Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold22

Parameters: 2 7 7 80 10 50 500

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500

Length: 1964558
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31

Warning! 137786 characters in sequence are not A, C, G, or T


File 5 of 6

Found at i:1112814 original size:32 final size:31

Alignment explanation

Indices: 1112759--1112837 Score: 79 Period size: 31 Copynumber: 2.5 Consensus size: 31 1112749 ATTCGGATTT * * 1112759 TTTTGTTAAGTCGCT-CATGAAATCAAGAAGGG 1 TTTTGTTAAGTCG-TACATAAAATC-AGAAGGA * *** 1112791 TTTTGTTAAGTCGTACTTAAAATCATTCGGA 1 TTTTGTTAAGTCGTACATAAAATCAGAAGGA 1112822 TTTTGTTAAGTCGTAC 1 TTTTGTTAAGTCGTAC 1112838 CAGGAATAAT Statistics Matches: 40, Mismatches: 6, Indels: 3 0.82 0.12 0.06 Matches are distributed among these distances: 31 20 0.50 32 20 0.50 ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39 Consensus pattern (31 bp): TTTTGTTAAGTCGTACATAAAATCAGAAGGA Found at i:1112850 original size:31 final size:30 Alignment explanation

Indices: 1112791--1112855 Score: 78 Period size: 31 Copynumber: 2.1 Consensus size: 30 1112781 TCAAGAAGGG * * 1112791 TTTTGTTAAGTCGTACTTAAAATCATTCGGA 1 TTTTGTTAAGTCGTACTCAAAATAATTC-GA * 1112822 TTTTGTTAAGTCGTAC-CAGGAATAATTCGA 1 TTTTGTTAAGTCGTACTCA-AAATAATTCGA 1112852 TTTT 1 TTTT 1112856 TTCATCTTTT Statistics Matches: 30, Mismatches: 3, Indels: 3 0.83 0.08 0.08 Matches are distributed among these distances: 30 7 0.23 31 23 0.77 ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43 Consensus pattern (30 bp): TTTTGTTAAGTCGTACTCAAAATAATTCGA Found at i:1114162 original size:437 final size:437 Alignment explanation

Indices: 1113410--1114391 Score: 1883 Period size: 437 Copynumber: 2.2 Consensus size: 437 1113400 ATATTTACAA 1113410 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA 1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA * * * 1113475 AGTCTTTAATATGTAGCCCTTTACTGAGAAATATTTTGTGAAATGTTATAGAAGCAAATATGTTT 66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT * 1113540 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTTATATGTTACGTAATTAAGGGGTTTT 131 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT * 1113605 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGATAAATATTTTGTATTGCAG 196 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG 1113670 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC 261 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC 1113735 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT 326 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT 1113800 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT 391 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT * * 1113847 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGTTCTAC 1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA * 1113912 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGTAATGTTATAGAAGCAAATATGTTT 66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT 1113977 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT 131 ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT 1114042 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG 196 AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG 1114107 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC 261 TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC 1114172 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT 326 GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT 1114237 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT 391 AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT * 1114284 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGGGCTCTAA 1 GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA 1114349 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAA 66 AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAA 1114392 GGTTGTTAAA Statistics Matches: 533, Mismatches: 12, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 437 533 1.00 ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31 Consensus pattern (437 bp): GACCTTTTATTTGATATCAAGAAAAAGGGGCTGGCCCCTCAAATTAGGGGACGAAAGTGCTCTAA AGTCTTTAATTTGTAGCCCTTTACTGAGAGATGTTTTGTGAAATGTTATAGAAGCAAATATGTTT ATCTCACAGTTATGTATCCAAGCAGTGTAAATATTTTGTCATATGTTACGTAATTAAGGGGTTTT AGGGGCCAAAAGTCCAAAATTTTGATCATCCATATCTCAGAAAGGAAAAATATTTTGTATTGCAG TACAGAAGAAAAGTTGTTCAAAATGATGTTCTTAACAATATGCAACCGTCAAAATTTCGTTAAAC GGCCCCTAAAAGGAGATAAGGGACCGGCCCCTAAAACCTACTTTCTCATATATCTCTAGAACGGT AACGAATTTTTACACACTTGTAGAACAAAATGTGTTCAGAATTAAAT Found at i:1117690 original size:2 final size:2 Alignment explanation

Indices: 1117683--1117745 Score: 126 Period size: 2 Copynumber: 31.5 Consensus size: 2 1117673 TCTTTTCAAA 1117683 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1117725 AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG A 1117746 TCTTATTTGT Statistics Matches: 61, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 61 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1124212 original size:2 final size:2 Alignment explanation

Indices: 1124205--1124260 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 1124195 GCCATTGTAT 1124205 GA GA GA 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 GA GA GA 1124247 GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA 1124261 TATGGACAGA Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1130256 original size:33 final size:34 Alignment explanation

Indices: 1130208--1130271 Score: 112 Period size: 33 Copynumber: 1.9 Consensus size: 34 1130198 AAAAAGGCAG * 1130208 AGAGAGAGAGAGAATGGCACAGAGCTAGAGAGAA 1 AGAGAGAGAGAGAATGGCACAGAGATAGAGAGAA 1130242 AGAGA-AGAGAGAATGGCACAGAGATAGAGA 1 AGAGAGAGAGAGAATGGCACAGAGATAGAGA 1130272 AAGGCAGAGA Statistics Matches: 29, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 33 24 0.83 34 5 0.17 ACGTcount: A:0.48, C:0.08, G:0.38, T:0.06 Consensus pattern (34 bp): AGAGAGAGAGAGAATGGCACAGAGATAGAGAGAA Found at i:1130272 original size:18 final size:18 Alignment explanation

Indices: 1130210--1130290 Score: 62 Period size: 18 Copynumber: 4.7 Consensus size: 18 1130200 AAAGGCAGAG * 1130210 AGAGAGAGAGAATGGCAC 1 AGAGATAGAGAATGGCAC * * 1130228 AGAGCTAGAG-A--G-AA 1 AGAGATAGAGAATGGCAC * 1130242 AGAGAAGAGAGAATGGCAC 1 AGAG-ATAGAGAATGGCAC * * 1130261 AGAGATAGAGAAAGGCAG 1 AGAGATAGAGAATGGCAC * 1130279 AGAGATAAAGAA 1 AGAGATAGAGAA 1130291 AGAGAGAGAG Statistics Matches: 48, Mismatches: 10, Indels: 10 0.71 0.15 0.15 Matches are distributed among these distances: 14 5 0.10 15 5 0.10 16 1 0.02 17 1 0.02 18 31 0.65 19 5 0.10 ACGTcount: A:0.51, C:0.07, G:0.36, T:0.06 Consensus pattern (18 bp): AGAGATAGAGAATGGCAC Found at i:1130291 original size:18 final size:18 Alignment explanation

Indices: 1130251--1130301 Score: 59 Period size: 18 Copynumber: 2.8 Consensus size: 18 1130241 AAGAGAAGAG * * * 1130251 AGAATGGCACAGAGATAG 1 AGAAAGGCAGAGAGATAA 1130269 AGAAAGGCAGAGAGATAA 1 AGAAAGGCAGAGAGATAA 1130287 AGAAAGAG-AGAGAGA 1 AGAAAG-GCAGAGAGA 1130302 AACTGTAAGA Statistics Matches: 29, Mismatches: 3, Indels: 2 0.85 0.09 0.06 Matches are distributed among these distances: 18 28 0.97 19 1 0.03 ACGTcount: A:0.53, C:0.06, G:0.35, T:0.06 Consensus pattern (18 bp): AGAAAGGCAGAGAGATAA Found at i:1132664 original size:2 final size:2 Alignment explanation

Indices: 1132657--1132712 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 1132647 GCAGTGAACT 1132657 GA GA GA 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 GA GA GA 1132699 GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA 1132713 TTGCCTTGAC Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1133228 original size:20 final size:20 Alignment explanation

Indices: 1133203--1133269 Score: 125 Period size: 20 Copynumber: 3.4 Consensus size: 20 1133193 TGGAATGATT 1133203 ACATGTAATAATCTATTCTG 1 ACATGTAATAATCTATTCTG * 1133223 ACATGTAATATTCTATTCTG 1 ACATGTAATAATCTATTCTG 1133243 ACATGTAATAATCTATTCTG 1 ACATGTAATAATCTATTCTG 1133263 ACATGTA 1 ACATGTA 1133270 TGTCTTTAAT Statistics Matches: 45, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 45 1.00 ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40 Consensus pattern (20 bp): ACATGTAATAATCTATTCTG Found at i:1136441 original size:2 final size:2 Alignment explanation

Indices: 1136434--1136460 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1136424 AACAGAGGTG 1136434 CT CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT C 1136461 ATTTTATCTT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:1136556 original size:2 final size:2 Alignment explanation

Indices: 1136546--1136634 Score: 65 Period size: 2 Copynumber: 45.5 Consensus size: 2 1136536 TGCACACACG * * * * 1136546 CT CT GT CT CT CC CT CT CT CT CT CC CT CT CT CT CT CC CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT * * * * * * * 1136588 CT C- CA CT CT TT CT CT CC CT CT C- CT CT CT TT AT TT TT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1136628 CT CT CT C 1 CT CT CT C 1136635 ATCTTTCATC Statistics Matches: 68, Mismatches: 17, Indels: 4 0.76 0.19 0.04 Matches are distributed among these distances: 1 2 0.03 2 66 0.97 ACGTcount: A:0.02, C:0.49, G:0.01, T:0.47 Consensus pattern (2 bp): CT Found at i:1136561 original size:12 final size:12 Alignment explanation

Indices: 1136546--1136614 Score: 97 Period size: 12 Copynumber: 5.9 Consensus size: 12 1136536 TGCACACACG * 1136546 CTCTGTCTCTCC 1 CTCTCTCTCTCC 1136558 CTCTCTCTCTCC 1 CTCTCTCTCTCC 1136570 CTCTCTCTCTCC 1 CTCTCTCTCTCC * 1136582 CTCTCTCTC-CA 1 CTCTCTCTCTCC * 1136593 CTCTTTCTCTCC 1 CTCTCTCTCTCC 1136605 CTCTC-CTCTC 1 CTCTCTCTCTC 1136615 TTTATTTTTC Statistics Matches: 51, Mismatches: 5, Indels: 3 0.86 0.08 0.05 Matches are distributed among these distances: 11 14 0.27 12 37 0.73 ACGTcount: A:0.01, C:0.55, G:0.01, T:0.42 Consensus pattern (12 bp): CTCTCTCTCTCC Found at i:1141557 original size:16 final size:17 Alignment explanation

Indices: 1141536--1141568 Score: 59 Period size: 16 Copynumber: 2.0 Consensus size: 17 1141526 GATTTCTCTG 1141536 ATAAAAAATGA-AAAAA 1 ATAAAAAATGAGAAAAA 1141552 ATAAAAAATGAGAAAAA 1 ATAAAAAATGAGAAAAA 1141569 CCCCTGTAGG Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 11 0.69 17 5 0.31 ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12 Consensus pattern (17 bp): ATAAAAAATGAGAAAAA Found at i:1160085 original size:48 final size:48 Alignment explanation

Indices: 1160009--1160146 Score: 154 Period size: 48 Copynumber: 2.9 Consensus size: 48 1159999 CACTGTCAGC * 1160009 AATGTCAGGTATGTTGATGTAAATAGAGGTAACTGCTAGGTGGGTCAA 1 AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCTAGGTGGGTCAA * * * * 1160057 AATGTCAAGTGTGTTGATGTAAAAAGAGGTAACTG-TCAGGTGTGTCGA 1 AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCT-AGGTGGGTCAA * * * ** 1160105 AATGTCCGGTTTGTCGATG-AAAATAGATTTAACTGCTAGGTG 1 AATGTCAGGTATGTTGATGTAAAA-AGAGGTAACTGCTAGGTG 1160147 AGTTATTATG Statistics Matches: 76, Mismatches: 11, Indels: 6 0.82 0.12 0.06 Matches are distributed among these distances: 47 5 0.07 48 70 0.92 49 1 0.01 ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30 Consensus pattern (48 bp): AATGTCAGGTATGTTGATGTAAAAAGAGGTAACTGCTAGGTGGGTCAA Found at i:1162902 original size:32 final size:32 Alignment explanation

Indices: 1162857--1162984 Score: 195 Period size: 32 Copynumber: 4.0 Consensus size: 32 1162847 GAGGAGAAGT * 1162857 AGTG-TGATTGGCTGAAATGTAGAGCTCAGAG 1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG * 1162888 AGTGCTGATTGGCTGAAATGTACAGCTCAGTG 1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG * * * 1162920 AGTGCTTATTGGCTGAAATATACAGCTCAGTG 1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG * 1162952 AGTGCTGATTGGCTGAAATGTACAGCTAAGAG 1 AGTGCTGATTGGCTGAAATGTACAGCTCAGAG 1162984 A 1 A 1162985 CTGTGAATGA Statistics Matches: 88, Mismatches: 8, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 31 4 0.05 32 84 0.95 ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27 Consensus pattern (32 bp): AGTGCTGATTGGCTGAAATGTACAGCTCAGAG Found at i:1165338 original size:15 final size:15 Alignment explanation

Indices: 1165318--1165347 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 1165308 TGGTGTTTGG 1165318 GTACATACATGTACT 1 GTACATACATGTACT 1165333 GTACATACATGTACT 1 GTACATACATGTACT 1165348 AATTTTCAGT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33 Consensus pattern (15 bp): GTACATACATGTACT Found at i:1171035 original size:12 final size:12 Alignment explanation

Indices: 1171018--1171044 Score: 54 Period size: 12 Copynumber: 2.2 Consensus size: 12 1171008 GTTGGTGCGC 1171018 CATTACCATCAG 1 CATTACCATCAG 1171030 CATTACCATCAG 1 CATTACCATCAG 1171042 CAT 1 CAT 1171045 CAAGGACGCC 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:0.33, C:0.33, G:0.07, T:0.26 Consensus pattern (12 bp): CATTACCATCAG Found at i:1173507 original size:23 final size:23 Alignment explanation

Indices: 1173477--1173525 Score: 73 Period size: 23 Copynumber: 2.1 Consensus size: 23 1173467 CAATGTTTAG 1173477 TGACCTCAATA-TATACTGACATT 1 TGACCTCAATACTA-ACTGACATT * 1173500 TGACCTCAATACTAATTGACATT 1 TGACCTCAATACTAACTGACATT 1173523 TGA 1 TGA 1173526 ATCCAATACT Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 23 22 0.92 24 2 0.08 ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35 Consensus pattern (23 bp): TGACCTCAATACTAACTGACATT Found at i:1177512 original size:31 final size:31 Alignment explanation

Indices: 1177428--1177668 Score: 113 Period size: 31 Copynumber: 7.9 Consensus size: 31 1177418 GTTTCATTGT * * ** * 1177428 TGATATTGACACTTACATGGCCTGTCTACGC 1 TGATATAGACACTTAAATGGTTTGTCTACAC * * 1177459 TGATATAGACACATAAAAGGTTTGTCTACAC 1 TGATATAGACACTTAAATGGTTTGTCTACAC * * 1177490 TGATATAGACACTTAAATGGTTTGTCAATAC 1 TGATATAGACACTTAAATGGTTTGTCTACAC *** ** 1177521 TGGGGTAGATTCTTACAA-GG--T-T-TACAC 1 TGATATAGACACTTA-AATGGTTTGTCTACAC * * * * * 1177548 TGACATAGGCACTTCAATAGTTTGTCTACAT 1 TGATATAGACACTTAAATGGTTTGTCTACAC * * **** 1177579 TGATATAGACACATACATAACATGTCTACAC 1 TGATATAGACACTTAAATGGTTTGTCTACAC * * * 1177610 TGA-AGTAGACAC-TAACAAGGTTTGCCTAAAC 1 TGATA-TAGACACTTAA-ATGGTTTGTCTACAC * 1177641 TGA-AGTAGACAATTACAA-GGTTTGTCTA 1 TGATA-TAGACACTTA-AATGGTTTGTCTA 1177669 TACTTGGGTA Statistics Matches: 154, Mismatches: 46, Indels: 20 0.70 0.21 0.09 Matches are distributed among these distances: 26 2 0.01 27 12 0.08 28 1 0.01 29 2 0.01 30 4 0.03 31 127 0.82 32 5 0.03 33 1 0.01 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31 Consensus pattern (31 bp): TGATATAGACACTTAAATGGTTTGTCTACAC Found at i:1177977 original size:31 final size:31 Alignment explanation

Indices: 1177934--1178152 Score: 172 Period size: 31 Copynumber: 6.8 Consensus size: 31 1177924 TTACTACACT * * * * 1177934 GTTTTTCTACACTAAAATAGACACTTACTTG 1 GTTTGTCTACACTGATATAGACACTTACATG * * 1177965 GTTTGTCTACACTAATACATGTAAAGACACTTAATATATG 1 GTTTGTCTACACTGAT--A--T--AGACAC-T--TACATG * * * 1178005 GGTTGCCTACACTGATATAGACACTTACAAG 1 GTTTGTCTACACTGATATAGACACTTACATG * * * 1178036 GTTTGTCTACATTGAAATAGACA--TATATG 1 GTTTGTCTACACTGATATAGACACTTACATG * * * 1178065 GTTTGTTTACAATGATATAGACACTTACATA 1 GTTTGTCTACACTGATATAGACACTTACATG * * * 1178096 GCTTGTCTACACTGATATAGACACTTAAAAG 1 GTTTGTCTACACTGATATAGACACTTACATG * 1178127 GTGTGTCTACACTGATATAGACACTT 1 GTTTGTCTACACTGATATAGACACTT 1178153 GATATATGGC Statistics Matches: 149, Mismatches: 28, Indels: 22 0.75 0.14 0.11 Matches are distributed among these distances: 29 24 0.16 31 90 0.60 33 2 0.01 34 6 0.04 35 1 0.01 36 1 0.01 37 6 0.04 38 2 0.01 40 17 0.11 ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34 Consensus pattern (31 bp): GTTTGTCTACACTGATATAGACACTTACATG Found at i:1178081 original size:60 final size:60 Alignment explanation

Indices: 1177998--1178152 Score: 186 Period size: 60 Copynumber: 2.5 Consensus size: 60 1177988 AAGACACTTA * * * * 1177998 ATATATGGGTTGCCTACACTGATATAGACACTTACA-AGGTTTGTCTACATTGAAATAGAC 1 ATATATGGTTTGTCTACACTGATATAGACACTTACATA-GCTTGTCTACACTGAAATAGAC * * * 1178058 ATATATGGTTTGTTTACAATGATATAGACACTTACATAGCTTGTCTACACTGATATAGAC 1 ATATATGGTTTGTCTACACTGATATAGACACTTACATAGCTTGTCTACACTGAAATAGAC * * * 1178118 ACTTAAAAGGTGTGTCTACACTGATATAGACACTT 1 A--TATATGGTTTGTCTACACTGATATAGACACTT 1178153 GATATATGGC Statistics Matches: 80, Mismatches: 12, Indels: 4 0.83 0.12 0.04 Matches are distributed among these distances: 60 52 0.65 61 1 0.01 62 27 0.34 ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34 Consensus pattern (60 bp): ATATATGGTTTGTCTACACTGATATAGACACTTACATAGCTTGTCTACACTGAAATAGAC Found at i:1180727 original size:189 final size:188 Alignment explanation

Indices: 1180367--1180745 Score: 618 Period size: 189 Copynumber: 2.0 Consensus size: 188 1180357 AATCAGTAAT * * 1180367 CAAGTTAATCTTTAGTTTCTTCTTATTATGTCATTTTTTTATTTTTACTAAGTTAACTGTGTTAG 1 CAAGTAAATCTTTAGTTTCTTC-T-TTATGTCATTTTTTTATTATTACTAAGTTAACTGTGTTAG * * 1180432 GCCAAAATAATTATCTTTTCTTTCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGG 64 GCCAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGG * * 1180497 CCAAAACAATTAATCTAAACTTTCTCATGCGGAACATTTCAAAATAAAATGTTGCAGGTA 129 CCAAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA 1180557 CAAGTAAATCTTTAGTTTCTTC-TTATGTCATTTATTTTAAATTATTACTAAGTTAACTGTGTTA 1 CAAGTAAATCTTTAGTTTCTTCTTTATGTCATTT-TTTT--ATTATTACTAAGTTAACTGTGTTA * 1180621 GGCCAAAAAAATTATCTTTTCTATCTGAGGCAA-TTAATGAATTGATAATAAGTTAACAGATATG 63 GGCCAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATG * * 1180685 GCCAAAACAATTAATCTTAAGTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA 128 GCCAAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA 1180746 TTTAACTTTT Statistics Matches: 177, Mismatches: 9, Indels: 7 0.92 0.05 0.04 Matches are distributed among these distances: 187 11 0.06 188 4 0.02 189 88 0.50 190 74 0.42 ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39 Consensus pattern (188 bp): CAAGTAAATCTTTAGTTTCTTCTTTATGTCATTTTTTTATTATTACTAAGTTAACTGTGTTAGGC CAAAAAAATTATCTTTTCTATCTCAGGCAATTTAATGAATTGATAATAAGTTAACAGATATGGCC AAAACAATTAATCTAAACTTTCTCATGCGAAACATTTCAAAATAAAATGTTACAGGTA Found at i:1186598 original size:2 final size:2 Alignment explanation

Indices: 1186591--1186620 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 1186581 CTGTTCTTTA 1186591 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1186621 AAAAATAAGC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1190423 original size:30 final size:29 Alignment explanation

Indices: 1190384--1190445 Score: 106 Period size: 30 Copynumber: 2.1 Consensus size: 29 1190374 AATTAGGAAT * 1190384 CTACAGTACTTATTAGAATTGCATATGCA 1 CTACAGTACTTACTAGAATTGCATATGCA 1190413 CTACATGTACTTACTAGAATTGCATATGCA 1 CTACA-GTACTTACTAGAATTGCATATGCA 1190443 CTA 1 CTA 1190446 TCAAGGAAAG Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 29 5 0.16 30 26 0.84 ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34 Consensus pattern (29 bp): CTACAGTACTTACTAGAATTGCATATGCA Found at i:1191291 original size:14 final size:14 Alignment explanation

Indices: 1191272--1191299 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 1191262 ATCACTCATG 1191272 AAGTGAACAAATAT 1 AAGTGAACAAATAT 1191286 AAGTGAACAAATAT 1 AAGTGAACAAATAT 1191300 CTGGATTCTG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21 Consensus pattern (14 bp): AAGTGAACAAATAT Found at i:1192252 original size:46 final size:46 Alignment explanation

Indices: 1192185--1192415 Score: 453 Period size: 46 Copynumber: 5.0 Consensus size: 46 1192175 TCTTTGCATA 1192185 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1192231 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1192277 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1192323 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG * 1192369 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTACCAG 1 CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG 1192415 C 1 C 1192416 ATGGTCAAAA Statistics Matches: 184, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 46 184 1.00 ACGTcount: A:0.18, C:0.32, G:0.13, T:0.37 Consensus pattern (46 bp): CCCATACTTACTGCAGCTATCTCTTTGTCTCTGATTGCATTCCCAG Found at i:1198477 original size:2 final size:2 Alignment explanation

Indices: 1198470--1198524 Score: 83 Period size: 2 Copynumber: 27.5 Consensus size: 2 1198460 AGACATTCCT * * * 1198470 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TT TC TC TT TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1198512 TC TC TC TC TC TC T 1 TC TC TC TC TC TC T 1198525 GGGAATAGAC Statistics Matches: 47, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 2 47 1.00 ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56 Consensus pattern (2 bp): TC Found at i:1202028 original size:2 final size:2 Alignment explanation

Indices: 1202023--1202059 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 1202013 AAAAAATTAA 1202023 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1202060 AAAACATTAG Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1207922 original size:80 final size:80 Alignment explanation

Indices: 1207833--1208019 Score: 311 Period size: 80 Copynumber: 2.3 Consensus size: 80 1207823 GGGGTAACTA * * 1207833 ATTAAAGGTAAGTCAGTATTACCTACAGTCAAATTTGCAAGTAAGTCAATTGAATTTTACCTGTG 1 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG * 1207898 CTCACTGGGCAAGTT 66 CTCACTAGGCAAGTT * 1207913 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAGGTAAGTCAATTGAATTTTACCTGTG 1 ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG * 1207978 CTCACTAGGTAAGTT 66 CTCACTAGGCAAGTT * 1207993 ATTATAGGTAAGTCAGTTTTGACCTAC 1 ATTATAGGTAAGTCAGTATT-ACCTAC 1208020 TTCAGGTCCA Statistics Matches: 100, Mismatches: 6, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 80 94 0.94 81 6 0.06 ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34 Consensus pattern (80 bp): ATTATAGGTAAGTCAGTATTACCTACAGTCAAATCTGCAAGTAAGTCAATTGAATTTTACCTGTG CTCACTAGGCAAGTT Found at i:1211395 original size:21 final size:21 Alignment explanation

Indices: 1211351--1211396 Score: 58 Period size: 21 Copynumber: 2.2 Consensus size: 21 1211341 AAATCATTTA * 1211351 TATTGTATGATATTTATTAAG 1 TATTGTATGATATTTATGAAG * 1211372 TATTG-ATGAATATTTATGAGG 1 TATTGTATG-ATATTTATGAAG 1211393 TATT 1 TATT 1211397 AATATTTATA Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 20 3 0.14 21 19 0.86 ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50 Consensus pattern (21 bp): TATTGTATGATATTTATGAAG Found at i:1214182 original size:24 final size:24 Alignment explanation

Indices: 1214155--1214271 Score: 135 Period size: 24 Copynumber: 4.9 Consensus size: 24 1214145 CAATTAAACT * 1214155 TAATATTCAAGTCAGCATGTAACC 1 TAATATTCAAGTCAGCATTTAACC * * * 1214179 TAATATCCAAGTCAGTATTTAACT 1 TAATATTCAAGTCAGCATTTAACC * * * 1214203 TGATATTCAAGACAACATTTAACC 1 TAATATTCAAGTCAGCATTTAACC * ** 1214227 TAATATTTAAGTCAGCATTTAATT 1 TAATATTCAAGTCAGCATTTAACC * 1214251 TAATGTTCAAGTCAGCATTTA 1 TAATATTCAAGTCAGCATTTA 1214272 TATACTCTAA Statistics Matches: 75, Mismatches: 18, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 24 75 1.00 ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36 Consensus pattern (24 bp): TAATATTCAAGTCAGCATTTAACC Found at i:1214226 original size:48 final size:48 Alignment explanation

Indices: 1214151--1214271 Score: 161 Period size: 48 Copynumber: 2.5 Consensus size: 48 1214141 ATAGCAATTA * * 1214151 AACTTAATATTCAAGTCAGCATGTAACCTAATATCCAAGTCAGTATTT 1 AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT * * * ** 1214199 AACTTGATATTCAAGACAACATTTAACCTAATATTTAAGTCAGCATTT 1 AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT * * 1214247 AATTTAATGTTCAAGTCAGCATTTA 1 AACTTAATATTCAAGTCAGCATTTA 1214272 TATACTCTAA Statistics Matches: 61, Mismatches: 12, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 48 61 1.00 ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36 Consensus pattern (48 bp): AACTTAATATTCAAGTCAGCATTTAACCTAATATCCAAGTCAGCATTT Found at i:1216238 original size:166 final size:166 Alignment explanation

Indices: 1215917--1216443 Score: 864 Period size: 166 Copynumber: 3.2 Consensus size: 166 1215907 AGAATCATCT * 1215917 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTT 1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC * 1215982 GACCCTCCATTGT-GCCCCACCCTACACCCAGGGGTCATGATTTTCACAACTTTGAATCTACACT 66 GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT * * 1216046 ATCTGAGGATGCTTCCACACAAGTTTCAGCTTCCCA 131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA * 1216082 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAGCTTC 1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC * 1216147 GACCCTCCATTGTGGCCCCACCCTACATCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT 66 GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT * 1216212 ACCTGAGGATCCTTCCACACAAGTTTCAGCTTTCCA 131 ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA * 1216248 GGCTGATTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC 1 GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC * * * * * 1216313 GACCCCCCATTGTGGCCCCA-CCTAACCCCCGGGGGCCATGAATTTCACAACTTTGAATTTACAC 66 GACCCTCCATTGTGGCCCCACCCT-ACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACAC * 1216377 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCT 130 TACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA * 1216414 GGCT--TTATGGTTCTTGAGAAGAAGATTTTT 1 GGCTGATTA-GTTTC-TGAGAAGAAGATTTTT 1216444 GAAAAATTCT Statistics Matches: 339, Mismatches: 19, Indels: 7 0.93 0.05 0.02 Matches are distributed among these distances: 164 3 0.01 165 82 0.24 166 254 0.75 ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33 Consensus pattern (166 bp): GGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTC GACCCTCCATTGTGGCCCCACCCTACACCCAGGGGTCATGAATTTCACAACTTTGAATCTACACT ACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCA Found at i:1218619 original size:18 final size:18 Alignment explanation

Indices: 1218574--1218621 Score: 53 Period size: 19 Copynumber: 2.6 Consensus size: 18 1218564 GTGCATACAT * * 1218574 TTAATTTGAGGTTTATAC 1 TTAACTTGAGGTTGATAC 1218592 TTAGACTTGAGGTTGAGTA- 1 TTA-ACTTGAGGTTGA-TAC 1218611 TTAACTTGAGG 1 TTAACTTGAGG 1218622 AGAGTTGGTG Statistics Matches: 26, Mismatches: 2, Indels: 4 0.81 0.06 0.12 Matches are distributed among these distances: 18 11 0.42 19 13 0.50 20 2 0.08 ACGTcount: A:0.27, C:0.06, G:0.25, T:0.42 Consensus pattern (18 bp): TTAACTTGAGGTTGATAC Found at i:1220715 original size:2 final size:2 Alignment explanation

Indices: 1220708--1220755 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 1220698 AATGATTGTG 1220708 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1220750 CT CT CT 1 CT CT CT 1220756 TACAGTAAAA Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1221317 original size:18 final size:20 Alignment explanation

Indices: 1221278--1221317 Score: 57 Period size: 19 Copynumber: 2.0 Consensus size: 20 1221268 CACAACCAGT 1221278 AAGTAATTCTTTGCAATAAA 1 AAGTAATTCTTTGCAATAAA 1221298 AAGTAA-TC-TTGCAGATAAA 1 AAGTAATTCTTTGCA-ATAAA 1221317 A 1 A 1221318 TTGTAAATAT Statistics Matches: 19, Mismatches: 0, Indels: 3 0.86 0.00 0.14 Matches are distributed among these distances: 18 5 0.26 19 8 0.42 20 6 0.32 ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30 Consensus pattern (20 bp): AAGTAATTCTTTGCAATAAA Found at i:1229226 original size:24 final size:24 Alignment explanation

Indices: 1229199--1229248 Score: 100 Period size: 24 Copynumber: 2.1 Consensus size: 24 1229189 TGGTGTATTT 1229199 ACCTGTATTTAAAAACAGTTTAAC 1 ACCTGTATTTAAAAACAGTTTAAC 1229223 ACCTGTATTTAAAAACAGTTTAAC 1 ACCTGTATTTAAAAACAGTTTAAC 1229247 AC 1 AC 1229249 ATTTGGTATT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 26 1.00 ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32 Consensus pattern (24 bp): ACCTGTATTTAAAAACAGTTTAAC Found at i:1237360 original size:22 final size:20 Alignment explanation

Indices: 1237335--1237393 Score: 77 Period size: 19 Copynumber: 3.0 Consensus size: 20 1237325 AATTTGAGAT * 1237335 AACGAATTCTTAAATTTGTTAA 1 AACGAATT-TTAAA-TCGTTAA 1237357 AACGAA-TTTAAATCGTTAA 1 AACGAATTTTAAATCGTTAA 1237376 AACGAA-TTTAAATCGTTA 1 AACGAATTTTAAATCGTTA 1237394 TAACAAAATT Statistics Matches: 36, Mismatches: 1, Indels: 3 0.90 0.03 0.08 Matches are distributed among these distances: 19 24 0.67 20 5 0.14 21 1 0.03 22 6 0.17 ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36 Consensus pattern (20 bp): AACGAATTTTAAATCGTTAA Found at i:1237376 original size:19 final size:19 Alignment explanation

Indices: 1237352--1237393 Score: 84 Period size: 19 Copynumber: 2.2 Consensus size: 19 1237342 TCTTAAATTT 1237352 GTTAAAACGAATTTAAATC 1 GTTAAAACGAATTTAAATC 1237371 GTTAAAACGAATTTAAATC 1 GTTAAAACGAATTTAAATC 1237390 GTTA 1 GTTA 1237394 TAACAAAATT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 23 1.00 ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33 Consensus pattern (19 bp): GTTAAAACGAATTTAAATC Found at i:1240261 original size:21 final size:21 Alignment explanation

Indices: 1240227--1240306 Score: 117 Period size: 21 Copynumber: 3.8 Consensus size: 21 1240217 AATTTAATGC * * 1240227 TATGCTATGGTATGCGATTT- 1 TATGCTATGCTATGAGATTTG * 1240247 TAATGATATGCTATGAGATTTG 1 T-ATGCTATGCTATGAGATTTG 1240269 TATGCTATGCTATGAGATTTG 1 TATGCTATGCTATGAGATTTG 1240290 TATGCTATGCTATGAGA 1 TATGCTATGCTATGAGA 1240307 AATTGAAATG Statistics Matches: 54, Mismatches: 4, Indels: 3 0.89 0.07 0.05 Matches are distributed among these distances: 20 1 0.02 21 52 0.96 22 1 0.02 ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41 Consensus pattern (21 bp): TATGCTATGCTATGAGATTTG Found at i:1240348 original size:10 final size:10 Alignment explanation

Indices: 1240330--1240362 Score: 57 Period size: 10 Copynumber: 3.3 Consensus size: 10 1240320 GGCTTAATGA 1240330 TATGGTATGC 1 TATGGTATGC * 1240340 TATGCTATGC 1 TATGGTATGC 1240350 TATGGTATGC 1 TATGGTATGC 1240360 TAT 1 TAT 1240363 AAGATTTGAA Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 10 21 1.00 ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42 Consensus pattern (10 bp): TATGGTATGC Found at i:1240529 original size:10 final size:10 Alignment explanation

Indices: 1240511--1240544 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 1240501 AATAATGTTG * 1240511 TATGCTATGC 1 TATGGTATGC 1240521 TATGGTATGC 1 TATGGTATGC * 1240531 TATGGTATGA 1 TATGGTATGC 1240541 TATG 1 TATG 1240545 ACGAATGCGA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41 Consensus pattern (10 bp): TATGGTATGC Found at i:1240530 original size:15 final size:15 Alignment explanation

Indices: 1240510--1240544 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 1240500 AAATAATGTT 1240510 GTATGCTATGCTATG 1 GTATGCTATGCTATG * 1240525 GTATGCTATGGTATG 1 GTATGCTATGCTATG * 1240540 ATATG 1 GTATG 1240545 ACGAATGCGA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40 Consensus pattern (15 bp): GTATGCTATGCTATG Found at i:1240594 original size:21 final size:21 Alignment explanation

Indices: 1240569--1240643 Score: 114 Period size: 21 Copynumber: 3.6 Consensus size: 21 1240559 ATGAGATTGT * * 1240569 ATGCTATGGTATGAAATTCCA 1 ATGCTATGCTATGAGATTCCA * 1240590 ATGCTATGCTATGAGATCCCA 1 ATGCTATGCTATGAGATTCCA * 1240611 ATGCTATGCTATGAGATTTCA 1 ATGCTATGCTATGAGATTCCA 1240632 ATGCTATGCTAT 1 ATGCTATGCTAT 1240644 CCTATGGTGT Statistics Matches: 49, Mismatches: 5, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 49 1.00 ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35 Consensus pattern (21 bp): ATGCTATGCTATGAGATTCCA Found at i:1240921 original size:49 final size:49 Alignment explanation

Indices: 1240835--1240941 Score: 160 Period size: 49 Copynumber: 2.2 Consensus size: 49 1240825 GCAAACATAA * * * 1240835 GGCTTAACATTTACTTCCCGAAGAATGACAAAATTGTATAACTTCCTTT 1 GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT * * * 1240884 GGCTAAACATATACTTCCCGAAAAAGGACATATTTGTATAACTTCCTTT 1 GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT 1240933 GGCTTAACA 1 GGCTTAACA 1240942 AGCTCTTCCC Statistics Matches: 51, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 49 51 1.00 ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33 Consensus pattern (49 bp): GGCTTAACATATACTTCCCGAAAAAGGACAAAATTGTATAACTTCCTTT Found at i:1243678 original size:22 final size:21 Alignment explanation

Indices: 1243653--1243726 Score: 64 Period size: 23 Copynumber: 3.5 Consensus size: 21 1243643 AAACTTTGAA 1243653 ATAACGAATTCAAGAATTTGTT 1 ATAACGAATTCAA-AATTTGTT * 1243675 ATAAC-AGATT--AAATTCGTT 1 ATAACGA-ATTCAAAATTTGTT * 1243694 AAAACGAATTCCTAAAATTTGTT 1 ATAACGAATT-C-AAAATTTGTT * 1243717 ATAACAAATT 1 ATAACGAATT 1243727 TAATTCAATA Statistics Matches: 41, Mismatches: 5, Indels: 11 0.72 0.09 0.19 Matches are distributed among these distances: 19 14 0.34 20 2 0.05 21 1 0.02 22 8 0.20 23 16 0.39 ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35 Consensus pattern (21 bp): ATAACGAATTCAAAATTTGTT Found at i:1243701 original size:41 final size:41 Alignment explanation

Indices: 1243655--1243801 Score: 127 Period size: 41 Copynumber: 3.6 Consensus size: 41 1243645 ACTTTGAAAT * 1243655 AACGAATTCAAGAATTTGTTATAACAGATTAAATTCGTTAA 1 AACGAATTCAAGAATTCGTTATAACAGATTAAATTCGTTAA * * * ** * 1243696 AACGAATTCCTAA-AATTTGTTATAACAAATTTAATTCAATAT 1 AACGAATT-C-AAGAATTCGTTATAACAGATTAAATTCGTTAA * * * * * * 1243738 AACGGATTAAAAAATTCATTATAAC-GATTTAGATTCGTTTA 1 AACGAATTCAAGAATTCGTTATAACAGA-TTAAATTCGTTAA * 1243779 AACAAATTCAAGAATTCGTTATA 1 AACGAATTCAAGAATTCGTTATA 1243802 TCAAATTCAA Statistics Matches: 81, Mismatches: 21, Indels: 8 0.74 0.19 0.07 Matches are distributed among these distances: 40 3 0.04 41 44 0.54 42 32 0.40 43 2 0.02 ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35 Consensus pattern (41 bp): AACGAATTCAAGAATTCGTTATAACAGATTAAATTCGTTAA Found at i:1243798 original size:22 final size:22 Alignment explanation

Indices: 1243770--1243811 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 1243760 AACGATTTAG 1243770 ATTCGTT-TAAACAAATTCAAGA 1 ATTCGTTAT-AACAAATTCAAGA * 1243792 ATTCGTTATATCAAATTCAA 1 ATTCGTTATAACAAATTCAA 1243812 ATATATTTTT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 17 0.94 23 1 0.06 ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36 Consensus pattern (22 bp): ATTCGTTATAACAAATTCAAGA Found at i:1257955 original size:30 final size:30 Alignment explanation

Indices: 1257915--1258013 Score: 153 Period size: 30 Copynumber: 3.3 Consensus size: 30 1257905 AAAAAGAGGA * * * 1257915 CATAGAATTCTTATATCTGTCTTAGGGCGG 1 CATAGGATTCTTATATCTGACTTAGGACGG * 1257945 CATAGGATTCTAATATCTGACTTAGGACGG 1 CATAGGATTCTTATATCTGACTTAGGACGG * 1257975 CATAGGATTCTTATATCTGACTCAGGACGG 1 CATAGGATTCTTATATCTGACTTAGGACGG 1258005 CATAGGATT 1 CATAGGATT 1258014 ATTCTTTCTG Statistics Matches: 63, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 30 63 1.00 ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32 Consensus pattern (30 bp): CATAGGATTCTTATATCTGACTTAGGACGG Found at i:1258024 original size:30 final size:30 Alignment explanation

Indices: 1257915--1258026 Score: 125 Period size: 30 Copynumber: 3.7 Consensus size: 30 1257905 AAAAAGAGGA * * * * * 1257915 CATAGAATTCTTATATCTGTCTTAGGGCGG 1 CATAGGATTATTATATCTGACTCAGGACGG * * * 1257945 CATAGGATTCTAATATCTGACTTAGGACGG 1 CATAGGATTATTATATCTGACTCAGGACGG * 1257975 CATAGGATTCTTATATCTGACTCAGGACGG 1 CATAGGATTATTATATCTGACTCAGGACGG * * 1258005 CATAGGATTATTCTTTCTGACT 1 CATAGGATTATTATATCTGACT 1258027 AAGGGCGATA Statistics Matches: 73, Mismatches: 9, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 30 73 1.00 ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35 Consensus pattern (30 bp): CATAGGATTATTATATCTGACTCAGGACGG Found at i:1258170 original size:19 final size:20 Alignment explanation

Indices: 1258146--1258187 Score: 77 Period size: 20 Copynumber: 2.1 Consensus size: 20 1258136 GACTTGGAAC 1258146 GACATA-AATTCTTTTATCT 1 GACATATAATTCTTTTATCT 1258165 GACATATAATTCTTTTATCT 1 GACATATAATTCTTTTATCT 1258185 GAC 1 GAC 1258188 TTAGGACGGC Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 19 6 0.27 20 16 0.73 ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45 Consensus pattern (20 bp): GACATATAATTCTTTTATCT Found at i:1258216 original size:25 final size:25 Alignment explanation

Indices: 1258182--1258246 Score: 94 Period size: 25 Copynumber: 2.6 Consensus size: 25 1258172 AATTCTTTTA * 1258182 TCTGACTTAGGACGGCTTAGAGAAT 1 TCTGACTTAGGACGACTTAGAGAAT * * * 1258207 TCTGACTTAGGTCGACTTAGATAGT 1 TCTGACTTAGGACGACTTAGAGAAT 1258232 TCTGACTTAGGACGA 1 TCTGACTTAGGACGA 1258247 GATAAAGTTC Statistics Matches: 35, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 25 35 1.00 ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31 Consensus pattern (25 bp): TCTGACTTAGGACGACTTAGAGAAT Found at i:1262217 original size:7 final size:7 Alignment explanation

Indices: 1262202--1262268 Score: 71 Period size: 7 Copynumber: 9.6 Consensus size: 7 1262192 TTTAGATATT 1262202 GAATCTC 1 GAATCTC * 1262209 GAATTTC 1 GAATCTC * 1262216 GAATCTT 1 GAATCTC 1262223 GAATCTC 1 GAATCTC * * 1262230 GTATTTC 1 GAATCTC 1262237 GAATCTC 1 GAATCTC * * * 1262244 GTATTTT 1 GAATCTC 1262251 GAATCTC 1 GAATCTC 1262258 GAATCTC 1 GAATCTC 1262265 GAAT 1 GAAT 1262269 GATCCTTCTC Statistics Matches: 46, Mismatches: 14, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 7 46 1.00 ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39 Consensus pattern (7 bp): GAATCTC Found at i:1263007 original size:22 final size:22 Alignment explanation

Indices: 1262982--1263044 Score: 81 Period size: 25 Copynumber: 2.7 Consensus size: 22 1262972 ATCAAATAAA 1262982 TTTAAAAGAACATAATAAAGGT 1 TTTAAAAGAACATAATAAAGGT 1263004 TTTAAAAGAAGTCCATAATAAAGGT 1 TTTAAAAGAA---CATAATAAAGGT * * 1263029 TATAAAAGAAAATAAT 1 TTTAAAAGAACATAAT 1263045 GGAGATAAGG Statistics Matches: 36, Mismatches: 2, Indels: 6 0.82 0.05 0.14 Matches are distributed among these distances: 22 15 0.42 25 21 0.58 ACGTcount: A:0.56, C:0.05, G:0.13, T:0.27 Consensus pattern (22 bp): TTTAAAAGAACATAATAAAGGT Found at i:1267014 original size:2 final size:2 Alignment explanation

Indices: 1267007--1267060 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1266997 TATTTTAGAG 1267007 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1267049 CT CT CT CT CT CT 1 CT CT CT CT CT CT 1267061 TTATAATTAT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1271282 original size:4 final size:4 Alignment explanation

Indices: 1271273--1271303 Score: 62 Period size: 4 Copynumber: 7.8 Consensus size: 4 1271263 GAGACATTTC 1271273 TATT TATT TATT TATT TATT TATT TATT TAT 1 TATT TATT TATT TATT TATT TATT TATT TAT 1271304 ACATTCATAC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 27 1.00 ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74 Consensus pattern (4 bp): TATT Found at i:1273346 original size:12 final size:12 Alignment explanation

Indices: 1273329--1273358 Score: 51 Period size: 12 Copynumber: 2.5 Consensus size: 12 1273319 NNNNNNNCCC 1273329 CCCCCCCCCCCG 1 CCCCCCCCCCCG * 1273341 CCCCCCCCCCCT 1 CCCCCCCCCCCG 1273353 CCCCCC 1 CCCCCC 1273359 GATGCTACAT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 17 1.00 ACGTcount: A:0.00, C:0.93, G:0.03, T:0.03 Consensus pattern (12 bp): CCCCCCCCCCCG Found at i:1273801 original size:21 final size:21 Alignment explanation

Indices: 1273744--1273797 Score: 58 Period size: 21 Copynumber: 2.6 Consensus size: 21 1273734 TTTTCTCGCT 1273744 TGTCAACATACTTAT-GTTGCA 1 TGTCAACATA-TTATCGTTGCA ** 1273765 TGTTGACATGATTATCG-TGCA 1 TGTCAACAT-ATTATCGTTGCA 1273786 TGTCAACATATT 1 TGTCAACATATT 1273798 TATCTCGCAT Statistics Matches: 27, Mismatches: 4, Indels: 5 0.75 0.11 0.14 Matches are distributed among these distances: 20 3 0.11 21 22 0.81 22 2 0.07 ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39 Consensus pattern (21 bp): TGTCAACATATTATCGTTGCA Found at i:1273807 original size:21 final size:21 Alignment explanation

Indices: 1273733--1273807 Score: 57 Period size: 21 Copynumber: 3.6 Consensus size: 21 1273723 TTTGGTGCCG * 1273733 ATTT-TCTCGCTTGTCAACAT 1 ATTTATCTCGCATGTCAACAT * * * ** 1273753 ACTTATGTTGCATGTTGACAT 1 ATTTATCTCGCATGTCAACAT 1273774 GA-TTATCGT-GCATGTCAACAT 1 -ATTTATC-TCGCATGTCAACAT 1273795 ATTTATCTCGCAT 1 ATTTATCTCGCAT 1273808 TTCGACATTT Statistics Matches: 41, Mismatches: 9, Indels: 9 0.69 0.15 0.15 Matches are distributed among these distances: 20 5 0.12 21 34 0.83 22 2 0.05 ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41 Consensus pattern (21 bp): ATTTATCTCGCATGTCAACAT Found at i:1282000 original size:13 final size:13 Alignment explanation

Indices: 1281978--1282054 Score: 57 Period size: 13 Copynumber: 5.7 Consensus size: 13 1281968 TACACCAATT * 1281978 CATCATTACATTA 1 CATCAATACATTA 1281991 CATCAATACATTA 1 CATCAATACATTA * * 1282004 TATTAATACGTTATTA 1 CATCAATAC---ATTA * * 1282020 TATCATTACATTA 1 CATCAATACATTA * 1282033 TCA-CATTACATTA 1 -CATCAATACATTA 1282046 CATCAATAC 1 CATCAATAC 1282055 CAACTATCAA Statistics Matches: 52, Mismatches: 7, Indels: 10 0.75 0.10 0.14 Matches are distributed among these distances: 12 2 0.04 13 38 0.73 14 1 0.02 16 11 0.21 ACGTcount: A:0.40, C:0.19, G:0.01, T:0.39 Consensus pattern (13 bp): CATCAATACATTA Found at i:1297639 original size:12 final size:12 Alignment explanation

Indices: 1297622--1297664 Score: 52 Period size: 11 Copynumber: 3.6 Consensus size: 12 1297612 ATGAAGTGTT * 1297622 GTTTTTCGAAAA 1 GTTTTTCAAAAA 1297634 GTTTTTCCAAAAA 1 GTTTTT-CAAAAA * 1297647 ATTTTT-AAAAA 1 GTTTTTCAAAAA 1297658 GTTTTTC 1 GTTTTTC 1297665 GTCAATTCAT Statistics Matches: 26, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 11 10 0.38 12 6 0.23 13 10 0.38 ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47 Consensus pattern (12 bp): GTTTTTCAAAAA Found at i:1300039 original size:38 final size:38 Alignment explanation

Indices: 1299988--1300060 Score: 128 Period size: 38 Copynumber: 1.9 Consensus size: 38 1299978 GAATTAACTT * * 1299988 TGTTGTGAAAGTATTTATTAAAACAAAAGTTGCCTGTA 1 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCTGTA 1300026 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCT 1 TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCT 1300061 CTCTTGGAAC Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 38 33 1.00 ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36 Consensus pattern (38 bp): TGTTGTGAAAGTATTTAATAAAACAAAAATTGCCTGTA Found at i:1307151 original size:16 final size:16 Alignment explanation

Indices: 1307132--1307168 Score: 74 Period size: 16 Copynumber: 2.3 Consensus size: 16 1307122 AGTTCGGTTA 1307132 AAAATTTTCCAGAAAC 1 AAAATTTTCCAGAAAC 1307148 AAAATTTTCCAGAAAC 1 AAAATTTTCCAGAAAC 1307164 AAAAT 1 AAAAT 1307169 AACTTACCTG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 21 1.00 ACGTcount: A:0.54, C:0.16, G:0.05, T:0.24 Consensus pattern (16 bp): AAAATTTTCCAGAAAC Found at i:1312857 original size:42 final size:42 Alignment explanation

Indices: 1312793--1313259 Score: 580 Period size: 42 Copynumber: 11.1 Consensus size: 42 1312783 ACTATATGAA * * * * 1312793 CATGTATATAGAGGTGATTTCACGCCATTGTGGTTTTATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG * 1312835 CATGTAGATAGAGGTGACTTCACGCCATTGTCG-TTATATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTA-ATAAG * * ** * * * * 1312877 CATGTAGACAGAGGCAACCTCAGGCCATTGTGGTTTTATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG * * * * * * 1312919 CATGTAGATAGAGATGGCTTCACCCCATTGTCGTTTTATATG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG ** * * 1312961 TTTGT-AGTCAGAGGTGACTTCACGCCATTGCCGTTTAATAAG 1 CATGTAAAT-AGAGGTGACTTCACGCCATTGTCGTTTAATAAG 1313003 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG ** * 1313045 CATGTAAATAGAGGTGACTTCACGCCATTG-CAGTTTTTTCAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTC-GTTTAATAAG * * * 1313087 CATGTGAATAGAGGTGACTTCACGCCATTGCCGTGTAATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG * 1313129 CATGTAAATAGAGGTGACTTCACGCCATTGTCATTTAATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG * * * 1313171 CATGTAAATAGAGTTGACTTCACGCCATTGTCATTCAATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG * 1313213 CATGTAAATAGAGGTGACTTCACGCCATTGTCATTTAATAAG 1 CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG 1313255 CATGT 1 CATGT 1313260 TAATTGACTT Statistics Matches: 368, Mismatches: 51, Indels: 12 0.85 0.12 0.03 Matches are distributed among these distances: 41 4 0.01 42 359 0.98 43 5 0.01 ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32 Consensus pattern (42 bp): CATGTAAATAGAGGTGACTTCACGCCATTGTCGTTTAATAAG Found at i:1313735 original size:42 final size:42 Alignment explanation

Indices: 1313666--1313891 Score: 283 Period size: 42 Copynumber: 5.4 Consensus size: 42 1313656 AATCAGTGCC * ** * 1313666 GGTGACTCCACGCCATTATCGTTATATAAGCATGTAGATAGA 1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA * ** 1313708 AGTGACTTCACGCCATTGCCGTGATATAAGCATGTAGATAGA 1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA * * * * 1313750 GTTGACTTCACGCCATTGTCGTTTAATAAGCATGTAAATAGA 1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA * * * 1313792 GGTGACTTCACGCCATTGCAC-TTTTTTAAGCATTTTAGATATA 1 GGTGACTTCACGCCATTGC-CGTTTTATAAGCA-TGTAGATAGA * * 1313835 GGTGACTTCGCGCCATTGCCGTTTTATAAGCATGTAAATAGA 1 GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA 1313877 GGTGACTTCACGCCA 1 GGTGACTTCACGCCA 1313892 GGTGACTTCA Statistics Matches: 156, Mismatches: 25, Indels: 6 0.83 0.13 0.03 Matches are distributed among these distances: 42 120 0.77 43 36 0.23 ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31 Consensus pattern (42 bp): GGTGACTTCACGCCATTGCCGTTTTATAAGCATGTAGATAGA Found at i:1313896 original size:15 final size:15 Alignment explanation

Indices: 1313876--1313906 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 1313866 ATGTAAATAG 1313876 AGGTGACTTCACGCC 1 AGGTGACTTCACGCC * 1313891 AGGTGACTTCATGCC 1 AGGTGACTTCACGCC 1313906 A 1 A 1313907 TTGTCGTTTA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.23, C:0.29, G:0.26, T:0.23 Consensus pattern (15 bp): AGGTGACTTCACGCC Found at i:1313933 original size:57 final size:57 Alignment explanation

Indices: 1313834--1313948 Score: 167 Period size: 57 Copynumber: 2.0 Consensus size: 57 1313824 TTTTAGATAT * * 1313834 AGGTGACTTCGCGCCATTGCCGTTTTATAAGCATGTAAATAGAGGTGACTTCACGCC 1 AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC * * * * * 1313891 AGGTGACTTCATGCCATTGTCGTTTAATACGCATTTAGATAGAGGTGACTTCACGCC 1 AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC 1313948 A 1 A 1313949 TTGCCGTTTC Statistics Matches: 51, Mismatches: 7, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 57 51 1.00 ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30 Consensus pattern (57 bp): AGGTGACTTCACGCCATTGCCGTTTAATAAGCATGTAAATAGAGGTGACTTCACGCC Found at i:1313950 original size:42 final size:42 Alignment explanation

Indices: 1313891--1314454 Score: 620 Period size: 42 Copynumber: 13.4 Consensus size: 42 1313881 ACTTCACGCC * * * 1313891 AGGTGACTTCATGCCATTGTCGTTTAATACGCATTTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * ** * 1313933 AGGTGACTTCACGCCATTGCCGTTTCTTAAGGATGTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * ** 1313975 AGGTGACTTCACGCCATTGCCGTTTTTTAAGCATG-AGAATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAG-ATAG * * * 1314017 AGGTGACTTCACGTCATTGTGGATTT-ATAAGCATGTAGAAAG 1 AGGTGACTTCACGCCATTGTCG-TTTAATAAGCATGTAGATAG * ** * * * * 1314059 AGTTGACTTCACGTTATTGTCGTTTTATTAGCACGAAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * * 1314101 AGGTGACTTCACGCCATTGTCATTTAATAAGCATGTAAATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * * * ** 1314143 AGTTGACTTCCCGCCATTGCCGTTTTTTAAGCATGTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * 1314185 AGGTGACTTCACGCCATTGCCG-TTATATAAGCATGTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG * * 1314227 AGGTGACTTCACGCCATTGTCG-TTATATAAGCATGAAGATAT 1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG * * * * 1314269 AGGTGACCTCACGCTATTGTC-ATTATATAAGCATGTAGAAAG 1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG * * * 1314311 AGGTGACTTCACGCCATTTTCGTTTTATAAGCATGTAGATAT 1 AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG * * 1314353 AGGTGATTTCACGCCATTGTCG-TTATATAAGTATGTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG * * * * * 1314395 AGGTGGCTTCATGCTATTGCCG-TAATATAAGCATGTAGATAG 1 AGGTGACTTCACGCCATTGTCGTTTA-ATAAGCATGTAGATAG 1314437 AGGTGACTTCACGCCATT 1 AGGTGACTTCACGCCATT 1314455 TTGGTGTACT Statistics Matches: 443, Mismatches: 71, Indels: 16 0.84 0.13 0.03 Matches are distributed among these distances: 41 9 0.02 42 427 0.96 43 7 0.02 ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33 Consensus pattern (42 bp): AGGTGACTTCACGCCATTGTCGTTTAATAAGCATGTAGATAG Found at i:1315608 original size:22 final size:22 Alignment explanation

Indices: 1315583--1315626 Score: 79 Period size: 22 Copynumber: 2.0 Consensus size: 22 1315573 GAAAAAACCC * 1315583 CGGTTTAACAAAGACGGAAAAT 1 CGGTTTAACAAAGACAGAAAAT 1315605 CGGTTTAACAAAGACAGAAAAT 1 CGGTTTAACAAAGACAGAAAAT 1315627 AGCATTTACC Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 21 1.00 ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18 Consensus pattern (22 bp): CGGTTTAACAAAGACAGAAAAT Found at i:1318146 original size:2 final size:2 Alignment explanation

Indices: 1318139--1318178 Score: 80 Period size: 2 Copynumber: 20.0 Consensus size: 2 1318129 AGTATTTACA 1318139 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1318179 GTGCGTGCGC Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 38 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:1320844 original size:2 final size:2 Alignment explanation

Indices: 1320837--1320863 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 1320827 ATGCAAAATA 1320837 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC T 1320864 GAATTACTGA Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 25 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): TC Found at i:1321349 original size:2 final size:2 Alignment explanation

Indices: 1321342--1321419 Score: 133 Period size: 2 Copynumber: 40.0 Consensus size: 2 1321332 AGAGGTATGT * 1321342 TC TC TC TC TC TC -C TC TC TC TC TC TC TC AC TC -C TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1321382 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1321420 GTTATTTAAT Statistics Matches: 72, Mismatches: 2, Indels: 4 0.92 0.03 0.05 Matches are distributed among these distances: 1 2 0.03 2 70 0.97 ACGTcount: A:0.01, C:0.51, G:0.00, T:0.47 Consensus pattern (2 bp): TC Found at i:1325728 original size:42 final size:42 Alignment explanation

Indices: 1325638--1326807 Score: 1486 Period size: 42 Copynumber: 27.8 Consensus size: 42 1325628 TCCACATGCT * * * * * 1325638 TGAAGTCACCTCTATGTACA-GGTTGATAAAA-GACAATGACG 1 TGAAGTCACCTCTATTTACATGCTT-AAAAAACGTCAATGGCG * * ** 1325679 TGAAGTCACCTCTATCTACATGATTATTAAACGTCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG 1325721 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG * * * 1325763 TGAAGTCACCTCTATTTACATGCTTCAAAAACGGCGATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG * 1325805 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCA 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG 1325847 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG 1325889 TGAAGTCACCTCTATTTACATGCTTAAAAAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * * ** 1325931 TGAAGTCACCTCTATCTACATGCTTTAGGAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * ** * 1325973 TGAAGTCACCTCTATCTACATGCTTATTAAACGACAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG * * * * 1326015 TGAAGTCACCTCTATCTACATGATTATAAAACGGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG * 1326057 TGAAGTCACCTCTATTTACATGCTTTAAAAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * * 1326099 TGAAGTCACCTCTATCTACATGCTTATAAAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG ** * * 1326141 TGAAGTCACCTCTATTTACATGCTTATTAAACGGCAATGGCA 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG 1326183 TGAAGTCACCTCTATTTACATGCCTTAAAAAAC-TGCAATGGCG 1 TGAAGTCACCTCTATTTACATG-CTTAAAAAACGT-CAATGGCG 1326226 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-TGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * * * ** 1326268 TGAAGTCACCTCTCTCTACATGATTATTAAACAG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-GTCAATGGCG 1326310 TGAAGTCACCTCTATTTACATGCTTAAAAAAC-TGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * * * 1326352 TGAAGTCACCTCTATTTACATGCTTTAGAAACCG-CAATGGCA 1 TGAAGTCACCTCTATTTACATGC-TTAAAAAACGTCAATGGCG * 1326394 TGAAGTCACCTCTATCTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG 1326436 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG * 1326478 TGAAGTCACCTCTATCTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG 1326520 TGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG * * * 1326562 TGAAGTCACTTCTATCTACATGCTT-AAAAACGACAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG * * 1326603 TGAAGTCACCTCTATCTACATGCTTATAAAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * 1326645 TGAAGTCACCTCTATTTACATGCTTATAAAA-GTGCAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAACGT-CAATGGCG * 1326687 TAAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG 1 TGAAGTCACCTCTATTTACATGCTTAAAAAA-CGTCAATGGCG * 1326729 TGCAGTCACCTCTATTTACATGCCTTAAAAAAC-TGCAATGGCG 1 TGAAGTCACCTCTATTTACATG-CTTAAAAAACGT-CAATGGCG 1326772 TGAAGTCACCTCTATTAATTTACATGCTTAAAAAAC 1 TGAAGTCACCTC---T-ATTTACATGCTTAAAAAAC 1326808 TTCACGACAA Statistics Matches: 1024, Mismatches: 74, Indels: 57 0.89 0.06 0.05 Matches are distributed among these distances: 40 3 0.00 41 71 0.07 42 851 0.83 43 78 0.08 44 1 0.00 46 11 0.01 47 9 0.01 ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28 Consensus pattern (42 bp): TGAAGTCACCTCTATTTACATGCTTAAAAAACGTCAATGGCG Found at i:1325876 original size:126 final size:126 Alignment explanation

Indices: 1325638--1326787 Score: 1643 Period size: 126 Copynumber: 9.1 Consensus size: 126 1325628 TCCACATGCT * * * * * 1325638 TGAAGTCACCTCTATGTACA-GGTTGATAAAA-GACAATGACGTGAAGTCACCTCTATCTACATG 1 TGAAGTCACCTCTATTTACATGCTT-ATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG * ** 1325701 ATTATTAAA-CGTCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG 65 CTTAAAAAACCG-CAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * 1325763 TGAAGTCACCTCTATTTACATGCTTCA-AAAACGGCGATGGCGTGAAGTCACCTCTATTTACATG 1 TGAAGTCACCTCTATTTACATGCTT-ATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG * 1325827 CTTAAAAAACCGCAATGGCATGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG 65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * * 1325889 TGAAGTCACCTCTATTTACATGCTTA-AAAAAGTGCAATGGCGTGAAGTCACCTCTATCTACATG 1 TGAAGTCACCTCTATTTACATGCTTATAAAACG-GCAATGGCGTGAAGTCACCTCTATTTACATG * ** ** * ** 1325953 CTTTAGGAAGTGCAATGGCGTGAAGTCACCTCTATCTACATGCTTATTAAA-CGACAATGGCG 65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCG-CAATGGCG * * 1326015 TGAAGTCACCTCTATCTACATGATTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC 1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC * ** * * ** 1326080 TTTAAAAAGTGCAATGGCGTGAAGTCACCTCTATCTACATGCTTATAAAAGTGCAATGGCG 66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * * 1326141 TGAAGTCACCTCTATTTACATGCTTATTAAACGGCAATGGCATGAAGTCACCTCTATTTACATGC 1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATG- * * 1326206 CTTAAAAAACTGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACTGCAATGGCG 65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * * * * * 1326268 TGAAGTCACCTCTCTCTACATGATTATTAAACAGCAATGGCGTGAAGTCACCTCTATTTACATGC 1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC * * * * 1326333 TTAAAAAACTGCAATGGCGTGAAGTCACCTCTATTTACATGCTTTAGAAACCGCAATGGCA 66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * * * 1326394 TGAAGTCACCTCTATCTACATGCTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGC 1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC * 1326459 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATCTACATGCTTAAAAAACCGCAATGGCG 66 TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * * * * 1326520 TGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCGTGAAGTCACTTCTATCTACATGC 1 TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC * * ** 1326585 TT-AAAAA-CGACAATGGCGTGAAGTCACCTCTATCTACATGCTTATAAAAGTGCAATGGCG 66 TTAAAAAACCG-CAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG * 1326645 TGAAGTCACCTCTATTTACATGCTTATAAAA-GTGCAATGGCGTAAAGTCACCTCTATTTACATG 1 TGAAGTCACCTCTATTTACATGCTTATAAAACG-GCAATGGCGTGAAGTCACCTCTATTTACATG * * 1326709 CTTAAAAAACCGCAATGGCGTGCAGTCACCTCTATTTACATGCCTTAAAAAACTGCAATGGCG 65 CTTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATG-CTTAAAAAACCGCAATGGCG 1326772 TGAAGTCACCTCTATT 1 TGAAGTCACCTCTATT 1326788 AATTTACATG Statistics Matches: 938, Mismatches: 74, Indels: 24 0.91 0.07 0.02 Matches are distributed among these distances: 124 2 0.00 125 144 0.15 126 632 0.67 127 160 0.17 ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28 Consensus pattern (126 bp): TGAAGTCACCTCTATTTACATGCTTATAAAACGGCAATGGCGTGAAGTCACCTCTATTTACATGC TTAAAAAACCGCAATGGCGTGAAGTCACCTCTATTTACATGCTTAAAAAACCGCAATGGCG Found at i:1328350 original size:43 final size:43 Alignment explanation

Indices: 1328289--1328583 Score: 222 Period size: 43 Copynumber: 6.9 Consensus size: 43 1328279 AAATCTTTTT * 1328289 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAAC 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC * 1328332 TCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAATTAAC 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC * * * ** 1328375 TCGTAATAACGAGATCTTTTCTTGTAATTAGGAGAT-CTTTTC 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC * * ** * * *** 1328417 TCGTAATGACGAGATAATTAACTCGTAATAACGAGAT-CTTTTT 1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAAC * * * ** * * ** 1328460 TCGTAATTAGGAGATAATTAACTCGTAATAACGAGAT-CTTTTC 1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAAC * * * ** * ** 1328503 TCGTTATTACGAGATAATTAACTCATAATTACGAG-TTCTCT-AC 1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAAT-TAAC 1328546 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA 1328584 AAATATTTTC Statistics Matches: 216, Mismatches: 32, Indels: 8 0.84 0.12 0.03 Matches are distributed among these distances: 42 33 0.15 43 182 0.84 44 1 0.00 ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36 Consensus pattern (43 bp): TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAAC Found at i:1328474 original size:107 final size:107 Alignment explanation

Indices: 1328281--1328583 Score: 423 Period size: 107 Copynumber: 2.8 Consensus size: 107 1328271 TTTTATATAA * * 1328281 ATCTTTT-TTCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCGTAATAACGAG 1 ATCTTTTCTT-GTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG * 1328345 ATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAG 65 ATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG * * 1328388 ATCTTTTCTTGTAATTAGGAGATCTTTTCTCGTAATGACGAGATAATTAACTCGTAATAACGAGA 1 ATCTTTTCTTGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGA * * 1328453 TCTTTTTTCGTAATTAGGAGATAATTAACTCGTAATAACGAG 66 TCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG * * * ** * ** 1328495 ATCTTTTCTCGTTATTACGAGATAATTAACTCATAATTACGAG-TTCTCT-ACTCGTAATAACGA 1 ATCTTTTCTTGTAATTACGAGAT-CTTTTCTCGTAATTACGAGATAAT-TAACTCGTAATAACGA 1328558 GATCTTTTCTCGTAATTACGAGATAA 64 GATCTTTTCTCGTAATTACGAGATAA 1328584 AAATATTTTC Statistics Matches: 174, Mismatches: 19, Indels: 6 0.87 0.10 0.03 Matches are distributed among these distances: 107 157 0.90 108 17 0.10 ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37 Consensus pattern (107 bp): ATCTTTTCTTGTAATTACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAGA TCTTTTCTCGTAATTACGAGATAATTAACTCGTAATAACGAG Found at i:1328506 original size:64 final size:64 Alignment explanation

Indices: 1328289--1328583 Score: 288 Period size: 64 Copynumber: 4.6 Consensus size: 64 1328279 AAATCTTTTT * * * 1328289 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCGTAATAACGAGATCTTTTC 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC * ** * * ** * * * 1328353 TCGTAATAACGAGATAATTAACTCGTAATAACGAGAT-CTTTTCTTGTAATTAGGAGATCTTTTC 1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC * * ** * * *** * * * 1328417 TCGTAATGACGAGATAATTAACTCGTAATAACGAGAT-CTTTTTTCGTAATTAGGAGATAATTAA 1 TCGTAATAACGAGAT-CTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGAT-CTTTA 1328481 C 64 C * * * * 1328482 TCGTAATAACGAGATCTTTTCTCGTTATTACGAGATAATTAACTCATAATTACGAGTTCTCTAC 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC 1328546 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA 1 TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA 1328584 AAATATTTTC Statistics Matches: 194, Mismatches: 34, Indels: 6 0.83 0.15 0.03 Matches are distributed among these distances: 64 147 0.76 65 47 0.24 ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36 Consensus pattern (64 bp): TCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAATTAACTCGTAATTACGAGATCTTTAC Found at i:1342235 original size:438 final size:437 Alignment explanation

Indices: 1341291--1343153 Score: 2494 Period size: 437 Copynumber: 4.3 Consensus size: 437 1341281 ATAAACGTAT * ** * *** 1341291 TATTATGCTT-TTGTAACATTTCACAAAATATATCTCAGTAAATCGCTACA-AATACAATTTTTT 1 TATT-TGCTTCTT-TAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTA-AAGACTTT * * * 1341354 AGAGCCTTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAAGCCAT 63 AGAGCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCAT * * * ** * * 1341419 TTAATTCTA-ATCACATTTTTTTGAATC-AGTGTTT-GGGATTTGTTACCGTTTTTGAGATATTT 128 TTAATTCTACA-CAAATTTTGTTCAA-CAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATAT * * 1341481 GAGAAAGAATGTTTTAGGGGCCGATCCCTAATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAA 191 GAGAAAGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAA * * * * * * ** ** 1341546 GGTTGCATATTACTT-AGGACATCACTTTGAGCATCTTTCCTTCTATACTGCATTTTAAAATCCT 256 GGTTGCAT-TTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATT * * * 1341610 TTTCGTTTCTGAGATATGGGTGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCCTAATTACG 320 TTTCCTTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACG * * * * * * 1341675 TAACATATAATAAAATCATTACATTGTTTGGATACATTAC-TGTTAGAAAAACA 385 TAACACATAATAAAATCATTACATTGCTTGAATACATAACAT-TGAGATAAACA * * * * 1341728 TATTTGCTTCTTTAACATTTCACAAAATATCTCTTAGTAAAGGGCTACAGATGAAAAACTTTCGA 1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA ** * * 1341793 GCCCTTTAATCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATAACAGATAAAAGGTCATTTA 66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA * * * * * * 1341858 ATTCTACACACATTTTGTTCAATAAGTATTTAAAAATGTGTTACCGTTCTTGAGATATTTGAGAA 131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA ** * * * 1341923 AGAATATTTTAGGGGCCGATCCCTTATTTCCTTTTAGGGGCCGTTTAACGATATTTTGAAAGTTG 196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG * * * * * 1341988 CATATTTCTT-AGGACATCATTTTGAGCATCTTTTCTTCTGTGCTGCATTTCAAAATCCTTTTTC 261 CAT-TTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAAT-ATTTTTC * * * ** * 1342052 TTTTCTGAGATATGGGTGATCGAAATTTTGGACTTTTGGCCCCTAAAAACCCTTGGTTAGGTAAC 324 CTTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAAC * * * 1342117 ACATGATTAAATCATTACATTGCTT-AGATACATAAC-TGTAAGATAAACA 389 ACATAATAAAATCATTACATTGCTTGA-ATACATAACAT-TGAGATAAACA 1342166 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA 1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA * * 1342231 GCCCTTTGGTCCCCTAATTTTAGGGGCCAGCTCCTTTTTCTTGATATCAAATAAAAGGTCATTTA 66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA * 1342296 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTAGAGATATATGAGAA 131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA * * * * * 1342361 AGAAGGTTTTAGGGGCTGGTCCCTTATCTCCTTTTAGGGGGCTTTTAACGAAATTTTGACGGTTG 196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG * * * 1342426 CATTTTGTTAAGAACATCATTTTGAACAACTTTTCTTTTGTACTGCATTACAAAATATTTTTCCT 261 CATTTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCCT * * 1342491 TTCTGAAATATGGGAGATCGAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC 326 TTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC * 1342556 ATCATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA 391 ATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA * * * 1342603 CATTTGCTTCTATAACATTTCACAAAATATCTCTCAGTAAAAGGCTACAGATTAAAGACTTTAGA 1 TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA 1342668 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA 66 GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA * * * * 1342733 ATTCTACACAAAATTTGTTAAACAAGTGTTTAGAAATTCGTTACCGTTCTGGAGATATATGAGAA 131 ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA * * * * * 1342798 ATAAGGTTTTAGGGGCCGTTCCCTTATCTCCTTTTAGGGGCCGTTAAACGAAATTTTGACGATTG 196 AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG * * 1342863 CATTTTGTTAAGAACATCATTTTGAACAAT-TTTTCTTCTGTACTGCATTACAAAATATTTGTCC 261 CATTTTCTTAAGAACATCATTTTGAAC-ATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCC * * * 1342927 TTTCTGAGATATGGGAGATCAAAATTTGGGAGTTTTGCCCCCTAAAAACCCTTAATTACGTAACA 325 TTTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACA 1342992 CATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA 390 CATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA * * * * * * * * * 1343040 TATTTGCTTCTATAATC-TATT-ACAAAATATCCCTCGGTAAAGAGTTACGGGTAAAAGATTTTA 1 TATTTGCTTCTTTAA-CAT-TTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTA 1343103 GAGCCCTTTAGGT-CCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCA 64 GAGCCCTTT-GGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCA 1343154 GCTGAAAGAT Statistics Matches: 1281, Mismatches: 131, Indels: 28 0.89 0.09 0.02 Matches are distributed among these distances: 436 127 0.10 437 764 0.60 438 390 0.30 ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36 Consensus pattern (437 bp): TATTTGCTTCTTTAACATTTCACAAAATATCTCTCAGTAAAGGGCTACAGATTAAAGACTTTAGA GCCCTTTGGTCCCCTAATTTGAGGGGCCAGCCCCTTTTTCTTGATATCAAATAAAAGGTCATTTA ATTCTACACAAATTTTGTTCAACAAGTGTTTAGAAATTTGTTACCGTTCTTGAGATATATGAGAA AGAAGGTTTTAGGGGCCGATCCCTTATCTCCTTTTAGGGGCCGTTTAACGAAATTTTGAAGGTTG CATTTTCTTAAGAACATCATTTTGAACATCTTTTCTTCTGTACTGCATTACAAAATATTTTTCCT TTCTGAGATATGGGAGATCAAAATTTTGGACTTTTGGCCCCTAAAAACCCTTAATTACGTAACAC ATAATAAAATCATTACATTGCTTGAATACATAACATTGAGATAAACA Found at i:1343806 original size:115 final size:115 Alignment explanation

Indices: 1343604--1343835 Score: 410 Period size: 115 Copynumber: 2.0 Consensus size: 115 1343594 AATAATAGGG * * * 1343604 AAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAATAAAAAGAAA 1 AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA * * 1343669 CCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT 66 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT * 1343719 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA 1 AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA 1343784 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT 66 CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT 1343834 AA 1 AA 1343836 TAATGAAGAA Statistics Matches: 111, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 115 111 1.00 ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15 Consensus pattern (115 bp): AAAAAGAAACCGAAGAATAACAAGAAGGTCTTCCGTTGAAAACGGAAGACCCTAATAAAAAGAAA CCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAAAAT Found at i:1343826 original size:56 final size:56 Alignment explanation

Indices: 1343604--1343829 Score: 380 Period size: 56 Copynumber: 4.0 Consensus size: 56 1343594 AATAATAGGG * * * * 1343604 AAAAAGAAACCGAAGAATAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT 1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT * 1343660 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGGAAACGGAAGACCCTAATAAT 1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCC---TAAT 1343719 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT 1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT 1343775 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAA 1 AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAA 1343830 AAATAATAAT Statistics Matches: 163, Mismatches: 4, Indels: 6 0.94 0.02 0.03 Matches are distributed among these distances: 56 108 0.66 59 55 0.34 ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15 Consensus pattern (56 bp): AAAAAGAAACCGAAGAATAACAAGAGGGTCTTCCGTTGAAAACGGAAGACCCTAAT Found at i:1347730 original size:129 final size:130 Alignment explanation

Indices: 1347405--1347918 Score: 895 Period size: 130 Copynumber: 4.0 Consensus size: 130 1347395 GTCATTACCC 1347405 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT 1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT 1347470 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA 66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA * * 1347535 TTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT 1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT * * ** * 1347600 ACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATGGAGACTTCTTAAC-CC 66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA * 1347664 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCATTGT 1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT 1347729 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA 66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA * * * 1347794 TTGTTTCACTTTCTTATAGTTTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT 1 TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT * * * 1347859 ACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA 66 ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTA 1347919 CATCTGTTAC Statistics Matches: 361, Mismatches: 22, Indels: 2 0.94 0.06 0.01 Matches are distributed among these distances: 129 121 0.34 130 240 0.66 ACGTcount: A:0.25, C:0.25, G:0.10, T:0.39 Consensus pattern (130 bp): TTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCACTGT ACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAACTCA Found at i:1347860 original size:259 final size:259 Alignment explanation

Indices: 1347401--1347918 Score: 1000 Period size: 259 Copynumber: 2.0 Consensus size: 259 1347391 TGAAGTCATT 1347401 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 1 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 1347466 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA 66 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA 1347531 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 131 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA ** 1347596 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATGGAGACTTCTTA 196 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA 1347660 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 1 ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA * 1347725 TTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA 66 CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA * 1347790 CTCATTGTTTCACTTTCTTATAGTTTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 131 CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA 1347855 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA 196 CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA 1347919 CATCTGTTAC Statistics Matches: 255, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 259 255 1.00 ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39 Consensus pattern (259 bp): ACCCTTGTATCACTTTCTCATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA CTGTACCCTCACAATCAGCTCCTTTATTTGATTTTTTAACTTAGACAAAAATATAGACTTCTTAA CTCATTGTTTCACTTTCTTATAGTGTTGTAACCTACCCTGTATCCAAGTGTACCCTTTGTACCCA CTGTACCCTCACCATCAGCTCCTTTATTTGATTTTTTAACTTTGACAAAAATAAAGACTTCTTA Found at i:1349367 original size:24 final size:25 Alignment explanation

Indices: 1349340--1349391 Score: 97 Period size: 25 Copynumber: 2.1 Consensus size: 25 1349330 TTTATCTCAC 1349340 TTTAA-TTTTTTTTAGATTCTTCTG 1 TTTAAGTTTTTTTTAGATTCTTCTG 1349364 TTTAAGTTTTTTTTAGATTCTTCTG 1 TTTAAGTTTTTTTTAGATTCTTCTG 1349389 TTT 1 TTT 1349392 TGTAGGGTCA Statistics Matches: 27, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 24 5 0.19 25 22 0.81 ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67 Consensus pattern (25 bp): TTTAAGTTTTTTTTAGATTCTTCTG Found at i:1363552 original size:54 final size:55 Alignment explanation

Indices: 1363450--1363565 Score: 173 Period size: 54 Copynumber: 2.1 Consensus size: 55 1363440 AGACGAAGAA * ** 1363450 GTGCTGTAAATCGTTAATTATTATATCCACTACGAGTGATCAACTAGACAAAAAT 1 GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAACTAGACAAAAAT * 1363505 GTGCTGTAAATCGTT-ATCATTATATCCACTATGAGCCATC-ACTTAGACAAAAAT 1 GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAAC-TAGACAAAAAT 1363559 GTGCTGT 1 GTGCTGT 1363566 TATATATAGT Statistics Matches: 56, Mismatches: 4, Indels: 3 0.89 0.06 0.05 Matches are distributed among these distances: 53 2 0.04 54 39 0.70 55 15 0.27 ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32 Consensus pattern (55 bp): GTGCTGTAAATCGTTAATCATTATATCCACTACGAGCCATCAACTAGACAAAAAT Found at i:1364574 original size:215 final size:214 Alignment explanation

Indices: 1364203--1364631 Score: 849 Period size: 215 Copynumber: 2.0 Consensus size: 214 1364193 AACAGCGGTA 1364203 AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT 1 AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT 1364268 TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA 66 TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA 1364333 AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA 131 AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA 1364398 TTCTGGGGGCCATGCAAAT 196 TTCTGGGGGCCATGCAAAT 1364417 NAATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCA 1 -AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCA 1364482 TTTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAAT 65 TTTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAAT 1364547 AAAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAA 130 AAAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAA 1364612 ATTCTGGGGGCCATGCAAAT 195 ATTCTGGGGGCCATGCAAAT 1364632 TATTTCAATA Statistics Matches: 214, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 215 214 1.00 ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32 Consensus pattern (214 bp): AATTCTAAAATGTATTTTAAAAGGTAATGTTAGCCCTTGTATGAAAAATTTCGGATGGTAGTCAT TTTTTCCGGGATCCAGACCGAGAGCTACATATATGCAGCTAAGGTAACTAATAATGCTTCCAATA AAATACTTTGTTTATTAATGCAAGCTTTTAAGAAAGCAATACAGCCTACTCCGGATATATTGAAA TTCTGGGGGCCATGCAAAT Found at i:1365457 original size:15 final size:17 Alignment explanation

Indices: 1365420--1365464 Score: 67 Period size: 17 Copynumber: 2.8 Consensus size: 17 1365410 ATTTATTTCT 1365420 ATTTCAAAATAAGCGGA 1 ATTTCAAAATAAGCGGA 1365437 ATTTCAAAATAAGC-G- 1 ATTTCAAAATAAGCGGA * 1365452 ATTTCAATATAAG 1 ATTTCAAAATAAG 1365465 TGGAGTAAGC Statistics Matches: 27, Mismatches: 1, Indels: 2 0.90 0.03 0.07 Matches are distributed among these distances: 15 12 0.44 16 1 0.04 17 14 0.52 ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29 Consensus pattern (17 bp): ATTTCAAAATAAGCGGA Found at i:1368748 original size:2 final size:2 Alignment explanation

Indices: 1368741--1368765 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 1368731 AAATTGCAAT 1368741 GA GA GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA G 1368766 GGGGGCGTTG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:1371613 original size:11 final size:11 Alignment explanation

Indices: 1371597--1371628 Score: 55 Period size: 11 Copynumber: 2.9 Consensus size: 11 1371587 CTTAGAAGTC * 1371597 AAGAAATATAG 1 AAGAAATAAAG 1371608 AAGAAATAAAG 1 AAGAAATAAAG 1371619 AAGAAATAAA 1 AAGAAATAAA 1371629 AGAATCATTA Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 20 1.00 ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12 Consensus pattern (11 bp): AAGAAATAAAG Found at i:1373234 original size:10 final size:10 Alignment explanation

Indices: 1373200--1373249 Score: 50 Period size: 10 Copynumber: 5.0 Consensus size: 10 1373190 AATACATCAC 1373200 AATATTGTA- 1 AATATTGTAT 1373209 ACATA-TGATAT 1 A-ATATTG-TAT * 1373220 TATATTGTAT 1 AATATTGTAT * 1373230 AATATAGTAT 1 AATATTGTAT 1373240 AATATTGTAT 1 AATATTGTAT 1373250 TGTATGATAT Statistics Matches: 33, Mismatches: 4, Indels: 7 0.75 0.09 0.16 Matches are distributed among these distances: 9 3 0.09 10 28 0.85 11 2 0.06 ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46 Consensus pattern (10 bp): AATATTGTAT Found at i:1373234 original size:20 final size:20 Alignment explanation

Indices: 1373200--1373259 Score: 61 Period size: 20 Copynumber: 3.0 Consensus size: 20 1373190 AATACATCAC 1373200 AATATTGTA-ACATATGATAT 1 AATATTGTATA-ATATGATAT * 1373220 TATATTGTATAATAT-AGTAT 1 AATATTGTATAATATGA-TAT ** 1373240 AATATTGTATTGTATGATAT 1 AATATTGTATAATATGATAT 1373260 CGTATCATAT Statistics Matches: 33, Mismatches: 4, Indels: 6 0.77 0.09 0.14 Matches are distributed among these distances: 19 1 0.03 20 30 0.91 21 2 0.06 ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47 Consensus pattern (20 bp): AATATTGTATAATATGATAT Found at i:1373250 original size:25 final size:25 Alignment explanation

Indices: 1373216--1373270 Score: 74 Period size: 25 Copynumber: 2.2 Consensus size: 25 1373206 GTAACATATG 1373216 ATATTATATTGTATAATATAGTATA 1 ATATTATATTGTATAATATAGTATA * * * * 1373241 ATATTGTATTGTATGATATCGTATC 1 ATATTATATTGTATAATATAGTATA 1373266 ATATT 1 ATATT 1373271 TGATACACAA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 26 1.00 ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49 Consensus pattern (25 bp): ATATTATATTGTATAATATAGTATA Found at i:1373299 original size:22 final size:23 Alignment explanation

Indices: 1373256--1373299 Score: 63 Period size: 24 Copynumber: 1.9 Consensus size: 23 1373246 GTATTGTATG 1373256 ATATCGTATCATATTTGATACACA 1 ATATCGTATCATA-TTGATACACA * 1373280 ATATTGTATCATA-TGATACA 1 ATATCGTATCATATTGATACA 1373300 ATATAATTTG Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 22 7 0.37 24 12 0.63 ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39 Consensus pattern (23 bp): ATATCGTATCATATTGATACACA Found at i:1373351 original size:15 final size:15 Alignment explanation

Indices: 1373333--1373661 Score: 128 Period size: 15 Copynumber: 21.6 Consensus size: 15 1373323 TCATATCATG * * 1373333 ATACAATATCATCTG 1 ATACAATATCATATT * * 1373348 ATACAGTATGATATT 1 ATACAATATCATATT * 1373363 ATATAATA-CAATATT 1 ATACAATATC-ATATT * 1373378 ATACAATATCATTTT 1 ATACAATATCATATT 1373393 ATACAATATCATATCATAT 1 ATACAATATC--AT-AT-T 1373412 GATACAATATCATATT 1 -ATACAATATCATATT * 1373428 ATACAGTATCATATT 1 ATACAATATCATATT * 1373443 ATATAATATC---TT 1 ATACAATATCATATT * 1373455 AT--AATATCATATA 1 ATACAATATCATATT * 1373468 ATACAATTTCATGTATTAT 1 ATACAATATCA--TA-T-T 1373487 ATAACAATAT-ATTATAT 1 AT-ACAATATCA-TAT-T * 1373504 AAACCAATATCATATT 1 ATA-CAATATCATATT * ** * 1373520 ATACATTATTGTATC 1 ATACAATATCATATT * * 1373535 ATACAATATGATATA 1 ATACAATATCATATT * 1373550 ATTATAATATACA-A-T 1 A-TACAATAT-CATATT ** * 1373565 AT--TGTATCATATG 1 ATACAATATCATATT * 1373578 ATACAAAATCATA-T 1 ATACAATATCATATT * * * 1373592 ATTGCAATATAATATG 1 A-TACAATATCATATT * * 1373608 AAACAATATCAT-TCG 1 ATACAATATCATAT-T * 1373623 ATAAAATAAT-ATATT 1 ATACAAT-ATCATATT 1373638 ATACAATATCATATT 1 ATACAATATCATATT * 1373653 CTACAATAT 1 ATACAATAT 1373662 TGTATAATAA Statistics Matches: 233, Mismatches: 50, Indels: 62 0.68 0.14 0.18 Matches are distributed among these distances: 10 6 0.03 11 2 0.01 12 8 0.03 13 5 0.02 14 5 0.02 15 142 0.61 16 18 0.08 17 20 0.09 18 7 0.03 19 4 0.02 20 16 0.07 ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39 Consensus pattern (15 bp): ATACAATATCATATT Found at i:1373408 original size:5 final size:5 Alignment explanation

Indices: 1373398--1373466 Score: 52 Period size: 5 Copynumber: 13.8 Consensus size: 5 1373388 ATTTTATACA * * * * 1373398 ATATC ATATC ATATG ATA-C AATATC ATATT ATA-C AGTATC ATATT ATATA 1 ATATC ATATC ATATC ATATC -ATATC ATATC ATATC A-TATC ATATC ATATC * * 1373448 ATATC TTATA ATATC ATAT 1 ATATC ATATC ATATC ATAT 1373467 AATACAATTT Statistics Matches: 49, Mismatches: 11, Indels: 8 0.72 0.16 0.12 Matches are distributed among these distances: 4 1 0.02 5 45 0.92 6 3 0.06 ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42 Consensus pattern (5 bp): ATATC Found at i:1373408 original size:20 final size:20 Alignment explanation

Indices: 1373383--1373426 Score: 70 Period size: 20 Copynumber: 2.2 Consensus size: 20 1373373 ATATTATACA * * 1373383 ATATCATTTTATACAATATC 1 ATATCATATGATACAATATC 1373403 ATATCATATGATACAATATC 1 ATATCATATGATACAATATC 1373423 ATAT 1 ATAT 1373427 TATACAGTAT Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 22 1.00 ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41 Consensus pattern (20 bp): ATATCATATGATACAATATC Found at i:1373424 original size:35 final size:35 Alignment explanation

Indices: 1373338--1373446 Score: 120 Period size: 35 Copynumber: 3.3 Consensus size: 35 1373328 TCATGATACA * * * * 1373338 ATATCATCTGATACAGTATGATATTATATAATA-C 1 ATATCATATGATACAATATCATATTATACAATATC * 1373372 A-AT-AT-T-ATACAATATCATTTTATACAATATC 1 ATATCATATGATACAATATCATATTATACAATATC * 1373403 ATATCATATGATACAATATCATATTATACAGTATC 1 ATATCATATGATACAATATCATATTATACAATATC * 1373438 ATATTATAT 1 ATATCATAT 1373447 AATATCTTAT Statistics Matches: 63, Mismatches: 7, Indels: 9 0.80 0.09 0.11 Matches are distributed among these distances: 30 19 0.30 31 3 0.05 32 4 0.06 33 4 0.06 34 2 0.03 35 31 0.49 ACGTcount: A:0.43, C:0.12, G:0.05, T:0.40 Consensus pattern (35 bp): ATATCATATGATACAATATCATATTATACAATATC Found at i:1373441 original size:20 final size:19 Alignment explanation

Indices: 1373383--1373472 Score: 62 Period size: 20 Copynumber: 4.8 Consensus size: 19 1373373 ATATTATACA * 1373383 ATATCATTTTATACAATATC 1 ATATCATATTATAC-ATATC * 1373403 ATATCATATGATAC--A-- 1 ATATCATATTATACATATC 1373418 ATATCATATTATACAGTATC 1 ATATCATATTATACA-TATC * * * * 1373438 ATATTATATAATATCTTATA 1 ATATCATATTATA-CATATC * 1373458 ATATCATATAATACA 1 ATATCATATTATACA 1373473 ATTTCATGTA Statistics Matches: 55, Mismatches: 9, Indels: 13 0.71 0.12 0.17 Matches are distributed among these distances: 15 13 0.24 17 1 0.02 18 1 0.02 19 1 0.02 20 38 0.69 21 1 0.02 ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41 Consensus pattern (19 bp): ATATCATATTATACATATC Found at i:1373457 original size:10 final size:10 Alignment explanation

Indices: 1373397--1373470 Score: 69 Period size: 10 Copynumber: 7.4 Consensus size: 10 1373387 CATTTTATAC 1373397 AATATCATAT 1 AATATCATAT * * * 1373407 CATATGATAC 1 AATATCATAT 1373417 AATATCATAT 1 AATATCATAT * 1373427 TATA-CAGTAT 1 AATATCA-TAT * * 1373437 CATATTATAT 1 AATATCATAT * 1373447 AATATCTTAT 1 AATATCATAT 1373457 AATATCATAT 1 AATATCATAT 1373467 AATA 1 AATA 1373471 CAATTTCATG Statistics Matches: 49, Mismatches: 13, Indels: 4 0.74 0.20 0.06 Matches are distributed among these distances: 9 2 0.04 10 46 0.94 11 1 0.02 ACGTcount: A:0.46, C:0.11, G:0.03, T:0.41 Consensus pattern (10 bp): AATATCATAT Found at i:1373718 original size:15 final size:15 Alignment explanation

Indices: 1373333--1373718 Score: 97 Period size: 15 Copynumber: 25.2 Consensus size: 15 1373323 TCATATCATG * * 1373333 ATACAATATCATCTG 1 ATACAATATCATATA * * * 1373348 ATACAGTATGATATT 1 ATACAATATCATATA * * 1373363 ATATAATA-CAATATT 1 ATACAATATC-ATATA * * 1373378 ATACAATATCATTTT 1 ATACAATATCATATA 1373393 ATACAATATCATATCATA 1 ATACAATATC--AT-ATA * 1373411 TGATACAATATCATATT 1 --ATACAATATCATATA * * 1373428 ATACAGTATCATATT 1 ATACAATATCATATA * 1373443 ATATAATATC-T-T- 1 ATACAATATCATATA 1373455 AT--AATATCATATA 1 ATACAATATCATATA * 1373468 ATACAATTTCATGTATTA 1 ATACAATATCA--TA-TA 1373486 TATAACAATAT-ATTATA 1 -AT-ACAATATCA-TATA * * 1373503 TAAACCAATATCATATT 1 -ATA-CAATATCATATA * ** * 1373520 ATACATTATTGTATC 1 ATACAATATCATATA * 1373535 ATACAATATGATATA 1 ATACAATATCATATA * 1373550 ATTATAATATACA-AT- 1 A-TACAATAT-CATATA ** * 1373565 AT--TGTATCATATG 1 ATACAATATCATATA * 1373578 ATACAAAATCATATA 1 ATACAATATCATATA * * * 1373593 TTGCAATATAATATGA 1 ATACAATATCATAT-A * 1373609 A-ACAATATCAT-TCG 1 ATACAATATCATAT-A * * 1373623 ATAAAATAAT-ATATT 1 ATACAAT-ATCATATA * 1373638 ATACAATATCATATT 1 ATACAATATCATATA * * 1373653 CTACAATATTGTATAATAA 1 ATACAATA-T-CAT-AT-A 1373672 TATACAATA-C-TATA 1 -ATACAATATCATATA 1373686 CATAACAATATC--ATA 1 -AT-ACAATATCATATA 1373701 ATACAATATCATATA 1 ATACAATATCATATA 1373716 ATA 1 ATA 1373719 ATGTACAAAA Statistics Matches: 277, Mismatches: 55, Indels: 78 0.68 0.13 0.19 Matches are distributed among these distances: 10 6 0.02 11 3 0.01 12 8 0.03 13 13 0.05 14 11 0.04 15 158 0.57 16 20 0.07 17 22 0.08 18 10 0.04 19 3 0.01 20 23 0.08 ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38 Consensus pattern (15 bp): ATACAATATCATATA Found at i:1379683 original size:327 final size:326 Alignment explanation

Indices: 1379052--1380138 Score: 1497 Period size: 327 Copynumber: 3.3 Consensus size: 326 1379042 TGAAATAGGG * * * 1379052 GTGAAATGCTAAAATATTACAAAGTTCGGGT-AGCTAACTGAGCCCCTGTAGGGGTCATAGGTGC 1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC * * * ** * * 1379116 CCTC-TAACACTTATTATGAATATATACCTCCTGAGGTTCTCTACCTTATCCAAGTGTTTGCAAG 66 CCTCGT-ACGCTTATGATG---A-ATA-CTTCTGAGGCCCTCTACCTAATCCAAGTGTTTCCAAG * * 1379180 TTCTTGTGGTCAATCTCAAGTGAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGATCCT-C 125 TTCTTGTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGA-GCTAC 1379244 TTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACAC 189 TTGGTGGTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACAC * * 1379309 TGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGTGATAATGGCCCGCCTTTCACCCCT 254 TGCCCTGGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCT 1379374 ATATCATT 319 ATATCATT * * * * * 1379382 GTGAAATGCTAAAATATGAGAGAGTTCGGGTGAGCTAACTGAACCCTTGTAGGGGCCATAGGTGC 1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC * * * * 1379447 CCTCGTACGCTTATTATGAATACTTCTTGAGGTCCTCAACCTAATCCAAGTGTTTTCAAGTTCTT 66 CCTCGTACGCTTATGATGAATACTTC-TGAGGCCCTCTACCTAATCCAAGTGTTTCCAAGTTCTT * * 1379512 GTGGTCAATCTTAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCTTGGGAGCTACTTGGTG 130 GTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTG * 1379577 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAACAGCCCTCATAGGTCCTCTACACTGCCCT 195 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCT * 1379642 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGTCCGCCTTTCACCCCTATATCA 260 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCTATATCA 1379707 TT 325 TT * * 1379709 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTTACTGGGCCCTTGCAGGGGTCATAGGTGC 1 GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC * * * 1379774 CCTCGTACGCTTATGATGAATACCTCTGAGGCCCTCTACCTAATCCTAA-TGTTTCCCAGTTTTT 66 CCTCGTACGCTTATGATGAATACTTCTGAGGCCCTCTACCTAATCC-AAGTGTTTCCAAGTTCTT * * * * 1379838 GTGATCAAACTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCGGGGAGCGACTTGGTG 130 GTGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTG * * * * * 1379903 GTACCCCTACAGCCCGAATTTGAGACCGGGAAATAGTATCAC-CATAGGTCCTCTACACTGCCTT 195 GTACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCT * * * ** * * * * 1379967 GGCATTCGTTTGCTTTACACTTCAAAGATAAAA-ATGATATTGGACCGCTTTTCATCCATATATC 260 GGTATCCGTTTGATGCACACTTCAAAGATAAAAGA-GATAATGGACCGCCTTTCACCCCTATATC ** 1380031 GCT 324 ATT ** * * 1380034 GAAAAATGCT-AAATAAT-ACAAAGTTCGGGTGAGCTAACTGGGCCCTTGCAGGGGTTATAGGTG 1 GTGAAATGCTAAAAT-ATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTG * 1380097 CCCTCTTACGCTTATGATGAATACCTTCTGAGGCCCTCTACC 65 CCCTCGTACGCTTATGATGAATA-CTTCTGAGGCCCTCTACC 1380139 CTGGGAGCCA Statistics Matches: 686, Mismatches: 63, Indels: 21 0.89 0.08 0.03 Matches are distributed among these distances: 324 71 0.10 325 101 0.15 326 131 0.19 327 308 0.45 328 1 0.00 330 28 0.04 331 45 0.07 332 1 0.00 ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27 Consensus pattern (326 bp): GTGAAATGCTAAAATATGACAAAGTTCGGGTGAGCTAACTGAGCCCTTGCAGGGGTCATAGGTGC CCTCGTACGCTTATGATGAATACTTCTGAGGCCCTCTACCTAATCCAAGTGTTTCCAAGTTCTTG TGGTCAATCTCAAGTCAGATATAAACCCCTGAAATGAGCCAGAACCCCTGGGAGCTACTTGGTGG TACCCCTACAGCCCAAATTTGAGACCGGGAAATAATAGCCCTCATAGGTCCTCTACACTGCCCTG GTATCCGTTTGATGCACACTTCAAAGATAAAAGAGATAATGGACCGCCTTTCACCCCTATATCAT T Found at i:1380818 original size:13 final size:13 Alignment explanation

Indices: 1380800--1380824 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 1380790 TTTTATGGGC 1380800 TTAGTGGCTGCTG 1 TTAGTGGCTGCTG 1380813 TTAGTGGCTGCT 1 TTAGTGGCTGCT 1380825 TGCTTCAGCC Statistics Matches: 12, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 12 1.00 ACGTcount: A:0.08, C:0.16, G:0.36, T:0.40 Consensus pattern (13 bp): TTAGTGGCTGCTG Found at i:1382117 original size:2 final size:2 Alignment explanation

Indices: 1382110--1382163 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1382100 TCATCATATA 1382110 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1382152 AG AG AG AG AG AG 1 AG AG AG AG AG AG 1382164 TACCAGTGTG Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1382499 original size:2 final size:2 Alignment explanation

Indices: 1382492--1382546 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1382482 TTGTAAAATA 1382492 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1382534 TC TC TC TC TC TC T 1 TC TC TC TC TC TC T 1382547 GTGTACTTTT Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1384017 original size:19 final size:20 Alignment explanation

Indices: 1383993--1384037 Score: 65 Period size: 19 Copynumber: 2.3 Consensus size: 20 1383983 GTAACGATAT * 1383993 CCACGGAGTAACACA-GTGG 1 CCACGGAGTAACACAGGCGG * 1384012 CCACGGAGTTACACAGGCGG 1 CCACGGAGTAACACAGGCGG 1384032 CCACGG 1 CCACGG 1384038 TGCGACACGG Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 19 14 0.61 20 9 0.39 ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09 Consensus pattern (20 bp): CCACGGAGTAACACAGGCGG Found at i:1387033 original size:16 final size:16 Alignment explanation

Indices: 1387010--1387059 Score: 64 Period size: 16 Copynumber: 3.1 Consensus size: 16 1387000 CGTCACATTG 1387010 CCATTTGACACAAATA 1 CCATTTGACACAAATA * * * 1387026 CTATTTGATACAATTA 1 CCATTTGACACAAATA * 1387042 CCATTTGACACAATTA 1 CCATTTGACACAAATA 1387058 CC 1 CC 1387060 CGATGTCCAA Statistics Matches: 29, Mismatches: 5, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 16 29 1.00 ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32 Consensus pattern (16 bp): CCATTTGACACAAATA Found at i:1388231 original size:46 final size:46 Alignment explanation

Indices: 1388181--1388268 Score: 131 Period size: 46 Copynumber: 1.9 Consensus size: 46 1388171 AAAATGTTTT * * 1388181 TATCTCGTAATTACGAGAAAAGATCTCGTTATTACGAGAAAATAAA 1 TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAATAAA * * * 1388227 TATCTCGTTATTACGAAAAAAAATCTTGTTATTATGAGAAAA 1 TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAA 1388269 GAGACCTCAT Statistics Matches: 37, Mismatches: 5, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 46 37 1.00 ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32 Consensus pattern (46 bp): TATCTCGTAATTACGAAAAAAAATCTCGTTATTACGAGAAAATAAA Found at i:1388268 original size:21 final size:21 Alignment explanation

Indices: 1388182--1388268 Score: 93 Period size: 21 Copynumber: 4.0 Consensus size: 21 1388172 AAATGTTTTT * * 1388182 ATCTCGTAATTACGAGAAAAG 1 ATCTCGTTATTACGAGAAAAA 1388203 ATCTCGTTATTACGAGAAAATAAA 1 ATCTCGTTATTACGAG--AA-AAA * 1388227 TATCTCGTTATTACGAAAAAAA 1 -ATCTCGTTATTACGAGAAAAA * * 1388249 ATCTTGTTATTATGAGAAAA 1 ATCTCGTTATTACGAGAAAA 1388269 GAGACCTCAT Statistics Matches: 56, Mismatches: 6, Indels: 8 0.80 0.09 0.11 Matches are distributed among these distances: 21 32 0.57 22 3 0.05 23 4 0.07 24 2 0.04 25 15 0.27 ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31 Consensus pattern (21 bp): ATCTCGTTATTACGAGAAAAA Found at i:1388428 original size:43 final size:43 Alignment explanation

Indices: 1388349--1388444 Score: 138 Period size: 43 Copynumber: 2.2 Consensus size: 43 1388339 TATTCTTATT * * * * * 1388349 ATTACGAGAAAAGATCTTGTTTTTACGCGTTAATTATCTCGTA 1 ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA * 1388392 ATTACGAGAAAAGATATAGTTATTAAGAGTTCATTATCTCGTA 1 ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA 1388435 ATTACGAGAA 1 ATTACGAGAA 1388445 TTGGTCTAAT Statistics Matches: 47, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 43 47 1.00 ACGTcount: A:0.36, C:0.11, G:0.17, T:0.35 Consensus pattern (43 bp): ATTACGAGAAAAGATATAGTTATTAAGAGTTAATTATCTCGTA Found at i:1389183 original size:21 final size:21 Alignment explanation

Indices: 1389151--1389312 Score: 153 Period size: 21 Copynumber: 7.6 Consensus size: 21 1389141 TAACTCGTTA 1389151 TAATAAACGAGATCTTTTCTCG 1 TAAT-AACGAGATCTTTTCTCG * * * 1389173 TTATTACGAGATCTTTTTTCG 1 TAATAACGAGATCTTTTCTCG * * * 1389194 TAATAACGACATAATTATCTCG 1 TAATAACGAGAT-CTTTTCTCG * 1389216 TAATAACGAAATCTTTTCTCG 1 TAATAACGAGATCTTTTCTCG * ** * 1389237 TAATAACGAGATAATTAGCCCG 1 TAATAACGAGAT-CTTTTCTCG * * 1389259 TTATAACGAGATCTTTTCTCA 1 TAATAACGAGATCTTTTCTCG * 1389280 TAATAACGAGATATTTTCTCG 1 TAATAACGAGATCTTTTCTCG * * 1389301 TTATCACGAGAT 1 TAATAACGAGAT 1389313 ATCTTTTATG Statistics Matches: 110, Mismatches: 28, Indels: 5 0.77 0.20 0.03 Matches are distributed among these distances: 21 74 0.67 22 36 0.33 ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37 Consensus pattern (21 bp): TAATAACGAGATCTTTTCTCG Found at i:1389199 original size:43 final size:43 Alignment explanation

Indices: 1389168--1389312 Score: 193 Period size: 43 Copynumber: 3.4 Consensus size: 43 1389158 CGAGATCTTT * * * 1389168 TCTCGTTATTACGAGATCTTTTTTCGTAATAACGACATAATTA 1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA * * 1389211 TCTCGTAATAACGAAATCTTTTCTCGTAATAACGAGATAATTA 1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA * * * * 1389254 GCCCGTTATAACGAGATCTTTTCTCATAATAACGAGAT-ATTT 1 TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA * 1389296 TCTCGTTATCACGAGAT 1 TCTCGTTATAACGAGAT 1389313 ATCTTTTATG Statistics Matches: 88, Mismatches: 14, Indels: 1 0.85 0.14 0.01 Matches are distributed among these distances: 42 17 0.19 43 71 0.81 ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37 Consensus pattern (43 bp): TCTCGTTATAACGAGATCTTTTCTCGTAATAACGAGATAATTA Found at i:1391635 original size:19 final size:18 Alignment explanation

Indices: 1391611--1391668 Score: 68 Period size: 16 Copynumber: 3.3 Consensus size: 18 1391601 CTTAACATTG 1391611 TTTTTTGTTTGTTTGGTTT 1 TTTTTTGTTTGTTT-GTTT 1391630 TTTTTTGGTTT-TTTGTTT 1 TTTTTT-GTTTGTTTGTTT * 1391648 TTTTGTG-TTGTTT-TTT 1 TTTTTTGTTTGTTTGTTT 1391664 TTTTT 1 TTTTT 1391669 GGTGTTTATT Statistics Matches: 35, Mismatches: 2, Indels: 7 0.80 0.05 0.16 Matches are distributed among these distances: 16 9 0.26 17 4 0.11 18 9 0.26 19 9 0.26 20 4 0.11 ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83 Consensus pattern (18 bp): TTTTTTGTTTGTTTGTTT Found at i:1391652 original size:27 final size:29 Alignment explanation

Indices: 1391610--1391664 Score: 87 Period size: 27 Copynumber: 2.0 Consensus size: 29 1391600 ACTTAACATT 1391610 GTTTTTTGTTTGTTTG-GTT-TTTTTTTG 1 GTTTTTTGTTTGTTTGTGTTGTTTTTTTG * 1391637 GTTTTTTGTTTTTTTGTGTTGTTTTTTT 1 GTTTTTTGTTTGTTTGTGTTGTTTTTTT 1391665 TTTTGGTGTT Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 27 15 0.60 28 3 0.12 29 7 0.28 ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80 Consensus pattern (29 bp): GTTTTTTGTTTGTTTGTGTTGTTTTTTTG Found at i:1391673 original size:18 final size:17 Alignment explanation

Indices: 1391627--1391675 Score: 66 Period size: 17 Copynumber: 2.9 Consensus size: 17 1391617 GTTTGTTTGG 1391627 TTTTTTTTTGGT-TTTT 1 TTTTTTTTTGGTGTTTT * 1391643 TGTTTTTTT-GTGTTGTT 1 TTTTTTTTTGGTGTT-TT 1391660 TTTTTTTTTGGTGTTT 1 TTTTTTTTTGGTGTTT 1391676 ATTGTTCTTA Statistics Matches: 28, Mismatches: 2, Indels: 5 0.80 0.06 0.14 Matches are distributed among these distances: 15 2 0.07 16 10 0.36 17 11 0.39 18 5 0.18 ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82 Consensus pattern (17 bp): TTTTTTTTTGGTGTTTT Found at i:1398716 original size:12 final size:12 Alignment explanation

Indices: 1398695--1398736 Score: 50 Period size: 12 Copynumber: 3.5 Consensus size: 12 1398685 CAAAATTTAT * 1398695 ATCATCATCATC 1 ATCATTATCATC 1398707 ATCATTATCATC 1 ATCATTATCATC * 1398719 ATCA-TACTCAGC 1 ATCATTA-TCATC 1398731 ATCATT 1 ATCATT 1398737 TTACCAAGAT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 11 2 0.08 12 23 0.88 13 1 0.04 ACGTcount: A:0.33, C:0.29, G:0.02, T:0.36 Consensus pattern (12 bp): ATCATTATCATC Found at i:1405010 original size:9 final size:9 Alignment explanation

Indices: 1404996--1405025 Score: 51 Period size: 9 Copynumber: 3.3 Consensus size: 9 1404986 TTTTCTTGTG 1404996 TTTGTGTTT 1 TTTGTGTTT 1405005 TTTGTGTTT 1 TTTGTGTTT * 1405014 TTTATGTTT 1 TTTGTGTTT 1405023 TTT 1 TTT 1405026 CACTGAATGT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80 Consensus pattern (9 bp): TTTGTGTTT Found at i:1408632 original size:107 final size:105 Alignment explanation

Indices: 1408448--1408659 Score: 300 Period size: 107 Copynumber: 2.0 Consensus size: 105 1408438 GAAAGATAAT * * * 1408448 GACCGGACACGAATTTTGCACTTTTTCTGCAAGTGACCTTGACCTTGCCCAAATGACCTTGGGTC 1 GACCGGACACGAATTTTGCACTTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGGATC * * 1408513 AAAGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTG 66 AAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG * * 1408553 GACCGGACACTAATTTTGCACTTTTTTTTTTCCAA-CGACCTTGACCTTGCCCAAATGACCTTGG 1 GACCGGACACGAATTTTGCAC---TTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGG * * * 1408617 ATCAAGGTCATGACACACCCTTAGTTCATAAGCAATCTTTGTG 63 ATCAAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG 1408660 TGAATTAACA Statistics Matches: 94, Mismatches: 10, Indels: 4 0.87 0.09 0.04 Matches are distributed among these distances: 105 20 0.21 107 65 0.69 108 9 0.10 ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31 Consensus pattern (105 bp): GACCGGACACGAATTTTGCACTTTTTCTCCAAGCGACCTTGACCTTGCCCAAATGACCTTGGATC AAAGTCATGACACACCCTTAGGTCATAAGCAATATTTGTG Found at i:1408819 original size:146 final size:146 Alignment explanation

Indices: 1408551--1409002 Score: 683 Period size: 146 Copynumber: 3.1 Consensus size: 146 1408541 GCAATATTTG * * * ** 1408551 TGGACCGGACACTAATTTTGCACTTTTTTTTTTCCAACGACCTTGACCTTGCCCAAATGACCTTG 1 TGGACCGGACACAAATTTTGCAC--TTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTG * * 1408616 GATCAAGGTCATGACACACCCTTAGTTCATAAGCAATCTTTGTGTGAA-TTAACAACTTCCAATA 64 GGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTT-ACAACTTCCAATA 1408680 ATTCTCCATAAGAAAGATA 128 ATTCTCCATAAGAAAGATA 1408699 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG 1 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG * * 1408764 TCAAGGTCATGACACACCCTTAGGTCATAGGCAATCTTTGTGTGAAGTTAGAACTTCCAATAATT 66 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTACAACTTCCAATAATT 1408829 CTCCATAAGAAAGATA 131 CTCCATAAGAAAGATA * * * ** * 1408845 TGGACCGGACACGAATTTTGTATTTTTTCTGCCAGTGACCTTGACCTTGCCGGAATGACCTTGTG 1 TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG * ** 1408910 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG-TATTAACTTCCAATGTT 66 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTA-CAACTTCCAATAAT 1408974 TCTCCATAAGAAAGATA 130 TCTCCATAAGAAAGATA * 1408991 TGGACCGAACAC 1 TGGACCGGACAC 1409003 GATTGCACAG Statistics Matches: 282, Mismatches: 20, Indels: 6 0.92 0.06 0.02 Matches are distributed among these distances: 145 2 0.01 146 256 0.91 147 2 0.01 148 22 0.08 ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30 Consensus pattern (146 bp): TGGACCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGG TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTTACAACTTCCAATAATT CTCCATAAGAAAGATA Found at i:1409026 original size:12 final size:12 Alignment explanation

Indices: 1409009--1409042 Score: 68 Period size: 12 Copynumber: 2.8 Consensus size: 12 1408999 ACACGATTGC 1409009 ACAGACGGACGG 1 ACAGACGGACGG 1409021 ACAGACGGACGG 1 ACAGACGGACGG 1409033 ACAGACGGAC 1 ACAGACGGAC 1409043 AAGGTGATTC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.35, C:0.26, G:0.38, T:0.00 Consensus pattern (12 bp): ACAGACGGACGG Found at i:1427266 original size:2 final size:2 Alignment explanation

Indices: 1427259--1427322 Score: 110 Period size: 2 Copynumber: 32.0 Consensus size: 2 1427249 TTCATGTGCG * 1427259 CT CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT * 1427301 CT CT CT CT CT CT TT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT 1427323 NNNNNNNNNN Statistics Matches: 58, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 58 1.00 ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50 Consensus pattern (2 bp): CT Done.