-ATTAT 1 ATTTGCATGATTATTAATT-T 21669234 ATTTGCATG---A-TAATTT 1 ATTTGCATGATTATTAATTT * * 21669250 ATTTGC----TTAATATTTT 1 ATTTGCATGATTATTAATTT * * 21669266 ATTTGTATGATTAGT-A--T 1 ATTTGCATGATTATTAATTT ** * 21669283 ATTTGTGTGATTTATTAATAT 1 ATTTGCATGA-TTATTAATTT * * * 21669304 GTTTGCATGATTGTTAATAT 1 ATTTGCATGATTATTAATTT * 21669324 GTTTGCATGATTATTAATTT 1 ATTTGCATGATTATTAATTT * * * 21669344 ATCTACATGATTATTAAGTT 1 ATTTGCATGATTATTAATTT * 21669364 ATTTGCATGATTATCAATTT 1 ATTTGCATGATTATTAATTT 21669384 ATTT 1 ATTT 21669388 ATTTGTGTAA Statistics Matches: 141, Mismatches: 21, Indels: 24 0.76 0.11 0.13 Matches are distributed among these distances: 15 1 0.01 16 18 0.13 17 14 0.10 18 4 0.03 19 1 0.01 20 95 0.67 21 8 0.06 ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52 Consensus pattern (20 bp): ATTTGCATGATTATTAATTT Found at i:21669480 original size:53 final size:52 Alignment explanation

Indices: 21669411--21669599 Score: 159 Period size: 53 Copynumber: 3.5 Consensus size: 52 21669401 CATGATTATT * * * * 21669411 ATTATATAATTGATTGCATGTTTATTGGCATGATTTATATTACTATTTACATG 1 ATTATATATTTAATTGCATGTTTATT-GCATGATTTATATTAATATTTGCATG * 21669464 ATTATATATTTAATTGCATAG-TTATTTACATTG-TTTATATATATATATTTTTGCATG 1 ATTATATATTTAATTGCAT-GTTTA-TTGCA-TGATTTATAT-TA-ATA--TTTGCATG * * * * 21669521 ATTATATATTTAATTGCATGTTTATCTGTA-GTATTTATATTATTAATTGTATG 1 ATTATATATTTAATTGCATGTTTAT-TGCATG-ATTTATATTAATATTTGCATG * * * 21669574 ATTATATACTTAATTACATGATTATT 1 ATTATATATTTAATTGCATGTTTATT 21669600 AATTTATTTA Statistics Matches: 112, Mismatches: 13, Indels: 23 0.76 0.09 0.16 Matches are distributed among these distances: 52 1 0.01 53 57 0.51 54 7 0.06 55 5 0.04 56 4 0.04 57 38 0.34 ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52 Consensus pattern (52 bp): ATTATATATTTAATTGCATGTTTATTGCATGATTTATATTAATATTTGCATG Found at i:21669537 original size:20 final size:20 Alignment explanation

Indices: 21669438--21669545 Score: 61 Period size: 20 Copynumber: 5.5 Consensus size: 20 21669428 ATGTTTATTG * 21669438 GCATGATT-TATATTACTATTT 1 GCATGATTATATATT--TAATT * 21669459 ACATGATTATATATTTAATT 1 GCATGATTATATATTTAATT * 21669479 GCAT-A--GT-TATTTACATT 1 GCATGATTATATATTTA-ATT * 21669496 GTTTAT-ATATATATATTT--TT 1 G--CATGAT-TATATATTTAATT 21669516 GCATGATTATATATTTAATT 1 GCATGATTATATATTTAATT * 21669536 GCATGTTTAT 1 GCATGATTAT 21669546 CTGTAGTATT Statistics Matches: 68, Mismatches: 8, Indels: 23 0.69 0.08 0.23 Matches are distributed among these distances: 16 6 0.09 17 5 0.07 18 11 0.16 19 6 0.09 20 21 0.31 21 7 0.10 22 7 0.10 23 5 0.07 ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53 Consensus pattern (20 bp): GCATGATTATATATTTAATT Found at i:21669558 original size:57 final size:52 Alignment explanation

Indices: 21669443--21669598 Score: 141 Period size: 57 Copynumber: 2.9 Consensus size: 52 21669433 TATTGGCATG * * * * * 21669443 ATTTATATTACTATTTACATGATTATATATTTAATTGCATAGTTATTTACATT 1 ATTTATATTATTAATTGCATGATTATATATTTAATTGCAT-GTTATCTACAGT * * ** 21669496 GTTTATATATATATATTTTTGCATGATTATATATTTAATTGCATGTTTATCTGTAGT 1 ATTTATAT-TAT-TA--ATTGCATGATTATATATTTAATTGCATG-TTATCTACAGT * * * 21669553 ATTTATATTATTAATTGTATGATTATATACTTAATTACATGATTAT 1 ATTTATATTATTAATTGCATGATTATATATTTAATTGCATG-TTAT 21669599 TAATTTATTT Statistics Matches: 85, Mismatches: 13, Indels: 10 0.79 0.12 0.09 Matches are distributed among these distances: 53 35 0.41 54 2 0.02 55 4 0.05 56 4 0.05 57 40 0.47 ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53 Consensus pattern (52 bp): ATTTATATTATTAATTGCATGATTATATATTTAATTGCATGTTATCTACAGT Found at i:21669704 original size:24 final size:24 Alignment explanation

Indices: 21669677--21669738 Score: 81 Period size: 24 Copynumber: 2.6 Consensus size: 24 21669667 TTATTATTAC * 21669677 ATGATTTTATATTTATTACATGAT 1 ATGATATTATATTTATTACATGAT * 21669701 ATGATATTATATGTTATTGCATGAT 1 ATGATATTATAT-TTATTACATGAT * 21669726 -TAATATTATATTT 1 ATGATATTATATTT 21669739 GAATGATATC Statistics Matches: 34, Mismatches: 3, Indels: 3 0.85 0.08 0.08 Matches are distributed among these distances: 23 2 0.06 24 21 0.62 25 11 0.32 ACGTcount: A:0.34, C:0.03, G:0.10, T:0.53 Consensus pattern (24 bp): ATGATATTATATTTATTACATGAT Found at i:21669707 original size:19 final size:19 Alignment explanation

Indices: 21669661--21669708 Score: 62 Period size: 19 Copynumber: 2.5 Consensus size: 19 21669651 TTATATATTT 21669661 ATATGAT-TATTATTACATG 1 ATATGATAT-TTATTACATG * * 21669680 ATTTTATATTTATTACATG 1 ATATGATATTTATTACATG 21669699 ATATGATATT 1 ATATGATATT 21669709 ATATGTTATT Statistics Matches: 24, Mismatches: 4, Indels: 2 0.80 0.13 0.07 Matches are distributed among these distances: 19 23 0.96 20 1 0.04 ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52 Consensus pattern (19 bp): ATATGATATTTATTACATG Found at i:21669855 original size:20 final size:20 Alignment explanation

Indices: 21669832--21669917 Score: 86 Period size: 20 Copynumber: 4.3 Consensus size: 20 21669822 GATTTCATAA 21669832 TTATATATTTGCATGATATT 1 TTATATATTTGCATGATATT * 21669852 TTATAT-TATTGCATGACATT 1 TTATATAT-TTGCATGATATT * * 21669872 TTATATTATTAG-ATGATAAT 1 TTATA-TATTTGCATGATATT * * 21669892 TAATATATTTGCATAATATT 1 TTATATATTTGCATGATATT * 21669912 ATATAT 1 TTATAT 21669918 TTACATTATT Statistics Matches: 52, Mismatches: 10, Indels: 8 0.74 0.14 0.11 Matches are distributed among these distances: 19 6 0.12 20 42 0.81 21 3 0.06 22 1 0.02 ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51 Consensus pattern (20 bp): TTATATATTTGCATGATATT Found at i:21671397 original size:31 final size:33 Alignment explanation

Indices: 21671348--21671409 Score: 85 Period size: 31 Copynumber: 1.9 Consensus size: 33 21671338 CACACTTTTT * 21671348 TTTTTGTTTTTTGTTTTCTT-GTTTATATTTTGG 1 TTTTTGTTTTTAGTTTTCTTGGTTT-TATTTTGG 21671381 TTTTT-TTTTTAG-TTTCTTGGTTTTATTTT 1 TTTTTGTTTTTAGTTTTCTTGGTTTTATTTT 21671410 ATTTTTTCTA Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 31 12 0.44 32 10 0.37 33 5 0.19 ACGTcount: A:0.06, C:0.03, G:0.13, T:0.77 Consensus pattern (33 bp): TTTTTGTTTTTAGTTTTCTTGGTTTTATTTTGG Found at i:21671400 original size:20 final size:20 Alignment explanation

Indices: 21671343--21671409 Score: 61 Period size: 20 Copynumber: 3.5 Consensus size: 20 21671333 AGTTTCACAC * 21671343 TTTT-TTTTTT-GTTTTTTG 1 TTTTATTTTTTAGTTTTTGG * * 21671361 TTTTCTTGTTTA-TATTTTGG 1 TTTTATTTTTTAGT-TTTTGG 21671381 TTTT-TTTTTTAGTTTCTTGG 1 TTTTATTTTTTAGTTT-TTGG 21671401 TTTTATTTT 1 TTTTATTTT 21671410 ATTTTTTCTA Statistics Matches: 40, Mismatches: 3, Indels: 9 0.77 0.06 0.17 Matches are distributed among these distances: 18 4 0.10 19 14 0.35 20 18 0.45 21 4 0.10 ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79 Consensus pattern (20 bp): TTTTATTTTTTAGTTTTTGG Found at i:21671411 original size:38 final size:38 Alignment explanation

Indices: 21671343--21671416 Score: 89 Period size: 38 Copynumber: 1.9 Consensus size: 38 21671333 AGTTTCACAC * * 21671343 TTTTTTTTTTGTTTTTTGTTTTCTTGTTTATATTTTGG 1 TTTTTTTTTTGTTTTTGGTTTTCATGTTTATATTTTGG * 21671381 TTTTTTTTTTAGTTTCTTGGTTTT-AT-TTTATTTTTT 1 TTTTTTTTTT-GTTT-TTGGTTTTCATGTTTATATTTT 21671417 CTACTAACCT Statistics Matches: 31, Mismatches: 3, Indels: 4 0.82 0.08 0.11 Matches are distributed among these distances: 38 19 0.61 39 5 0.16 40 7 0.23 ACGTcount: A:0.07, C:0.03, G:0.11, T:0.80 Consensus pattern (38 bp): TTTTTTTTTTGTTTTTGGTTTTCATGTTTATATTTTGG Found at i:21671416 original size:31 final size:32 Alignment explanation

Indices: 21671343--21671416 Score: 82 Period size: 31 Copynumber: 2.3 Consensus size: 32 21671333 AGTTTCACAC * 21671343 TTTTTTTTTTGTTTTTTGTTTTCTTGTTTATA 1 TTTTTTTTTTGTTTTTAGTTTTCTTGTTTATA * 21671375 TTTTGGTTTTT-TTTTTAG-TTTCTTGGTTT-TA 1 TTTT-TTTTTTGTTTTTAGTTTTCTT-GTTTATA 21671406 TTTTATTTTTT 1 TTTT-TTTTTT 21671417 CTACTAACCT Statistics Matches: 36, Mismatches: 4, Indels: 5 0.80 0.09 0.11 Matches are distributed among these distances: 31 17 0.47 32 14 0.39 33 5 0.14 ACGTcount: A:0.07, C:0.03, G:0.11, T:0.80 Consensus pattern (32 bp): TTTTTTTTTTGTTTTTAGTTTTCTTGTTTATA Found at i:21671917 original size:26 final size:26 Alignment explanation

Indices: 21671868--21671918 Score: 68 Period size: 26 Copynumber: 2.0 Consensus size: 26 21671858 TTTGAGAATT * 21671868 TTTTAATAAAATAAAATTTTACTTGC 1 TTTTAATAAAATAAAATTTAACTTGC * 21671894 TTTTCATAAAAT-AAATTTGAACTTG 1 TTTTAATAAAATAAAATTT-AACTTG 21671919 ATTTAAGATT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 25 6 0.27 26 16 0.73 ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45 Consensus pattern (26 bp): TTTTAATAAAATAAAATTTAACTTGC Found at i:21672331 original size:22 final size:23 Alignment explanation

Indices: 21672282--21672337 Score: 73 Period size: 24 Copynumber: 2.5 Consensus size: 23 21672272 AGAAAAATAA * 21672282 AGAAAA-AAATAGGGAGAGAGAG 1 AGAAAAGAAAGAGGGAGAGAGAG 21672304 AGAAAAGGAAAGAGGGAGAGAG-G 1 AGAAAA-GAAAGAGGGAGAGAGAG 21672327 A-AAAAGAAAGA 1 AGAAAAGAAAGA 21672338 AAAATAAGAT Statistics Matches: 31, Mismatches: 1, Indels: 5 0.84 0.03 0.14 Matches are distributed among these distances: 21 6 0.19 22 10 0.32 23 2 0.06 24 13 0.42 ACGTcount: A:0.61, C:0.00, G:0.38, T:0.02 Consensus pattern (23 bp): AGAAAAGAAAGAGGGAGAGAGAG Found at i:21672473 original size:25 final size:24 Alignment explanation

Indices: 21672418--21672473 Score: 67 Period size: 25 Copynumber: 2.3 Consensus size: 24 21672408 TATTTTTTAA * * 21672418 AATTAATTTTTGTTAATTAGTTAT 1 AATTAATTTTTATTAATTAATTAT * * 21672442 GACTAATTTTATATTAATTAATTAT 1 AATTAATTTT-TATTAATTAATTAT 21672467 AATTAAT 1 AATTAAT 21672474 AATTACTTTT Statistics Matches: 25, Mismatches: 6, Indels: 1 0.78 0.19 0.03 Matches are distributed among these distances: 24 8 0.32 25 17 0.68 ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54 Consensus pattern (24 bp): AATTAATTTTTATTAATTAATTAT Found at i:21672978 original size:38 final size:36 Alignment explanation

Indices: 21672907--21672987 Score: 92 Period size: 39 Copynumber: 2.2 Consensus size: 36 21672897 TTAGTATTAA 21672907 AAAAATTCTAAAATAGTTTTAAAAATTATTGAAAAATTT 1 AAAAA-TCTAAAATAGTTTTAAAAATTATTG-AAAA-TT * ** 21672946 AAAAATCTAAAATATTTTTTTTAAATTA-TGAAAATT 1 AAAAATCTAAAATA-GTTTTAAAAATTATTGAAAATT 21672982 AAAAAT 1 AAAAAT 21672988 AAAAAATCTT Statistics Matches: 38, Mismatches: 3, Indels: 5 0.83 0.07 0.11 Matches are distributed among these distances: 36 8 0.21 37 4 0.11 38 11 0.29 39 15 0.39 ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40 Consensus pattern (36 bp): AAAAATCTAAAATAGTTTTAAAAATTATTGAAAATT Found at i:21673059 original size:24 final size:24 Alignment explanation

Indices: 21673032--21673081 Score: 75 Period size: 24 Copynumber: 2.1 Consensus size: 24 21673022 TTTCTAAAAT 21673032 AATTTTTAAAAATT-AAAAAAATAA 1 AATTTTT-AAAATTCAAAAAAATAA * 21673056 AATTTTTAAAATTCTAAAAAATAA 1 AATTTTTAAAATTCAAAAAAATAA 21673080 AA 1 AA 21673082 AACATCCTTA Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 23 6 0.25 24 18 0.75 ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34 Consensus pattern (24 bp): AATTTTTAAAATTCAAAAAAATAA Found at i:21673061 original size:23 final size:24 Alignment explanation

Indices: 21673027--21673081 Score: 69 Period size: 23 Copynumber: 2.4 Consensus size: 24 21673017 AAAAATTTCT * 21673027 AAAAT-AATTTTTAAAAATT-AAA 1 AAAATAAAATTTTAAAAATTCAAA * * 21673049 AAAATAAAATTTTTAAAATTCTAA 1 AAAATAAAATTTTAAAAATTCAAA 21673073 AAAATAAAA 1 AAAATAAAA 21673082 AACATCCTTA Statistics Matches: 28, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 22 5 0.18 23 12 0.43 24 11 0.39 ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33 Consensus pattern (24 bp): AAAATAAAATTTTAAAAATTCAAA Found at i:21673197 original size:17 final size:17 Alignment explanation

Indices: 21673166--21673208 Score: 61 Period size: 18 Copynumber: 2.5 Consensus size: 17 21673156 AAAAGAAAAC 21673166 TAAAACATTTTAAAA-TT 1 TAAAA-ATTTTAAAATTT 21673183 TAAAAATTTTCAAAATTT 1 TAAAAATTTT-AAAATTT 21673201 TAAAAATT 1 TAAAAATT 21673209 AGAAAATTCA Statistics Matches: 24, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 16 5 0.21 17 9 0.38 18 10 0.42 ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42 Consensus pattern (17 bp): TAAAAATTTTAAAATTT Found at i:21673199 original size:9 final size:9 Alignment explanation

Indices: 21673166--21673208 Score: 54 Period size: 9 Copynumber: 4.9 Consensus size: 9 21673156 AAAAGAAAAC 21673166 TAAAACATTT 1 TAAAA-ATTT 21673176 T-AAAA-TT 1 TAAAAATTT 21673183 TAAAAATTT 1 TAAAAATTT * 21673192 TCAAAATTT 1 TAAAAATTT 21673201 TAAAAATT 1 TAAAAATT 21673209 AGAAAATTCA Statistics Matches: 29, Mismatches: 2, Indels: 5 0.81 0.06 0.14 Matches are distributed among these distances: 7 3 0.10 8 5 0.17 9 20 0.69 10 1 0.03 ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42 Consensus pattern (9 bp): TAAAAATTT Found at i:21673491 original size:23 final size:24 Alignment explanation

Indices: 21673465--21673541 Score: 79 Period size: 24 Copynumber: 3.2 Consensus size: 24 21673455 TTTTCTTGGA 21673465 TTTAGTATT-AAATTTTTATG-ATT 1 TTTA-TATTAAAATTTTTATGAATT * * 21673488 TTTATTTTAAAATTTTTTTGAATT 1 TTTATATTAAAATTTTTATGAATT * * 21673512 TTTATTTTAATAATTTTT-TGCATT 1 TTTATATTAA-AATTTTTATGAATT 21673536 TTTATA 1 TTTATA 21673542 ATGCTTTTTA Statistics Matches: 47, Mismatches: 4, Indels: 5 0.84 0.07 0.09 Matches are distributed among these distances: 22 3 0.06 23 14 0.30 24 23 0.49 25 7 0.15 ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65 Consensus pattern (24 bp): TTTATATTAAAATTTTTATGAATT Found at i:21673512 original size:24 final size:23 Alignment explanation

Indices: 21673474--21673540 Score: 91 Period size: 24 Copynumber: 2.8 Consensus size: 23 21673464 ATTTAGTATT * 21673474 AAATTTTTATGATTTTTATTTTA 1 AAATTTTTTTGATTTTTATTTTA 21673497 AAATTTTTTTGAATTTTTATTTTA 1 AAATTTTTTTG-ATTTTTATTTTA 21673521 ATAA-TTTTTTGCATTTTTAT 1 A-AATTTTTTTG-ATTTTTAT 21673541 AATGCTTTTT Statistics Matches: 40, Mismatches: 2, Indels: 3 0.89 0.04 0.07 Matches are distributed among these distances: 23 10 0.25 24 28 0.70 25 2 0.05 ACGTcount: A:0.28, C:0.01, G:0.04, T:0.66 Consensus pattern (23 bp): AAATTTTTTTGATTTTTATTTTA Found at i:21673651 original size:28 final size:27 Alignment explanation

Indices: 21673612--21673681 Score: 95 Period size: 28 Copynumber: 2.6 Consensus size: 27 21673602 TTTCATATAT 21673612 ATTTTTTTAATTTTTAAAATATTTAAG 1 ATTTTTTTAATTTTTAAAATATTTAAG * * 21673639 ATTTTTTTGAATTTTTAAAATTTTTTAG 1 ATTTTTTT-AATTTTTAAAATATTTAAG ** 21673667 ATTTTTAAAATTTTT 1 ATTTTTTTAATTTTT 21673682 TGAATTGTTT Statistics Matches: 38, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 27 15 0.39 28 23 0.61 ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63 Consensus pattern (27 bp): ATTTTTTTAATTTTTAAAATATTTAAG Found at i:21673655 original size:19 final size:18 Alignment explanation

Indices: 21673633--21673687 Score: 67 Period size: 18 Copynumber: 3.0 Consensus size: 18 21673623 TTTTAAAATA 21673633 TTTAAGATTTTTTTGAATT 1 TTTAA-ATTTTTTTGAATT * 21673652 TTTAAAATTTTTT-AGATT 1 TTTAAATTTTTTTGA-ATT * 21673670 TTTAAAATTTTTTGAATT 1 TTTAAATTTTTTTGAATT 21673688 GTTTGTTTAA Statistics Matches: 33, Mismatches: 1, Indels: 5 0.85 0.03 0.13 Matches are distributed among these distances: 17 1 0.03 18 26 0.79 19 6 0.18 ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62 Consensus pattern (18 bp): TTTAAATTTTTTTGAATT Found at i:21673662 original size:18 final size:18 Alignment explanation

Indices: 21673641--21673687 Score: 78 Period size: 18 Copynumber: 2.6 Consensus size: 18 21673631 TATTTAAGAT 21673641 TTTTTTGAATTTTTAAAA 1 TTTTTTGAATTTTTAAAA 21673659 TTTTTT-AGATTTTTAAAA 1 TTTTTTGA-ATTTTTAAAA 21673677 TTTTTTGAATT 1 TTTTTTGAATT 21673688 GTTTGTTTAA Statistics Matches: 27, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 17 1 0.04 18 25 0.93 19 1 0.04 ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64 Consensus pattern (18 bp): TTTTTTGAATTTTTAAAA Found at i:21674782 original size:19 final size:18 Alignment explanation

Indices: 21674744--21674791 Score: 78 Period size: 18 Copynumber: 2.6 Consensus size: 18 21674734 ACATGTTTTA * 21674744 TTTTTATATTTAAGTATT 1 TTTTTATTTTTAAGTATT 21674762 TTTTTATTTTTAAGTATTT 1 TTTTTATTTTTAAGTA-TT 21674781 TTTTTATTTTT 1 TTTTTATTTTT 21674792 TAAATATACC Statistics Matches: 28, Mismatches: 1, Indels: 1 0.93 0.03 0.03 Matches are distributed among these distances: 18 15 0.54 19 13 0.46 ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75 Consensus pattern (18 bp): TTTTTATTTTTAAGTATT Found at i:21685207 original size:12 final size:12 Alignment explanation

Indices: 21685190--21685225 Score: 72 Period size: 12 Copynumber: 3.0 Consensus size: 12 21685180 TCACTTAAGT 21685190 TTTAGGATTTCA 1 TTTAGGATTTCA 21685202 TTTAGGATTTCA 1 TTTAGGATTTCA 21685214 TTTAGGATTTCA 1 TTTAGGATTTCA 21685226 AGTCTCACCT Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 24 1.00 ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50 Consensus pattern (12 bp): TTTAGGATTTCA Found at i:21685305 original size:19 final size:19 Alignment explanation

Indices: 21685263--21685306 Score: 52 Period size: 19 Copynumber: 2.3 Consensus size: 19 21685253 TTAAGGTTTT * * 21685263 AGGTTTCAGGTTTCGCCTA 1 AGGTTTCAAGTTTCACCTA * * 21685282 GGGTTTCAAGTTTCACTTA 1 AGGTTTCAAGTTTCACCTA 21685301 AGGTTT 1 AGGTTT 21685307 GAGATTTTAC Statistics Matches: 20, Mismatches: 5, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41 Consensus pattern (19 bp): AGGTTTCAAGTTTCACCTA Found at i:21685347 original size:26 final size:26 Alignment explanation

Indices: 21685308--21685361 Score: 90 Period size: 26 Copynumber: 2.1 Consensus size: 26 21685298 TTAAGGTTTG 21685308 AGATTTTACATTAGGGTTTCATTTTA 1 AGATTTTACATTAGGGTTTCATTTTA * * 21685334 AGATTTTGCTTTAGGGTTTCATTTTA 1 AGATTTTACATTAGGGTTTCATTTTA 21685360 AG 1 AG 21685362 GTTTCAAAAA Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 26 26 1.00 ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50 Consensus pattern (26 bp): AGATTTTACATTAGGGTTTCATTTTA Found at i:21685404 original size:19 final size:20 Alignment explanation

Indices: 21685367--21685404 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 21685357 TTAAGGTTTC * 21685367 AAAAATTTATGAACCTCTAT 1 AAAAATTTATGAACATCTAT * 21685387 AAAAATTTCT-AACATCTA 1 AAAAATTTATGAACATCTA 21685405 AATAGATTTT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 7 0.44 20 9 0.56 ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34 Consensus pattern (20 bp): AAAAATTTATGAACATCTAT Found at i:21687565 original size:18 final size:17 Alignment explanation

Indices: 21687542--21687628 Score: 77 Period size: 18 Copynumber: 4.8 Consensus size: 17 21687532 TTTTGTTGGT 21687542 TTTTTTATTTATTTATTG 1 TTTTTTATTTA-TTATTG 21687560 TTTTTTATATTATTATTTG 1 TTTTTTAT-TTATTA-TTG * * * 21687579 TTCTTTATTAATTATTA 1 TTTTTTATTTATTATTG 21687596 TTATTATTA-TTATTATTG 1 TT-TT-TTATTTATTATTG 21687614 TTGTTATTATTTATT 1 TT-TT-TTATTTATT 21687629 TTTTAATTAA Statistics Matches: 57, Mismatches: 7, Indels: 9 0.78 0.10 0.12 Matches are distributed among these distances: 17 4 0.07 18 32 0.56 19 21 0.37 ACGTcount: A:0.23, C:0.01, G:0.05, T:0.71 Consensus pattern (17 bp): TTTTTTATTTATTATTG Found at i:21687595 original size:3 final size:3 Alignment explanation

Indices: 21687583--21687624 Score: 57 Period size: 3 Copynumber: 13.7 Consensus size: 3 21687573 TATTTGTTCT * * 21687583 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTA TTA TT 1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT 21687625 TATTTTTTAA Statistics Matches: 36, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 3 33 0.92 4 3 0.08 ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67 Consensus pattern (3 bp): TTA Found at i:21698710 original size:27 final size:28 Alignment explanation

Indices: 21698657--21698731 Score: 80 Period size: 27 Copynumber: 2.6 Consensus size: 28 21698647 TAGTCATCAA 21698657 ATCATAATGTCAAAACATTTCCAAAATC 1 ATCATAATGTCAAAACATTTCCAAAATC * ** 21698685 ATCATTATGTC-AAACATTTCGTAAATC 1 ATCATAATGTCAAAACATTTCCAAAATC * * 21698712 ATAAATCAATATCAAAACAT 1 AT-CAT-AATGTCAAAACAT 21698732 GTCAATTCAT Statistics Matches: 38, Mismatches: 6, Indels: 4 0.79 0.12 0.08 Matches are distributed among these distances: 27 16 0.42 28 12 0.32 29 4 0.11 30 6 0.16 ACGTcount: A:0.47, C:0.19, G:0.04, T:0.31 Consensus pattern (28 bp): ATCATAATGTCAAAACATTTCCAAAATC Found at i:21704765 original size:22 final size:22 Alignment explanation

Indices: 21704740--21704870 Score: 90 Period size: 22 Copynumber: 6.0 Consensus size: 22 21704730 TTATGAATCT 21704740 TGCCCAGAAGAGC-TTGAAATTA 1 TGCCCAGAAGA-CTTTGAAATTA * 21704762 TG-CCATGAGGACTTTGAAATTA 1 TGCCCA-GAAGACTTTGAAATTA * * 21704784 TGCCCAGAAGACTTTTAAATTG 1 TGCCCAGAAGACTTTGAAATTA * * * * 21704806 TACGC-GAAGGACTTTGCAATTG 1 TGCCCAGAA-GACTTTGAAATTA ** * 21704828 TG-CTTGAAGGACTTTGCAATTA 1 TGCCCAGAA-GACTTTGAAATTA * * 21704850 TGCCTAAAAGACTTTGAAATT 1 TGCCCAGAAGACTTTGAAATT 21704871 GTGCTTGGAG Statistics Matches: 88, Mismatches: 15, Indels: 12 0.77 0.13 0.10 Matches are distributed among these distances: 21 7 0.08 22 74 0.84 23 7 0.08 ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31 Consensus pattern (22 bp): TGCCCAGAAGACTTTGAAATTA Found at i:21704841 original size:44 final size:43 Alignment explanation

Indices: 21704771--21704938 Score: 167 Period size: 44 Copynumber: 3.8 Consensus size: 43 21704761 ATGCCATGAG * ** * * 21704771 GACTTTGAAATTATGCCCAGAA-GACTTTTAAATTGTACGCGAAG 1 GACTTTGAAATTGTG-CTTGAAGGACTTTGAAATTGTAC-CGAAA * * * * * 21704815 GACTTTGCAATTGTGCTTGAAGGACTTTGCAATTATGCCTAAAA 1 GACTTTGAAATTGTGCTTGAAGGACTTTGAAATTGTACC-GAAA * * 21704859 GACTTTGAAATTGTGCTTGGAGGACTTTGAAATTGTACTTGAAA 1 GACTTTGAAATTGTGCTTGAAGGACTTTGAAATTGTAC-CGAAA * * 21704903 GACTTTGAAATTGTACTTGAAAGACTTTGAAATTGT 1 GACTTTGAAATTGTGCTTGAAGGACTTTGAAATTGT 21704939 GTTTATAGGA Statistics Matches: 101, Mismatches: 20, Indels: 6 0.80 0.16 0.05 Matches are distributed among these distances: 43 5 0.05 44 96 0.95 ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35 Consensus pattern (43 bp): GACTTTGAAATTGTGCTTGAAGGACTTTGAAATTGTACCGAAA Found at i:21704883 original size:66 final size:66 Alignment explanation

Indices: 21704769--21704939 Score: 207 Period size: 66 Copynumber: 2.6 Consensus size: 66 21704759 TTATGCCATG * * * * * * 21704769 AGGACTTTGAAATTATGCCCAGAAGACTTTTAAATTGTACGCGAAGGACTTTGCAATTGTGCTTG 1 AGGACTTTGAAATTATGCCTAAAAGACTTTGAAATTGTGCGCGAAGGACTTTGAAATTGTACTTG 21704834 A 66 A * ** * 21704835 AGGACTTTGCAATTATGCCTAAAAGACTTTGAAATTGTGCTTGGAGGACTTTGAAATTGTACTTG 1 AGGACTTTGAAATTATGCCTAAAAGACTTTGAAATTGTGCGCGAAGGACTTTGAAATTGTACTTG 21704900 A 66 A * * * * * 21704901 AAGACTTTGAAATTGTACTTGAAAGACTTTGAAATTGTG 1 AGGACTTTGAAATTATGCCTAAAAGACTTTGAAATTGTG 21704940 TTTATAGGAC Statistics Matches: 89, Mismatches: 16, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 66 89 1.00 ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34 Consensus pattern (66 bp): AGGACTTTGAAATTATGCCTAAAAGACTTTGAAATTGTGCGCGAAGGACTTTGAAATTGTACTTG A Found at i:21704884 original size:22 final size:22 Alignment explanation

Indices: 21704791--21704939 Score: 163 Period size: 22 Copynumber: 6.8 Consensus size: 22 21704781 TTATGCCCAG * * ** 21704791 AAGACTTTTAAATTGTACGCGA 1 AAGACTTTGAAATTGTGCTTGA * * 21704813 AGGACTTTGCAATTGTGCTTGA 1 AAGACTTTGAAATTGTGCTTGA * * * * * 21704835 AGGACTTTGCAATTATGCCTAA 1 AAGACTTTGAAATTGTGCTTGA * 21704857 AAGACTTTGAAATTGTGCTTGG 1 AAGACTTTGAAATTGTGCTTGA * * 21704879 AGGACTTTGAAATTGTACTTGA 1 AAGACTTTGAAATTGTGCTTGA * 21704901 AAGACTTTGAAATTGTACTTGA 1 AAGACTTTGAAATTGTGCTTGA 21704923 AAGACTTTGAAATTGTG 1 AAGACTTTGAAATTGTG 21704940 TTTATAGGAC Statistics Matches: 107, Mismatches: 20, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 107 1.00 ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35 Consensus pattern (22 bp): AAGACTTTGAAATTGTGCTTGA Found at i:21704902 original size:12 final size:12 Alignment explanation

Indices: 21704885--21704924 Score: 50 Period size: 12 Copynumber: 3.5 Consensus size: 12 21704875 TTGGAGGACT 21704885 TTGAAATTGTAC 1 TTGAAATTGTAC 21704897 TTGAAA--G-AC 1 TTGAAATTGTAC 21704906 TTTGAAATTGTAC 1 -TTGAAATTGTAC 21704919 TTGAAA 1 TTGAAA 21704925 GACTTTGAAA Statistics Matches: 24, Mismatches: 0, Indels: 8 0.75 0.00 0.25 Matches are distributed among these distances: 9 2 0.08 10 7 0.29 12 13 0.54 13 2 0.08 ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38 Consensus pattern (12 bp): TTGAAATTGTAC Found at i:21704949 original size:66 final size:66 Alignment explanation

Indices: 21704771--21704962 Score: 190 Period size: 66 Copynumber: 2.9 Consensus size: 66 21704761 ATGCCATGAG * * * * * * * 21704771 GACTTTGAAATTATGCCCAGAAGACTTTTAAATTGTACGC-GA-AGGACTTTGCAATTGTGCTTG 1 GACTTTGAAATTATACCTAAAAGACTTTGAAATTGT--GCTTAGAGGACTTTGAAATTGTACTTG * 21704834 AAG 64 AAA * * * 21704837 GACTTTGCAATTATGCCTAAAAGACTTTGAAATTGTGCTTGGAGGACTTTGAAATTGTACTTGAA 1 GACTTTGAAATTATACCTAAAAGACTTTGAAATTGTGCTTAGAGGACTTTGAAATTGTACTTGAA 21704902 A 66 A * * * * * * * 21704903 GACTTTGAAATTGTACTTGAAAGACTTTGAAATTGTGTTTATAGGACTTTCAAAGTGTAC 1 GACTTTGAAATTATACCTAAAAGACTTTGAAATTGTGCTTAGAGGACTTTGAAATTGTAC 21704963 CCAAAGGATT Statistics Matches: 105, Mismatches: 19, Indels: 4 0.82 0.15 0.03 Matches are distributed among these distances: 64 2 0.02 66 103 0.98 ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35 Consensus pattern (66 bp): GACTTTGAAATTATACCTAAAAGACTTTGAAATTGTGCTTAGAGGACTTTGAAATTGTACTTGAA A Found at i:21704951 original size:44 final size:43 Alignment explanation

Indices: 21704815--21704962 Score: 143 Period size: 44 Copynumber: 3.4 Consensus size: 43 21704805 GTACGCGAAG * * * * * * 21704815 GACTTTGCAATTGTGCTTGAAGGACTTTGCAATTATGCCTAAAA 1 GACTTTGAAATTGTACTTGAAGGACTTTGAAATTGTG-TTTAAA * * * * 21704859 GACTTTGAAATTGTGCTTGGAGGACTTTGAAATTGTACTTGAAA 1 GACTTTGAAATTGTACTTGAAGGACTTTGAAATTGT-GTTTAAA * * 21704903 GACTTTGAAATTGTACTTGAAAGACTTTGAAATTGTGTTTATAG 1 GACTTTGAAATTGTACTTGAAGGACTTTGAAATTGTGTTTA-AA * * 21704947 GACTTTCAAAGTGTAC 1 GACTTTGAAATTGTAC 21704963 CCAAAGGATT Statistics Matches: 87, Mismatches: 15, Indels: 4 0.82 0.14 0.04 Matches are distributed among these distances: 43 3 0.03 44 84 0.97 ACGTcount: A:0.30, C:0.11, G:0.22, T:0.36 Consensus pattern (43 bp): GACTTTGAAATTGTACTTGAAGGACTTTGAAATTGTGTTTAAA Found at i:21704976 original size:66 final size:66 Alignment explanation

Indices: 21704856--21704982 Score: 157 Period size: 66 Copynumber: 1.9 Consensus size: 66 21704846 ATTATGCCTA * * * ** 21704856 AAAGACTTTGAAATTGTGCTTGGAGGACTTTGAAATTGTACTTGAAAGACTTTGAAATTGTACTT 1 AAAGACTTTGAAATTGTGCTTAGAGGACTTTCAAAGTGTACTCCAAAGACTTTGAAATTGTACTT 21704921 G 66 G * * * * 21704922 AAAGACTTTGAAATTGTGTTTATAGGACTTTCAAAGTGTAC-CCAAAGGATTTTGAGATTGT 1 AAAGACTTTGAAATTGTGCTTAGAGGACTTTCAAAGTGTACTCCAAA-GACTTTGAAATTGT 21704983 TTAAAAATAT Statistics Matches: 51, Mismatches: 9, Indels: 2 0.82 0.15 0.03 Matches are distributed among these distances: 65 3 0.06 66 48 0.94 ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36 Consensus pattern (66 bp): AAAGACTTTGAAATTGTGCTTAGAGGACTTTCAAAGTGTACTCCAAAGACTTTGAAATTGTACTT G Found at i:21705036 original size:40 final size:41 Alignment explanation

Indices: 21704985--21705194 Score: 141 Period size: 41 Copynumber: 5.2 Consensus size: 41 21704975 GAGATTGTTT * 21704985 AAAAATATAAGGTTTTACCTTTA-A-GTC-TTGAAAATTTTTA 1 AAAAATTTAAGGTTTTA-C-TTAGAGGTCTTTGAAAATTTTTA * * 21705025 AAAAATTTAAGGTTTTACTTAGAGGTCTTTGAAATTTTTTC 1 AAAAATTTAAGGTTTTACTTAGAGGTCTTTGAAAATTTTTA ** * * * * 21705066 AAAAATTTAAAATTTTGCCT-GAAGGTC-TTG-GAA--TTAA 1 AAAAATTTAAGGTTTTACTTAG-AGGTCTTTGAAAATTTTTA *** * * * * 21705103 AAAAAAAAAAGGTTTT-GTTTGAAGGTCTTTGAAAATCTTTC 1 AAAAATTTAAGGTTTTACTTAG-AGGTCTTTGAAAATTTTTA ** * * 21705144 AAAAATTTAAAATTTTACTTAAAGGTCTTTGAAAATCTTTA 1 AAAAATTTAAGGTTTTACTTAGAGGTCTTTGAAAATTTTTA 21705185 AAAAATTTAA 1 AAAAATTTAA 21705195 AATTTTGTAT Statistics Matches: 130, Mismatches: 30, Indels: 19 0.73 0.17 0.11 Matches are distributed among these distances: 36 1 0.01 37 20 0.15 38 6 0.05 39 5 0.04 40 23 0.18 41 73 0.56 42 2 0.02 ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40 Consensus pattern (41 bp): AAAAATTTAAGGTTTTACTTAGAGGTCTTTGAAAATTTTTA Found at i:21705070 original size:41 final size:40 Alignment explanation

Indices: 21704972--21705075 Score: 115 Period size: 40 Copynumber: 2.6 Consensus size: 40 21704962 CCCAAAGGAT * * * 21704972 TTTGAGATTGTTTAAAAATATAAGGTTTTACCTTTAAGTC 1 TTTGAAATTTTTTAAAAATTTAAGGTTTTACCTTTAAGTC * 21705012 -TTGAAAATTTTTAAAAAATTTAAGGTTTTA-C-TTAGAGGTC 1 TTTG-AAATTTTTTAAAAATTTAAGGTTTTACCTTTA-A-GTC 21705052 TTTGAAATTTTTTCAAAAATTTAA 1 TTTGAAATTTTTT-AAAAATTTAA 21705076 AATTTTGCCT Statistics Matches: 54, Mismatches: 5, Indels: 9 0.79 0.07 0.13 Matches are distributed among these distances: 38 3 0.06 39 5 0.09 40 33 0.61 41 13 0.24 ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45 Consensus pattern (40 bp): TTTGAAATTTTTTAAAAATTTAAGGTTTTACCTTTAAGTC Found at i:21705092 original size:41 final size:41 Alignment explanation

Indices: 21705012--21705339 Score: 194 Period size: 41 Copynumber: 8.1 Consensus size: 41 21705002 CCTTTAAGTC * * ** * * 21705012 TTGAAAATTTTTAAAAAATTTAAGGTTTT-ACTTAGAGGTCT 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGA-AGGTCT * * 21705053 TTGAAATTTTTTCAAAAATTTAAAATTTTGCCTGAAGGTC- 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGAAGGTCT * *** ** 21705093 TTG-GAA---TT-AAAAAAAAAAAAGGTTTTGTTTGAAGGTCT 1 TTGAAAATCTTTCAAAAATTTAAAA--TTTTGCCTGAAGGTCT * * * 21705131 TTGAAAATCTTTCAAAAATTTAAAATTTTACTTAAAGGTCT 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGAAGGTCT * ** 21705172 TTGAAAATCTTTAAAAAATTTAAAATTTTGTATGAAGGTCT 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGAAGGTCT * * * * * * 21705213 TTG-AAATCATTCAAAGATTTAAGATTATGCTTGAAGGTTTT 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGAAGG-TCT * * * ** * * 21705254 TTGAAATTATTT-AAAAATCTAAGGTTTTG-CTCGAAAG-CC 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCT-GAAGGTCT * * 21705293 TTGAAAATCTTTCAAAATTTTAAGATTTTGCCT-AGAGGTCT 1 TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGA-AGGTCT * 21705334 TAGAAA 1 TTGAAA 21705340 TCATGTATTC Statistics Matches: 219, Mismatches: 52, Indels: 32 0.72 0.17 0.11 Matches are distributed among these distances: 35 9 0.04 36 2 0.01 37 13 0.06 38 3 0.01 39 14 0.06 40 47 0.21 41 112 0.51 42 10 0.05 43 9 0.04 ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40 Consensus pattern (41 bp): TTGAAAATCTTTCAAAAATTTAAAATTTTGCCTGAAGGTCT Found at i:21705282 original size:81 final size:82 Alignment explanation

Indices: 21705012--21705282 Score: 207 Period size: 78 Copynumber: 3.4 Consensus size: 82 21705002 CCTTTAAGTC * * * * ** 21705012 TTGAAAATTTTTAAAAAATTTAAGG-TTT-TACTTAGAGGTCTTTGAAATTTTTTCAAAAATTTA 1 TTGAAAATATTTAAAAAATCTAAGGTTTTGTA-TGA-AGGTCTTTGAAAATCATTCAAAAATTTA * * * * 21705075 AAATTTTGCCTGAAGGTC- 64 AAATTATACTTAAAGGTCT * * *** * * 21705093 TTG--GA-ATTAAAAAAAAAAAAGGTTTTGTTTGAAGGTCTTTGAAAATCTTTCAAAAATTTAAA 1 TTGAAAATATTTAAAAAATCTAAGGTTTTGTATGAAGGTCTTTGAAAATCATTCAAAAATTTAAA * 21705155 ATTTTACTTAAAGGTCT 66 ATTATACTTAAAGGTCT * * ** * * 21705172 TTGAAAATCTTTAAAAAATTTAAAATTTTGTATGAAGGTCTTTG-AAATCATTCAAAGATTTAAG 1 TTGAAAATATTTAAAAAATCTAAGGTTTTGTATGAAGGTCTTTGAAAATCATTCAAAAATTTAAA * * * 21705236 ATTATGCTTGAAGGTTTT 66 ATTATACTTAAAGG-TCT * 21705254 TTGAAATTATTT-AAAAATCTAAGGTTTTG 1 TTGAAAATATTTAAAAAATCTAAGGTTTTG 21705283 CTCGAAAGCC Statistics Matches: 149, Mismatches: 34, Indels: 14 0.76 0.17 0.07 Matches are distributed among these distances: 78 53 0.36 79 9 0.06 80 1 0.01 81 46 0.31 82 40 0.27 ACGTcount: A:0.38, C:0.06, G:0.14, T:0.41 Consensus pattern (82 bp): TTGAAAATATTTAAAAAATCTAAGGTTTTGTATGAAGGTCTTTGAAAATCATTCAAAAATTTAAA ATTATACTTAAAGGTCT Found at i:21707280 original size:10 final size:10 Alignment explanation

Indices: 21707265--21707340 Score: 62 Period size: 10 Copynumber: 7.0 Consensus size: 10 21707255 AGTTATTCAA 21707265 TTTTTTTCTT 1 TTTTTTTCTT * 21707275 TTTTTTCCCTT 1 TTTTTT-TCTT * 21707286 TTGTTTTCTT 1 TTTTTTTCTT * 21707296 TTGTTTTCTT 1 TTTTTTTCTT * 21707306 TTGTTTTCTT 1 TTTTTTTCTT 21707316 TTGTTCTTATCTT 1 TT-TT-TT-TCTT 21707329 TTGTTCTTTCTT 1 TT-TT-TTTCTT 21707341 ACATTTTTTT Statistics Matches: 58, Mismatches: 4, Indels: 6 0.85 0.06 0.09 Matches are distributed among these distances: 10 31 0.53 11 9 0.16 12 6 0.10 13 12 0.21 ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78 Consensus pattern (10 bp): TTTTTTTCTT Found at i:21707330 original size:13 final size:12 Alignment explanation

Indices: 21707290--21707340 Score: 65 Period size: 10 Copynumber: 4.5 Consensus size: 12 21707280 TCCCTTTTGT 21707290 TTTCTTTTG-T- 1 TTTCTTTTGTTC 21707300 TTTCTTTTG-T- 1 TTTCTTTTGTTC 21707310 TTTCTTTTGTTC 1 TTTCTTTTGTTC 21707322 TTATCTTTTGTTC 1 TT-TCTTTTGTTC 21707335 TTTCTT 1 TTTCTT 21707341 ACATTTTTTT Statistics Matches: 38, Mismatches: 0, Indels: 4 0.90 0.00 0.10 Matches are distributed among these distances: 10 19 0.50 11 1 0.03 12 6 0.16 13 12 0.32 ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76 Consensus pattern (12 bp): TTTCTTTTGTTC Found at i:21707875 original size:9 final size:9 Alignment explanation

Indices: 21707863--21707887 Score: 50 Period size: 9 Copynumber: 2.8 Consensus size: 9 21707853 TTCTTTTCTT 21707863 TTTTTTTCA 1 TTTTTTTCA 21707872 TTTTTTTCA 1 TTTTTTTCA 21707881 TTTTTTT 1 TTTTTTT 21707888 ATTCTTTGCA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 16 1.00 ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84 Consensus pattern (9 bp): TTTTTTTCA Found at i:21708529 original size:20 final size:19 Alignment explanation

Indices: 21708504--21708551 Score: 60 Period size: 20 Copynumber: 2.4 Consensus size: 19 21708494 AAAAACAACC 21708504 TTTTTTTCCCTTTCTTTTTA 1 TTTTTTTCCCTTT-TTTTTA * * 21708524 TTTTTTTCTCTTTTTTTTT 1 TTTTTTTCCCTTTTTTTTA 21708543 TCTTTTTTC 1 T-TTTTTTC 21708552 AAGGCATTTT Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 19 6 0.24 20 19 0.76 ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81 Consensus pattern (19 bp): TTTTTTTCCCTTTTTTTTA Found at i:21708550 original size:21 final size:20 Alignment explanation

Indices: 21708503--21708550 Score: 60 Period size: 21 Copynumber: 2.4 Consensus size: 20 21708493 AAAAAACAAC 21708503 CTTTTTTTCCCTTTCTTTTT 1 CTTTTTTTCCCTTTCTTTTT * * * 21708523 ATTTTTTTCTCTTTTTTTTTT 1 CTTTTTTTC-CCTTTCTTTTT 21708544 CTTTTTT 1 CTTTTTT 21708551 CAAGGCATTT Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 20 8 0.35 21 15 0.65 ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81 Consensus pattern (20 bp): CTTTTTTTCCCTTTCTTTTT Found at i:21711501 original size:23 final size:23 Alignment explanation

Indices: 21711462--21711506 Score: 65 Period size: 23 Copynumber: 2.0 Consensus size: 23 21711452 TTTGGTGATT 21711462 TTTTGTTTTTAGATTTTCTTTTTC 1 TTTTGTTTTTAGATTTT-TTTTTC * 21711486 TTTT-TTTTTAGTTTTTTTTTT 1 TTTTGTTTTTAGATTTTTTTTT 21711507 GTTTCCTGTG Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 22 5 0.25 23 11 0.55 24 4 0.20 ACGTcount: A:0.07, C:0.04, G:0.07, T:0.82 Consensus pattern (23 bp): TTTTGTTTTTAGATTTTTTTTTC Found at i:21712163 original size:27 final size:28 Alignment explanation

Indices: 21712125--21712178 Score: 85 Period size: 27 Copynumber: 2.0 Consensus size: 28 21712115 AATAAAAGAC 21712125 ATTTTCTTATTTTTT-ATTTTTTTCAAA 1 ATTTTCTTATTTTTTAATTTTTTTCAAA 21712152 ATTTT-TTAATTTTTTAATTTTTTTCAA 1 ATTTTCTT-ATTTTTTAATTTTTTTCAA 21712179 TTTTTGATTT Statistics Matches: 25, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 26 2 0.08 27 12 0.48 28 11 0.44 ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70 Consensus pattern (28 bp): ATTTTCTTATTTTTTAATTTTTTTCAAA Found at i:21712183 original size:27 final size:26 Alignment explanation

Indices: 21712125--21712191 Score: 66 Period size: 27 Copynumber: 2.6 Consensus size: 26 21712115 AATAAAAGAC * * 21712125 ATTTTCTTATTTTTTATTTTTTTCAAA 1 ATTTTTTTATTTTTTAATTTTTTC-AA * 21712152 ATTTTTTAATTTTTTAATTTTTTTC-A 1 ATTTTTTTATTTTTTAA-TTTTTTCAA * 21712178 A-TTTTTGATTTTTT 1 ATTTTTTTATTTTTT 21712192 TTAGGAAAAC Statistics Matches: 35, Mismatches: 4, Indels: 4 0.81 0.09 0.09 Matches are distributed among these distances: 25 12 0.34 26 2 0.06 27 14 0.40 28 7 0.20 ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73 Consensus pattern (26 bp): ATTTTTTTATTTTTTAATTTTTTCAA Found at i:21712190 original size:18 final size:17 Alignment explanation

Indices: 21712153--21712194 Score: 57 Period size: 18 Copynumber: 2.4 Consensus size: 17 21712143 TTTTTCAAAA * 21712153 TTTTTTAATTTTTTAAT 1 TTTTTTAATTTTTGAAT * 21712170 TTTTTTCAATTTTTGATT 1 TTTTTT-AATTTTTGAAT 21712188 TTTTTTA 1 TTTTTTA 21712195 GGAAAACAAA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 17 7 0.32 18 15 0.68 ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76 Consensus pattern (17 bp): TTTTTTAATTTTTGAAT Found at i:21713174 original size:22 final size:22 Alignment explanation

Indices: 21713141--21713183 Score: 70 Period size: 22 Copynumber: 2.0 Consensus size: 22 21713131 TAAGGATTGG 21713141 TTTTAGGATTTAGGGTTTAGGA 1 TTTTAGGATTTAGGGTTTAGGA 21713163 TTTTA-GAGTTTAGGGTTTAGG 1 TTTTAGGA-TTTAGGGTTTAGG 21713184 GCCTTAGGGT Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 21 2 0.10 22 18 0.90 ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47 Consensus pattern (22 bp): TTTTAGGATTTAGGGTTTAGGA Found at i:21713184 original size:7 final size:7 Alignment explanation

Indices: 21713142--21713202 Score: 59 Period size: 7 Copynumber: 8.4 Consensus size: 7 21713132 AAGGATTGGT * 21713142 TTTAGGA 1 TTTAGGG 21713149 TTTAGGG 1 TTTAGGG * 21713156 TTTAGGAT 1 TTTAGG-G * 21713164 TTTAGAG 1 TTTAGGG 21713171 TTTAGGG 1 TTTAGGG 21713178 TTTAGGG 1 TTTAGGG * 21713185 CCTTAGGG 1 -TTTAGGG * 21713193 TTTAAGG 1 TTTAGGG 21713200 TTT 1 TTT 21713203 CAAAATTGGG Statistics Matches: 44, Mismatches: 8, Indels: 4 0.79 0.14 0.07 Matches are distributed among these distances: 7 33 0.75 8 11 0.25 ACGTcount: A:0.20, C:0.03, G:0.33, T:0.44 Consensus pattern (7 bp): TTTAGGG Found at i:21713190 original size:22 final size:22 Alignment explanation

Indices: 21713149--21713202 Score: 63 Period size: 22 Copynumber: 2.5 Consensus size: 22 21713139 GGTTTTAGGA ** 21713149 TTTAGGGTTTAGGATTTTAGAG 1 TTTAGGGTTTAGGACCTTAGAG * * 21713171 TTTAGGGTTTAGGGCCTTAGGG 1 TTTAGGGTTTAGGACCTTAGAG * 21713193 TTTAAGGTTT 1 TTTAGGGTTT 21713203 CAAAATTGGG Statistics Matches: 27, Mismatches: 5, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 22 27 1.00 ACGTcount: A:0.19, C:0.04, G:0.33, T:0.44 Consensus pattern (22 bp): TTTAGGGTTTAGGACCTTAGAG Found at i:21714868 original size:144 final size:141 Alignment explanation

Indices: 21714693--21714950 Score: 299 Period size: 144 Copynumber: 1.8 Consensus size: 141 21714683 TTTTAATGCA * * 21714693 CCAAAAATCATTAAATAATTTAAAAATATGATCTATAA-TGTTTCACGAAAAACTAA-CTTCAGA 1 CCAAAAATCATCAAATAATTT-AAAATATGATCCA-AAGTGTTTCACGAAAAACTAACCTT-AGA * * * 21714756 AAGGTTAAATTACAAAAATACCCTTAAAAGGTA-TTTTAGTGATTTCACACCTTGTGAGGTACGA 63 AAAGTCAAATTAC-AAAATACCCTT-AAAGGTATTTTTA-TAATTTCACACCTTGTGAGGTACGA 21714820 TTAAGATTTTTAATATT 125 TTAAGATTTTTAATATT * * * ** 21714837 CCAAAAATTATCAAATAATATT-AAATCATGATCCAAAGTTTTTCATGAAATTCTAACCTTAGAA 1 CCAAAAATCATCAAATAAT-TTAAAAT-ATGATCCAAAGTGTTTCACGAAAAACTAACCTTAGAA * * * 21714901 AAGTCAATTTACAAAGTACCCTTAAGGGTATTTTTATAATTTCACACCTT 64 AAGTCAAATTACAAAATACCCTTAAAGGTATTTTTATAATTTCACACCTT 21714951 TTAAAGTATA Statistics Matches: 96, Mismatches: 13, Indels: 12 0.79 0.11 0.10 Matches are distributed among these distances: 142 19 0.20 143 21 0.22 144 51 0.53 145 5 0.05 ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34 Consensus pattern (141 bp): CCAAAAATCATCAAATAATTTAAAATATGATCCAAAGTGTTTCACGAAAAACTAACCTTAGAAAA GTCAAATTACAAAATACCCTTAAAGGTATTTTTATAATTTCACACCTTGTGAGGTACGATTAAGA TTTTTAATATT Found at i:21716646 original size:24 final size:24 Alignment explanation

Indices: 21716614--21716670 Score: 114 Period size: 24 Copynumber: 2.4 Consensus size: 24 21716604 AGCCTATCAA 21716614 TCAAAGGCTATATCAATCAAAATG 1 TCAAAGGCTATATCAATCAAAATG 21716638 TCAAAGGCTATATCAATCAAAATG 1 TCAAAGGCTATATCAATCAAAATG 21716662 TCAAAGGCT 1 TCAAAGGCT 21716671 TGGAAACATT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 33 1.00 ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25 Consensus pattern (24 bp): TCAAAGGCTATATCAATCAAAATG Found at i:21721889 original size:66 final size:66 Alignment explanation

Indices: 21721753--21721889 Score: 184 Period size: 66 Copynumber: 2.1 Consensus size: 66 21721743 GGGGTAAAAT * * * * 21721753 ATTGTTATCAACTACCTATATGTTCAATTGAATATTCTCCAAGTCAGTTACAACCACTCCCTGTG 1 ATTGTTATCAACTACCTATATATTCAATTGAATATTCTCCAAGTCAATTACAACCAATCCCTATG * 21721818 T 66 A ** * * * 21721819 ATTGTTATCAACTATTTATATATTCAATTGAATATTTTGCAAGTCAATTACAACCAATTCCTATG 1 ATTGTTATCAACTACCTATATATTCAATTGAATATTCTCCAAGTCAATTACAACCAATCCCTATG 21721884 A 66 A 21721885 ATTGT 1 ATTGT 21721890 GGATTGGTAG Statistics Matches: 61, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 66 61 1.00 ACGTcount: A:0.32, C:0.19, G:0.09, T:0.39 Consensus pattern (66 bp): ATTGTTATCAACTACCTATATATTCAATTGAATATTCTCCAAGTCAATTACAACCAATCCCTATG A Found at i:21730257 original size:38 final size:38 Alignment explanation

Indices: 21730214--21730292 Score: 149 Period size: 38 Copynumber: 2.1 Consensus size: 38 21730204 CTACAGCGTT * 21730214 ACCATTATTTTAGTTTTTTATTTTCACTTGATTTTTAA 1 ACCATTATTTTAGGTTTTTATTTTCACTTGATTTTTAA 21730252 ACCATTATTTTAGGTTTTTATTTTCACTTGATTTTTAA 1 ACCATTATTTTAGGTTTTTATTTTCACTTGATTTTTAA 21730290 ACC 1 ACC 21730293 TATGAAATTT Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 38 40 1.00 ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57 Consensus pattern (38 bp): ACCATTATTTTAGGTTTTTATTTTCACTTGATTTTTAA Found at i:21730432 original size:18 final size:19 Alignment explanation

Indices: 21730406--21730441 Score: 56 Period size: 18 Copynumber: 1.9 Consensus size: 19 21730396 TATTTAAAAG * 21730406 TATTTTTTCTCT-TTTTTT 1 TATTCTTTCTCTCTTTTTT 21730424 TATTCTTTCTCTCTTTTT 1 TATTCTTTCTCTCTTTTT 21730442 CAATTTTCAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 11 0.69 19 5 0.31 ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78 Consensus pattern (19 bp): TATTCTTTCTCTCTTTTTT Found at i:21730562 original size:18 final size:18 Alignment explanation

Indices: 21730518--21730555 Score: 60 Period size: 18 Copynumber: 2.1 Consensus size: 18 21730508 GGAGAGGAAC 21730518 TAATTTATTTTTGGAACAA 1 TAATTT-TTTTTGGAACAA 21730537 TAATTTTTTTTGGAA-AA 1 TAATTTTTTTTGGAACAA 21730554 TA 1 TA 21730556 TCTTTTTCAA Statistics Matches: 19, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 17 4 0.21 18 9 0.47 19 6 0.32 ACGTcount: A:0.37, C:0.03, G:0.11, T:0.50 Consensus pattern (18 bp): TAATTTTTTTTGGAACAA Found at i:21730675 original size:23 final size:23 Alignment explanation

Indices: 21730637--21730696 Score: 70 Period size: 23 Copynumber: 2.7 Consensus size: 23 21730627 TGAAATAATT * * 21730637 TTAAATAATA-AAATTTTATTAA 1 TTAAATAATATTAATTTAATTAA * 21730659 CTT-ATTAATATTAATTTAATTAA 1 -TTAAATAATATTAATTTAATTAA 21730682 TTAAATAATATTAAT 1 TTAAATAATATTAAT 21730697 AATAATTGAA Statistics Matches: 31, Mismatches: 4, Indels: 4 0.79 0.10 0.10 Matches are distributed among these distances: 22 8 0.26 23 23 0.74 ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48 Consensus pattern (23 bp): TTAAATAATATTAATTTAATTAA Found at i:21741641 original size:103 final size:103 Alignment explanation

Indices: 21741320--21741656 Score: 453 Period size: 109 Copynumber: 3.2 Consensus size: 103 21741310 TAAATCTATT * * ** * * 21741320 TATGGCTTCCTTT-TTTAATATTTCTTCATGTTTCAATCC-CCATAAAACAAGCCAACTATAGTC 1 TATGGCTTTCTTTCATTAATATTTCTTCATGTTTCAATCCAAAAAAAAAAAAGCCAACTATAGTC 21741383 CCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG 66 CCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG * * * 21741421 TATGGCTTTCTTTCATAAATATTTCTTCATGTTTCAATCCAAAGAAAAAAAAAAAATAGCTAACC 1 TATGGCTTTCTTTCATTAATATTTCTTCATGTTTCAATCC-----AAAAAAAAAAA-AGCCAACT ** 21741486 ATAGTCCGAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG 60 ATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG * 21741530 TATAGCTTTCTTTCATTAATATTTCTTCATGTTTCAATCCAAAAAAAAAAAAGCCAACTATAGTC 1 TATGGCTTTCTTTCATTAATATTTCTTCATGTTTCAATCCAAAAAAAAAAAAGCCAACTATAGTC * * * 21741595 CCCACCTAATTTAAATAAAGCTTTAGTTTTCATCTTTA 66 CCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG ** 21741633 TATGGCTTTCTTTTTTTAATATTT 1 TATGGCTTTCTTTCATTAATATTT 21741657 TTCTATTCTT Statistics Matches: 205, Mismatches: 23, Indels: 14 0.85 0.10 0.06 Matches are distributed among these distances: 101 12 0.06 102 24 0.12 103 66 0.32 104 11 0.05 108 6 0.03 109 86 0.42 ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41 Consensus pattern (103 bp): TATGGCTTTCTTTCATTAATATTTCTTCATGTTTCAATCCAAAAAAAAAAAAGCCAACTATAGTC CCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTG Found at i:21741678 original size:103 final size:104 Alignment explanation

Indices: 21741363--21741680 Score: 381 Period size: 103 Copynumber: 3.0 Consensus size: 104 21741353 CAATCCCCAT * 21741363 AAAACAAGCCAACTATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT 1 AAAAAAAGCCAACTATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT * * * ** 21741428 TTCTTTCATAAATATTTCTTCATGTTTCAATCCAAAGAAAAAA 66 TTCTTTCATTAATATTTCTTC-T-ATTC-TTCC-ATCAAAAAA * * ** * 21741471 AAAAAATAGCTAACCATAGTCCGAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATAGC 1 AAAAAA-AGCCAACTATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGC * * 21741536 TTTCTTTCATTAATATTTCTTC-ATGT-TTCAATCCAAAAA 65 TTTCTTTCATTAATATTTCTTCTAT-TCTTCCATCAAAAAA * * * 21741575 AAAAAAAGCCAACTATAGTCCCCACCTAATTTAAATAAAGCTTTAGTTTTCATCTTTATATGGCT 1 AAAAAAAGCCAACTATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT ** ** 21741640 TTCTTTTTTTAATATTT-TTCTATTCTTCCATCTTAAAA 66 TTCTTTCATTAATATTTCTTCTATTCTTCCATCAAAAAA 21741678 AAA 1 AAA 21741681 CCCATGCAAC Statistics Matches: 180, Mismatches: 26, Indels: 13 0.82 0.12 0.06 Matches are distributed among these distances: 102 4 0.02 103 81 0.45 104 12 0.07 105 2 0.01 106 1 0.01 107 1 0.01 108 5 0.03 109 74 0.41 ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39 Consensus pattern (104 bp): AAAAAAAGCCAACTATAGTCCCCACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT TTCTTTCATTAATATTTCTTCTATTCTTCCATCAAAAAA Found at i:21746472 original size:24 final size:24 Alignment explanation

Indices: 21746440--21746491 Score: 86 Period size: 24 Copynumber: 2.2 Consensus size: 24 21746430 TCATCATGTG * * 21746440 GCAGATAGAAGTAGAAATGCAGAA 1 GCAGATAGAAGTAAAAATACAGAA 21746464 GCAGATAGAAGTAAAAATACAGAA 1 GCAGATAGAAGTAAAAATACAGAA 21746488 GCAG 1 GCAG 21746492 CCTGGCAGAT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.52, C:0.10, G:0.27, T:0.12 Consensus pattern (24 bp): GCAGATAGAAGTAAAAATACAGAA Found at i:21748773 original size:107 final size:107 Alignment explanation

Indices: 21748625--21748920 Score: 448 Period size: 107 Copynumber: 2.8 Consensus size: 107 21748615 CAATCCCCAT * * ** 21748625 AAAACAAGCCAACTATAGTCCCCGCCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT 1 AAAAAAAGCCAACCATAGTCCCAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT * 21748690 TTCTTTCATTAATATTTCTTCATGTTTCAATCCAAAAAAAAA 66 TTCTTTCATTAATATTTCTTCATGGTTCAATCCAAAAAAAAA * * * * 21748732 AAAAATAGCTAACCATAGTCCGAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATAGCT 1 AAAAAAAGCCAACCATAGTCCCAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT 21748797 TTCTTTCATTAATATTTCTTCATGGTTCAATCCAAAAAAAAA 66 TTCTTTCATTAATATTTCTTCATGGTTCAATCCAAAAAAAAA * * * * * 21748839 AAAAAAAGCCAACTATAGTCCCCACCTAATTTAAATAAAGCTTTAGTTTTCATCTTTATATGGCT 1 AAAAAAAGCCAACCATAGTCCCAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT ** 21748904 TTCTTTTTTTAATATTT 66 TTCTTTCATTAATATTT 21748921 TTCTATTCTT Statistics Matches: 169, Mismatches: 20, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 107 169 1.00 ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39 Consensus pattern (107 bp): AAAAAAAGCCAACCATAGTCCCAACCTATTTTAAACAAAGCTTTAGTTTTCATCTTTGTATGGCT TTCTTTCATTAATATTTCTTCATGGTTCAATCCAAAAAAAAA Found at i:21750502 original size:52 final size:50 Alignment explanation

Indices: 21750414--21750529 Score: 126 Period size: 52 Copynumber: 2.3 Consensus size: 50 21750404 ATCAAAGTCC * ** * * 21750414 TTGAGACTTTAAAAATCTCATTTAAAAATGGTTCCCCTTAAAT-AGAGGTT 1 TTGAAACTTTAAAAATCTCATTTAAAAATGACTCCCCAT-AATCAGAGGCT * * * 21750464 TTGAAGCTTTAAAAAGTCTTATTTGAGAAATGACTCCCCATAATCAGAGGCT 1 TTGAAACTTTAAAAA-TCTCATTT-AAAAATGACTCCCCATAATCAGAGGCT 21750516 TTGAAACTTTAAAA 1 TTGAAACTTTAAAA 21750530 TTTAAAATAT Statistics Matches: 54, Mismatches: 9, Indels: 4 0.81 0.13 0.06 Matches are distributed among these distances: 50 13 0.24 51 10 0.19 52 31 0.57 ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34 Consensus pattern (50 bp): TTGAAACTTTAAAAATCTCATTTAAAAATGACTCCCCATAATCAGAGGCT Found at i:21750718 original size:59 final size:58 Alignment explanation

Indices: 21750629--21750795 Score: 162 Period size: 59 Copynumber: 2.8 Consensus size: 58 21750619 TTAGAACTTT * 21750629 AAAAATCTTGTATGAAAAT-GGTTTCCCCTAAACAGAGGCTTTGAAACTTTCTTT-T-TTAA 1 AAAAATCTTGTTTGAAAATGGGTTT--CCTAAACAGAGGCTTTGAAACTTT-TTTCTCTT-A * * 21750688 AAAAATCTTGTTTGAAAATGGGTATTCCTAAACAGAAGCTTTGAAACTCTTTTTCTCTTT 1 AAAAATCTTGTTTGAAAATGGGT-TTCCTAAACAGAGGCTTTGAAACT-TTTTTCTCTTA ** * * * * 21750748 TTAAATCTT-TTTGAAAATGGCTCCTCCCAAACAGAGGCTGTGAAACTT 1 AAAAATCTTGTTTGAAAATGGGT-TTCCTAAACAGAGGCTTTGAAACTT 21750796 AAAAAATATA Statistics Matches: 92, Mismatches: 11, Indels: 11 0.81 0.10 0.10 Matches are distributed among these distances: 58 1 0.01 59 74 0.80 60 13 0.14 61 4 0.04 ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37 Consensus pattern (58 bp): AAAAATCTTGTTTGAAAATGGGTTTCCTAAACAGAGGCTTTGAAACTTTTTTCTCTTA Found at i:21751782 original size:24 final size:24 Alignment explanation

Indices: 21751755--21751806 Score: 70 Period size: 24 Copynumber: 2.2 Consensus size: 24 21751745 TTTTATTGTT 21751755 TTTTGCCTTT-TGTTTTGTTTTCTC 1 TTTTGCCTTTCT-TTTTGTTTTCTC ** 21751779 TTTTTTCTTTCTTTTTGTTTTCTC 1 TTTTGCCTTTCTTTTTGTTTTCTC 21751803 TTTT 1 TTTT 21751807 TTTGTCTCAT Statistics Matches: 25, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 24 24 0.96 25 1 0.04 ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77 Consensus pattern (24 bp): TTTTGCCTTTCTTTTTGTTTTCTC Found at i:21751783 original size:13 final size:13 Alignment explanation

Indices: 21751767--21751807 Score: 59 Period size: 13 Copynumber: 3.3 Consensus size: 13 21751757 TTGCCTTTTG 21751767 TTTTGTTTTCTCT 1 TTTTGTTTTCTCT * 21751780 TTTT-TCTT-TCT 1 TTTTGTTTTCTCT 21751791 TTTTGTTTTCTCT 1 TTTTGTTTTCTCT 21751804 TTTT 1 TTTT 21751808 TTGTCTCATT Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 11 7 0.29 12 6 0.25 13 11 0.46 ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80 Consensus pattern (13 bp): TTTTGTTTTCTCT Found at i:21767140 original size:98 final size:96 Alignment explanation

Indices: 21767025--21767262 Score: 274 Period size: 98 Copynumber: 2.4 Consensus size: 96 21767015 ACCCATCTAG * * * * 21767025 ACAAAACTTTAG--TTCATCTATATACGGCTTCCTTT-TTTAATATTTCATGTTTCAATCCC-TA 1 ACAAAGCTTTAGTTTTCATCTTTATATGGCTT-CTTTCTTTAATA---CATGTTTCAATCCCAAA * 21767086 AAAAACAAGCCAACCATAGTCCCCACCT-ATTTTAA 62 AAAAAAAAGCCAACCATAGTCCCCA-CTGATTTTAA 21767121 ACAAAGCTTTAGTTTTCATCTTTATATGGCATTCTTTCTTT-A-ACATGTTTCAATCCCAAAAAA 1 ACAAAGCTTTAGTTTTCATCTTTATATGGC-TTCTTTCTTTAATACATGTTTCAATCCC---AAA * * 21767184 AAAAAAAAGCCAGCCTTAGTCCCCACTGATTTTAA 62 AAAAAAAAGCCAACCATAGTCCCCACTGATTTTAA 21767219 ACAAAGCTTTAGTTTTCATCTTTATATGGCTTTCTTTCTTTAAT 1 ACAAAGCTTTAGTTTTCATCTTTATATGGC-TTCTTTCTTTAAT 21767263 TTTTTCTATT Statistics Matches: 123, Mismatches: 8, Indels: 18 0.83 0.05 0.12 Matches are distributed among these distances: 94 14 0.11 96 11 0.09 97 3 0.02 98 89 0.72 99 6 0.05 ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38 Consensus pattern (96 bp): ACAAAGCTTTAGTTTTCATCTTTATATGGCTTCTTTCTTTAATACATGTTTCAATCCCAAAAAAA AAAAGCCAACCATAGTCCCCACTGATTTTAA Done.