Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_pilon, 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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 6 of 19

Found at i:1056376 original size:24 final size:24

Alignment explanation

Indices: 1056344--1056390 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 1056334 CTCTAAAATC 1056344 TAAAACTCTCAAACAT-TCAAACTT 1 TAAAACTCTCAAAC-TCTCAAACTT * 1056368 TAAAACTCTTAAACTCTCAAACT 1 TAAAACTCTCAAACTCTCAAACT 1056391 AATAAAATGG Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 23 1 0.05 24 20 0.95 ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30 Consensus pattern (24 bp): TAAAACTCTCAAACTCTCAAACTT Found at i:1056396 original size:16 final size:16 Alignment explanation

Indices: 1056346--1056396 Score: 50 Period size: 16 Copynumber: 3.2 Consensus size: 16 1056336 CTAAAATCTA 1056346 AAACTCTCAAAC-ATT 1 AAACTCTCAAACTATT * * * 1056361 CAAACTTTAAAACTCTT 1 -AAACTCTCAAACTATT * 1056378 AAACTCTCAAACTAAT 1 AAACTCTCAAACTATT 1056394 AAA 1 AAA 1056397 ATGGCTCATA Statistics Matches: 27, Mismatches: 7, Indels: 2 0.75 0.19 0.06 Matches are distributed among these distances: 16 25 0.93 17 2 0.07 ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27 Consensus pattern (16 bp): AAACTCTCAAACTATT Found at i:1059667 original size:57 final size:57 Alignment explanation

Indices: 1059603--1059743 Score: 237 Period size: 57 Copynumber: 2.5 Consensus size: 57 1059593 CTAAAGTAAA * * 1059603 AAAGAAAAATATATGTGAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGCAT 1 AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT * 1059660 AATGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT 1 AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT * * 1059717 AAAGAAATATATGTGTAAAAGGAATTA 1 AAAGAAAAATATATGTAAAAGGAATTA 1059744 TTTTAGGCAT Statistics Matches: 78, Mismatches: 6, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 57 78 1.00 ACGTcount: A:0.52, C:0.05, G:0.18, T:0.24 Consensus pattern (57 bp): AAAGAAAAATATATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAT Found at i:1059761 original size:37 final size:37 Alignment explanation

Indices: 1059708--1059780 Score: 110 Period size: 37 Copynumber: 2.0 Consensus size: 37 1059698 GGCTAGAAAC * * 1059708 TTTAGGAATAAAGAAATATATGTGTAAAAGGAATTAT 1 TTTAGGAATAAAGAAATATATATGTAAAAAGAATTAT * * 1059745 TTTAGGCATAACGAAATATATATGTAAAAAGAATTA 1 TTTAGGAATAAAGAAATATATATGTAAAAAGAATTA 1059781 AACTAAAGTA Statistics Matches: 32, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 37 32 1.00 ACGTcount: A:0.49, C:0.03, G:0.16, T:0.32 Consensus pattern (37 bp): TTTAGGAATAAAGAAATATATATGTAAAAAGAATTAT Found at i:1059831 original size:49 final size:49 Alignment explanation

Indices: 1059759--1059860 Score: 177 Period size: 49 Copynumber: 2.1 Consensus size: 49 1059749 GGCATAACGA 1059759 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG 1 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG * ** 1059808 AATATATGTGTAAATGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG 1 AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG 1059857 AATA 1 AATA 1059861 AAGAAATATA Statistics Matches: 50, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 49 50 1.00 ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27 Consensus pattern (49 bp): AATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG Found at i:1059877 original size:143 final size:145 Alignment explanation

Indices: 1059606--1059879 Score: 435 Period size: 143 Copynumber: 1.9 Consensus size: 145 1059596 AAGTAAAAAA * * 1059606 GAAAAATATATGTGAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGCATAATGAAAAATA 1 GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG-A-AAT----AATA 1059671 TATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAA 60 TATGTAAAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAA 1059736 AGGAATTATTTTAGGCATAAC 125 AGGAATTATTTTAGGCATAAC * * 1059757 GAAATATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGG-AAT-ATATGTGTA 1 GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAATAATATATGTA * 1059820 AATGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAA 66 AAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAA 1059880 ATCATTATGT Statistics Matches: 118, Mismatches: 5, Indels: 8 0.90 0.04 0.06 Matches are distributed among these distances: 143 67 0.57 148 3 0.03 151 48 0.41 ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26 Consensus pattern (145 bp): GAAAAATATATGTAAAAAGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAAATAATATATGTA AAAGGAATTAAACTAAAGTAAGGCTAGAAACTTTAGGAATAAAGAAATATATGTGTAAAAGGAAT TATTTTAGGCATAAC Found at i:1062469 original size:15 final size:15 Alignment explanation

Indices: 1062435--1062481 Score: 60 Period size: 15 Copynumber: 3.2 Consensus size: 15 1062425 CTTTCACCTA * 1062435 ATTTTAAAAATA-AC 1 ATTTTAATAATATAC * 1062449 ATTTTAATAATATAT 1 ATTTTAATAATATAC * 1062464 ATTTTAATTATATAC 1 ATTTTAATAATATAC 1062479 ATT 1 ATT 1062482 ATAAATATCT Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 14 11 0.39 15 17 0.61 ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49 Consensus pattern (15 bp): ATTTTAATAATATAC Found at i:1063506 original size:20 final size:20 Alignment explanation

Indices: 1063483--1063527 Score: 67 Period size: 20 Copynumber: 2.3 Consensus size: 20 1063473 TAAAGTAGTG 1063483 TAAAATGTT-TTAAAATAAA 1 TAAAATGTTATTAAAATAAA 1063502 -ATAAATGTTATTAAAATAAA 1 TA-AAATGTTATTAAAATAAA 1063522 TAAAAT 1 TAAAAT 1063528 CAGATAAATT Statistics Matches: 23, Mismatches: 0, Indels: 5 0.82 0.00 0.18 Matches are distributed among these distances: 18 1 0.04 19 7 0.30 20 14 0.61 21 1 0.04 ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36 Consensus pattern (20 bp): TAAAATGTTATTAAAATAAA Found at i:1063509 original size:19 final size:19 Alignment explanation

Indices: 1063485--1063525 Score: 66 Period size: 19 Copynumber: 2.2 Consensus size: 19 1063475 AAGTAGTGTA 1063485 AAATGTT-TTAAAATAAAAT 1 AAATGTTATTAAAAT-AAAT 1063504 AAATGTTATTAAAATAAAT 1 AAATGTTATTAAAATAAAT 1063523 AAA 1 AAA 1063526 ATCAGATAAA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 19 14 0.67 20 7 0.33 ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34 Consensus pattern (19 bp): AAATGTTATTAAAATAAAT Found at i:1066868 original size:16 final size:16 Alignment explanation

Indices: 1066847--1066880 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 1066837 TTTCTCCAAG 1066847 TCAATCGTAATTGACA 1 TCAATCGTAATTGACA * 1066863 TCAATCTTAATTGACA 1 TCAATCGTAATTGACA 1066879 TC 1 TC 1066881 CACCCCTTCA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35 Consensus pattern (16 bp): TCAATCGTAATTGACA Found at i:1074597 original size:2 final size:2 Alignment explanation

Indices: 1074590--1074615 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 1074580 TTTTATTTTG 1074590 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 1074616 GTTTTTCATC 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:1075237 original size:12 final size:12 Alignment explanation

Indices: 1075220--1075246 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 1075210 TTGCAATGTC 1075220 TGGTCGTGGCGG 1 TGGTCGTGGCGG 1075232 TGGTCGTGGCGG 1 TGGTCGTGGCGG 1075244 TGG 1 TGG 1075247 AGGCCGTGGC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 15 1.00 ACGTcount: A:0.00, C:0.15, G:0.59, T:0.26 Consensus pattern (12 bp): TGGTCGTGGCGG Found at i:1075473 original size:30 final size:30 Alignment explanation

Indices: 1075383--1075550 Score: 165 Period size: 30 Copynumber: 5.3 Consensus size: 30 1075373 TACCCCGCCT * * ** 1075383 CCTCCTCAGTCGGCTCCAGCTCATCAACCA 1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA 1075413 CCTCCTCAGGCGCTCCGGCTCCGGCGGCTCGGCAACCA 1 CCTCCTCA-G-G---CGGCT-C--CGGCTCGGCAACCA * 1075451 CCTCCTCAGACGGCTCCGGCTCGGCAACCA 1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA * * * * 1075481 CCTCTTCAGGCGGCTCCGACTCGGCAATCT 1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA * * 1075511 CCTCCCCAGGCGGCTCCGGCTCGGCAACCT 1 CCTCCTCAGGCGGCTCCGGCTCGGCAACCA 1075541 CCTCCTCAGG 1 CCTCCTCAGG 1075551 AGGTTCCTGC Statistics Matches: 115, Mismatches: 15, Indels: 16 0.79 0.10 0.11 Matches are distributed among these distances: 30 82 0.71 31 1 0.01 32 1 0.01 33 5 0.04 35 5 0.04 36 1 0.01 37 1 0.01 38 19 0.17 ACGTcount: A:0.14, C:0.46, G:0.23, T:0.17 Consensus pattern (30 bp): CCTCCTCAGGCGGCTCCGGCTCGGCAACCA Found at i:1087058 original size:3 final size:3 Alignment explanation

Indices: 1087050--1087074 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 1087040 ATCATGTTAT 1087050 TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA T 1087075 GTAGTCAAAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:1089030 original size:101 final size:105 Alignment explanation

Indices: 1088857--1089114 Score: 339 Period size: 101 Copynumber: 2.5 Consensus size: 105 1088847 AACTTCCTCT * * 1088857 TCCTT-TTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGATGCTGATATATCTC 1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACAC-TTCTGGAAATGTTGATGATGATATATCTC * * * * 1088921 TTTCTGTGATAGAATC-ACGCAAAATGTTGAACAAGTTC-T- 65 CTTATGTGATAGAATCGA-GCAAAAGGTTAAACAAGTTCTTC * * * 1088960 T-C-TCTTCAGATGAATTATTCTCATTATGAACACTTCTGGAAATGTTGATGATGATCTATCTCC 1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGATGATATATCTCC ** 1089023 TTATGTGATAGCGTCGAGCAAAAGGTTAAACAAGTTCTTC 66 TTATGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTC * 1089063 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCTTCTGGAAATGTTGAT 1 TCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTCTGGAAATGTTGAT 1089115 CTTCAAAAGA Statistics Matches: 134, Mismatches: 14, Indels: 11 0.84 0.09 0.07 Matches are distributed among these distances: 101 58 0.43 102 29 0.22 103 2 0.01 104 1 0.01 105 27 0.20 106 17 0.13 ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39 Consensus pattern (105 bp): TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGATGATATATCTCC TTATGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTC Found at i:1089383 original size:41 final size:40 Alignment explanation

Indices: 1089296--1089396 Score: 141 Period size: 41 Copynumber: 2.5 Consensus size: 40 1089286 AAGGCTGAAC * * * * 1089296 AAGTTCTTCTCACTATGAAC-TTCTTTTTCCTCTTCAGAT 1 AAGTTCTTCTCATTATGAACTTTCTTCTCCCTCTTCAAAT 1089335 AAGTTCTTCTCATTATGAACTTTCTTCTCCCTTCTTCAAAT 1 AAGTTCTTCTCATTATGAACTTTCTTCTCCC-TCTTCAAAT * 1089376 GAGTTCTTCTCATTATGAACT 1 AAGTTCTTCTCATTATGAACT 1089397 CTATCTGGCA Statistics Matches: 55, Mismatches: 5, Indels: 2 0.89 0.08 0.03 Matches are distributed among these distances: 39 19 0.35 40 8 0.15 41 28 0.51 ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46 Consensus pattern (40 bp): AAGTTCTTCTCATTATGAACTTTCTTCTCCCTCTTCAAAT Found at i:1089495 original size:113 final size:113 Alignment explanation

Indices: 1089338--1089657 Score: 514 Period size: 113 Copynumber: 2.8 Consensus size: 113 1089328 TTCAGATAAG * * * * 1089338 TTCTTCTCATTATGAACTTTCTTCTCCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCTATCT 1 TTCTTCTCATTATGAAC-TTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCT * * * 1089403 GGCAATGCTGATCCATCAAGTGATAAATTCGAGCGAAAGGTTGAACAAA 65 GGCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA * 1089452 TTCTTCTCATTTTGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG 1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG * * 1089517 GCAATGTTGATCCCTCAAGTGATGAATTCGAGCAAAAGGTTGAACAAG 66 GCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA * * * 1089565 TTCTTCTCATTATGAACTTTCTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAGCTCTACCTG 1 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG 1089630 GCAATGTTGATCCATCAAGTGATGAATT 66 GCAATGTTGATCCATCAAGTGATGAATT 1089658 TGAATATTTG Statistics Matches: 191, Mismatches: 15, Indels: 1 0.92 0.07 0.00 Matches are distributed among these distances: 113 175 0.92 114 16 0.08 ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38 Consensus pattern (113 bp): TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG GCAATGTTGATCCATCAAGTGATGAATTCGAGCAAAAGGTTGAACAAA Found at i:1091636 original size:36 final size:36 Alignment explanation

Indices: 1091550--1091647 Score: 101 Period size: 36 Copynumber: 2.7 Consensus size: 36 1091540 TTACTTCTTG * * 1091550 CTGAGATGAGCCTCCAAGAATG-CCCAAATATTCATA 1 CTGACATGAGCCTTCAA-AATGCCCCAAATATTCATA * * * 1091586 TTGTCGTGAGCCTTCAAAATGCCCCAAATATTCATA 1 CTGACATGAGCCTTCAAAATGCCCCAAATATTCATA ** 1091622 CTGACATG-GACCTTCAGGATGCCCCA 1 CTGACATGAG-CCTTCAAAATGCCCCA 1091648 CATGAATCAT Statistics Matches: 50, Mismatches: 10, Indels: 4 0.78 0.16 0.06 Matches are distributed among these distances: 35 5 0.10 36 45 0.90 ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24 Consensus pattern (36 bp): CTGACATGAGCCTTCAAAATGCCCCAAATATTCATA Found at i:1099231 original size:3 final size:3 Alignment explanation

Indices: 1099223--1099247 Score: 50 Period size: 3 Copynumber: 8.3 Consensus size: 3 1099213 ATCATGTTAT 1099223 TTA TTA TTA TTA TTA TTA TTA TTA T 1 TTA TTA TTA TTA TTA TTA TTA TTA T 1099248 GTAGTCAAAT Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 22 1.00 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (3 bp): TTA Found at i:1099301 original size:3 final size:3 Alignment explanation

Indices: 1099293--1099321 Score: 58 Period size: 3 Copynumber: 9.7 Consensus size: 3 1099283 ATATGACTAC 1099293 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT 1099322 TAAATATATT 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:0.66, C:0.00, G:0.00, T:0.34 Consensus pattern (3 bp): ATA Found at i:1099350 original size:14 final size:13 Alignment explanation

Indices: 1099299--1099360 Score: 52 Period size: 15 Copynumber: 4.3 Consensus size: 13 1099289 CTACATAATA * 1099299 ATAATAATAATAAT 1 ATAAAAATAA-AAT * 1099313 AATAATAATTAAATAT 1 -ATAA-AAATAAA-AT 1099329 ATTAAAAATAAACAT 1 A-TAAAAATAAA-AT 1099344 ATAAAAATAAAAT 1 ATAAAAATAAAAT 1099357 ATAA 1 ATAA 1099361 CTAAATGGTG Statistics Matches: 40, Mismatches: 4, Indels: 8 0.77 0.08 0.15 Matches are distributed among these distances: 13 6 0.15 14 10 0.25 15 15 0.38 16 9 0.22 ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31 Consensus pattern (13 bp): ATAAAAATAAAAT Found at i:1099366 original size:15 final size:14 Alignment explanation

Indices: 1099331--1099360 Score: 53 Period size: 14 Copynumber: 2.2 Consensus size: 14 1099321 TTAAATATAT 1099331 TAAAAATAAACATA 1 TAAAAATAAACATA 1099345 TAAAAATAAA-ATA 1 TAAAAATAAACATA 1099358 TAA 1 TAA 1099361 CTAAATGGTG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 6 0.38 14 10 0.62 ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23 Consensus pattern (14 bp): TAAAAATAAACATA Found at i:1103963 original size:48 final size:48 Alignment explanation

Indices: 1103892--1103986 Score: 172 Period size: 48 Copynumber: 2.0 Consensus size: 48 1103882 AAAATAATGG * 1103892 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCATCAACACAGCAA 1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA * 1103940 CACTCTTTGAATCAGAAAGTGTTGTCTATGGTGGCACCAACACAGCA 1 CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCA 1103987 GCACCGGCAC Statistics Matches: 45, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 48 45 1.00 ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25 Consensus pattern (48 bp): CACTCTTTGAATCAGAAAGTGTTGCCTATGGTGGCACCAACACAGCAA Found at i:1106065 original size:20 final size:19 Alignment explanation

Indices: 1106048--1106085 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 19 1106038 AAATTTAATT * 1106048 TTTTTAAATAATTATTAAAA 1 TTTTCAAATAATT-TTAAAA 1106068 TTTTCAAATAATTTTAAA 1 TTTTCAAATAATTTTAAA 1106086 TGATAATTGA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 19 5 0.29 20 12 0.71 ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50 Consensus pattern (19 bp): TTTTCAAATAATTTTAAAA Found at i:1106246 original size:23 final size:22 Alignment explanation

Indices: 1106214--1106277 Score: 67 Period size: 24 Copynumber: 2.8 Consensus size: 22 1106204 AATTTTTAAA 1106214 TTTTAATAATTTTAA-AAATATT 1 TTTTAATAA-TTTAATAAATATT 1106236 TTTTACATAATTTAATAAATAATT 1 TTTTA-ATAATTTAATAAAT-ATT * * 1106260 ATATAATTAATTTAATAA 1 TTTTAA-TAATTTAATAA 1106278 TAAAAATAGA Statistics Matches: 36, Mismatches: 2, Indels: 6 0.82 0.05 0.14 Matches are distributed among these distances: 22 10 0.28 23 9 0.25 24 17 0.47 ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50 Consensus pattern (22 bp): TTTTAATAATTTAATAAATATT Found at i:1119220 original size:48 final size:48 Alignment explanation

Indices: 1119147--1119241 Score: 145 Period size: 48 Copynumber: 2.0 Consensus size: 48 1119137 TTGATGAAGT 1119147 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC 1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC * * * * * 1119195 ACGAGGCATCTCCTCGATATGCGTATGTATGTGTGTGTTTATGTATA 1 ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATA 1119242 TACCCAAGCA Statistics Matches: 42, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 48 42 1.00 ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38 Consensus pattern (48 bp): ACGAGACATCTACTCGATATACGTATGTATATGTATGTTTATGTATAC Found at i:1120061 original size:31 final size:32 Alignment explanation

Indices: 1120005--1120070 Score: 98 Period size: 31 Copynumber: 2.1 Consensus size: 32 1119995 GCTTAATAAA * * 1120005 CTTAACGAGCAACGACTCGAGCAATAAATTTT 1 CTTAACGAGCAACAACTAGAGCAATAAATTTT * 1120037 CTTAACGAG-AACAAGTAGAGCAATAAATTTT 1 CTTAACGAGCAACAACTAGAGCAATAAATTTT 1120068 CTT 1 CTT 1120071 TACAAGCACG Statistics Matches: 31, Mismatches: 3, Indels: 1 0.89 0.09 0.03 Matches are distributed among these distances: 31 22 0.71 32 9 0.29 ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27 Consensus pattern (32 bp): CTTAACGAGCAACAACTAGAGCAATAAATTTT Found at i:1120563 original size:78 final size:78 Alignment explanation

Indices: 1120478--1120635 Score: 221 Period size: 78 Copynumber: 2.0 Consensus size: 78 1120468 AGAAAAAAAT * * 1120478 AACATTTTAAG-TAGCGCCCAATATTAACATTTCCGGTAAAAAAATAATAATTT-AGATAACGCT 1 AACATTTT-AGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAG-TAACGCT 1120541 TTACCAGAAATGTTA 64 TTACCAGAAATGTTA * * * * 1120556 AACATTTTAGTTAGCACCTAATATTAACATTTCTAGTAAAAAAATAATATTTTAAGTAACGTTTT 1 AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAGTAACGCTTT * 1120621 ACTAGAAATGTTA 66 ACCAGAAATGTTA 1120634 AA 1 AA 1120636 AAATATTAAT Statistics Matches: 71, Mismatches: 7, Indels: 4 0.87 0.09 0.05 Matches are distributed among these distances: 77 2 0.03 78 67 0.94 79 2 0.03 ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34 Consensus pattern (78 bp): AACATTTTAGTTAGCACCCAATATTAACATTTCCAGTAAAAAAATAATAATTTAAGTAACGCTTT ACCAGAAATGTTA Found at i:1123688 original size:22 final size:23 Alignment explanation

Indices: 1123660--1123704 Score: 83 Period size: 22 Copynumber: 2.0 Consensus size: 23 1123650 GGAATAACAA 1123660 TGCCAGTGATTGGTGA-TTAAAG 1 TGCCAGTGATTGGTGATTTAAAG 1123682 TGCCAGTGATTGGTGATTTAAAG 1 TGCCAGTGATTGGTGATTTAAAG 1123705 ATTCTTATCA Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 22 16 0.73 23 6 0.27 ACGTcount: A:0.27, C:0.09, G:0.31, T:0.33 Consensus pattern (23 bp): TGCCAGTGATTGGTGATTTAAAG Found at i:1126875 original size:21 final size:21 Alignment explanation

Indices: 1126799--1126880 Score: 69 Period size: 20 Copynumber: 4.0 Consensus size: 21 1126789 AAATGACCAA ** 1126799 CAAATTCGCAACGCGA-ACTC 1 CAAATTCGCAACGCGATTTTC * * * 1126819 CAATTTCGCAACTC-AGTTTC 1 CAAATTCGCAACGCGATTTTC *** 1126839 CAAATTCGCGTTGCGATTTTC 1 CAAATTCGCAACGCGATTTTC 1126860 CAAATTCGCAACGCGAATTTT 1 CAAATTCGCAACGCG-ATTTT 1126881 GTTGTAGCAA Statistics Matches: 46, Mismatches: 13, Indels: 4 0.73 0.21 0.06 Matches are distributed among these distances: 19 1 0.02 20 23 0.50 21 17 0.37 22 5 0.11 ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29 Consensus pattern (21 bp): CAAATTCGCAACGCGATTTTC Found at i:1130160 original size:18 final size:18 Alignment explanation

Indices: 1130137--1130172 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 1130127 AAGCAAAAAG * 1130137 AAATCAAAATCGCAATCA 1 AAATCAAAATCCCAATCA 1130155 AAATCAAAATCCCAATCA 1 AAATCAAAATCCCAATCA 1130173 CAACCGGCTT 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:0.56, C:0.25, G:0.03, T:0.17 Consensus pattern (18 bp): AAATCAAAATCCCAATCA Found at i:1130483 original size:20 final size:20 Alignment explanation

Indices: 1130460--1130541 Score: 83 Period size: 20 Copynumber: 4.1 Consensus size: 20 1130450 TCGCATTACA * 1130460 AATTTGGCTTTCACGTTGCG 1 AATTTGACTTTCACGTTGCG ** 1130480 AATTTGACTTTTGCGTTGCG 1 AATTTGACTTTCACGTTGCG * * *** 1130500 AATTTGACTATCGCAACGCG 1 AATTTGACTTTCACGTTGCG * 1130520 AATTTGACTTTCGCGTTGCG 1 AATTTGACTTTCACGTTGCG 1130540 AA 1 AA 1130542 AGTGTACCTT Statistics Matches: 50, Mismatches: 12, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 20 50 1.00 ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37 Consensus pattern (20 bp): AATTTGACTTTCACGTTGCG Found at i:1130734 original size:63 final size:64 Alignment explanation

Indices: 1130600--1130746 Score: 235 Period size: 63 Copynumber: 2.3 Consensus size: 64 1130590 ACTTTAAAAC 1130600 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA 1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA *** * * 1130664 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAATAATTCTTATTTCCTCATCAATTA 1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA 1130727 AACAAATCAAC-TTTACAAAT 1 AACAAATCAACTTTTACAAAT 1130747 ACATCAATTT Statistics Matches: 78, Mismatches: 5, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 62 9 0.12 63 35 0.45 64 34 0.44 ACGTcount: A:0.52, C:0.18, G:0.02, T:0.29 Consensus pattern (64 bp): AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA Found at i:1132115 original size:21 final size:21 Alignment explanation

Indices: 1132089--1132224 Score: 112 Period size: 21 Copynumber: 6.5 Consensus size: 21 1132079 GTGAATCGGG * 1132089 CTCTTGAACGGTGGGAGGGAC 1 CTCTTGAACGGTGGGAGGGGC * ** 1132110 CTCTTGAACGATGACAGGGGC 1 CTCTTGAACGGTGGGAGGGGC * 1132131 CTCTTGAACTGTGGGAGGGGC 1 CTCTTGAACGGTGGGAGGGGC ** * 1132152 CTCTTGAA-GGATGATAGCGGC 1 CTCTTGAACGG-TGGGAGGGGC * * * * 1132173 CTCTTGAATGATAGGAGAGGC 1 CTCTTGAACGGTGGGAGGGGC * * * * 1132194 CTTTTGAACGATAGGAGAGGC 1 CTCTTGAACGGTGGGAGGGGC 1132215 CTCTTGAACG 1 CTCTTGAACG 1132225 ATGACAGGTG Statistics Matches: 93, Mismatches: 20, Indels: 4 0.79 0.17 0.03 Matches are distributed among these distances: 20 1 0.01 21 91 0.98 22 1 0.01 ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23 Consensus pattern (21 bp): CTCTTGAACGGTGGGAGGGGC Found at i:1132148 original size:42 final size:41 Alignment explanation

Indices: 1132089--1132223 Score: 139 Period size: 42 Copynumber: 3.2 Consensus size: 41 1132079 GTGAATCGGG * * 1132089 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC 1 CTCTTGAACTGTGGGAGGG-CCTCTTGAACGATGACAGAGGC * * * 1132131 CTCTTGAACTGTGGGAGGGGCCTCTTGAAGGATGATAGCGGC 1 CTCTTGAACTGTGGGA-GGGCCTCTTGAACGATGACAGAGGC * * * 1132173 CTCTTGAA-TGATAGGAGAGGCCTTTTGAACGAT-AGGAGAGGC 1 CTCTTGAACTG-TGGGAG-GGCCTCTTGAACGATGA-CAGAGGC 1132215 CTCTTGAAC 1 CTCTTGAAC 1132224 GATGACAGGT Statistics Matches: 79, Mismatches: 9, Indels: 9 0.81 0.09 0.09 Matches are distributed among these distances: 41 4 0.05 42 72 0.91 43 3 0.04 ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23 Consensus pattern (41 bp): CTCTTGAACTGTGGGAGGGCCTCTTGAACGATGACAGAGGC Found at i:1134326 original size:20 final size:20 Alignment explanation

Indices: 1134281--1134326 Score: 56 Period size: 20 Copynumber: 2.3 Consensus size: 20 1134271 TTGTGTTGCG * * 1134281 AGTTTCGCGTTGCGATTTTC 1 AGTTTCGCGTTGCGAATTTA * * 1134301 ATTTTCGTGTTGCGAATTTA 1 AGTTTCGCGTTGCGAATTTA 1134321 AGTTTC 1 AGTTTC 1134327 AAATAGTCTT Statistics Matches: 21, Mismatches: 5, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 20 21 1.00 ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48 Consensus pattern (20 bp): AGTTTCGCGTTGCGAATTTA Found at i:1134668 original size:22 final size:22 Alignment explanation

Indices: 1134642--1134699 Score: 80 Period size: 22 Copynumber: 2.6 Consensus size: 22 1134632 GATGAAGATA 1134642 GACGGATTTCGCCGGAGATAAG 1 GACGGATTTCGCCGGAGATAAG * ** 1134664 GACGGATTTCGTCGGAGATGGG 1 GACGGATTTCGCCGGAGATAAG * 1134686 GACGGATGTCGCCG 1 GACGGATTTCGCCG 1134700 TAAAGAGTGA Statistics Matches: 31, Mismatches: 5, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 22 31 1.00 ACGTcount: A:0.21, C:0.19, G:0.41, T:0.19 Consensus pattern (22 bp): GACGGATTTCGCCGGAGATAAG Found at i:1135123 original size:22 final size:22 Alignment explanation

Indices: 1135096--1135143 Score: 78 Period size: 22 Copynumber: 2.2 Consensus size: 22 1135086 GGAGATAAAT 1135096 GGATTTCACCGGAGATGGGGAC 1 GGATTTCACCGGAGATGGGGAC ** 1135118 GGATTTCGTCGGAGATGGGGAC 1 GGATTTCACCGGAGATGGGGAC 1135140 GGAT 1 GGAT 1135144 GTCGCCATAG Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21 Consensus pattern (22 bp): GGATTTCACCGGAGATGGGGAC Found at i:1135301 original size:451 final size:451 Alignment explanation

Indices: 1134455--1135307 Score: 1483 Period size: 451 Copynumber: 1.9 Consensus size: 451 1134445 ATTTACTAAG 1134455 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT 1 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT 1134520 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT 66 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT * * 1134585 TGATTTTCCATTTCTGACCGTGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAGACGGATT 131 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT * * 1134650 TCGCCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCGTAAAGAGTGAAAGAT 196 TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAAAGAT * * * 1134715 GGAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATATTGTATATATTT 261 GAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATTT * 1134780 GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGTG 326 GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGCG 1134845 CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA 391 CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA * 1134906 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAGTAT 1 CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT * 1134971 GAAAAATCTAATAATAATACAAAATTTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT 66 GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT * * 1135036 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGGAGATAAATGGATT 131 TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT ** * 1135101 TCACCGGAGATGGGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAGAGAGT-AAGAGA 196 TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAA-AGA * * * 1135165 TGAAGATGGGACTGAGTTGTGATTTAGGGTTTTAAGTTATGATTTACGATTATACTATTTATATT 260 TGAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATT ** * * * 1135230 TGTGTTGCGAAATAAATATTGTGTTTTGAATTCGAAATTAAAATTCGCGTTGCGAAAATAAACGC 325 TGTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGC 1135295 GCTTTGCGAATTT 390 GCTTTGCGAATTT 1135308 AACTTGTGTT Statistics Matches: 378, Mismatches: 23, Indels: 2 0.94 0.06 0.00 Matches are distributed among these distances: 450 2 0.01 451 376 0.99 ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32 Consensus pattern (451 bp): CAATCTAAGTGAAATGGTTAATCTATTACTGAAATTACCAGTAAATTTATCATCAATTTAAATAT GAAAAATCTAATAATAATACAAAAATTTCAAAATAAAAATAATTAAAAAACTAACCCTCGGTGGT TGATTTTCCATTTCTGACCATGAATGGTTGTGAGGGTGGCTCTGAGAGATGAAGATAAACGGATT TCACCGGAGATAAGGACGGATTTCGTCGGAGATGGGGACGGATGTCGCCATAAAGAGTGAAAGAT GAAGATGGGACTGAGTTGTGATTTAGGGGTTTAAGTTATAATTTACGATTATACTATATATATTT GTGTTGCGAAATAAATATTGTGTTTCAAATTCAAAAATAAAATTCGCGTTGCGAAAAAAAACGCG CTTTGCGAATTTGATTTCTGTGTTGCGAATTACAAATTCGCGTTGCGATTTTCCAAATTCA Found at i:1135324 original size:18 final size:20 Alignment explanation

Indices: 1135298--1135345 Score: 64 Period size: 20 Copynumber: 2.5 Consensus size: 20 1135288 TAAACGCGCT 1135298 TTGCGAATTTAAC-T-TGTG 1 TTGCGAATTTAACTTATGTG * * 1135316 TTGCAAATTTGACTTATGTG 1 TTGCGAATTTAACTTATGTG 1135336 TTGCGAATTT 1 TTGCGAATTT 1135346 GGAAACTGAG Statistics Matches: 25, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 18 11 0.44 19 1 0.04 20 13 0.52 ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46 Consensus pattern (20 bp): TTGCGAATTTAACTTATGTG Found at i:1141856 original size:11 final size:12 Alignment explanation

Indices: 1141828--1141860 Score: 50 Period size: 11 Copynumber: 2.8 Consensus size: 12 1141818 GTATTATGAA 1141828 TTTTCAAATATTG 1 TTTTCAAATA-TG 1141841 TTTTCAAATA-G 1 TTTTCAAATATG 1141852 TTTTCAAAT 1 TTTTCAAAT 1141861 CCAAATCCAA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 10 0.50 13 10 0.50 ACGTcount: A:0.33, C:0.09, G:0.06, T:0.52 Consensus pattern (12 bp): TTTTCAAATATG Found at i:1145365 original size:23 final size:23 Alignment explanation

Indices: 1145337--1145405 Score: 70 Period size: 23 Copynumber: 3.0 Consensus size: 23 1145327 ACATCTTATA * 1145337 TGGCACTTCGGTGCATTTCTATAC- 1 TGGCACTTAGGTGCATTT-T-TACG * 1145361 T-GCACTTAGGTGCAATTTTACG 1 TGGCACTTAGGTGCATTTTTACG * * 1145383 TGGCACTTTGGTGCATTTATACG 1 TGGCACTTAGGTGCATTTTTACG 1145406 AGCTGTGGTT Statistics Matches: 38, Mismatches: 5, Indels: 5 0.79 0.10 0.10 Matches are distributed among these distances: 21 3 0.08 22 2 0.05 23 32 0.84 24 1 0.03 ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38 Consensus pattern (23 bp): TGGCACTTAGGTGCATTTTTACG Found at i:1150637 original size:23 final size:23 Alignment explanation

Indices: 1150609--1150677 Score: 79 Period size: 23 Copynumber: 3.0 Consensus size: 23 1150599 ACATCTTATA 1150609 TGGCACTTCGGTGCATTTCTATAC- 1 TGGCACTTCGGTGCATTT-T-TACG * * 1150633 T-GCACTTAGGTGCAATTTTACG 1 TGGCACTTCGGTGCATTTTTACG * 1150655 TGGCACTTCGGTGCATTTATACG 1 TGGCACTTCGGTGCATTTTTACG 1150678 AGCTGTGGTT Statistics Matches: 38, Mismatches: 5, Indels: 5 0.79 0.10 0.10 Matches are distributed among these distances: 21 3 0.08 22 2 0.05 23 32 0.84 24 1 0.03 ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36 Consensus pattern (23 bp): TGGCACTTCGGTGCATTTTTACG Found at i:1151584 original size:20 final size:20 Alignment explanation

Indices: 1151559--1151596 Score: 60 Period size: 20 Copynumber: 1.9 Consensus size: 20 1151549 CTATATATAT 1151559 ATTTGGTTTTGATT-GTTTGA 1 ATTTGG-TTTGATTAGTTTGA 1151579 ATTTGGTTTGATTAGTTT 1 ATTTGGTTTGATTAGTTT 1151597 ATATTGATTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 19 7 0.41 20 10 0.59 ACGTcount: A:0.16, C:0.00, G:0.24, T:0.61 Consensus pattern (20 bp): ATTTGGTTTGATTAGTTTGA Found at i:1157781 original size:24 final size:25 Alignment explanation

Indices: 1157736--1157787 Score: 61 Period size: 24 Copynumber: 2.1 Consensus size: 25 1157726 CCATAAGGAT * 1157736 TGTGACACAAGAAAAG-AGAAAACG 1 TGTGACACAAGAAAAGAAAAAAACG * * * 1157760 TGTGCCACAAGAACATAAAAAAACG 1 TGTGACACAAGAAAAGAAAAAAACG 1157785 TGT 1 TGT 1157788 TACAAGGATA Statistics Matches: 23, Mismatches: 4, Indels: 1 0.82 0.14 0.04 Matches are distributed among these distances: 24 13 0.57 25 10 0.43 ACGTcount: A:0.50, C:0.15, G:0.21, T:0.13 Consensus pattern (25 bp): TGTGACACAAGAAAAGAAAAAAACG Found at i:1158554 original size:10 final size:10 Alignment explanation

Indices: 1158541--1158573 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 1158531 TTTCTTTTTC 1158541 TTTTTTATTT 1 TTTTTTATTT 1158551 TTTTTTA-TT 1 TTTTTTATTT * 1158560 TTTTTAATTT 1 TTTTTTATTT 1158570 TTTT 1 TTTT 1158574 AACAAGTTAT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 9 8 0.38 10 13 0.62 ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88 Consensus pattern (10 bp): TTTTTTATTT Found at i:1158574 original size:9 final size:9 Alignment explanation

Indices: 1158541--1158575 Score: 52 Period size: 9 Copynumber: 3.9 Consensus size: 9 1158531 TTTCTTTTTC * 1158541 TTTTTTATT 1 TTTTTTAAT * 1158550 TTTTTTTAT 1 TTTTTTAAT 1158559 TTTTTTAAT 1 TTTTTTAAT 1158568 TTTTTTAA 1 TTTTTTAA 1158576 CAAGTTATCT Statistics Matches: 23, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 9 23 1.00 ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83 Consensus pattern (9 bp): TTTTTTAAT Found at i:1164009 original size:24 final size:24 Alignment explanation

Indices: 1163940--1164000 Score: 122 Period size: 24 Copynumber: 2.5 Consensus size: 24 1163930 CCATAAGGAT 1163940 TGTGCCACAAGAAAAGAGAAAACG 1 TGTGCCACAAGAAAAGAGAAAACG 1163964 TGTGCCACAAGAAAAGAGAAAACG 1 TGTGCCACAAGAAAAGAGAAAACG 1163988 TGTGCCACAAGAA 1 TGTGCCACAAGAA 1164001 CATAAAAAAA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 37 1.00 ACGTcount: A:0.48, C:0.18, G:0.25, T:0.10 Consensus pattern (24 bp): TGTGCCACAAGAAAAGAGAAAACG Found at i:1170197 original size:24 final size:25 Alignment explanation

Indices: 1170152--1170203 Score: 70 Period size: 24 Copynumber: 2.1 Consensus size: 25 1170142 CCATAAGGAT * 1170152 TGTGCCACAAGAAAAG-AGAAAACG 1 TGTGCCACAAGAAAAGAAAAAAACG * * 1170176 TGTGCCACAAGAACATAAAAAAACG 1 TGTGCCACAAGAAAAGAAAAAAACG 1170201 TGT 1 TGT 1170204 TACAAGGATA Statistics Matches: 24, Mismatches: 3, Indels: 1 0.86 0.11 0.04 Matches are distributed among these distances: 24 14 0.58 25 10 0.42 ACGTcount: A:0.48, C:0.17, G:0.21, T:0.13 Consensus pattern (25 bp): TGTGCCACAAGAAAAGAAAAAAACG Found at i:1171403 original size:19 final size:21 Alignment explanation

Indices: 1171360--1171405 Score: 60 Period size: 21 Copynumber: 2.3 Consensus size: 21 1171350 TTCTTCTTTT * 1171360 AAATTTTTGTTTTAGATCTTT 1 AAATTTTTGTTTTAGATCTTC * 1171381 AAATTTTTTTTTTA-A-CTTC 1 AAATTTTTGTTTTAGATCTTC 1171400 AAATTT 1 AAATTT 1171406 CTTATAATTG Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 19 9 0.39 20 1 0.04 21 13 0.57 ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61 Consensus pattern (21 bp): AAATTTTTGTTTTAGATCTTC Found at i:1173750 original size:18 final size:18 Alignment explanation

Indices: 1173727--1173763 Score: 65 Period size: 18 Copynumber: 2.1 Consensus size: 18 1173717 TATGCTTTTC 1173727 GCTGATGACATTGTCATA 1 GCTGATGACATTGTCATA * 1173745 GCTGATGACATTGTTATA 1 GCTGATGACATTGTCATA 1173763 G 1 G 1173764 TTGCTGAAAC Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35 Consensus pattern (18 bp): GCTGATGACATTGTCATA Found at i:1176969 original size:41 final size:41 Alignment explanation

Indices: 1176904--1177060 Score: 208 Period size: 41 Copynumber: 3.8 Consensus size: 41 1176894 GGAAGTTTAG * * 1176904 TGGATTTACCATTCGGGATAAATTTCACTTTGGAATATTAA 1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA * * * * * 1176945 TGGGTTCACCATTCAGGATGAATTTCAC-TTCGAATTATTAG 1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAA-TATTAA * * 1176986 TGGATTCACCCTTCGGGATTAATTTCACTTTAGAATATTAA 1 TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA * 1177027 TGGATTCACCCTTCGGGATTAATTTCACTTTGGA 1 TGGATTCACCATTCGGGATTAATTTCACTTTGGA 1177061 TTATCACTGC Statistics Matches: 101, Mismatches: 13, Indels: 4 0.86 0.11 0.03 Matches are distributed among these distances: 40 5 0.05 41 91 0.90 42 5 0.05 ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38 Consensus pattern (41 bp): TGGATTCACCATTCGGGATTAATTTCACTTTGGAATATTAA Found at i:1177047 original size:22 final size:22 Alignment explanation

Indices: 1176981--1177049 Score: 56 Period size: 22 Copynumber: 3.3 Consensus size: 22 1176971 ACTTCGAATT * 1176981 ATTAGTGGATTCACCCTTCGGG 1 ATTAATGGATTCACCCTTCGGG * * ** 1177003 ATTAAT---TTCA-CTTTAGAAT 1 ATTAATGGATTCACCCTTCG-GG 1177022 ATTAATGGATTCACCCTTCGGG 1 ATTAATGGATTCACCCTTCGGG 1177044 ATTAAT 1 ATTAAT 1177050 TTCACTTTGG Statistics Matches: 33, Mismatches: 9, Indels: 10 0.63 0.17 0.19 Matches are distributed among these distances: 18 4 0.12 19 10 0.30 22 15 0.45 23 4 0.12 ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38 Consensus pattern (22 bp): ATTAATGGATTCACCCTTCGGG Found at i:1177064 original size:82 final size:82 Alignment explanation

Indices: 1176900--1177056 Score: 242 Period size: 82 Copynumber: 1.9 Consensus size: 82 1176890 TCGAGGAAGT * * * 1176900 TTAGTGGATTTACCATTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCATTCAGGATG 1 TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG 1176965 AATTTCACTTCGAATTA 66 AATTTCACTTCGAATTA * * * * * 1176982 TTAGTGGATTCACCCTTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCCTTCGGGATT 1 TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG 1177047 AATTTCACTT 66 AATTTCACTT 1177057 TGGATTATCA Statistics Matches: 67, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 82 67 1.00 ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39 Consensus pattern (82 bp): TTAGTGGATTCACCATTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATG AATTTCACTTCGAATTA Found at i:1177080 original size:41 final size:41 Alignment explanation

Indices: 1176915--1177081 Score: 120 Period size: 41 Copynumber: 4.1 Consensus size: 41 1176905 GGATTTACCA * * * ** * * 1176915 TTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCA 1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC * * * * * * * 1176956 TTCAGGATGAATTTCAC-TTCGAATTATTAGTGGATTCACCC 1 TTCGGGATTAATTTCACTTTAGAA-TATCAATGCATCCACCC * * * 1176997 TTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCC 1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC * * * * * 1177038 TTCGGGATTAATTTCACTTTGGATTATCACTGCCTCCTCCC 1 TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC 1177079 TTC 1 TTC 1177082 AAGACAGACT Statistics Matches: 106, Mismatches: 18, Indels: 4 0.83 0.14 0.03 Matches are distributed among these distances: 40 5 0.05 41 96 0.91 42 5 0.05 ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38 Consensus pattern (41 bp): TTCGGGATTAATTTCACTTTAGAATATCAATGCATCCACCC Found at i:1177080 original size:82 final size:82 Alignment explanation

Indices: 1176915--1177081 Score: 208 Period size: 82 Copynumber: 2.0 Consensus size: 82 1176905 GGATTTACCA * * 1176915 TTCGGGATAAATTTCACTTTGGAATATTAATGGGTTCACCATTCAGGATGAATTTCACTTCGAAT 1 TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT * * * * 1176980 TATTAGTGGATTCACCC 66 TATCACTGCATCCACCC * * * * * * 1176997 TTCGGGATTAATTTCACTTTAGAATATTAATGGATTCACCCTTCGGGATTAATTTCACTTTGGAT 1 TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT * * 1177062 TATCACTGCCTCCTCCC 66 TATCACTGCATCCACCC 1177079 TTC 1 TTC 1177082 AAGACAGACT Statistics Matches: 71, Mismatches: 14, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 82 71 1.00 ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38 Consensus pattern (82 bp): TTCGGGATAAATTTCACTTTAGAATATTAATGGATTCACCATTCAGGATGAATTTCACTTCGAAT TATCACTGCATCCACCC Found at i:1177576 original size:21 final size:21 Alignment explanation

Indices: 1177546--1177593 Score: 87 Period size: 21 Copynumber: 2.3 Consensus size: 21 1177536 TAATTTTCAA * 1177546 ACATTATTGCACCTAATTTTG 1 ACATTGTTGCACCTAATTTTG 1177567 ACATTGTTGCACCTAATTTTG 1 ACATTGTTGCACCTAATTTTG 1177588 ACATTG 1 ACATTG 1177594 CAATATTAGG Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42 Consensus pattern (21 bp): ACATTGTTGCACCTAATTTTG Found at i:1182193 original size:21 final size:21 Alignment explanation

Indices: 1182163--1182210 Score: 87 Period size: 21 Copynumber: 2.3 Consensus size: 21 1182153 TAATTTTCAA * 1182163 ACATTATTGCACCTAATTTTG 1 ACATTGTTGCACCTAATTTTG 1182184 ACATTGTTGCACCTAATTTTG 1 ACATTGTTGCACCTAATTTTG 1182205 ACATTG 1 ACATTG 1182211 CAATATTAGG Statistics Matches: 26, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42 Consensus pattern (21 bp): ACATTGTTGCACCTAATTTTG Found at i:1183326 original size:40 final size:40 Alignment explanation

Indices: 1183271--1183356 Score: 118 Period size: 40 Copynumber: 2.1 Consensus size: 40 1183261 TTACCACTCG * * * * 1183271 GGATGAATTTTACTTTGGATTATTAGTGTATTCACCTTTC 1 GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC * 1183311 GGATGAATTTCACTTTGGAATATTAGTGGGTTCACCATTC 1 GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC 1183351 GAGATG 1 G-GATG 1183357 TTTAAAATAT Statistics Matches: 40, Mismatches: 5, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 40 36 0.90 41 4 0.10 ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41 Consensus pattern (40 bp): GGATGAATTTCACTTTGGAATATTAGTGGATTCACCATTC Found at i:1184073 original size:21 final size:21 Alignment explanation

Indices: 1184038--1184079 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 1184028 GCACTAATAC * 1184038 ACTAAAGTGCCTTAGCGTTGA 1 ACTAAAGTGCCTTAGCATTGA ** 1184059 ACTAAAGTGTTTTAGCATTGA 1 ACTAAAGTGCCTTAGCATTGA 1184080 TGGGTGAACC Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33 Consensus pattern (21 bp): ACTAAAGTGCCTTAGCATTGA Found at i:1187050 original size:76 final size:77 Alignment explanation

Indices: 1186883--1187174 Score: 333 Period size: 77 Copynumber: 3.8 Consensus size: 77 1186873 AAAAGCTGAA * * * * ** 1186883 AATGTCATGGTTCACTGAGAAACATGTTGCGATCTAGAATTTTACTATTTTTATTAATAAAATAA 1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG * * 1186948 CTTGCGCCCAAG 66 GTTGCGCACAAG * * * 1186960 AATGTCATGATTCACTGAGAAATATGTTACGATCTAGAATGTTAATA-TTTTATTAATAAAATGG 1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG * * 1187024 GTTGCGCTCAAT 66 GTTGCGCACAAG * * * * * 1187036 AATGTCATGGTTCACTAATAAATAGGTTGCGATTTGGAATGTTAATATTTTTATAAATAAAATGG 1 AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG * 1187101 GTTGCACACAAG 66 GTTGCGCACAAG * 1187113 AATGTTATGGTTCACTAAGAAAGTGA-GTTGCGATCT-GTAATGTTAAT-TTTTCTATT-ATAAA 1 AATGTCATGGTTCACTAAGAAA-T-ATGTTGCGATCTAG-AATGTTAATATTTT-TATTAATAAA 1187174 A 62 A 1187175 AATTCGAAAG Statistics Matches: 185, Mismatches: 25, Indels: 10 0.84 0.11 0.05 Matches are distributed among these distances: 76 64 0.35 77 98 0.53 78 22 0.12 79 1 0.01 ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37 Consensus pattern (77 bp): AATGTCATGGTTCACTAAGAAATATGTTGCGATCTAGAATGTTAATATTTTTATTAATAAAATGG GTTGCGCACAAG Found at i:1187436 original size:123 final size:124 Alignment explanation

Indices: 1187276--1187499 Score: 342 Period size: 124 Copynumber: 1.8 Consensus size: 124 1187266 TTTACAAAAA 1187276 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTAT-AAATTCAAAAGTAT 1 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT * * 1187340 CGATACTTTTGAAAAAATATTCATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG 66 AGATACTTTTGAAAAAATATACATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG * * * ** * * 1187399 TATCGATACTTTTAACTTTGAAATTTAAAATATCATTTTTTATTTTTTTTAAAATTCAAAATTAT 1 TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT * * 1187464 AGATACTTTTGAAAAAGTATACTTACTTTCGAATTT 66 AGATACTTTTGAAAAAATATACATACTTTCGAATTT 1187500 TTTATAATAG Statistics Matches: 89, Mismatches: 11, Indels: 1 0.88 0.11 0.01 Matches are distributed among these distances: 123 44 0.49 124 45 0.51 ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42 Consensus pattern (124 bp): TATCGATACTTTTAAATTCGAAAGTTAAAATATCATTTTACATTTTTTATAAAATTCAAAAGTAT AGATACTTTTGAAAAAATATACATACTTTCGAATTTAAAAAAATGAAAAGACTGCAAAG Found at i:1187553 original size:17 final size:17 Alignment explanation

Indices: 1187531--1187564 Score: 68 Period size: 17 Copynumber: 2.0 Consensus size: 17 1187521 TTTCAGATCG 1187531 CAACTTGTTTTCTTTGT 1 CAACTTGTTTTCTTTGT 1187548 CAACTTGTTTTCTTTGT 1 CAACTTGTTTTCTTTGT 1187565 GAATCATAAT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.12, C:0.18, G:0.12, T:0.59 Consensus pattern (17 bp): CAACTTGTTTTCTTTGT Found at i:1187763 original size:77 final size:77 Alignment explanation

Indices: 1187592--1187924 Score: 363 Period size: 77 Copynumber: 4.4 Consensus size: 77 1187582 TGTGCAGTCT * * * * 1187592 ATTTTATTTATAAAATTATTAACATTCCATATCACAACTTATTTATTAGTG-ATCATTGACA-T- 1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCA-TGACATTC * * 1187654 TTGGGCGCAACCC 65 TTGGACGCAACTC * * * * 1187667 ATTTTATTAATAAAAATATTAATATTCCATATCGCATCCTATTTATTAATGAACCATGACATTCT 1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT * * 1187732 TGGGCGTAACTC 66 TGGACGCAACTC * * * * * * 1187744 ATTTTATTAATAAAAATATTAACATTTCAGATCACAACCTTTTTCTTAGTAAATCATGACATTCT 1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT * 1187809 TGAACGCAACAT- 66 TGGACGCAAC-TC * *** * * 1187821 ATTTTATTAATAAAAATATTAACATTCCAAATTGTAACCTAATTCTTAATGAAAT-ATGACATTC 1 ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATG-AATCATGACATTC 1187885 TTGGACGCAAC-C 65 TTGGACGCAACTC 1187897 AATTTTATTAATAAAAATATTAACATTC 1 -ATTTTATTAATAAAAATATTAACATTC 1187925 TAGATTATAT Statistics Matches: 218, Mismatches: 33, Indels: 12 0.83 0.13 0.05 Matches are distributed among these distances: 75 49 0.22 76 4 0.02 77 161 0.74 78 4 0.02 ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38 Consensus pattern (77 bp): ATTTTATTAATAAAAATATTAACATTCCATATCACAACCTATTTATTAATGAATCATGACATTCT TGGACGCAACTC Found at i:1187884 original size:154 final size:152 Alignment explanation

Indices: 1187592--1187929 Score: 412 Period size: 154 Copynumber: 2.2 Consensus size: 152 1187582 TGTGCAGTCT * * * * 1187592 ATTTTATTTATAAAATTATTAACATTCCATATCACAACTTATTTATTAGTGATCATTGACATTTG 1 ATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTATTAGTAATCATTGACATTTG ** * * * * * * 1187657 GGCGCAACCCATTTTATTAATAAAAATATTAATATTCCATATCGCATCCTATTTATTAATGAACC 66 AACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATGAAAC * * 1187722 ATGACATTCTTGGGCGTAACTC- 131 ATGACATTCTTGGACGCAAC-CA * * 1187744 ATTTTATTAATAAAAATATTAACATTTCAGATCACAACCTT-TTTCTTAGTAAATCA-TGACATT 1 ATTTTATTAATAAAAATATTAACATTCCAGATCACAA-CTTATTTATTAGT-AATCATTGACA-T * * * * 1187807 CTTGAACGCAACATATTTTATTAATAAAAATATTAACATTCCAAATTGTAACCTAATTCTTAATG 63 -TTGAACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATG * 1187872 AAATATGACATTCTTGGACGCAACCA 127 AAACATGACATTCTTGGACGCAACCA * 1187898 ATTTTATTAATAAAAATATTAACATTCTAGAT 1 ATTTTATTAATAAAAATATTAACATTCCAGAT 1187930 TATATGTTTC Statistics Matches: 158, Mismatches: 23, Indels: 8 0.84 0.12 0.04 Matches are distributed among these distances: 152 46 0.29 153 9 0.06 154 103 0.65 ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38 Consensus pattern (152 bp): ATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTATTAGTAATCATTGACATTTG AACGCAACACATTTTATTAATAAAAATATTAACATTCCAAATCGCAACCTAATTATTAATGAAAC ATGACATTCTTGGACGCAACCA Found at i:1187924 original size:40 final size:40 Alignment explanation

Indices: 1187725--1187925 Score: 102 Period size: 40 Copynumber: 5.2 Consensus size: 40 1187715 ATGAACCATG * * 1187725 ACATTCTTGGGCGTAACTC-ATTTTATTAATAAAAATATTA 1 ACATTCTTGGACGCAAC-CAATTTTATTAATAAAAATATTA ** * * * * * 1187765 ACATT-TCAGATCACAACC-TTTTTCTTAGT--AAATCA-TG 1 ACATTCTTGGA-CGCAACCAATTTTATTAATAAAAAT-ATTA * 1187802 ACATTCTTGAACGCAA-CATATTTTATTAATAAAAATATTA 1 ACATTCTTGGACGCAACCA-ATTTTATTAATAAAAATATTA *** * * * * * 1187842 ACATTC-CAAATTGTAACCTAA--TTCTTAAT-GAAATA-TG 1 ACATTCTTGGA-CGCAACC-AATTTTATTAATAAAAATATTA 1187879 ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA 1 ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA 1187919 ACATTCT 1 ACATTCT 1187926 AGATTATATG Statistics Matches: 113, Mismatches: 32, Indels: 32 0.64 0.18 0.18 Matches are distributed among these distances: 36 3 0.03 37 26 0.23 38 24 0.21 39 26 0.23 40 31 0.27 41 2 0.02 42 1 0.01 ACGTcount: A:0.39, C:0.16, G:0.07, T:0.37 Consensus pattern (40 bp): ACATTCTTGGACGCAACCAATTTTATTAATAAAAATATTA Found at i:1205754 original size:24 final size:24 Alignment explanation

Indices: 1205722--1205770 Score: 98 Period size: 24 Copynumber: 2.0 Consensus size: 24 1205712 GAAACAACTT 1205722 GTAACAGATGAGATTAAAAGAGTA 1 GTAACAGATGAGATTAAAAGAGTA 1205746 GTAACAGATGAGATTAAAAGAGTA 1 GTAACAGATGAGATTAAAAGAGTA 1205770 G 1 G 1205771 CAAGTTTAAT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20 Consensus pattern (24 bp): GTAACAGATGAGATTAAAAGAGTA Found at i:1206134 original size:20 final size:20 Alignment explanation

Indices: 1206109--1206240 Score: 108 Period size: 20 Copynumber: 6.6 Consensus size: 20 1206099 AACACAGAAA 1206109 TCAAATTCGCAACGC-GATAG 1 TCAAATTCGCAACGCGGA-AG * * * * 1206129 TCAAATTCGTAACACAGAAT 1 TCAAATTCGCAACGCGGAAG * * * ** 1206149 TCAAATTTGTAACACAAAAG 1 TCAAATTCGCAACGCGGAAG * 1206169 TCAAATT-GATAACGC-GATAG 1 TCAAATTCG-CAACGCGGA-AG * * 1206189 TCAAATTCACAATGCGGAAG 1 TCAAATTCGCAACGCGGAAG 1206209 TCAAATTCGCAACGCGGAAG 1 TCAAATTCGCAACGCGGAAG 1206229 TCAAATTCGCAA 1 TCAAATTCGCAA 1206241 AGCAGAACAA Statistics Matches: 94, Mismatches: 13, Indels: 10 0.80 0.11 0.09 Matches are distributed among these distances: 19 2 0.02 20 88 0.94 21 4 0.04 ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22 Consensus pattern (20 bp): TCAAATTCGCAACGCGGAAG Found at i:1206153 original size:40 final size:39 Alignment explanation

Indices: 1206095--1206240 Score: 125 Period size: 40 Copynumber: 3.7 Consensus size: 39 1206085 TATTTGTAAA * 1206095 TCGTAACACAGAAATCAAATTCGCAACGCGATAGTCAAAT 1 TCGTAACACAGAAGTCAAATTCGCAACGCGA-AGTCAAAT * * * * * 1206135 TCGTAACACAGAATTCAAATTTGTAACACAAAAGTCAAAT 1 TCGTAACACAGAAGTCAAATTCGCAACGC-GAAGTCAAAT * * * 1206175 T-GATAACGC-GATAGTCAAATTCACAATGCGGAAGTCAAAT 1 TCG-TAACACAGA-AGTCAAATTCGCAACGC-GAAGTCAAAT * * * 1206215 TCGCAACGCGGAAGTCAAATTCGCAA 1 TCGTAACACAGAAGTCAAATTCGCAA 1206241 AGCAGAACAA Statistics Matches: 85, Mismatches: 16, Indels: 10 0.77 0.14 0.09 Matches are distributed among these distances: 39 3 0.04 40 78 0.92 41 4 0.05 ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21 Consensus pattern (39 bp): TCGTAACACAGAAGTCAAATTCGCAACGCGAAGTCAAAT Found at i:1206213 original size:60 final size:60 Alignment explanation

Indices: 1206097--1206240 Score: 148 Period size: 60 Copynumber: 2.4 Consensus size: 60 1206087 TTTGTAAATC ** * 1206097 GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCGTAACACAGAATTCAAATTT 1 GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT * ** * * 1206157 GTAACACA-AAAGTCAAATT-GATAACGCGATAGTCAAATTCACAATGCGGAAGTCAAATTC 1 GTAACACAGAAA-TCAAATTCG-CAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT * * * * 1206217 GCAACGCGGAAGTCAAATTCGCAA 1 GTAACACAGAAATCAAATTCGCAA 1206241 AGCAGAACAA Statistics Matches: 67, Mismatches: 13, Indels: 8 0.76 0.15 0.09 Matches are distributed among these distances: 59 4 0.06 60 60 0.90 61 3 0.04 ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21 Consensus pattern (60 bp): GTAACACAGAAATCAAATTCGCAACGCGATAGTCAAATTCACAACACAGAAGTCAAATTT Found at i:1206385 original size:22 final size:20 Alignment explanation

Indices: 1206350--1206392 Score: 50 Period size: 22 Copynumber: 2.0 Consensus size: 20 1206340 TCACTCTCTA * 1206350 CGGCGACATCCGTCCCTATCTC 1 CGGCGAAATCCGT--CTATCTC * 1206372 CGGCGAAATTCGTCTATCTC 1 CGGCGAAATCCGTCTATCTC 1206392 C 1 C 1206393 ATCTCTCAGA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 20 8 0.42 22 11 0.58 ACGTcount: A:0.16, C:0.40, G:0.19, T:0.26 Consensus pattern (20 bp): CGGCGAAATCCGTCTATCTC Found at i:1209005 original size:21 final size:21 Alignment explanation

Indices: 1208958--1209056 Score: 85 Period size: 21 Copynumber: 4.7 Consensus size: 21 1208948 GATGCACCTA * ** 1208958 TCATCATTCAAGAGTCATCTC 1 TCATCATTCAAGAGGCCCCTC 1208979 -CTATCATTCAAGAGGCCCCTC 1 TC-ATCATTCAAGAGGCCCCTC * 1209000 TCATCA-TCGAAGAAGCCCCTC 1 TCATCATTC-AAGAGGCCCCTC * * * * 1209021 CCACCGTTCAAGAGGCCCCTG 1 TCATCATTCAAGAGGCCCCTC * 1209042 TCATCGTTCAAGAGG 1 TCATCATTCAAGAGG 1209057 TCCCGCCCGC Statistics Matches: 63, Mismatches: 11, Indels: 8 0.77 0.13 0.10 Matches are distributed among these distances: 20 3 0.05 21 57 0.90 22 3 0.05 ACGTcount: A:0.25, C:0.34, G:0.17, T:0.23 Consensus pattern (21 bp): TCATCATTCAAGAGGCCCCTC Found at i:1209005 original size:42 final size:41 Alignment explanation

Indices: 1208958--1209055 Score: 99 Period size: 42 Copynumber: 2.3 Consensus size: 41 1208948 GATGCACCTA * * * 1208958 TCATCATTCAAGAGTCATCTCCTATCATTCAAGAGGCCCCTC 1 TCATCATTCAAGAG-CACCTCCCACCATTCAAGAGGCCCCTC * * * 1209000 TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG 1 TCATCATTC-AAG-AGCACCTCCCACCATTCAAGAGGCCCCTC * 1209042 TCATCGTTCAAGAG 1 TCATCATTCAAGAG 1209056 GTCCCGCCCG Statistics Matches: 46, Mismatches: 7, Indels: 7 0.77 0.12 0.12 Matches are distributed among these distances: 41 4 0.09 42 38 0.83 43 4 0.09 ACGTcount: A:0.26, C:0.35, G:0.16, T:0.23 Consensus pattern (41 bp): TCATCATTCAAGAGCACCTCCCACCATTCAAGAGGCCCCTC Found at i:1209070 original size:42 final size:42 Alignment explanation

Indices: 1208985--1209076 Score: 114 Period size: 42 Copynumber: 2.2 Consensus size: 42 1208975 TCTCCTATCA * 1208985 TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCTCCCACCG 1 TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACCG * * * * * 1209027 TTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGCCCGCCG 1 TTCAAGAGGCCCCTCTCATC-ATCGAAGAAGCCCCGCCCACCG 1209069 TTCAAGAG 1 TTCAAGAG 1209077 CCCGATTCAC Statistics Matches: 43, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 42 41 0.95 43 2 0.05 ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18 Consensus pattern (42 bp): TTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCACCG Found at i:1210551 original size:66 final size:65 Alignment explanation

Indices: 1210392--1210567 Score: 257 Period size: 66 Copynumber: 2.6 Consensus size: 65 1210382 TGGTGTACAC 1210392 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA 1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA 1210456 TAATTA 60 TAATTA * * 1210462 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAATAATT 1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAATAATT 1210526 A 65 A 1210527 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT 1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT 1210568 GTTTTAAATT Statistics Matches: 101, Mismatches: 2, Indels: 10 0.89 0.02 0.09 Matches are distributed among these distances: 64 17 0.17 65 19 0.19 66 40 0.40 67 1 0.01 68 4 0.04 69 20 0.20 ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54 Consensus pattern (65 bp): TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTA Found at i:1210678 original size:20 final size:20 Alignment explanation

Indices: 1210630--1210678 Score: 64 Period size: 20 Copynumber: 2.5 Consensus size: 20 1210620 ACAAATTCAT 1210630 AACGCGAAAGGTAAATTCGC 1 AACGCGAAAGGTAAATTCGC * * 1210650 AAAGTGAAA-GTAAAATTCGC 1 AACGCGAAAGGT-AAATTCGC 1210670 AACGCGAAA 1 AACGCGAAA 1210679 TAAGCGCTGC Statistics Matches: 24, Mismatches: 4, Indels: 2 0.80 0.13 0.07 Matches are distributed among these distances: 19 2 0.08 20 22 0.92 ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14 Consensus pattern (20 bp): AACGCGAAAGGTAAATTCGC Found at i:1213453 original size:24 final size:24 Alignment explanation

Indices: 1213402--1213455 Score: 63 Period size: 24 Copynumber: 2.2 Consensus size: 24 1213392 ACATCATCAT ** * 1213402 TGACTAAGATCAAAGTCCGGGTAT 1 TGACTAAGATCAAAGTCCGAATAC * * 1213426 TGACTAAGATCAAATTTCGAATAC 1 TGACTAAGATCAAAGTCCGAATAC 1213450 TGACTA 1 TGACTA 1213456 GTACTCACAA Statistics Matches: 25, Mismatches: 5, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28 Consensus pattern (24 bp): TGACTAAGATCAAAGTCCGAATAC Found at i:1213586 original size:12 final size:12 Alignment explanation

Indices: 1213565--1213598 Score: 50 Period size: 12 Copynumber: 2.8 Consensus size: 12 1213555 GGTTGTGGGT * 1213565 TTTGAGATTGTG 1 TTTGATATTGTG 1213577 TTTGATATTGTG 1 TTTGATATTGTG * 1213589 TTTGGTATTG 1 TTTGATATTG 1213599 AAAATGTGGT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 12 20 1.00 ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56 Consensus pattern (12 bp): TTTGATATTGTG Found at i:1214412 original size:19 final size:18 Alignment explanation

Indices: 1214369--1214415 Score: 58 Period size: 18 Copynumber: 2.6 Consensus size: 18 1214359 CAAAACATTT 1214369 GTGTTGCGAAACTAAAAC 1 GTGTTGCGAAACTAAAAC * * * 1214387 CTGTTGCGAAATTAAATTC 1 GTGTTGCGAAACTAAA-AC 1214406 GTGTTGCGAA 1 GTGTTGCGAA 1214416 TTCGAAAATC Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 18 14 0.58 19 10 0.42 ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30 Consensus pattern (18 bp): GTGTTGCGAAACTAAAAC Found at i:1214449 original size:19 final size:19 Alignment explanation

Indices: 1214408--1214459 Score: 61 Period size: 19 Copynumber: 2.7 Consensus size: 19 1214398 TTAAATTCGT * 1214408 GTTGCGAATTCGAAAATCTA 1 GTTGCGAATTTG-AAATCTA 1214428 GTTGCGAATTTGAAAT-TAA 1 GTTGCGAATTTGAAATCT-A * 1214447 GTTACGAATTTGA 1 GTTGCGAATTTGA 1214460 CTTTTGTGTT Statistics Matches: 29, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 18 1 0.03 19 17 0.59 20 11 0.38 ACGTcount: A:0.35, C:0.10, G:0.21, T:0.35 Consensus pattern (19 bp): GTTGCGAATTTGAAATCTA Found at i:1214476 original size:20 final size:20 Alignment explanation

Indices: 1214451--1214493 Score: 77 Period size: 20 Copynumber: 2.1 Consensus size: 20 1214441 AATTAAGTTA * 1214451 CGAATTTGACTTTTGTGTTG 1 CGAATTTGACTTCTGTGTTG 1214471 CGAATTTGACTTCTGTGTTG 1 CGAATTTGACTTCTGTGTTG 1214491 CGA 1 CGA 1214494 TTTACAAATT Statistics Matches: 22, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44 Consensus pattern (20 bp): CGAATTTGACTTCTGTGTTG Found at i:1214536 original size:20 final size:20 Alignment explanation

Indices: 1214511--1214560 Score: 91 Period size: 20 Copynumber: 2.5 Consensus size: 20 1214501 ATTCGCGTTG 1214511 CGAAATTGGAAACTGTGTTA 1 CGAAATTGGAAACTGTGTTA * 1214531 CGAAATTGGAAACTGTGTTG 1 CGAAATTGGAAACTGTGTTA 1214551 CGAAATTGGA 1 CGAAATTGGA 1214561 GTTTGCGTTG Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 20 29 1.00 ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28 Consensus pattern (20 bp): CGAAATTGGAAACTGTGTTA Found at i:1214570 original size:20 final size:20 Alignment explanation

Indices: 1214505--1214574 Score: 86 Period size: 20 Copynumber: 3.5 Consensus size: 20 1214495 TTACAAATTC 1214505 GCGTTGCGAAATTGGAAACT 1 GCGTTGCGAAATTGGAAACT * * 1214525 GTGTTACGAAATTGGAAACT 1 GCGTTGCGAAATTGGAAACT * *** 1214545 GTGTTGCGAAATTGGAGTTT 1 GCGTTGCGAAATTGGAAACT 1214565 GCGTTGCGAA 1 GCGTTGCGAA 1214575 TTTGTTGGTC Statistics Matches: 43, Mismatches: 7, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 43 1.00 ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30 Consensus pattern (20 bp): GCGTTGCGAAATTGGAAACT Found at i:1216922 original size:2 final size:2 Alignment explanation

Indices: 1216915--1216950 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 1216905 GAGGGAAAAC 1216915 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1216951 AACTTAACAG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1218375 original size:21 final size:21 Alignment explanation

Indices: 1218345--1218397 Score: 56 Period size: 20 Copynumber: 2.6 Consensus size: 21 1218335 TTTAAACAAT * 1218345 AACTAAAATAAATGAAAT-TAA 1 AACTATAATAAATGAAATAT-A * 1218366 AACTATAAT-ATTGAAATATA 1 AACTATAATAAATGAAATATA * 1218386 AACAATAATAAA 1 AACTATAATAAA 1218398 ATTTGTAATT Statistics Matches: 26, Mismatches: 4, Indels: 4 0.76 0.12 0.12 Matches are distributed among these distances: 20 16 0.62 21 10 0.38 ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26 Consensus pattern (21 bp): AACTATAATAAATGAAATATA Found at i:1219779 original size:3 final size:3 Alignment explanation

Indices: 1219766--1219817 Score: 72 Period size: 3 Copynumber: 18.0 Consensus size: 3 1219756 ATTTATTATT * * 1219766 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TAA -AA TAA TTA 1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA 1219812 TAA TAA 1 TAA TAA 1219818 ATCAAAAAAT Statistics Matches: 43, Mismatches: 4, Indels: 4 0.84 0.08 0.08 Matches are distributed among these distances: 2 4 0.09 3 39 0.91 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (3 bp): TAA Found at i:1219780 original size:9 final size:8 Alignment explanation

Indices: 1219773--1219831 Score: 57 Period size: 9 Copynumber: 6.9 Consensus size: 8 1219763 ATTTAATAAA 1219773 AATAATAAT 1 AATAA-AAT 1219782 AATAATAAT 1 AATAA-AAT 1219791 AATAAAAT 1 AATAAAAT 1219799 AATAAAAT 1 AATAAAAT * 1219807 AATTATAAT 1 AA-TAAAAT 1219816 AAATCAAAA- 1 -AAT-AAAAT 1219825 AATAAAA 1 AATAAAA 1219832 CACAAATGGA Statistics Matches: 45, Mismatches: 2, Indels: 8 0.82 0.04 0.15 Matches are distributed among these distances: 7 4 0.09 8 16 0.36 9 20 0.44 10 5 0.11 ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27 Consensus pattern (8 bp): AATAAAAT Found at i:1221028 original size:80 final size:79 Alignment explanation

Indices: 1220929--1221083 Score: 247 Period size: 80 Copynumber: 1.9 Consensus size: 79 1220919 TTGCGCGTTC * * 1220929 TTGATTTGAGTATTTTGTTTAGGGTTGCGAGATCTATATAAAATTTGGGTTAGATTTAAGTAATG 1 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAA-TTAGGTTAGATTTAAGTAATG * 1220994 TTTGCATTTTGGTTA 65 TTTACATTTTGGTTA * * * 1221009 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATGTAAAATTAGGTTTGATTTACGTAATGT 1 TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGT 1221074 TTACATTTTG 66 TTACATTTTG 1221084 TTTACTAATC Statistics Matches: 69, Mismatches: 6, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 79 28 0.41 80 41 0.59 ACGTcount: A:0.25, C:0.05, G:0.24, T:0.47 Consensus pattern (79 bp): TTGATTTGAGTATTGTGTTTAGGGTTGCGAGATCTATATAAAATTAGGTTAGATTTAAGTAATGT TTACATTTTGGTTA Found at i:1223390 original size:18 final size:18 Alignment explanation

Indices: 1223358--1223392 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 1223348 TTCATTGCCA ** 1223358 TGGATTACATGACTGTTC 1 TGGATTACAAAACTGTTC 1223376 TGGATTACAAAACTGTT 1 TGGATTACAAAACTGTT 1223393 TTTGCATAAT Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37 Consensus pattern (18 bp): TGGATTACAAAACTGTTC Found at i:1227940 original size:34 final size:34 Alignment explanation

Indices: 1227897--1227963 Score: 116 Period size: 34 Copynumber: 2.0 Consensus size: 34 1227887 GATGAACTAT * 1227897 CAATTTAGGGCATTGAATATCGGAACTCTATGTC 1 CAATTTAGGGCATTGAATATCGGAACCCTATGTC * 1227931 CAATTTAGGGTATTGAATATCGGAACCCTATGT 1 CAATTTAGGGCATTGAATATCGGAACCCTATGT 1227964 GCTTGCCTTT Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 34 31 1.00 ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33 Consensus pattern (34 bp): CAATTTAGGGCATTGAATATCGGAACCCTATGTC Found at i:1241119 original size:18 final size:18 Alignment explanation

Indices: 1241093--1241138 Score: 56 Period size: 18 Copynumber: 2.6 Consensus size: 18 1241083 TCACGGAATG * * 1241093 TAAGATTACTGGCGTGAA 1 TAAGATTACTGACGAGAA * * 1241111 TAGGATTACCGACGAGAA 1 TAAGATTACTGACGAGAA 1241129 TAAGATTACT 1 TAAGATTACT 1241139 AGGAATGTTG Statistics Matches: 22, Mismatches: 6, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 18 22 1.00 ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26 Consensus pattern (18 bp): TAAGATTACTGACGAGAA Found at i:1241844 original size:20 final size:20 Alignment explanation

Indices: 1241805--1241845 Score: 55 Period size: 20 Copynumber: 2.0 Consensus size: 20 1241795 CCAGATCAGT ** 1241805 CCAAGATGTAGGGTGTAAGC 1 CCAAGATGTAGGGTCAAAGC * 1241825 CCAAGATGTTGGGTCAAAGC 1 CCAAGATGTAGGGTCAAAGC 1241845 C 1 C 1241846 TTACCCCACG Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.29, C:0.20, G:0.32, T:0.20 Consensus pattern (20 bp): CCAAGATGTAGGGTCAAAGC Found at i:1245195 original size:18 final size:19 Alignment explanation

Indices: 1245172--1245209 Score: 60 Period size: 19 Copynumber: 2.1 Consensus size: 19 1245162 CGCTTCTTCT 1245172 CTACTTAT-AGTATCGATA 1 CTACTTATCAGTATCGATA * 1245190 CTACTTTTCAGTATCGATA 1 CTACTTATCAGTATCGATA 1245209 C 1 C 1245210 CTATTCTTGG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 18 7 0.39 19 11 0.61 ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39 Consensus pattern (19 bp): CTACTTATCAGTATCGATA Found at i:1251232 original size:22 final size:22 Alignment explanation

Indices: 1251183--1251232 Score: 91 Period size: 22 Copynumber: 2.3 Consensus size: 22 1251173 CAACATGTTC * 1251183 TTCATACACCCAAATCATGTAA 1 TTCATCCACCCAAATCATGTAA 1251205 TTCATCCACCCAAATCATGTAA 1 TTCATCCACCCAAATCATGTAA 1251227 TTCATC 1 TTCATC 1251233 ATTCAGGCAT Statistics Matches: 27, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 22 27 1.00 ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30 Consensus pattern (22 bp): TTCATCCACCCAAATCATGTAA Found at i:1257884 original size:22 final size:22 Alignment explanation

Indices: 1257855--1257914 Score: 59 Period size: 27 Copynumber: 2.5 Consensus size: 22 1257845 GTGTAAATTA 1257855 TTTTGGTTGTTTGA-TGTTTTG 1 TTTTGGTTGTTTGATTGTTTTG 1257876 TTTTCGGTTGTTAGCTTGATTGTTTTG 1 TTTT-GGTTG-T---TTGATTGTTTTG 1257903 TTTTTGGTTGTT 1 -TTTTGGTTGTT 1257915 GGCTTGACTG Statistics Matches: 32, Mismatches: 0, Indels: 12 0.73 0.00 0.27 Matches are distributed among these distances: 21 4 0.12 22 5 0.16 23 2 0.06 26 5 0.16 27 12 0.38 28 4 0.12 ACGTcount: A:0.05, C:0.03, G:0.27, T:0.65 Consensus pattern (22 bp): TTTTGGTTGTTTGATTGTTTTG Found at i:1257902 original size:27 final size:26 Alignment explanation

Indices: 1257865--1257931 Score: 98 Period size: 27 Copynumber: 2.5 Consensus size: 26 1257855 TTTTGGTTGT 1257865 TTGATGTTTTGTTTTCGGTTGTTAGC 1 TTGATGTTTTGTTTTCGGTTGTTAGC * * 1257891 TTGATTGTTTTGTTTTTGGTTGTTGGC 1 TTGA-TGTTTTGTTTTCGGTTGTTAGC 1257918 TTGACTGTTTTGTT 1 TTGA-TGTTTTGTT 1257932 GTAGCATATT Statistics Matches: 37, Mismatches: 3, Indels: 1 0.90 0.07 0.02 Matches are distributed among these distances: 26 4 0.11 27 33 0.89 ACGTcount: A:0.06, C:0.06, G:0.27, T:0.61 Consensus pattern (26 bp): TTGATGTTTTGTTTTCGGTTGTTAGC Found at i:1258449 original size:29 final size:29 Alignment explanation

Indices: 1258414--1258497 Score: 109 Period size: 29 Copynumber: 2.9 Consensus size: 29 1258404 TTAAATTTTT ** 1258414 AAAAGTTATAAAATCGTTATTG-AAGTTTC 1 AAAAGTTATAAAATAATTATTGTAA-TTTC * * 1258443 AGAAGTTATAAAATAATTATTGTAATTTT 1 AAAAGTTATAAAATAATTATTGTAATTTC 1258472 AAAAGTTATAAAATAATTATT-TAATT 1 AAAAGTTATAAAATAATTATTGTAATT 1258498 AATCGGACTG Statistics Matches: 49, Mismatches: 5, Indels: 3 0.86 0.09 0.05 Matches are distributed among these distances: 28 5 0.10 29 42 0.86 30 2 0.04 ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42 Consensus pattern (29 bp): AAAAGTTATAAAATAATTATTGTAATTTC Found at i:1259118 original size:20 final size:20 Alignment explanation

Indices: 1259093--1259166 Score: 69 Period size: 20 Copynumber: 3.5 Consensus size: 20 1259083 ATCCGACTCG 1259093 AAATATTATATTTATTAAAA 1 AAATATTATATTTATTAAAA * 1259113 AAATATTATTTTTATTCAATAA 1 AAATATTATATTTATT-AA-AA * * 1259135 AAATA-GAGATTTAATTAAAA 1 AAATATTATATTT-ATTAAAA * 1259155 ATAATAATATAT 1 A-AATATTATAT 1259167 AAAAAGATAT Statistics Matches: 43, Mismatches: 6, Indels: 8 0.75 0.11 0.14 Matches are distributed among these distances: 20 18 0.42 21 12 0.28 22 13 0.30 ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42 Consensus pattern (20 bp): AAATATTATATTTATTAAAA Found at i:1259834 original size:188 final size:188 Alignment explanation

Indices: 1259517--1259892 Score: 752 Period size: 188 Copynumber: 2.0 Consensus size: 188 1259507 TTTCCCCAGG 1259517 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT 1 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT 1259582 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG 66 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG 1259647 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT 131 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT 1259705 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT 1 TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT 1259770 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG 66 TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG 1259835 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT 131 AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT 1259893 CCTCCTGCGA Statistics Matches: 188, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 188 188 1.00 ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31 Consensus pattern (188 bp): TGAATTATACATCTTTTTCTTCAGTTTTCAATTCTCCATTTCTATTCTTCCTTTTAGCTGACTGT TTAATCCATTTTTATAGAAAACAATGAGTCGGAGAGCGAACAGTCCAGAGCTGGAACTGACGCTG AACTCATCGCCACCAAGGGCGCCAAACCAACAAGTTGGGTCGCCGAACACGTCGGTTT Found at i:1261591 original size:84 final size:85 Alignment explanation

Indices: 1261450--1261609 Score: 313 Period size: 84 Copynumber: 1.9 Consensus size: 85 1261440 TGGAAGAAAA 1261450 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACC-AAACG 1 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG 1261514 ATGAAGACGTAAATGCATAG 66 ATGAAGACGTAAATGCATAG 1261534 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG 1 AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG 1261599 ATGAAGACGTA 66 ATGAAGACGTA 1261610 GAAATATGCA Statistics Matches: 75, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 84 59 0.79 85 16 0.21 ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23 Consensus pattern (85 bp): AGGACTAAGGATCAATATTGAAAAGACAGAGTATTTATGTTCAAACTTCAGTGGGAACCAAAACG ATGAAGACGTAAATGCATAG Found at i:1264215 original size:17 final size:18 Alignment explanation

Indices: 1264178--1264216 Score: 62 Period size: 18 Copynumber: 2.2 Consensus size: 18 1264168 ATATTTTGTA 1264178 TTTAAATTATTTAAGTAT 1 TTTAAATTATTTAAGTAT * 1264196 TTTAATTTATTTAA-TAT 1 TTTAAATTATTTAAGTAT 1264213 TTTA 1 TTTA 1264217 CTTATATAAT Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 17 7 0.35 18 13 0.65 ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62 Consensus pattern (18 bp): TTTAAATTATTTAAGTAT Found at i:1265968 original size:50 final size:50 Alignment explanation

Indices: 1265894--1265993 Score: 175 Period size: 50 Copynumber: 2.0 Consensus size: 50 1265884 AGCAGCCACC * 1265894 GTATCCAGCGACTTACATACCGCAACCATAAATGATGCCGCCA-CGCCTT 1 GTATCCAGCGACCTACATACCGCAACCATAAATGATGCCGCCACCGCCTT 1265943 GTATCCAGCGACACTACATACCGCAACCATAAATGATGCCGCCACCGCCTT 1 GTATCCAGCGAC-CTACATACCGCAACCATAAATGATGCCGCCACCGCCTT 1265994 TCCATTACCA Statistics Matches: 48, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 49 12 0.25 50 30 0.62 51 6 0.12 ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19 Consensus pattern (50 bp): GTATCCAGCGACCTACATACCGCAACCATAAATGATGCCGCCACCGCCTT Found at i:1269727 original size:34 final size:34 Alignment explanation

Indices: 1269684--1269768 Score: 152 Period size: 34 Copynumber: 2.5 Consensus size: 34 1269674 TATGATTGAT 1269684 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA 1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA * 1269718 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA 1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA * 1269752 ATCTCGGCGTCTTCAGT 1 CTCTCGGCGTCTTCAGT 1269769 GCTGTGCATG Statistics Matches: 49, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 34 49 1.00 ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35 Consensus pattern (34 bp): CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA Found at i:1269874 original size:23 final size:23 Alignment explanation

Indices: 1269844--1269887 Score: 88 Period size: 23 Copynumber: 1.9 Consensus size: 23 1269834 TTGAGCAGGG 1269844 CTGCACGTCTGCATGTGGGGGTC 1 CTGCACGTCTGCATGTGGGGGTC 1269867 CTGCACGTCTGCATGTGGGGG 1 CTGCACGTCTGCATGTGGGGG 1269888 GCATGCAATT Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 23 21 1.00 ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25 Consensus pattern (23 bp): CTGCACGTCTGCATGTGGGGGTC Found at i:1269894 original size:23 final size:22 Alignment explanation

Indices: 1269841--1269894 Score: 81 Period size: 23 Copynumber: 2.4 Consensus size: 22 1269831 GGGTTGAGCA 1269841 GGGCTGCACGTCTGCATGTGGG 1 GGGCTGCACGTCTGCATGTGGG * 1269863 GGTCCTGCACGTCTGCATGTGGG 1 GG-GCTGCACGTCTGCATGTGGG 1269886 GGGCATGCA 1 GGGC-TGCA 1269895 ATTGTTGGAT Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 22 3 0.11 23 25 0.89 ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22 Consensus pattern (22 bp): GGGCTGCACGTCTGCATGTGGG Found at i:1270099 original size:41 final size:41 Alignment explanation

Indices: 1270042--1270119 Score: 138 Period size: 41 Copynumber: 1.9 Consensus size: 41 1270032 GAGACTGCTA * 1270042 GGGCTAAGGCAATTCACAATTACAGAAGTAGTGAGAGTTTG 1 GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG * 1270083 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG 1 GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAG 1270120 CCTGAGAGGG Statistics Matches: 35, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 41 35 1.00 ACGTcount: A:0.35, C:0.14, G:0.31, T:0.21 Consensus pattern (41 bp): GGGCTAAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG Found at i:1270617 original size:20 final size:20 Alignment explanation

Indices: 1270592--1270632 Score: 57 Period size: 20 Copynumber: 2.0 Consensus size: 20 1270582 TTATAAAAAG * 1270592 TTAGTA-TACTATGCTTGAAT 1 TTAGTATTAATATGCTT-AAT 1270612 TTAGTATTAATATGCTTAAT 1 TTAGTATTAATATGCTTAAT 1270632 T 1 T 1270633 GGTTAAATTT Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 10 0.53 21 9 0.47 ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49 Consensus pattern (20 bp): TTAGTATTAATATGCTTAAT Found at i:1270649 original size:172 final size:173 Alignment explanation

Indices: 1270362--1270720 Score: 564 Period size: 172 Copynumber: 2.1 Consensus size: 173 1270352 TTGTAAAGTT * * * 1270362 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGATAT 1 TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATAT * 1270427 ACTATGCTGAAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T 66 ACTATGCTGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT * 1270490 GGATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA 131 -GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA * * 1270534 TTAGGGATCGTTTTGTAAAATTTGAGAAATTTAAGGAATTAGAGTAAATTATAAAAAGTT-AGTA 1 TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGA-TA * 1270598 TACTATGCTTG-AATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA 65 TACTATGC-TGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTA * * 1270662 GTGATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA 129 GTGATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA * 1270707 TTAGGGATCATTTT 1 TTAGGGATCGTTTT 1270721 ATATTTGATG Statistics Matches: 172, Mismatches: 11, Indels: 7 0.91 0.06 0.04 Matches are distributed among these distances: 171 1 0.01 172 108 0.63 173 62 0.36 174 1 0.01 ACGTcount: A:0.40, C:0.04, G:0.18, T:0.37 Consensus pattern (173 bp): TTAGGGATCGTTTTGTAAAATTTAAGAAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGATAT ACTATGCTGAAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT GATTAAATTGCAAACTTTGAAAATGTTGAGAACCAAATAGTAA Found at i:1272976 original size:14 final size:14 Alignment explanation

Indices: 1272959--1273642 Score: 99 Period size: 14 Copynumber: 48.3 Consensus size: 14 1272949 AAGTCAAGTA 1272959 ATTATTATTAAATC 1 ATTATTATTAAATC ** 1272973 ATTAAAATTAAATC 1 ATTATTATTAAATC ** * * 1272987 ATTAAAATTAAGTA 1 ATTATTATTAAATC 1273001 ATTATTATT-AA-- 1 ATTATTATTAAATC 1273012 ATTATTA--AAAT- 1 ATTATTATTAAATC * * * * 1273023 A-AATCATTAAGTA 1 ATTATTATTAAATC 1273036 ATTATTATTAAATC 1 ATTATTATTAAATC * 1273050 ATTAAATCATTAAATC 1 ATT--ATTATTAAATC * 1273066 ATTAATCATT-AA-- 1 ATT-ATTATTAAATC * 1273078 ATTATTATTAAAGC 1 ATTATTATTAAATC * 1273092 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC * * 1273106 ---ATTA--AAGTA 1 ATTATTATTAAATC 1273115 ATTATTATTAAATC 1 ATTATTATTAAATC * * * 1273129 ATTAAATCTTAAAGTA 1 ATT-ATTATTAAA-TC * 1273145 ATTATTATTAAAAC 1 ATTATTATTAAATC * 1273159 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC * * * 1273173 ATTA-AAGTAATTATT 1 ATTATTATTAA--ATC * * 1273188 ATTAATCATTAAAGTA 1 ATT-ATTATTAAA-TC 1273204 ATTATTATTAAATC 1 ATTATTATTAAATC * 1273218 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC * * 1273232 ATTAAATCATTAAATT 1 ATT--ATTATTAAATC * * * * 1273248 A-AATCATTAAGTA 1 ATTATTATTAAATC 1273261 ATTATTATTAAATC 1 ATTATTATTAAATC ** 1273275 ATTAAAATT-AATC 1 ATTATTATTAAATC * * * 1273288 ATTA-AAGTAATTATT 1 ATTATTATTAA--ATC * * 1273303 ATTAATCATTAAAGTT 1 ATT-ATTATTAAA-TC * * * 1273319 A-AATCATTAAAGTA 1 ATTATTATTAAA-TC 1273333 ATTATTATTAAATC 1 ATTATTATTAAATC * * 1273347 ATTA-AAGTTAAATA 1 ATTATTA-TTAAATC 1273361 ATTATTA-TAAATC 1 ATTATTATTAAATC * 1273374 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC * * * 1273388 ATTA-AAGTAATATT 1 ATTATTATTAA-ATC * 1273402 ATTAAATCATTAAATC 1 ATT--ATTATTAAATC * * 1273418 ATAAATCATTAAAGT- 1 AT-TATTATTAAA-TC 1273433 ATTATTATTAAATC 1 ATTATTATTAAATC * 1273447 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC 1273461 ATTAATCATTAAAATTAAATC 1 A-T--T-ATT---ATTAAATC * 1273482 ATTA-AAGTTAAATC 1 ATTATTA-TTAAATC * 1273496 ATTAAATCATTAAA-- 1 ATT--ATTATTAAATC * * 1273510 ATTAATCATTAAAGTA 1 ATT-ATTATTAAA-TC 1273526 ATTATTATTAAATC 1 ATTATTATTAAATC ** * 1273540 ATTAAAATTCAATC 1 ATTATTATTAAATC * * 1273554 ATTAAAGTATT--ATT 1 ATT--ATTATTAAATC * * * 1273568 ATTAATCATTAAGTT 1 ATT-ATTATTAAATC * * 1273583 A-AATTATTAAAGTA 1 ATTATTATTAAA-TC 1273597 ATTATTATTAAATC 1 ATTATTATTAAATC * * 1273611 ATTA-AAGTTAAATA 1 ATTATTA-TTAAATC 1273625 ATTATTATTAAATC 1 ATTATTATTAAATC 1273639 ATTA 1 ATTA 1273643 AAGTTATAAT Statistics Matches: 499, Mismatches: 98, Indels: 146 0.67 0.13 0.20 Matches are distributed among these distances: 9 3 0.01 10 5 0.01 11 14 0.03 12 17 0.03 13 66 0.13 14 230 0.46 15 83 0.17 16 53 0.11 17 16 0.03 18 2 0.00 20 1 0.00 21 8 0.02 22 1 0.00 ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41 Consensus pattern (14 bp): ATTATTATTAAATC Found at i:1272978 original size:8 final size:8 Alignment explanation

Indices: 1272965--1273559 Score: 216 Period size: 8 Copynumber: 81.8 Consensus size: 8 1272955 AGTAATTATT 1272965 ATTAAATC 1 ATTAAATC 1272973 ATTAAA-- 1 ATTAAATC 1272979 ATTAAATC 1 ATTAAATC 1272987 ATTAAA-- 1 ATTAAATC * * 1272993 ATTAAGTA 1 ATTAAATC * 1273001 ATT--ATT 1 ATTAAATC * 1273007 ATTAAATT 1 ATTAAATC 1273015 ATTAAA-- 1 ATTAAATC 1273021 A-TAAATC 1 ATTAAATC * * 1273028 ATTAAGTA 1 ATTAAATC * 1273036 ATT--ATT 1 ATTAAATC 1273042 ATTAAATC 1 ATTAAATC 1273050 ATTAAATC 1 ATTAAATC 1273058 ATTAAATC 1 ATTAAATC 1273066 ATT-AATC 1 ATTAAATC * 1273073 ATTAAATTATT 1 ATT-AA--ATC * 1273084 ATTAAAGC 1 ATTAAATC 1273092 ATTAAA-- 1 ATTAAATC * 1273098 GTTAAATC 1 ATTAAATC * 1273106 ATTAAAGTA 1 ATTAAA-TC * 1273115 ATT--ATT 1 ATTAAATC 1273121 ATTAAATC 1 ATTAAATC 1273129 ATTAAATC 1 ATTAAATC * 1273137 -TTAAAGTA 1 ATTAAA-TC * 1273145 ATT--ATT 1 ATTAAATC * 1273151 ATTAAAAC 1 ATTAAATC 1273159 ATTAAA-- 1 ATTAAATC * 1273165 GTTAAATC 1 ATTAAATC * 1273173 ATTAAAGTA 1 ATTAAA-TC * 1273182 ATT--ATT 1 ATTAAATC 1273188 ATT-AATC 1 ATTAAATC * 1273195 ATTAAAGTA 1 ATTAAA-TC * 1273204 ATT--ATT 1 ATTAAATC 1273210 ATTAAATC 1 ATTAAATC 1273218 ATTAAA-- 1 ATTAAATC * 1273224 GTTAAATC 1 ATTAAATC 1273232 ATTAAATC 1 ATTAAATC 1273240 ATT-AA-- 1 ATTAAATC 1273245 ATTAAATC 1 ATTAAATC * * 1273253 ATTAAGTA 1 ATTAAATC * 1273261 ATT--ATT 1 ATTAAATC 1273267 ATTAAATC 1 ATTAAATC 1273275 ATTAAA-- 1 ATTAAATC 1273281 ATT-AATC 1 ATTAAATC * 1273288 ATTAAAGTA 1 ATTAAA-TC * 1273297 ATT--ATT 1 ATTAAATC 1273303 ATT-AATC 1 ATTAAATC 1273310 ATTAAA-- 1 ATTAAATC * 1273316 GTTAAATC 1 ATTAAATC * 1273324 ATTAAAGTA 1 ATTAAA-TC * 1273333 ATT--ATT 1 ATTAAATC 1273339 ATTAAATC 1 ATTAAATC 1273347 ATTAAA-- 1 ATTAAATC * * 1273353 GTTAAATA 1 ATTAAATC * 1273361 ATT--ATT 1 ATTAAATC 1273367 A-TAAATC 1 ATTAAATC 1273374 ATTAAA-- 1 ATTAAATC * 1273380 GTTAAATC 1 ATTAAATC 1273388 ATTAAAGT- 1 ATTAAA-TC * * 1273396 A--ATATT 1 ATTAAATC 1273402 ATTAAATC 1 ATTAAATC 1273410 ATTAAATC 1 ATTAAATC 1273418 A-TAAATC 1 ATTAAATC 1273425 ATTAAAGT- 1 ATTAAA-TC * 1273433 ATT--ATT 1 ATTAAATC 1273439 ATTAAATC 1 ATTAAATC 1273447 ATTAAA-- 1 ATTAAATC * 1273453 GTTAAATC 1 ATTAAATC 1273461 ATT-AATC 1 ATTAAATC 1273468 ATTAAA-- 1 ATTAAATC 1273474 ATTAAATC 1 ATTAAATC 1273482 ATTAAA-- 1 ATTAAATC * 1273488 GTTAAATC 1 ATTAAATC 1273496 ATTAAATC 1 ATTAAATC 1273504 ATTAAA-- 1 ATTAAATC 1273510 ATT-AATC 1 ATTAAATC * 1273517 ATTAAAGTA 1 ATTAAA-TC * 1273526 ATT--ATT 1 ATTAAATC 1273532 ATTAAATC 1 ATTAAATC 1273540 ATTAAA-- 1 ATTAAATC * 1273546 ATTCAATC 1 ATTAAATC 1273554 ATTAAA 1 ATTAAA 1273560 GTATTATTAT Statistics Matches: 444, Mismatches: 62, Indels: 162 0.66 0.09 0.24 Matches are distributed among these distances: 5 14 0.03 6 121 0.27 7 55 0.12 8 218 0.49 9 29 0.07 10 2 0.00 11 5 0.01 ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40 Consensus pattern (8 bp): ATTAAATC Found at i:1273172 original size:36 final size:37 Alignment explanation

Indices: 1273130--1273524 Score: 426 Period size: 35 Copynumber: 11.0 Consensus size: 37 1273120 TATTAAATCA * 1273130 TTAAATC-TTAAAGTAATTATTATTAAAACATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273166 TTAAATCATTAAAGTAATTATTATT-AATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG * 1273202 TAATTATTATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAA- 1 ---------TTAAATCATTAAAG-TAATTATTATTAAATCATTAAAG * 1273246 TTAAATCATT-AAGTAATTATTATTAAATCATTAAAA 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273282 TT-AATCATTAAAGTAATTATTATT-AATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273317 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273354 --------TTAAA-TAATTATTA-TAAATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273381 TTAAATCATTAAAGTAA-TATTATTAAATCATTAAA- 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273416 TCATAAATCATTAAAGT-ATTATTATTAAATCATTAAAG 1 T--TAAATCATTAAAGTAATTATTATTAAATCATTAAAG * ** 1273454 TTAAATCATT-AA-TCATTAAAATTAAATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG * ** 1273489 TTAAATCATTAAA-TCATTAAAATT-AATCATTAAAG 1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273524 T 1 T 1273525 AATTATTATT Statistics Matches: 319, Mismatches: 6, Indels: 69 0.81 0.02 0.18 Matches are distributed among these distances: 27 13 0.04 28 9 0.03 29 5 0.02 33 3 0.01 34 4 0.01 35 99 0.31 36 93 0.29 37 60 0.19 38 1 0.00 44 5 0.02 45 24 0.08 46 3 0.01 ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40 Consensus pattern (37 bp): TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG Found at i:1273194 original size:22 final size:22 Alignment explanation

Indices: 1273169--1273317 Score: 140 Period size: 22 Copynumber: 6.5 Consensus size: 22 1273159 ATTAAAGTTA 1273169 AATCATTAAAGTAATTATTATT 1 AATCATTAAAGTAATTATTATT 1273191 AATCATTAAAGTAATTATTATT 1 AATCATTAAAGTAATTATTATT * 1273213 AAATCATTAAAGTTAA--ATCATT 1 -AATCATTAAAG-TAATTATTATT * * * 1273235 AAATCATTAAATTAAATCATTAAGT 1 -AATCATTAAAGT-AATTATT-ATT * * * ** 1273260 AATTATTATTAAATCATTAAAATT 1 AATCATTA--AAGTAATTATTATT 1273284 AATCATTAAAGTAATTATTATT 1 AATCATTAAAGTAATTATTATT 1273306 AATCATTAAAGT 1 AATCATTAAAGT 1273318 TAAATCATTA Statistics Matches: 103, Mismatches: 16, Indels: 16 0.76 0.12 0.12 Matches are distributed among these distances: 21 1 0.01 22 62 0.60 23 11 0.11 24 21 0.20 25 5 0.05 26 3 0.03 ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42 Consensus pattern (22 bp): AATCATTAAAGTAATTATTATT Found at i:1273341 original size:129 final size:130 Alignment explanation

Indices: 1272993--1273628 Score: 718 Period size: 129 Copynumber: 4.9 Consensus size: 130 1272983 AATCATTAAA * * 1272993 ATTAAGTAATTATTATTAAATTATTAAAATAAATCATT-AAGTAATTATTATTAAATCATTAAAT 1 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAA- * * * * * 1273057 CATTAAATCATTAATCATTAAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTA 65 -GTTAAATCATTAA--AGT-AATTATTATTAAATCATTAAAGTTAAATCATTAAA-TCATTA-AA 1273122 TTAAATC 124 TTAAATC * * * ** * * * 1273129 ATT-A--AA-TCTTA--AAGTAATTATTATTAAAACATTAAAGTTAA--ATCATTAAAGTAATTA 1 ATTAAGTAATTATTATTAAATCATTAAAATT-AATCATTAAAG-TAATTATTATTAAA-TCATTA * 1273186 TTA-TT-AATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTA 63 -AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTA 1273249 AATC 127 AATC 1273253 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATT-AATCATTAAAG 1 ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG * 1273317 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATAAATCATTAAAGT 66 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTT--A-AATCA-T-TAAATCATTAAA-T 1273382 TAAATC 125 TAAATC * 1273388 ATTAAAGTAA-TATTATTAAATCATTAAATCATAAATCATTAAAGT-ATTATTATTAAATCATTA 1 ATT-AAGTAATTATTATTAAATCATTAAA--ATTAATCATTAAAGTAATTATTATTAAATCATTA * ** 1273451 AAGTTAAATCATT-AA-TCATTAAAATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATT- 63 AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATT-AAATTA 1273513 AATC 127 AATC 1273517 ATTAAAGTAATTATTATTAAATCATTAAAATTCAATCATTAAAGT-ATTATTATT-AATCATT-A 1 ATT-AAGTAATTATTATTAAATCATTAAAATT-AATCATTAAAGTAATTATTATTAAATCATTAA * * 1273579 AGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTA 64 AGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTA 1273629 TTATTAAATC Statistics Matches: 435, Mismatches: 35, Indels: 67 0.81 0.07 0.12 Matches are distributed among these distances: 124 11 0.03 125 6 0.01 126 34 0.08 127 17 0.04 128 25 0.06 129 122 0.28 130 55 0.13 131 19 0.04 132 20 0.05 133 8 0.02 134 12 0.03 135 51 0.12 136 20 0.05 137 35 0.08 ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41 Consensus pattern (130 bp): ATTAAGTAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAATCATTAAATTAAATC Found at i:1273597 original size:71 final size:73 Alignment explanation

Indices: 1273402--1273675 Score: 272 Period size: 71 Copynumber: 3.9 Consensus size: 73 1273392 AAGTAATATT ** * 1273402 ATTAAATCATTAAA-TCATAAATCATTAAAGT-ATTATTATTAAATCATTAAAGTTAA--ATCAT 1 ATTAAATCATTAAAGT--TAAATCATTAAA-TCATTAAAATTAAATCATTAAAG-TAATTATTAT 1273463 T-AATCATTAAA 62 TAAATCATTAAA 1273474 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATT-AATCATTAAAGTAATTATTATTAAA 1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA 1273538 TCATTAAA 66 TCATTAAA * * * * * 1273546 ATTCAATCATTAAAG-TATTATTATT-AATCATT-AAGTTAAATTATTAAAGTAATTATTATTAA 1 ATTAAATCATTAAAGTTA-AATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA 1273608 ATCATTAAA 65 ATCATTAAA * * * * * 1273617 GTTAAATAATTATTA-TTAAATCATTAAA--GTTATAATTAAAT--TTAAA-TAATTATTATTAA 1 ATTAAATCATTA-AAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA 1273676 TATGTACTCG Statistics Matches: 174, Mismatches: 17, Indels: 26 0.80 0.08 0.12 Matches are distributed among these distances: 68 13 0.07 69 8 0.05 70 18 0.10 71 86 0.49 72 48 0.28 73 1 0.01 ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42 Consensus pattern (73 bp): ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA TCATTAAA Found at i:1273626 original size:28 final size:29 Alignment explanation

Indices: 1273589--1273648 Score: 113 Period size: 28 Copynumber: 2.1 Consensus size: 29 1273579 AGTTAAATTA 1273589 TTAAAGTAATTATTATTAAATCATTAAAG 1 TTAAAGTAATTATTATTAAATCATTAAAG 1273618 TTAAA-TAATTATTATTAAATCATTAAAG 1 TTAAAGTAATTATTATTAAATCATTAAAG 1273646 TTA 1 TTA 1273649 TAATTAAATT Statistics Matches: 31, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 28 26 0.84 29 5 0.16 ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43 Consensus pattern (29 bp): TTAAAGTAATTATTATTAAATCATTAAAG Found at i:1273633 original size:229 final size:227 Alignment explanation

Indices: 1273043--1273644 Score: 759 Period size: 229 Copynumber: 2.7 Consensus size: 227 1273033 GTAATTATTA * 1273043 TTAAATCATTAAATCATTAAATCATTAATCATT--A--AATTATTATTAAAGCATTAAAGTTAAA 1 TTAAATCATTAAATCATTAAA--ATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAA * * * 1273104 TCATTAAAGTAATTATTATTAA--A-TCA-TTAAA-TCTTAAAGTAATTATTATTAAAACATTAA 64 TCATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAA * * * * 1273164 AGTTAAATCATTA-AAGT-AATTATT--ATTAATCATTAAAGTAATTATTATTAAATCATTAAAG 129 AGTTAAATAATTATTATTAAATCATTAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAG 1273225 TTAAATCATTAAATCATTAAATTAAATCATTAAG 194 TTAAATCATTAAATCATTAAATTAAATCATTAAG * 1273259 -TAATTATTATTAAATCATTAAAATTAATCATTAAAGTAATTATTATT-AATCATTAAAGTTAAA 1 TTAA--ATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAA * * * 1273322 TCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATAAATCATTA-AAGTTAAA 64 TCATTAAAGTAATTATTATT-AATCATT-AAGTT--A-AATTATTA-AAGTAATTATTA-TTAAA 1273386 TCATTAAAG-----TAA-TATTATTAAATCATTAAATCATAAATCATTAAAGT-ATTATTATTAA 122 TCATTAAAGTTAAATAATTATTATTAAATCATTAAAT--T-AATCATTAAAGTAATTATTATTAA 1273444 ATCATTAAAGTTAAATCATT-AATCATTAAAATTAAATCATTAAAG 184 ATCATTAAAGTTAAATCATTAAATCATT-AAATTAAATCATT-AAG * * 1273489 TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAATTCAATC 1 TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATC 1273554 ATTAAAGT-ATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG 66 ATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG 1273618 TTAAATAATTATTATTAAATCATTAAA 131 TTAAATAATTATTATTAAATCATTAAA 1273645 GTTATAATTA Statistics Matches: 332, Mismatches: 18, Indels: 59 0.81 0.04 0.14 Matches are distributed among these distances: 215 13 0.04 217 17 0.05 218 35 0.11 219 12 0.04 221 1 0.00 222 1 0.00 223 24 0.07 224 15 0.05 225 7 0.02 226 1 0.00 227 9 0.03 228 22 0.07 229 133 0.40 230 39 0.12 231 3 0.01 ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41 Consensus pattern (227 bp): TTAAATCATTAAATCATTAAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATC ATTAAAGTAATTATTATTAATCATTAAGTTAAATTATTAAAGTAATTATTATTAAATCATTAAAG TTAAATAATTATTATTAAATCATTAAATTAATCATTAAAGTAATTATTATTAAATCATTAAAGTT AAATCATTAAATCATTAAATTAAATCATTAAG Found at i:1273636 original size:20 final size:19 Alignment explanation

Indices: 1273611--1273675 Score: 60 Period size: 20 Copynumber: 3.3 Consensus size: 19 1273601 TTATTAAATC 1273611 ATTAAAGTTAAATAATTATT 1 ATTAAA-TTAAATAATTATT * * * 1273631 ATTAAATCATTAA-AGTTATA 1 ATTAAAT--TAAATAATTATT 1273651 ATTAAATTTAAATAATTATT 1 ATTAAA-TTAAATAATTATT 1273671 ATTAA 1 ATTAA 1273676 TATGTACTCG Statistics Matches: 35, Mismatches: 6, Indels: 8 0.71 0.12 0.16 Matches are distributed among these distances: 19 4 0.11 20 27 0.77 21 4 0.11 ACGTcount: A:0.51, C:0.02, G:0.03, T:0.45 Consensus pattern (19 bp): ATTAAATTAAATAATTATT Found at i:1273675 original size:14 final size:14 Alignment explanation

Indices: 1273585--1273675 Score: 66 Period size: 14 Copynumber: 6.6 Consensus size: 14 1273575 ATTAAGTTAA 1273585 ATTATTAAAGTAATT 1 ATTATTAAA-TAATT * 1273600 ATTATTAAATCATT 1 ATTATTAAATAATT * 1273614 A-AAGTTAAATAATT 1 ATTA-TTAAATAATT * 1273628 ATTATTAAATCATT 1 ATTATTAAATAATT * 1273642 A-AAGTT--ATAATT 1 ATTA-TTAAATAATT * 1273654 A-AATTTAAATAATT 1 ATTA-TTAAATAATT 1273668 ATTATTAA 1 ATTATTAA 1273676 TATGTACTCG Statistics Matches: 61, Mismatches: 9, Indels: 13 0.73 0.11 0.16 Matches are distributed among these distances: 12 10 0.16 13 2 0.03 14 38 0.62 15 11 0.18 ACGTcount: A:0.49, C:0.02, G:0.03, T:0.45 Consensus pattern (14 bp): ATTATTAAATAATT Found at i:1277073 original size:42 final size:42 Alignment explanation

Indices: 1277014--1277101 Score: 142 Period size: 42 Copynumber: 2.1 Consensus size: 42 1277004 AACAAATCTC * * 1277014 ACGCTTCAGGCGAATCTCACGCTTCGACC-CTAAAGCATACAG 1 ACGCTTCAGACGAATCTCACGCTTCGACCAC-AAAGAATACAG 1277056 ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG 1 ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG 1277098 ACGC 1 ACGC 1277102 ATGCAGAACG Statistics Matches: 43, Mismatches: 2, Indels: 2 0.91 0.04 0.04 Matches are distributed among these distances: 42 42 0.98 43 1 0.02 ACGTcount: A:0.32, C:0.33, G:0.18, T:0.17 Consensus pattern (42 bp): ACGCTTCAGACGAATCTCACGCTTCGACCACAAAGAATACAG Found at i:1279423 original size:23 final size:22 Alignment explanation

Indices: 1279390--1279457 Score: 75 Period size: 21 Copynumber: 3.1 Consensus size: 22 1279380 TGCCATATAA * 1279390 AATGTCTCGAAGGACCTCGTAG 1 AATGTCCCGAAGGACCTCGTAG * * 1279412 AATTGTCCCGAAGGACCACATA- 1 AA-TGTCCCGAAGGACCTCGTAG * * 1279434 TATATCCCGAAGGACCTCGTAG 1 AATGTCCCGAAGGACCTCGTAG 1279456 AA 1 AA 1279458 CCCTCGACTC Statistics Matches: 36, Mismatches: 8, Indels: 4 0.75 0.17 0.08 Matches are distributed among these distances: 21 16 0.44 22 4 0.11 23 16 0.44 ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21 Consensus pattern (22 bp): AATGTCCCGAAGGACCTCGTAG Done.