Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold471

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: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29

Warning! 143812 characters in sequence are not A, C, G, or T


File 2 of 4

Found at i:644 original size:172 final size:172

Alignment explanation

Indices: 347--1143 Score: 1382 Period size: 172 Copynumber: 4.6 Consensus size: 172 337 GTATCGAGTC * * 347 TATCGACCAAGGCTGATTTTCGAACTTGACCAACGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * * 412 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGGT-AAACT 66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC- * 476 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG 130 GGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * 519 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * 584 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGGT-AAACT 66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC- * 648 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG 130 GGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * 691 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT 756 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG 66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG * 821 GAGTCATTATTGTGGTCATAGTCCCATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * * 863 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT ** 928 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTTCATAAAACG 66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG * * * 993 GAGTCATTATAGTGGTCAAAGTTCGATAACTCCAACAAAAAG 131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG * * 1035 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT 1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT * 1100 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA 66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAA 1144 AAAAGTGTGA Statistics Matches: 607, Mismatches: 17, Indels: 2 0.97 0.03 0.00 Matches are distributed among these distances: 172 603 0.99 173 4 0.01 ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30 Consensus pattern (172 bp): TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG Found at i:1170 original size:8 final size:8 Alignment explanation

Indices: 1152--1251 Score: 83 Period size: 8 Copynumber: 12.5 Consensus size: 8 1142 AAAAAAGTGT * 1152 GACGGACG 1 GACGCACG * 1160 GACGCAAG 1 GACGCACG * 1168 GACACACG 1 GACGCACG 1176 GACGCACG 1 GACGCACG * * 1184 GACCCACA 1 GACGCACG * * 1192 GACACACA 1 GACGCACG * 1200 GACCCACG 1 GACGCACG * 1208 GACACACG 1 GACGCACG * 1216 GACCCACG 1 GACGCACG * 1224 GACCCACG 1 GACGCACG * 1232 GACCCACG 1 GACGCACG * 1240 GACACACG 1 GACGCACG 1248 GACG 1 GACG 1252 GACGCCCGGC Statistics Matches: 78, Mismatches: 14, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 8 78 1.00 ACGTcount: A:0.32, C:0.40, G:0.28, T:0.00 Consensus pattern (8 bp): GACGCACG Found at i:1178 original size:16 final size:16 Alignment explanation

Indices: 1157--1250 Score: 125 Period size: 16 Copynumber: 5.9 Consensus size: 16 1147 AGTGTGACGG * * * 1157 ACGGACGCAAGGACAC 1 ACGGACACACGGACCC * 1173 ACGGACGCACGGACCC 1 ACGGACACACGGACCC * * 1189 ACAGACACACAGACCC 1 ACGGACACACGGACCC 1205 ACGGACACACGGACCC 1 ACGGACACACGGACCC * 1221 ACGGACCCACGGACCC 1 ACGGACACACGGACCC 1237 ACGGACACACGGAC 1 ACGGACACACGGAC 1251 GGACGCCCGG Statistics Matches: 69, Mismatches: 9, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 69 1.00 ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00 Consensus pattern (16 bp): ACGGACACACGGACCC Found at i:1184 original size:24 final size:24 Alignment explanation

Indices: 1152--1251 Score: 103 Period size: 24 Copynumber: 4.2 Consensus size: 24 1142 AAAAAAGTGT * * 1152 GACGGACGGACGCAAGGACACACG 1 GACGCACGGACCCAAGGACACACG * 1176 GACGCACGGACCCACA-GACACACA 1 GACGCACGGACCCA-AGGACACACG * * * * 1200 GACCCACGGACACACGGACCCACG 1 GACGCACGGACCCAAGGACACACG * * 1224 GACCCACGGACCCACGGACACACG 1 GACGCACGGACCCAAGGACACACG 1248 GACG 1 GACG 1252 GACGCCCGGC Statistics Matches: 63, Mismatches: 11, Indels: 4 0.81 0.14 0.05 Matches are distributed among these distances: 24 62 0.98 25 1 0.02 ACGTcount: A:0.32, C:0.40, G:0.28, T:0.00 Consensus pattern (24 bp): GACGCACGGACCCAAGGACACACG Found at i:7496 original size:1 final size:1 Alignment explanation

Indices: 7490--7514 Score: 50 Period size: 1 Copynumber: 25.0 Consensus size: 1 7480 CTCCCTTAAG 7490 TTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTT 7515 CAATCTTAAG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 24 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:24316 original size:16 final size:16 Alignment explanation

Indices: 24292--24324 Score: 57 Period size: 16 Copynumber: 2.1 Consensus size: 16 24282 AACTGAAGTG 24292 GGACAGACAGACGGAC 1 GGACAGACAGACGGAC * 24308 GGACGGACAGACGGAC 1 GGACAGACAGACGGAC 24324 G 1 G 24325 CAGAGGAAAG Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 16 1.00 ACGTcount: A:0.33, C:0.24, G:0.42, T:0.00 Consensus pattern (16 bp): GGACAGACAGACGGAC Found at i:27406 original size:14 final size:14 Alignment explanation

Indices: 27387--27413 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 27377 CAAACATAAT 27387 TATAGATACAAACA 1 TATAGATACAAACA 27401 TATAGATACAAAC 1 TATAGATACAAAC 27414 TTCTATACTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22 Consensus pattern (14 bp): TATAGATACAAACA Found at i:35917 original size:41 final size:40 Alignment explanation

Indices: 35855--36681 Score: 801 Period size: 41 Copynumber: 20.0 Consensus size: 40 35845 TGATACATGG * * * 35855 ACAGGAGTCAAACAGCTGTTATACAAGTCAAGGGATCAAT 1 ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * ** * * * * 35895 ACTGTGAGTCATACAGAAGTTATACAAATCAAAGGATCACT 1 ACAG-GAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT 35936 ACCAGGAGTCATACAGTTGTTATATACCAGTCAAGGGATCAAT 1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT * 35979 ACTAGGAGTCATACAGTTGTTATATACCAGTCAAGAGATCAAT 1 AC-AGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT * * 36022 ACTAGGAGTTATACAGTTGTTATATACCAATCAAGGGATCAAT 1 AC-AGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT * * * 36065 ---GGTTGTAATAC--TAG---T--CAGTCAAGGGATCAAT 1 ACAGG-AGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * 36096 ACCAGGAGTCATACAGTTATTATACTACTCAAGGGATCAAT 1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * * * 36137 GCCAGGAGTCATGCCGTTGTTATGCCAGTCAAAGGATCAAT 1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * 36178 ACCGGGAGTGATACAGTTGTTATACCAGTCAAAGGATCAAT 1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT *** * 36219 ACCCCAGTCATACAGTTGTTATACTAGTCAAGGGATCAAT 1 ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * 36259 GCCAGGAGTCATACAGTTGTTACACTAGTCAAGGGATCAAT 1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * 36300 ACCAGGAGTCATACAGTTGTTATATACCAATCAAGGGATCAAT 1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT * 36343 ACCAGGAGTCATACAGTTGTAATACTAGTCAGTCAAGGGATCAAT 1 A-CAGGAGTCATACAGTTGT--TA-TA-CCAGTCAAGGGATCAAT * * 36388 ACCAGGAGTCATACAGATGTTATACTAGTCAAGGGATCAAT 1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * 36429 GCCAGGAGTCATACAGTTGTTATGCCAGTCAAGGGATCAAT 1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * 36470 ACCGGGAGTGATACAGTTGTTATACCAGTCAAAGGATCAAT 1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * 36511 ACCAGGAGTCATACAGTTGTTATACCAGTCAAAGGATCAAT 1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * 36552 ACCAGGAGTCATACAGTTGGAATACTAGTCAGTCAAGGGATCAAT 1 A-CAGGAGTCATACAGTT-G-TTA-TA-CCAGTCAAGGGATCAAT * * 36597 GCCAGGAGTCATACAGTTGTTATACCAGTCAATGGATCAAT 1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT * * * 36638 ACCGGGAGTCATACAGCTGTTATATACCAGTCAAGAGATCAAT 1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT 36681 A 1 A 36682 TATAAATAGT Statistics Matches: 666, Mismatches: 85, Indels: 69 0.81 0.10 0.08 Matches are distributed among these distances: 31 15 0.02 33 1 0.00 34 6 0.01 35 2 0.00 36 1 0.00 38 2 0.00 39 3 0.00 40 42 0.06 41 349 0.52 42 12 0.02 43 163 0.24 44 5 0.01 45 65 0.10 ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25 Consensus pattern (40 bp): ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT Found at i:46950 original size:23 final size:23 Alignment explanation

Indices: 46922--47121 Score: 171 Period size: 23 Copynumber: 8.7 Consensus size: 23 46912 TATTTCTTAA * 46922 TGACAATTGCTGTCTAGTCCTAC 1 TGACAATTGCTGTCTATTCCTAC * 46945 TTACAATTGCTGTCTAATTCCTAC 1 TGACAATTGCTGTCT-ATTCCTAC * * 46969 TGAC-TTTGCTGTCTTTTTCCTAC 1 TGACAATTGCTGTC-TATTCCTAC * * * 46992 TGACAATTGTTAG-ATATT-CTGC 1 TGACAATTGCT-GTCTATTCCTAC * 47014 TGACAATTGCTATC---TCCTAC 1 TGACAATTGCTGTCTATTCCTAC ** * * 47034 TGGTAATTGCTGTCTTTTTCCTCC 1 TGACAATTGCTGTC-TATTCCTAC * 47058 TGACAATTGCTGTCTATTCCTGC 1 TGACAATTGCTGTCTATTCCTAC 47081 TGACAATTGCTGTCTATTTCCTAC 1 TGACAATTGCTGTCTA-TTCCTAC * 47105 AT-ACAATTACTGTCTAT 1 -TGACAATTGCTGTCTAT 47122 CTCTTCACCT Statistics Matches: 141, Mismatches: 24, Indels: 24 0.75 0.13 0.13 Matches are distributed among these distances: 19 1 0.01 20 14 0.10 22 13 0.09 23 60 0.43 24 51 0.36 25 2 0.01 ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42 Consensus pattern (23 bp): TGACAATTGCTGTCTATTCCTAC Found at i:47101 original size:47 final size:47 Alignment explanation

Indices: 46922--47121 Score: 173 Period size: 47 Copynumber: 4.4 Consensus size: 47 46912 TATTTCTTAA * * * * 46922 TGACAATTGCTGTCTAGTCCTACTTACAATTGCTGTCTAATTCCTAC 1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC * * ** * 46969 TGAC-TTTGCTGTCTTTTTCCTACTGACAATTG-T-TAGATATT-CTGC 1 TGACAATTGCTGTC-TATTCCTACTGACAATTGCTGTCTAT-TTCCTCC * ** * 47014 TGACAATTGCTATC---TCCTACTGGTAATTGCTGTCTTTTTCCTCC 1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC * * 47058 TGACAATTGCTGTCTATTCCTGCTGACAATTGCTGTCTATTTCCTACA 1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCT-CC * 47106 T-ACAATTACTGTCTAT 1 TGACAATTGCTGTCTAT 47122 CTCTTCACCT Statistics Matches: 120, Mismatches: 23, Indels: 20 0.74 0.14 0.12 Matches are distributed among these distances: 42 13 0.11 43 3 0.03 44 18 0.15 45 9 0.08 46 18 0.15 47 57 0.47 48 2 0.02 ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42 Consensus pattern (47 bp): TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC Found at i:52784 original size:19 final size:19 Alignment explanation

Indices: 52760--52816 Score: 98 Period size: 19 Copynumber: 3.0 Consensus size: 19 52750 ACAGAGATGA 52760 CTAGATGTACAGGTATTAC 1 CTAGATGTACAGGTATTAC 52779 CTAGATGTACAGGTATTAC 1 CTAGATGTACAGGTATTAC 52798 CTA-ATTGTACAGGTATTAC 1 CTAGA-TGTACAGGTATTAC 52817 TAACCATTCC Statistics Matches: 37, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 18 1 0.03 19 36 0.97 ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33 Consensus pattern (19 bp): CTAGATGTACAGGTATTAC Found at i:53961 original size:180 final size:182 Alignment explanation

Indices: 53651--54007 Score: 666 Period size: 180 Copynumber: 2.0 Consensus size: 182 53641 AAATTACACG 53651 GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAATGAT 1 GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAA-GAT 53716 CAGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAA 65 -AGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAA 53781 ATCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC 129 ATCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC 53835 NGGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTC-A-AT 1 -GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAAGAT 53898 -GAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAA 65 AGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAA 53962 TCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCC 130 TCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCC 54008 NTACATCATG Statistics Matches: 172, Mismatches: 0, Indels: 5 0.97 0.00 0.03 Matches are distributed among these distances: 180 110 0.64 182 2 0.01 184 1 0.01 185 59 0.34 ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29 Consensus pattern (182 bp): GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAAGATA GAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAAT CTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC Found at i:54389 original size:2 final size:2 Alignment explanation

Indices: 54382--54436 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 54372 TATACAAAAA 54382 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 54424 CT CT CT CT CT CT C 1 CT CT CT CT CT CT C 54437 ATTAATTTTT 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:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:58432 original size:2 final size:2 Alignment explanation

Indices: 58425--58465 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 58415 TTACAAGAAA 58425 CT CT CT CT CT CT CT 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 CT CT CT CT CT CT CT C 58466 ATTTTCAGCA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:63462 original size:133 final size:134 Alignment explanation

Indices: 63223--63490 Score: 520 Period size: 133 Copynumber: 2.0 Consensus size: 134 63213 AAGTAGAAAA 63223 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT 1 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT * 63288 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTTAATGA 66 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA 63353 TATG 131 TATG 63357 AGCACAGGGACATTATCCGACATACCTTGGAGAC-TAACCTGATCGGCGCATTTATTCATCAGGT 1 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT 63421 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA 66 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA 63486 TATG 131 TATG 63490 A 1 A 63491 ATACATATAA Statistics Matches: 133, Mismatches: 1, Indels: 1 0.99 0.01 0.01 Matches are distributed among these distances: 133 99 0.74 134 34 0.26 ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30 Consensus pattern (134 bp): AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA TATG Found at i:63812 original size:32 final size:32 Alignment explanation

Indices: 63776--63842 Score: 125 Period size: 32 Copynumber: 2.1 Consensus size: 32 63766 TACATGGATG * 63776 TAGGCTATGCCTGTCCACTTCTCAAAAGAGAA 1 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA 63808 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA 1 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA 63840 TAG 1 TAG 63843 AATTATAGTC Statistics Matches: 34, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 34 1.00 ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25 Consensus pattern (32 bp): TAGGCTATACCTGTCCACTTCTCAAAAGAGAA Found at i:71320 original size:12 final size:12 Alignment explanation

Indices: 71303--71327 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 71293 ATAAGATTGG 71303 TTTGTTTAATGT 1 TTTGTTTAATGT 71315 TTTGTTTAATGT 1 TTTGTTTAATGT 71327 T 1 T 71328 ACCAAATCTT Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68 Consensus pattern (12 bp): TTTGTTTAATGT Found at i:73056 original size:8 final size:8 Alignment explanation

Indices: 73043--73087 Score: 72 Period size: 8 Copynumber: 5.6 Consensus size: 8 73033 TGGTTTCACC 73043 CTGTCCGT 1 CTGTCCGT * 73051 CTGTCCTT 1 CTGTCCGT * 73059 CTGTCTGT 1 CTGTCCGT 73067 CTGTCCGT 1 CTGTCCGT 73075 CTGTCCGT 1 CTGTCCGT 73083 CTGTC 1 CTGTC 73088 TGTAGACGCA Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 8 33 1.00 ACGTcount: A:0.00, C:0.36, G:0.22, T:0.42 Consensus pattern (8 bp): CTGTCCGT Found at i:73067 original size:4 final size:4 Alignment explanation

Indices: 73043--73090 Score: 53 Period size: 4 Copynumber: 12.0 Consensus size: 4 73033 TGGTTTCACC * * * 73043 CTGT CCGT CTGT CCT-T CTGT CTGT CTGT CCGT CTGT CCGT CTGT CTGT 1 CTGT CTGT CTGT -CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT 73091 AGACGCAACT Statistics Matches: 36, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 3 2 0.06 4 32 0.89 5 2 0.06 ACGTcount: A:0.00, C:0.33, G:0.23, T:0.44 Consensus pattern (4 bp): CTGT Found at i:74407 original size:24 final size:24 Alignment explanation

Indices: 74363--74409 Score: 69 Period size: 24 Copynumber: 2.0 Consensus size: 24 74353 TTGATATTTA * 74363 TTTTTAATAAATAATATAATAACT 1 TTTTTAATAAAGAATATAATAACT 74387 TTTTTAATAAAAGAATA-AATAAC 1 TTTTTAAT-AAAGAATATAATAAC 74410 CAATAACAAT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 24 14 0.67 25 7 0.33 ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40 Consensus pattern (24 bp): TTTTTAATAAAGAATATAATAACT Found at i:75509 original size:51 final size:51 Alignment explanation

Indices: 75433--75562 Score: 224 Period size: 51 Copynumber: 2.5 Consensus size: 51 75423 TACCTTCAGG * * * 75433 ATCTAAGTGATAAAGTTAATGCAGTACAAATGCAGTACCTTTGATGCCTGT 1 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT 75484 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT 1 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT * 75535 ATCTAAATGATAAAGATAGTGCAGTACA 1 ATCTAAATGATAAAGATAATGCAGTACA 75563 CCTATGACAG Statistics Matches: 75, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 51 75 1.00 ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28 Consensus pattern (51 bp): ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT Found at i:76449 original size:24 final size:23 Alignment explanation

Indices: 76383--76452 Score: 81 Period size: 24 Copynumber: 3.0 Consensus size: 23 76373 AAGGCCTCTG 76383 GCAAACAGTTGCCGCAAATTT-- 1 GCAAACAGTTGCCGCAAATTTGC * * * 76404 GCAGAGAGTTTGTCGCAAATTTGC 1 GCAAACAG-TTGCCGCAAATTTGC 76428 GACAAACAGTTGCCGCAAATTTGC 1 G-CAAACAGTTGCCGCAAATTTGC 76452 G 1 G 76453 GCAGGTTCAG Statistics Matches: 39, Mismatches: 6, Indels: 5 0.78 0.12 0.10 Matches are distributed among these distances: 21 6 0.15 22 12 0.31 24 16 0.41 25 5 0.13 ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24 Consensus pattern (23 bp): GCAAACAGTTGCCGCAAATTTGC Found at i:76511 original size:59 final size:59 Alignment explanation

Indices: 76437--76693 Score: 442 Period size: 59 Copynumber: 4.4 Consensus size: 59 76427 CGACAAACAG * * 76437 TTGCCGCAAATTTGCGGCAGGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT 1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT * * * 76496 TTGCAGCAAAGTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGGAAACTGT 1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT * 76555 TTGCGGCAAATTTGCCGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT 1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT * 76614 TTGCGGCAAATTTGCAGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT 1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT * 76673 TTGCGGCAAATTTGCCGCAAG 1 TTGCGGCAAATTTGCGGCAAG 76694 CTTACAGATA Statistics Matches: 188, Mismatches: 10, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 59 188 1.00 ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30 Consensus pattern (59 bp): TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT Found at i:79268 original size:16 final size:15 Alignment explanation

Indices: 79232--79268 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 15 79222 CTGGTGGATG 79232 CTGGAGAAGTCGTAT 1 CTGGAGAAGTCGTAT 79247 CATGGAGAAGTCGTACT 1 C-TGGAGAAGTCGTA-T 79264 CTGGA 1 CTGGA 79269 AAAATCATAA Statistics Matches: 20, Mismatches: 0, Indels: 3 0.87 0.00 0.13 Matches are distributed among these distances: 15 1 0.05 16 17 0.85 17 2 0.10 ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24 Consensus pattern (15 bp): CTGGAGAAGTCGTAT Found at i:80509 original size:17 final size:17 Alignment explanation

Indices: 80487--80521 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 17 80477 AACTTTGTGG * 80487 GTGCGTATTATACACGA 1 GTGCGTACTATACACGA 80504 GTGCGTACTATACACGA 1 GTGCGTACTATACACGA 80521 G 1 G 80522 ACATTACGGT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 17 1.00 ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26 Consensus pattern (17 bp): GTGCGTACTATACACGA Found at i:84573 original size:70 final size:70 Alignment explanation

Indices: 84460--84599 Score: 208 Period size: 70 Copynumber: 2.0 Consensus size: 70 84450 TTTATGTGTC * * * ** 84460 AGCTTGCGTGATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGTAACTTATTGTTTGAATCA 1 AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA 84525 CAATG 66 CAATG * * * 84530 AGCTTGCGTAATGTTCCAAAGATTTAAATTCTCAATTGCTTGGTGGCAGCTAAACGTTTGAATCA 1 AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA 84595 CAATG 66 CAATG 84600 CAAGATGAGC Statistics Matches: 62, Mismatches: 8, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 70 62 1.00 ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34 Consensus pattern (70 bp): AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA CAATG Found at i:85187 original size:117 final size:118 Alignment explanation

Indices: 84974--85216 Score: 407 Period size: 117 Copynumber: 2.1 Consensus size: 118 84964 GGGAATCTGG * * * * 84974 CAGGTAATCATAATAAACATTTTTTTAGATGATATATTAAATACACAAAATGGCCCAAAAGATAA 1 CAGGCAATCATAATAAACA-TTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAA 85039 ATTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA 65 ATTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA * 85093 TAGGCAATCATAATAAACA-TTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA 1 CAGGCAATCATAATAAACATTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA * * 85157 TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATGACAAGATTGAAAGA 66 TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA 85210 CAGGCAA 1 CAGGCAA 85217 AAGATGCTTA Statistics Matches: 116, Mismatches: 8, Indels: 2 0.92 0.06 0.02 Matches are distributed among these distances: 117 99 0.85 119 17 0.15 ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24 Consensus pattern (118 bp): CAGGCAATCATAATAAACATTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA Found at i:88322 original size:16 final size:18 Alignment explanation

Indices: 88289--88327 Score: 55 Period size: 16 Copynumber: 2.3 Consensus size: 18 88279 TTTGTACATC 88289 AAAAAAGAAAGAAAAAGA 1 AAAAAAGAAAGAAAAAGA * 88307 AAAAAAG-AAG-ATAAGA 1 AAAAAAGAAAGAAAAAGA 88323 AAAAA 1 AAAAA 88328 TCAGCTAAAA Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 16 10 0.50 17 3 0.15 18 7 0.35 ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03 Consensus pattern (18 bp): AAAAAAGAAAGAAAAAGA Found at i:89240 original size:12 final size:12 Alignment explanation

Indices: 89223--89247 Score: 50 Period size: 12 Copynumber: 2.1 Consensus size: 12 89213 GAAAAAGTTC 89223 ATGCTTTAAGTG 1 ATGCTTTAAGTG 89235 ATGCTTTAAGTG 1 ATGCTTTAAGTG 89247 A 1 A 89248 AACTGAATGC Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 13 1.00 ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40 Consensus pattern (12 bp): ATGCTTTAAGTG Found at i:91232 original size:35 final size:35 Alignment explanation

Indices: 91185--91681 Score: 852 Period size: 35 Copynumber: 14.1 Consensus size: 35 91175 ATTGTGTTGT * * * 91185 AAAAGTGTGGGTGTAAGAAAATGGGGAAAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA * 91220 AAAAGTGGGGGTGTAAGAAAAAGGGGAAAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91255 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91290 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91325 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91360 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA * 91395 AAAAGTGGGGGTGTAAGAAAAAGGGGAAAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91430 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA ** 91465 AAAAAAGGGGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA ** 91500 AAAAGTGTTGGTGTAAGAAAAAGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91535 AAAAGTGGGGGTGTAAGAAAAAGGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAA-GGGGATAAGACAA 91571 AAAAGTGGGGGTGTAAGAAAAAGGGGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAA-GGGGATAAGACAA ** 91607 AAAAGTGGGGGTGTAAGAAAAAGGGGATATTACAAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGAC-AA * 91643 AAAAGTGTGGGTGTAAGAAAAA-GGGATAAGACAA 1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA 91677 AAAAG 1 AAAAG 91682 ATCGAGCGAA Statistics Matches: 442, Mismatches: 18, Indels: 5 0.95 0.04 0.01 Matches are distributed among these distances: 34 7 0.02 35 341 0.77 36 94 0.21 ACGTcount: A:0.49, C:0.03, G:0.36, T:0.12 Consensus pattern (35 bp): AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA Found at i:91566 original size:15 final size:15 Alignment explanation

Indices: 91548--91608 Score: 50 Period size: 18 Copynumber: 3.6 Consensus size: 15 91538 AGTGGGGGTG 91548 TAAGAAAAAGGGGGA 1 TAAGAAAAAGGGGGA * 91563 TAAGACAAAAAAGTGGGGGTG 1 TAAG---AAAAA--GGGGG-A 91584 TAAGAAAAAGGGGGA 1 TAAGAAAAAGGGGGA 91599 TAAGACAAAA 1 TAAGA-AAAA 91609 AAGTGGGGGT Statistics Matches: 37, Mismatches: 2, Indels: 13 0.71 0.04 0.25 Matches are distributed among these distances: 15 9 0.24 16 9 0.24 18 10 0.27 20 5 0.14 21 4 0.11 ACGTcount: A:0.52, C:0.03, G:0.34, T:0.10 Consensus pattern (15 bp): TAAGAAAAAGGGGGA Found at i:104183 original size:192 final size:191 Alignment explanation

Indices: 103856--104239 Score: 759 Period size: 192 Copynumber: 2.0 Consensus size: 191 103846 GGATATCTAT 103856 GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA 1 GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA 103921 TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT 66 TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT 103986 TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG 131 TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG 104047 NGCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTC 1 -GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTC 104112 ATCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGT 65 ATCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGT 104177 TTGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG 130 TTGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG 104239 G 1 G 104240 GGGGGGGGGG Statistics Matches: 192, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 191 1 0.01 192 191 0.99 ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36 Consensus pattern (191 bp): GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG Found at i:105718 original size:191 final size:190 Alignment explanation

Indices: 105393--105774 Score: 755 Period size: 191 Copynumber: 2.0 Consensus size: 190 105383 AAGTTGACTT 105393 TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC 1 TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC 105458 ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT 66 ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT 105523 TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG 131 TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG 105583 TNATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATG 1 T-ATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATG 105648 CATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATAT 65 CATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATAT 105713 TTTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG 130 TTTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG 105774 T 1 T 105775 TTTTTTTTTA Statistics Matches: 191, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 190 1 0.01 191 190 0.99 ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33 Consensus pattern (190 bp): TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG Found at i:107233 original size:11 final size:11 Alignment explanation

Indices: 107217--107248 Score: 64 Period size: 11 Copynumber: 2.9 Consensus size: 11 107207 CTGCATTTGC 107217 CGTGGGACTTA 1 CGTGGGACTTA 107228 CGTGGGACTTA 1 CGTGGGACTTA 107239 CGTGGGACTT 1 CGTGGGACTT 107249 GTTTTCCCCG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 21 1.00 ACGTcount: A:0.16, C:0.19, G:0.38, T:0.28 Consensus pattern (11 bp): CGTGGGACTTA Found at i:118161 original size:2 final size:2 Alignment explanation

Indices: 118156--118191 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 118146 ACTAACACAC 118156 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 118192 GCCGGTAAAA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:119166 original size:32 final size:32 Alignment explanation

Indices: 119125--119219 Score: 154 Period size: 32 Copynumber: 3.0 Consensus size: 32 119115 ATCAGAGTCA * 119125 TAAATAACATCTATATACGATGTTGTAACTCC 1 TAAATAACATCTATATACGGTGTTGTAACTCC 119157 TAAATAACATCTATATACGGTGTTGTAACTCC 1 TAAATAACATCTATATACGGTGTTGTAACTCC * * * 119189 TAAGTAACATCTATATGCGGTTTTGTAACTC 1 TAAATAACATCTATATACGGTGTTGTAACTC 119220 GATCCTAAGC Statistics Matches: 59, Mismatches: 4, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 59 1.00 ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36 Consensus pattern (32 bp): TAAATAACATCTATATACGGTGTTGTAACTCC Found at i:134392 original size:2 final size:2 Alignment explanation

Indices: 134385--134436 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 134375 TTTAGTGGTG 134385 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 134427 GA GA GA GA GA 1 GA GA GA GA GA 134437 AATCATAAAC Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:134686 original size:4 final size:4 Alignment explanation

Indices: 134677--134719 Score: 86 Period size: 4 Copynumber: 10.8 Consensus size: 4 134667 TAAAAACAAT 134677 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA 1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA 134720 AGATCATCCG Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 39 1.00 ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00 Consensus pattern (4 bp): AAAC Found at i:135349 original size:251 final size:251 Alignment explanation

Indices: 134906--135405 Score: 1000 Period size: 251 Copynumber: 2.0 Consensus size: 251 134896 ATGCCCGACA 134906 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA 1 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA 134971 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC 66 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC 135036 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT 131 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT 135101 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC 196 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC 135157 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA 1 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA 135222 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC 66 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC 135287 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT 131 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT 135352 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGC 196 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGC 135406 ATGGATTAAA Statistics Matches: 249, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 251 249 1.00 ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32 Consensus pattern (251 bp): GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC Found at i:153885 original size:38 final size:35 Alignment explanation

Indices: 153842--154014 Score: 103 Period size: 38 Copynumber: 4.6 Consensus size: 35 153832 GATTTCTTGC * 153842 AAGATTTCTAGGATATCCATCCTCAGATATATTATGAA 1 AAGATTTCT-GGATATCTATCCTCAGATAT-TTAT-AA * * * * * * 153880 AAGATTACTGGAATATCTATTCTTAGATGTCTTCCTAC 1 AAGATTTCTGG-ATATCTATCCTCAGATAT-TT-ATAA * ** * * 153918 AAGATTTCTGAGATATCTTTCCTTTGATGTCTACTAA 1 AAGATTTCTG-GATATCTATCCTCAGATATTTA-TAA * * * 153955 AAAATTTCTAGGATATCCATCCTCAGATATTTTATTAC 1 AAGATTTCT-GGATATCTATCCTCAGATA-TTTA-TAA 153993 AAGATTTCTGGGATATCTATCC 1 AAGATTTCT-GGATATCTATCC 154015 AAATAATTTA Statistics Matches: 102, Mismatches: 27, Indels: 12 0.72 0.19 0.09 Matches are distributed among these distances: 37 26 0.25 38 74 0.73 39 2 0.02 ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39 Consensus pattern (35 bp): AAGATTTCTGGATATCTATCCTCAGATATTTATAA Found at i:155099 original size:32 final size:32 Alignment explanation

Indices: 155058--155156 Score: 189 Period size: 32 Copynumber: 3.1 Consensus size: 32 155048 AAGGATGATT 155058 ATTTAGTGAGGGACCTTAAACTGTACTATTTC 1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC * 155090 ATTTAGTGAGGCACCTTAAACTGTACTATTTC 1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC 155122 ATTTAGTGAGGGACCTTAAACTGTACTATTTC 1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC 155154 ATT 1 ATT 155157 AAGAAACAAT Statistics Matches: 65, Mismatches: 2, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 32 65 1.00 ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38 Consensus pattern (32 bp): ATTTAGTGAGGGACCTTAAACTGTACTATTTC Found at i:155255 original size:21 final size:21 Alignment explanation

Indices: 155229--155273 Score: 90 Period size: 21 Copynumber: 2.1 Consensus size: 21 155219 TAAGCTGCAG 155229 TAACAATCCCAGTCAGGGCAA 1 TAACAATCCCAGTCAGGGCAA 155250 TAACAATCCCAGTCAGGGCAA 1 TAACAATCCCAGTCAGGGCAA 155271 TAA 1 TAA 155274 AACCCTCACG Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16 Consensus pattern (21 bp): TAACAATCCCAGTCAGGGCAA Found at i:157303 original size:23 final size:23 Alignment explanation

Indices: 157277--157320 Score: 70 Period size: 23 Copynumber: 1.9 Consensus size: 23 157267 AGTTATATTT * 157277 TTGGAGTAAAAATAGTTTCTGCC 1 TTGGAGTAAAAACAGTTTCTGCC * 157300 TTGGAGTAAAGACAGTTTCTG 1 TTGGAGTAAAAACAGTTTCTG 157321 TATTGTAACC Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 23 19 1.00 ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34 Consensus pattern (23 bp): TTGGAGTAAAAACAGTTTCTGCC Found at i:158168 original size:2 final size:2 Alignment explanation

Indices: 158163--158208 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 158153 TCTTATAATT 158163 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 158205 GA GA 1 GA GA 158209 CACTACACCC Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:158335 original size:2 final size:2 Alignment explanation

Indices: 158328--158354 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 158318 NNNNNNNNNN 158328 AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG A 158355 AACCTAACCC 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:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:158427 original size:2 final size:2 Alignment explanation

Indices: 158422--158460 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 158412 TTTTTTGATT 158422 GA GA GA GA GA GA GA 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 GA GA GA GA GA GA GA G 158461 GAATTAGCAT Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:160243 original size:2 final size:2 Alignment explanation

Indices: 160238--160264 Score: 54 Period size: 2 Copynumber: 13.5 Consensus size: 2 160228 TATATAATAA 160238 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 160265 AAAACATCTT 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:161561 original size:16 final size:15 Alignment explanation

Indices: 161537--161574 Score: 58 Period size: 16 Copynumber: 2.5 Consensus size: 15 161527 CTTATATTTG 161537 TGTCCATCCATCCATC 1 TGTCCATCCATCC-TC * 161553 TGTCTATCCATCCTC 1 TGTCCATCCATCCTC 161568 TGTCCAT 1 TGTCCAT 161575 TTATTCTCTC Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 15 8 0.40 16 12 0.60 ACGTcount: A:0.16, C:0.39, G:0.08, T:0.37 Consensus pattern (15 bp): TGTCCATCCATCCTC Found at i:161586 original size:2 final size:2 Alignment explanation

Indices: 161579--161672 Score: 147 Period size: 2 Copynumber: 47.5 Consensus size: 2 161569 GTCCATTTAT * 161579 TC TC TC TC TT TC TC TC -C ATC TC TC TC TC -C 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 * 161620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 161662 TC TC TC TC TC T 1 TC TC TC TC TC T 161673 AACAATAAAC Statistics Matches: 85, Mismatches: 4, Indels: 6 0.89 0.04 0.06 Matches are distributed among these distances: 1 2 0.02 2 82 0.96 3 1 0.01 ACGTcount: A:0.01, C:0.48, G:0.01, T:0.50 Consensus pattern (2 bp): TC Found at i:161784 original size:16 final size:16 Alignment explanation

Indices: 161763--161793 Score: 62 Period size: 16 Copynumber: 1.9 Consensus size: 16 161753 AATCCACACC 161763 GCACATTCAAAACCCA 1 GCACATTCAAAACCCA 161779 GCACATTCAAAACCC 1 GCACATTCAAAACCC 161794 CATTCTTCTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.42, C:0.39, G:0.06, T:0.13 Consensus pattern (16 bp): GCACATTCAAAACCCA Found at i:166208 original size:28 final size:25 Alignment explanation

Indices: 166150--166208 Score: 66 Period size: 25 Copynumber: 2.3 Consensus size: 25 166140 TCTTATGTCA 166150 CTATCATTTATTAATCATTTATCAT 1 CTATCATTTATTAATCATTTATCAT * * 166175 C-ATCATTATTTTAATCATCGTTTTCAT 1 CTATCATT-TATTAATCAT--TTATCAT 166202 CTATCAT 1 CTATCAT 166209 CATCTGAATG Statistics Matches: 28, Mismatches: 2, Indels: 5 0.80 0.06 0.14 Matches are distributed among these distances: 24 6 0.21 25 10 0.36 27 7 0.25 28 5 0.18 ACGTcount: A:0.29, C:0.19, G:0.02, T:0.51 Consensus pattern (25 bp): CTATCATTTATTAATCATTTATCAT Found at i:177778 original size:2 final size:2 Alignment explanation

Indices: 177771--177818 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 177761 TACATGCCCC 177771 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 177813 CT CT CT 1 CT CT CT 177819 ACTACCCCTC 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:178029 original size:2 final size:2 Alignment explanation

Indices: 178022--178149 Score: 89 Period size: 2 Copynumber: 63.0 Consensus size: 2 178012 NNNNNNNNNN * 178022 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CA CAT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T * ** * * * * * * * * 178065 CA CT CT CT GAG GT CA CAT CAG GT CA CA CA CT -T CT -T CT AT CT 1 CT CT CT CT -CT CT CT C-T C-T CT CT CT CT CT CT CT CT CT CT CT * 178106 GT 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 178148 CT 1 CT 178150 TTACATGCCT Statistics Matches: 100, Mismatches: 21, Indels: 10 0.76 0.16 0.08 Matches are distributed among these distances: 1 2 0.02 2 95 0.95 3 3 0.03 ACGTcount: A:0.09, C:0.44, G:0.05, T:0.43 Consensus pattern (2 bp): CT Found at i:179063 original size:184 final size:187 Alignment explanation

Indices: 178739--179111 Score: 576 Period size: 184 Copynumber: 2.0 Consensus size: 187 178729 TAAACAGGTA 178739 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGTAATATGTACAGTATGTATTGA 1 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTG--ATATGTACAGTATGTATTGA ** 178804 ATATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAATTGTGACTCTACATTGACAG 64 ATATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAA-TAAGACTCTACATTGACAG * 178869 ATACTGAGGTGTCAAGTTATCCAGGTCACACTGTTAT-CAGAGTAAGACTGATTATAGTG 128 ATACTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGTG * * 178928 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGAGGGATTATTG-TAT-TACA-TATGTATTGAAT 1 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGATATGTACAGTATGTATTGAAT * * 178990 ATCACATGTACACTATCAATATCTTAATAGATATATAGAGCCAAA-AAGACTCTACATTGACAGA 66 ATCACA--TACACTATCAATATCTTAAAAGATATACAGAGCCAAATAAGACTCTACATTGACAGA * * * 179054 TATTGAGGTGTCAATTTATCCAGGTCACACTGTTATAAAGAGTTAGACTGATTATAGT 129 TACTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGT 179112 ATTTCATTGG Statistics Matches: 171, Mismatches: 10, Indels: 10 0.90 0.05 0.05 Matches are distributed among these distances: 184 69 0.40 185 23 0.13 186 38 0.22 189 41 0.24 ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32 Consensus pattern (187 bp): TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGATATGTACAGTATGTATTGAAT ATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAATAAGACTCTACATTGACAGATA CTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGTG Found at i:184162 original size:2 final size:2 Alignment explanation

Indices: 184155--184195 Score: 66 Period size: 2 Copynumber: 20.5 Consensus size: 2 184145 TCTCCACAGC 184155 CT CT CT CT CT CT CT CT CT CT CT CT CT CGT -T CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT C 184196 GCGTTGTCTC Statistics Matches: 37, Mismatches: 0, Indels: 4 0.90 0.00 0.10 Matches are distributed among these distances: 1 1 0.03 2 35 0.95 3 1 0.03 ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49 Consensus pattern (2 bp): CT Found at i:184200 original size:16 final size:16 Alignment explanation

Indices: 184155--184205 Score: 70 Period size: 16 Copynumber: 3.3 Consensus size: 16 184145 TCTCCACAGC 184155 CTCTCTCTCTCTC--T 1 CTCTCTCTCTCTCGTT 184169 CTCTCTCTCTCTCGTT 1 CTCTCTCTCTCTCGTT * 184185 CTCTCTCTCTCGCGTT 1 CTCTCTCTCTCTCGTT * 184201 GTCTC 1 CTCTC 184206 AAGCGCGTGC Statistics Matches: 33, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 14 13 0.39 16 20 0.61 ACGTcount: A:0.00, C:0.45, G:0.08, T:0.47 Consensus pattern (16 bp): CTCTCTCTCTCTCGTT Found at i:184743 original size:2 final size:2 Alignment explanation

Indices: 184736--184783 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 184726 TAGCATTCAC 184736 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 184778 GA GA GA 1 GA GA GA 184784 TTAACTAAAC 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:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:185495 original size:35 final size:35 Alignment explanation

Indices: 185416--185495 Score: 88 Period size: 35 Copynumber: 2.3 Consensus size: 35 185406 AACTTCACGT * * * * 185416 AACTCGCTATAGCGCTAATTAGCAAAACTTAACGC 1 AACTCGCCATAGCGCTAATTAACAAAACCTAACAC * * * * 185451 GACTAGCCATAGCGCTAATTAACACAACCTCACAC 1 AACTCGCCATAGCGCTAATTAACAAAACCTAACAC 185486 AACTCGCCAT 1 AACTCGCCAT 185496 TGTGCTAACA Statistics Matches: 35, Mismatches: 10, Indels: 0 0.78 0.22 0.00 Matches are distributed among these distances: 35 35 1.00 ACGTcount: A:0.36, C:0.31, G:0.12, T:0.20 Consensus pattern (35 bp): AACTCGCCATAGCGCTAATTAACAAAACCTAACAC Found at i:185713 original size:31 final size:31 Alignment explanation

Indices: 185675--185754 Score: 97 Period size: 31 Copynumber: 2.6 Consensus size: 31 185665 TTAACATCAT * 185675 ATAACTCGCTATTGCGCTAACACAACTGCAC 1 ATAACTCGCAATTGCGCTAACACAACTGCAC * ** 185706 ATAACTCGCAAATGTTCTAACACAACTGCAC 1 ATAACTCGCAATTGCGCTAACACAACTGCAC * * * 185737 AAAACTCGCCATCGCGCT 1 ATAACTCGCAATTGCGCT 185755 TTTTGACACG Statistics Matches: 39, Mismatches: 10, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 31 39 1.00 ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21 Consensus pattern (31 bp): ATAACTCGCAATTGCGCTAACACAACTGCAC Found at i:186441 original size:26 final size:26 Alignment explanation

Indices: 186407--186465 Score: 109 Period size: 26 Copynumber: 2.3 Consensus size: 26 186397 GCATCACAAG * 186407 TTATGTTAAGTAGAATGAAAATTTTA 1 TTATTTTAAGTAGAATGAAAATTTTA 186433 TTATTTTAAGTAGAATGAAAATTTTA 1 TTATTTTAAGTAGAATGAAAATTTTA 186459 TTATTTT 1 TTATTTT 186466 CTCTTATTCT Statistics Matches: 32, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 26 32 1.00 ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49 Consensus pattern (26 bp): TTATTTTAAGTAGAATGAAAATTTTA Found at i:187759 original size:2 final size:2 Alignment explanation

Indices: 187754--187800 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 187744 ATCATATATA 187754 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 187796 TC TC T 1 TC TC T 187801 GCATTCACCC Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:190829 original size:2 final size:2 Alignment explanation

Indices: 190824--190849 Score: 52 Period size: 2 Copynumber: 13.0 Consensus size: 2 190814 ATTAATTCAA 190824 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 190850 NNNNNNNNNN Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 24 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:193731 original size:2 final size:2 Alignment explanation

Indices: 193689--193719 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 193679 ATATCTTCAT 193689 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 193720 ATGAAGGAGA Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:194786 original size:2 final size:2 Alignment explanation

Indices: 194779--194848 Score: 140 Period size: 2 Copynumber: 35.0 Consensus size: 2 194769 TGAATTATTT 194779 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 194821 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 194849 NNNNNNNNNN Statistics Matches: 68, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 68 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:197165 original size:21 final size:21 Alignment explanation

Indices: 197136--197242 Score: 108 Period size: 21 Copynumber: 5.0 Consensus size: 21 197126 GCTACACGCT * * 197136 CGCTAAACGGTTCACACGAAA 1 CGCTGAACGGTTTACACGAAA 197157 CGCTGAACGGTTTACACGAAA 1 CGCTGAACGGTTTACACGAAA ** * * 197178 CGCTGCGCGCTTTGTC-CGAAA 1 CGCTGAACGGTTT-ACACGAAA * 197199 CGCTTTGAAGCGATTTACACGAAA 1 CGC--TGAA-CGGTTTACACGAAA 197223 CGCTGAACGGTTTACACGAA 1 CGCTGAACGGTTTACACGAA 197243 TGATTAGTAG Statistics Matches: 70, Mismatches: 11, Indels: 10 0.77 0.12 0.11 Matches are distributed among these distances: 21 49 0.70 22 5 0.07 23 3 0.04 24 13 0.19 ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21 Consensus pattern (21 bp): CGCTGAACGGTTTACACGAAA Found at i:199943 original size:75 final size:75 Alignment explanation

Indices: 199820--199972 Score: 261 Period size: 75 Copynumber: 2.0 Consensus size: 75 199810 CTTGTTGAAA * * * * 199820 GTAAAAGGTTCTGAGTTCACCTGTTGTTTTACTATAACTACTGTATTACATTTAATACCATATTT 1 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC 199885 GTATGTACCT 66 GTATGTACCT * 199895 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTTCTGTATTACATTAAATACCATAGTC 1 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC 199960 GTATGTACCT 66 GTATGTACCT 199970 GTA 1 GTA 199973 TGTACAGCTA Statistics Matches: 73, Mismatches: 5, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 75 73 1.00 ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41 Consensus pattern (75 bp): GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC GTATGTACCT Found at i:200688 original size:2 final size:2 Alignment explanation

Indices: 200677--200722 Score: 85 Period size: 2 Copynumber: 23.5 Consensus size: 2 200667 ATCAAAGGTC 200677 AG AG -G 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 200718 AG AG A 1 AG AG A 200723 AAATTGGAAT Statistics Matches: 43, Mismatches: 0, Indels: 2 0.96 0.00 0.04 Matches are distributed among these distances: 1 1 0.02 2 42 0.98 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:200690 original size:198 final size:198 Alignment explanation

Indices: 200339--200708 Score: 686 Period size: 198 Copynumber: 1.9 Consensus size: 198 200329 CAATTTTAGA * 200339 ATTACCGGTATTTCTGTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA 1 ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA 200404 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC 66 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC * * * 200469 ATCAAAGGTCAGAGGTCAGAGAGAGGGCGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG 131 ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG 200534 AAT 196 AAT * 200537 ATTANCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA 1 ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA 200602 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC 66 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC * 200667 ATCAAAGGTCAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGA 131 ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGA 200709 GAGAGAGAGA Statistics Matches: 166, Mismatches: 6, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 198 166 1.00 ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23 Consensus pattern (198 bp): ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG AAT Found at i:205732 original size:8 final size:8 Alignment explanation

Indices: 205685--205825 Score: 160 Period size: 8 Copynumber: 17.6 Consensus size: 8 205675 GCGTCAGGTT * 205685 ATCAATAA 1 ATCAATCA * 205693 ATCCATCA 1 ATCAATCA 205701 ATCAGA-CA 1 ATCA-ATCA * 205709 ATAAATCA 1 ATCAATCA * 205717 GA-CAATAA 1 -ATCAATCA * 205725 ATCAATAA 1 ATCAATCA 205733 ATCAATCA 1 ATCAATCA * 205741 ATCCATCA 1 ATCAATCA 205749 ATCAATCA 1 ATCAATCA 205757 ATCAATCA 1 ATCAATCA * 205765 ATCAACCA 1 ATCAATCA 205773 ATCAATCA 1 ATCAATCA * 205781 ACCAATCA 1 ATCAATCA * 205789 ATCAACCA 1 ATCAATCA 205797 ATCAATCA 1 ATCAATCA 205805 ATCAATCA 1 ATCAATCA * 205813 ACCAATCA 1 ATCAATCA 205821 ATCAA 1 ATCAA 205826 CTGCCGAAGC Statistics Matches: 112, Mismatches: 17, Indels: 8 0.82 0.12 0.06 Matches are distributed among these distances: 7 2 0.02 8 108 0.96 9 2 0.02 ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21 Consensus pattern (8 bp): ATCAATCA Found at i:205739 original size:12 final size:12 Alignment explanation

Indices: 205685--205825 Score: 160 Period size: 12 Copynumber: 11.8 Consensus size: 12 205675 GCGTCAGGTT * * 205685 ATCAATAAATCC 1 ATCAATCAATCA 205697 ATCAATCAGA-CA 1 ATCAATCA-ATCA * 205709 ATAAATCAGA-CA 1 ATCAATCA-ATCA * * 205721 ATAAATCAATAA 1 ATCAATCAATCA * 205733 ATCAATCAATCC 1 ATCAATCAATCA 205745 ATCAATCAATCA 1 ATCAATCAATCA 205757 ATCAATCAATCA 1 ATCAATCAATCA * 205769 ACCAATCAATCA 1 ATCAATCAATCA * 205781 ACCAATCAATCA 1 ATCAATCAATCA * 205793 ACCAATCAATCA 1 ATCAATCAATCA * 205805 ATCAATCAACCA 1 ATCAATCAATCA 205817 ATCAATCAA 1 ATCAATCAA 205826 CTGCCGAAGC Statistics Matches: 116, Mismatches: 11, Indels: 4 0.89 0.08 0.03 Matches are distributed among these distances: 11 1 0.01 12 114 0.98 13 1 0.01 ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21 Consensus pattern (12 bp): ATCAATCAATCA Found at i:205742 original size:20 final size:20 Alignment explanation

Indices: 205685--205825 Score: 160 Period size: 20 Copynumber: 7.0 Consensus size: 20 205675 GCGTCAGGTT * * 205685 ATCAATAAATCCATCAATCA 1 ATCAATCAATCAATCAATCA * * 205705 GA-CAATAAATCAGA-CAATAA 1 -ATCAATCAATCA-ATCAATCA * * 205725 ATCAATAAATCAATCAATCC 1 ATCAATCAATCAATCAATCA 205745 ATCAATCAATCAATCAATCA 1 ATCAATCAATCAATCAATCA * * 205765 ATCAACCAATCAATCAACCA 1 ATCAATCAATCAATCAATCA * 205785 ATCAATCAACCAATCAATCA 1 ATCAATCAATCAATCAATCA * 205805 ATCAATCAACCAATCAATCA 1 ATCAATCAATCAATCAATCA 205825 A 1 A 205826 CTGCCGAAGC Statistics Matches: 106, Mismatches: 11, Indels: 7 0.85 0.09 0.06 Matches are distributed among these distances: 19 2 0.02 20 102 0.96 21 2 0.02 ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21 Consensus pattern (20 bp): ATCAATCAATCAATCAATCA Found at i:208353 original size:2 final size:2 Alignment explanation

Indices: 208346--208398 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 208336 TGAAACTTTG 208346 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 208388 GA GA GA GA GA G 1 GA GA GA GA GA G 208399 GTTTCTCCAT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:210068 original size:50 final size:50 Alignment explanation

Indices: 210016--210645 Score: 946 Period size: 50 Copynumber: 12.6 Consensus size: 50 210006 CAGGATGTAT * * * 210016 GTAGAGAATAACAGCTGTTTTGGTCAAATGTATGAAGG-TTCAGGATAAAT 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTT-AGGATAAAA * 210066 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * 210116 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * 210166 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * 210216 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * * * 210266 GTGGAAAATAACAGTTGTATTGGTCAAATGTATGAAGGCTGAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 210316 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * * 210366 GTAGAAATTAACAGTTGTTTTGGTAAAATGTATGAAGG-TTCAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTT-AGGATAAAA * * * 210416 GTAGAAATTAACAGTTGTTTTGGTCAAATGTATGAAAGCTTAGGATAAAT 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * * 210466 GTAGAAAATAACAGTTGTTTTGGTCAAATGTACGAAGGCTCAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * 210516 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA 1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA * * * * * 210566 GTAAAAAATAACAGTTGTTTTGGTAAAAAAAAGTATGAATG-TTATTG-TAAAA 1 GTAGAAAATAACAGTTGTTTTGGT---CAAATGTATGAAGGCTTA-GGATAAAA * * 210618 ATAGAAAATAACAGTT-TTCTGGTCAAAT 1 GTAGAAAATAACAGTTGTTTTGGTCAAAT 210646 TCTTTATGCA Statistics Matches: 539, Mismatches: 34, Indels: 16 0.92 0.06 0.03 Matches are distributed among these distances: 48 3 0.01 49 2 0.00 50 490 0.91 51 10 0.02 52 22 0.04 53 12 0.02 ACGTcount: A:0.41, C:0.06, G:0.23, T:0.29 Consensus pattern (50 bp): GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA Found at i:214283 original size:2 final size:2 Alignment explanation

Indices: 214278--214334 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 214268 GTGTGATGTC 214278 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 214320 AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG A 214335 TGAATGATTA Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:226589 original size:2 final size:2 Alignment explanation

Indices: 226582--226626 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 226572 TAGCAAAATT 226582 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 226624 GA G 1 GA G 226627 TCATCATTTG Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:226809 original size:4 final size:4 Alignment explanation

Indices: 226800--226870 Score: 142 Period size: 4 Copynumber: 17.8 Consensus size: 4 226790 AAATTAATGA 226800 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT 226848 ATCT ATCT ATCT ATCT ATCT ATC 1 ATCT ATCT ATCT ATCT ATCT ATC 226871 CTTTTTCTAC Statistics Matches: 67, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 67 1.00 ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49 Consensus pattern (4 bp): ATCT Found at i:227864 original size:267 final size:267 Alignment explanation

Indices: 227523--228320 Score: 1560 Period size: 267 Copynumber: 3.0 Consensus size: 267 227513 TTCAGAATAT * 227523 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCTCAAGTAAGCAATGAATTGCGCAATG 1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG * * 227588 GTATTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTATGTTTATTTTATTGTGTTTTATGT 66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT 227653 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA 131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA 227718 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT 196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT 227783 AGAATTA 261 AGAATTA 227790 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG 1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG 227855 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT 66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT 227920 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA 131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA 227985 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT 196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT 228050 AGAATTA 261 AGAATTA 228057 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG 1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG 228122 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT 66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT 228187 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA 131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA * 228252 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTTAAGTTCTGATACTT 196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT 228317 AGAA 261 AGAA 228321 CAGGGAAACA Statistics Matches: 527, Mismatches: 4, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 267 527 1.00 ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36 Consensus pattern (267 bp): AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT AGAATTA Found at i:228827 original size:4 final size:4 Alignment explanation

Indices: 228818--228863 Score: 65 Period size: 4 Copynumber: 11.0 Consensus size: 4 228808 TCTGCACTCC * 228818 AATA AATA AATA AATA ATGTAA AATA AATA AATA AATA AATA AATA 1 AATA AATA AATA AATA A-AT-A AATA AATA AATA AATA AATA AATA 228864 TACAGCTAAC Statistics Matches: 38, Mismatches: 2, Indels: 4 0.86 0.05 0.09 Matches are distributed among these distances: 4 34 0.89 5 2 0.05 6 2 0.05 ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26 Consensus pattern (4 bp): AATA Found at i:230963 original size:2 final size:2 Alignment explanation

Indices: 230956--230989 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 230946 GAAAAATAAT 230956 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 230990 TTGGATAATT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:234350 original size:62 final size:62 Alignment explanation

Indices: 234039--234347 Score: 545 Period size: 62 Copynumber: 5.0 Consensus size: 62 234029 ATAAAGCTAT 234039 AGAGTTTCCCTGAAATATA-TTT-AAAAAAA-ACACCAGTGGTTTCTGTAAATATACATAAA 1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA * 234098 AGAGTTTCCCTGAAATATA-TTTAAAAAAAATACACCAGTGCTTTCTGTAAATACATACATAAA 1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAAT--ATACATAAA 234161 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA 1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA 234223 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA 1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA * * 234285 ACACTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA 1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA 234347 A 1 A 234348 CACCAACGGC Statistics Matches: 241, Mismatches: 4, Indels: 7 0.96 0.02 0.03 Matches are distributed among these distances: 59 22 0.09 60 7 0.03 61 20 0.08 62 132 0.55 63 28 0.12 64 32 0.13 ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31 Consensus pattern (62 bp): AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA Found at i:239798 original size:10 final size:10 Alignment explanation

Indices: 239783--239809 Score: 54 Period size: 10 Copynumber: 2.7 Consensus size: 10 239773 CAAATACCAA 239783 AAAAAAAAAT 1 AAAAAAAAAT 239793 AAAAAAAAAT 1 AAAAAAAAAT 239803 AAAAAAA 1 AAAAAAA 239810 TTCATCGACA Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 17 1.00 ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07 Consensus pattern (10 bp): AAAAAAAAAT Found at i:251068 original size:53 final size:55 Alignment explanation

Indices: 250999--251110 Score: 194 Period size: 53 Copynumber: 2.1 Consensus size: 55 250989 GTGTTAATTT 250999 TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACA-A-GGTA 1 TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA 251052 TATAGAATGAAT-ATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA 1 TATAGAATG-ATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA 251107 TATA 1 TATA 251111 ACTGGATCTA Statistics Matches: 56, Mismatches: 0, Indels: 4 0.93 0.00 0.07 Matches are distributed among these distances: 53 45 0.80 54 3 0.05 55 8 0.14 ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38 Consensus pattern (55 bp): TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA Found at i:251404 original size:3 final size:3 Alignment explanation

Indices: 251396--251430 Score: 70 Period size: 3 Copynumber: 11.7 Consensus size: 3 251386 AAAAAGGACT 251396 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG 1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG 251431 TGTGGTGTAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 32 1.00 ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00 Consensus pattern (3 bp): AGA Found at i:261878 original size:15 final size:15 Alignment explanation

Indices: 261854--261892 Score: 51 Period size: 16 Copynumber: 2.5 Consensus size: 15 261844 CTTTAAATTT * 261854 AAAATAAAAAGTAAGA 1 AAAATAAAATGTAA-A * 261870 AAAATAAAATTTAAA 1 AAAATAAAATGTAAA 261885 AAAATAAA 1 AAAATAAA 261893 TAAAAATAAA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 9 0.43 16 12 0.57 ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18 Consensus pattern (15 bp): AAAATAAAATGTAAA Found at i:266198 original size:175 final size:174 Alignment explanation

Indices: 265902--266248 Score: 658 Period size: 175 Copynumber: 2.0 Consensus size: 174 265892 GTCTGTTGTT 265902 TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT 1 TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT * 265967 GAGATATCTCTTGGTGTTATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC 66 GAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC 266032 GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG 131 GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG 266076 NTGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGT 1 -TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGT * 266141 TGAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCTAAATGTTCAAGACC 65 TGAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACC * 266206 CGGAAGTTGACGACGATCGTTCGAATGATCTTGAGGAATACTT 130 CGGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTT 266249 TGATGCTGAC Statistics Matches: 169, Mismatches: 3, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 175 169 1.00 ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38 Consensus pattern (174 bp): TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT GAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG Found at i:268000 original size:166 final size:167 Alignment explanation

Indices: 267263--268388 Score: 1755 Period size: 166 Copynumber: 6.8 Consensus size: 167 267253 GTGAATATGC * * * * * * * 267263 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * * * * 267328 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAACATCTGCGATAAATAGCTGCTGAAA 66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * * 267393 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-- 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA * * 267428 AAAATAAACAAAGTAC-TCATTTAACAGGAAGATGACGTCCGATTGGTACAAAAATATATCCCAC 1 AAAATAAGCAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC * * * * 267492 GATATGGCATGCCTTAAAAAATACTGTGTTAAAATTTAAAGCATCTCCGATAAATAGCTGCTGAG 65 GATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG * 267557 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA 130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA * * * * * * 267594 AAAATAAACAAAGTCATTATTTAACAGGAAGTTG-CGTCTGATTGATACAAAAATATATCCCACA 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * 267658 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 267723 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA ** 267760 AAAATAAGCAAAGTCGTCATTTAACAATAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * * 267825 ATATGGCATGCCTTAACAAACACTGTCTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA 66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 267890 AATCTTTGACGAAAATTTGTTTGAAAA-TTTGGTTAA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA * * 267926 AAAATAAGCAAAGTTGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACG 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * 267991 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA * * 268056 ATTCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA 131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA * * 268092 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * 268157 ATATGGCATGCC-TATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG 66 ATATGGCATGCCTTA-ACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG 268221 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA 130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA * 268259 AAAATAAGCAAAGTCGTCATTTAACAAGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG 1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG * * 268324 ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA 66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA 268389 TAAATGCGAC Statistics Matches: 881, Mismatches: 70, Indels: 18 0.91 0.07 0.02 Matches are distributed among these distances: 165 266 0.30 166 372 0.42 167 241 0.27 168 2 0.00 ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29 Consensus pattern (167 bp): AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA Found at i:268421 original size:4 final size:4 Alignment explanation

Indices: 268412--268469 Score: 71 Period size: 4 Copynumber: 14.5 Consensus size: 4 268402 AATTTTTGTT * * * * * 268412 ACGG ACGG ACAG ACAG ACGG ACGG ACAG ACAG ACAG ACGG ACGG ACGG 1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG 268460 ACGG ACGG AC 1 ACGG ACGG AC 268470 AGACAGACAC Statistics Matches: 50, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 50 1.00 ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00 Consensus pattern (4 bp): ACGG Found at i:268433 original size:16 final size:16 Alignment explanation

Indices: 268412--268477 Score: 105 Period size: 16 Copynumber: 4.1 Consensus size: 16 268402 AATTTTTGTT 268412 ACGGACGGACAGACAG 1 ACGGACGGACAGACAG 268428 ACGGACGGACAGACAG 1 ACGGACGGACAGACAG * * * 268444 ACAGACGGACGGACGG 1 ACGGACGGACAGACAG 268460 ACGGACGGACAGACAG 1 ACGGACGGACAGACAG 268476 AC 1 AC 268478 ACACAAGGGT Statistics Matches: 44, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 16 44 1.00 ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00 Consensus pattern (16 bp): ACGGACGGACAGACAG Found at i:268437 original size:20 final size:20 Alignment explanation

Indices: 268412--268461 Score: 91 Period size: 20 Copynumber: 2.5 Consensus size: 20 268402 AATTTTTGTT 268412 ACGGACGGACAGACAGACGG 1 ACGGACGGACAGACAGACGG * 268432 ACGGACAGACAGACAGACGG 1 ACGGACGGACAGACAGACGG 268452 ACGGACGGAC 1 ACGGACGGAC 268462 GGACGGACAG Statistics Matches: 28, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 20 28 1.00 ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00 Consensus pattern (20 bp): ACGGACGGACAGACAGACGG Found at i:268448 original size:8 final size:8 Alignment explanation

Indices: 268415--268478 Score: 74 Period size: 8 Copynumber: 8.0 Consensus size: 8 268405 TTTTGTTACG 268415 GACGGACA 1 GACGGACA * * 268423 GACAGACG 1 GACGGACA 268431 GACGGACA 1 GACGGACA * 268439 GACAGACA 1 GACGGACA * 268447 GACGGACG 1 GACGGACA * 268455 GACGGACG 1 GACGGACA 268463 GACGGACA 1 GACGGACA * 268471 GACAGACA 1 GACGGACA 268479 CACAAGGGTA Statistics Matches: 47, Mismatches: 9, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 8 47 1.00 ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00 Consensus pattern (8 bp): GACGGACA Found at i:268474 original size:4 final size:4 Alignment explanation

Indices: 268419--268478 Score: 57 Period size: 4 Copynumber: 15.0 Consensus size: 4 268409 GTTACGGACG * * * * * * * 268419 GACA GACA GACG GACG GACA GACA GACA GACG GACG GACG GACG GACG 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA 268467 GACA GACA GACA 1 GACA GACA GACA 268479 CACAAGGGTA Statistics Matches: 52, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 4 52 1.00 ACGTcount: A:0.38, C:0.25, G:0.37, T:0.00 Consensus pattern (4 bp): GACA Found at i:270073 original size:20 final size:20 Alignment explanation

Indices: 270048--270121 Score: 71 Period size: 20 Copynumber: 3.7 Consensus size: 20 270038 AGTGCCATTT 270048 TTTACTGATAATTTCTGATA 1 TTTACTGATAATTTCTGATA * 270068 TTTACTGAT-ATTGTACTGTTA 1 TTTACTGATAATT-T-CTGATA * * * * 270089 -GTGCTGAGAATTGCTGATA 1 TTTACTGATAATTTCTGATA 270108 TTTACTGATAATTT 1 TTTACTGATAATTT 270122 TACTGCTGTT Statistics Matches: 40, Mismatches: 10, Indels: 8 0.69 0.17 0.14 Matches are distributed among these distances: 19 8 0.20 20 24 0.60 21 8 0.20 ACGTcount: A:0.27, C:0.09, G:0.16, T:0.47 Consensus pattern (20 bp): TTTACTGATAATTTCTGATA Found at i:270078 original size:10 final size:10 Alignment explanation

Indices: 270048--270117 Score: 54 Period size: 10 Copynumber: 7.0 Consensus size: 10 270038 AGTGCCATTT 270048 TTTACTGATAA 1 TTTACTGAT-A 270059 TTT-CTGATA 1 TTTACTGATA 270068 TTTACTGATA 1 TTTACTGATA * 270078 TTGTACTGTTA 1 TT-TACTGATA * * * 270089 -GTGCTGAGA 1 TTTACTGATA * * 270098 ATTGCTGATA 1 TTTACTGATA 270108 TTTACTGATA 1 TTTACTGATA 270118 ATTTTACTGC Statistics Matches: 47, Mismatches: 9, Indels: 7 0.75 0.14 0.11 Matches are distributed among these distances: 9 9 0.19 10 28 0.60 11 10 0.21 ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46 Consensus pattern (10 bp): TTTACTGATA Found at i:270142 original size:41 final size:40 Alignment explanation

Indices: 270050--270145 Score: 113 Period size: 40 Copynumber: 2.4 Consensus size: 40 270040 TGCCATTTTT * * 270050 TACTGATAATTTCTGATATTTACTGATATTGTACTGTTAG 1 TACTGATAATTGCTGATATTTACTGATATTGTACTGCTAG * * * 270090 TGCTGAGAATTGCTGATATTTACTGATAATTTTACTGCT-G 1 TACTGATAATTGCTGATATTTACTGAT-ATTGTACTGCTAG * 270130 TTATTGATAATTGCTG 1 -TACTGATAATTGCTG 270146 TTGGTTCTGA Statistics Matches: 46, Mismatches: 8, Indels: 3 0.81 0.14 0.05 Matches are distributed among these distances: 40 25 0.54 41 21 0.46 ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46 Consensus pattern (40 bp): TACTGATAATTGCTGATATTTACTGATATTGTACTGCTAG Found at i:270870 original size:2 final size:2 Alignment explanation

Indices: 270865--270900 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 270855 GGATAAATAA 270865 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 270901 CTACCATTTG Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:271296 original size:2 final size:2 Alignment explanation

Indices: 271289--271318 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 271279 ATGCTTAAAT 271289 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 271319 AGATAATCTA 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): TC Found at i:271439 original size:2 final size:2 Alignment explanation

Indices: 271434--271464 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 271424 CCCCCCCCCC 271434 CT CT 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 CT CT C 271465 ATTAATACTT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): CT Found at i:271846 original size:134 final size:134 Alignment explanation

Indices: 271606--271857 Score: 398 Period size: 134 Copynumber: 1.9 Consensus size: 134 271596 CAGAAAATTT * * * 271606 TTTGTATGTCTGGGATTAAGAATAACCTCAGAACTAACAGAGAGCACTCAGACTATACACACGAC 1 TTTGTATGTCTGGGATCAAGAATAACCTCAGAACTAACAGACAGCACTCAGAATATACACACGAC * * 271671 AGGGTGACCACGGCAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA 66 AGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA 271736 TTCG 131 TTCG * * 271740 TTTGTATGTCTGGGATCAAGAA-AACCCTCAGAACTAACAGACAGCGCTCAGAATATATACACGA 1 TTTGTATGTCTGGGATCAAGAATAA-CCTCAGAACTAACAGACAGCACTCAGAATATACACACGA ** * 271804 CAGAGTGACCGTGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTTGCAG 65 CAGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAG 271858 CCTCAGAATA Statistics Matches: 107, Mismatches: 10, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 133 2 0.02 134 105 0.98 ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23 Consensus pattern (134 bp): TTTGTATGTCTGGGATCAAGAATAACCTCAGAACTAACAGACAGCACTCAGAATATACACACGAC AGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA TTCG Found at i:272534 original size:10 final size:10 Alignment explanation

Indices: 272519--272696 Score: 80 Period size: 10 Copynumber: 17.7 Consensus size: 10 272509 TCAGTACCAA * 272519 CAGTAAATCT 1 CAGTAAATAT 272529 CAGTAAATAT 1 CAGTAAATAT * 272539 CAGTAATTAT 1 CAGTAAATAT ** 272549 CAG-AGCTCA- 1 CAGTAAAT-AT * * 272558 CAGCAAAAGCAT 1 CAG-TAAA-TAT 272570 CAGTAAATAT 1 CAGTAAATAT 272580 CAGTAAATAT 1 CAGTAAATAT ** * 272590 CAG-AACCAA 1 CAGTAAATAT * * 272599 CAGCAATTAT 1 CAGTAAATAT * * 272609 CAGT-AACAG 1 CAGTAAATAT 272618 CAGTAAAATTAT 1 CAGT-AAA-TAT 272630 CAGTAAATAT 1 CAGTAAATAT * * * 272640 CAGCAATTCT 1 CAGTAAATAT * * * 272650 CAG-CACTAA 1 CAGTAAATAT 272659 CAGTACAATAT 1 CAGTA-AATAT 272670 CAGTAAATAT 1 CAGTAAATAT 272680 CAG-AAACTAT 1 CAGTAAA-TAT 272690 CAGTAAA 1 CAGTAAA 272697 AAATGGCACT Statistics Matches: 124, Mismatches: 31, Indels: 25 0.69 0.17 0.14 Matches are distributed among these distances: 9 25 0.20 10 70 0.56 11 21 0.17 12 8 0.06 ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24 Consensus pattern (10 bp): CAGTAAATAT Found at i:282365 original size:13 final size:13 Alignment explanation

Indices: 282347--282371 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 282337 GGCTGAAGCT 282347 AGCAGCCACTAAC 1 AGCAGCCACTAAC 282360 AGCAGCCACTAA 1 AGCAGCCACTAA 282372 GCCCGTAGAA 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:0.40, C:0.36, G:0.16, T:0.08 Consensus pattern (13 bp): AGCAGCCACTAAC Found at i:283863 original size:303 final size:311 Alignment explanation

Indices: 283072--284692 Score: 2143 Period size: 303 Copynumber: 5.1 Consensus size: 311 283062 AAGAGACGGT * * * ** 283072 TTAGCTCACCCGAACTTTTTCATATTTTAGCATTTCACAATGATAAAGGGGTGAAAAGCGGGGCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA * * * * * 283137 TTATCTCTTTTATCTTTAAAGTGTGCATCAAACGGATGCCAGGGTAATGTAGGGGACCTATTGGG 66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG * * * * * * 283202 CTATTATTTCCCGGTCTCCAATTTGGGCTGTA-AGGGTACCACCAAGTGGCTTCCAAGGTTTCCG 131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGA-GGCACCACCAAGTGGCTCCCAGGGGTTCTG * * 283266 GCTCATTTCAGGGGTTTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAA 195 GCTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAA * * 283331 GTAGAGGACCTCAAGGGGTATTCATAATAAGCGCTAAATGGCACCTATGATCCCTGCAAGGGTTC 245 GTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTC 283396 AA 310 AA 283398 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA * 283463 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACGGATACCAGGGCAATGTAGGGGACCTATGGGG 66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG * * * 283528 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTGGCTCCCA-AGGTTTTCG 131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCT-G * 283592 GCTCATTTCAGGGGTTT-A-T-A-T-CT-CAC-A-AAACACTAGGATTAAGTATAGGACCTCAAA 195 GCTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAA * 283649 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGTTTCAA 260 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA 283701 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA 283766 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG 66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG * * 283831 CTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTGGCTCCCAGGGGTTCTGG 131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG * 283896 CTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAGGATTAAG 196 CTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAAG * * * 283961 TAGAGGACCTC-AAGGGTATTCATAATAAGCGTTGAAGGGCACCTATGACCCCTGCAAGGGTTCA 246 TAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCA 284025 A 311 A * * ** 284026 TTAGTTCACCCGAACTTTGTCATATTTTAGCATTTCACAATTATATAGGGGTGAAAGGCGGGGCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA * * * * * * * 284091 TTATCTCTTTTATTTTTAAAGTGTGCATTAAACGGATACCAGGGCAATGTAGGTGAGCAATGGGG 66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG * * * 284156 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTGGCTCCCA-AGGTTTTCG 131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCT-G * 284220 GCTCATTTCAGGGGTTT-A-T-A-T-CT-CA-TA-AAACACTAGGATTAAGTAGAGGACCTCAAA 195 GCTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAA * 284277 GGGTATTCATAATAAGCGCTAAATGGCACCTATGATCCCTGCAAGGGTTCAA 260 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA 284329 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA 284394 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG 66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG * * * 284459 CTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTGGATCCCAGGGGTTCTGG 131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG * 284524 CTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAGGATTAAG 196 CTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAAG * * * * 284589 TAGAGGACCTC-AAGGGTATTCATAACAAGCGTCT-AAGGGCACCTATGACCCCTGCAAGAGTTC 246 TAGAGGACCTCAAAGGGTATTCATAATAAGCGT-TAAATGGCACCTATGATCCCTGCAAGGGTTC 284652 AA 310 AA 284654 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA 1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA 284693 TTGAGACCGG Statistics Matches: 1163, Mismatches: 79, Indels: 107 0.86 0.06 0.08 Matches are distributed among these distances: 302 27 0.02 303 514 0.44 304 10 0.01 305 2 0.00 307 3 0.00 308 3 0.00 310 2 0.00 311 2 0.00 312 3 0.00 314 3 0.00 315 1 0.00 317 5 0.00 318 1 0.00 319 1 0.00 320 1 0.00 321 4 0.00 322 1 0.00 323 1 0.00 324 6 0.01 325 328 0.28 326 244 0.21 327 1 0.00 ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29 Consensus pattern (311 bp): TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG CTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAAG GGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA Found at i:284237 original size:325 final size:326 Alignment explanation

Indices: 283619--284692 Score: 1689 Period size: 325 Copynumber: 3.4 Consensus size: 326 283609 ATATCTCACA * * 283619 AAACACTAGGATTAAGTATAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGA 1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA * * 283684 TCCCTGCAAGGTTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG 66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG 283749 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT 131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT 283814 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG 196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG 283879 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG 261 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG 283944 G 326 G * 283945 AAACACTAGGATTAAGTAGAGGACCTC-AAGGGTATTCATAATAAGCGTTGAAGGGCACCTATGA 1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA * * 284009 CCCCTGCAAGGGTTCAATTAGTTCACCCGAACTTTGTCATATTTTAGCATTTCACAATTATATAG 66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG ** * * * * 284074 GGGTGAAAGGCGGGGCATTATCTCTTTTATTTTTAAAGTGTGCATTAAACGGATACCAGGGCAAT 131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT * * * * * * 284139 GTAGGTGAGCAATGGGGCTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTG 196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG * * * 284204 GCTCCCA-AGGTTTTCGGCTCATTTCAGGGGTTTATATCT--C-----A-T----------A--- 261 GCTCCCAGGGGTTCT-GGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTT 284247 -- 325 GG * * 284247 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGCTAAATGGCACCTATGA 1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA * 284312 TCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG 66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG 284377 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT 131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT 284442 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG 196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG * 284507 GATCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG 261 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG 284572 G 326 G * 284573 AAACACTAGGATTAAGTAGAGGACCTC-AAGGGTATTCATAACAAGCGTCT-AAGGGCACCTATG 1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGT-TAAAGGGCACCTATG * 284636 ACCCCTGCAAGAGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA 65 ACCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA 284693 TTGAGACCGG Statistics Matches: 672, Mismatches: 49, Indels: 55 0.87 0.06 0.07 Matches are distributed among these distances: 302 27 0.04 303 243 0.36 304 5 0.01 305 1 0.00 307 1 0.00 310 1 0.00 311 1 0.00 317 1 0.00 318 1 0.00 321 1 0.00 323 1 0.00 324 5 0.01 325 330 0.49 326 54 0.08 ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29 Consensus pattern (326 bp): AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG G Found at i:286364 original size:4 final size:4 Alignment explanation

Indices: 286357--286435 Score: 68 Period size: 4 Copynumber: 19.8 Consensus size: 4 286347 GCTACCGTGC * * * * * * 286357 GTGT GTGT GTGT GTGT GCGT GTGT GCGT GCGT GCGT GTGC GTGT GCGT 1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT * * * * 286405 GGGG GTGG GTGG GTGT GTGT GTGT GTGT GTG 1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTG 286436 CACCCCATTT Statistics Matches: 64, Mismatches: 11, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 4 64 1.00 ACGTcount: A:0.00, C:0.08, G:0.56, T:0.37 Consensus pattern (4 bp): GTGT Found at i:286368 original size:6 final size:6 Alignment explanation

Indices: 286357--286435 Score: 68 Period size: 6 Copynumber: 13.2 Consensus size: 6 286347 GCTACCGTGC * * * * * * 286357 GTGTGT GTGTGT GTGTGC GTGTGT GCGTGC GTGCGT GTGCGT GTGCGT 1 GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT * * * * 286405 GGGGGT GGGTGG GTGTGT GTGTGT GTGTGT G 1 GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT G 286436 CACCCCATTT Statistics Matches: 60, Mismatches: 13, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 6 60 1.00 ACGTcount: A:0.00, C:0.08, G:0.56, T:0.37 Consensus pattern (6 bp): GTGTGT Found at i:287254 original size:2 final size:2 Alignment explanation

Indices: 287247--287282 Score: 63 Period size: 2 Copynumber: 18.0 Consensus size: 2 287237 AAAAGAATTT * 287247 GA GA GA GA GA GA GA GA GA GA GA CA 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 287283 TTGTCAGTCT Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:290611 original size:21 final size:21 Alignment explanation

Indices: 290587--290676 Score: 135 Period size: 21 Copynumber: 4.3 Consensus size: 21 290577 CAATAGTGAT ** 290587 ATCATTATATGCAGTGGAAAC 1 ATCATTATATGCAGTGCTAAC 290608 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGCTAAC * * * 290629 ACCATTATATGTAGTGGTAAC 1 ATCATTATATGCAGTGCTAAC 290650 ATCATTATATGCAGTGCTAAC 1 ATCATTATATGCAGTGCTAAC 290671 ATCATT 1 ATCATT 290677 GTATACTGTA Statistics Matches: 61, Mismatches: 8, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 21 61 1.00 ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33 Consensus pattern (21 bp): ATCATTATATGCAGTGCTAAC Found at i:290997 original size:21 final size:21 Alignment explanation

Indices: 290948--290998 Score: 66 Period size: 21 Copynumber: 2.4 Consensus size: 21 290938 CAATTGCATG * * 290948 TAAAGCTTTCACCACAATACA 1 TAAAGGTTTAACCACAATACA * 290969 TAAAGGTTTAACCACCATACA 1 TAAAGGTTTAACCACAATACA * 290990 TAATGGTTT 1 TAAAGGTTT 290999 TAATACACCA Statistics Matches: 26, Mismatches: 4, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 21 26 1.00 ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29 Consensus pattern (21 bp): TAAAGGTTTAACCACAATACA Found at i:291315 original size:21 final size:21 Alignment explanation

Indices: 291291--291347 Score: 96 Period size: 21 Copynumber: 2.7 Consensus size: 21 291281 AAATTCCAGT * 291291 ATATAATGATGTTAGCACTGC 1 ATATAATGATGTTACCACTGC 291312 ATATAATGATGTTACCACTGC 1 ATATAATGATGTTACCACTGC * 291333 ATATAATGATATTAC 1 ATATAATGATGTTAC 291348 TATTGCAAAG Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 21 34 1.00 ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35 Consensus pattern (21 bp): ATATAATGATGTTACCACTGC Found at i:304632 original size:433 final size:433 Alignment explanation

Indices: 303826--305144 Score: 2026 Period size: 433 Copynumber: 3.0 Consensus size: 433 303816 AGTACTTTGA 303826 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA 1 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA 303891 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC 66 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC 303956 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC 131 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC 304021 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG 196 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG 304086 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT 261 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT 304151 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC 326 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC 304216 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT 391 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT 304259 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA 1 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA 304324 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC 66 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC 304389 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC 131 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC 304454 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG 196 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG 304519 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT 261 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT 304584 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC 326 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC * * * 304649 ACTATCTTTTACGGTTAATGAGGAGTAGCAATAAGAAGTATTT 391 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT * * * * * * * * * * 304692 TATACAAAAGGGGTAATAACTCTGTAACTTTTTA-AAGG-AAGGAGCCAAGGGGCTATATTTTAA 1 TGTACAATAGGGGCAATAACTCTATAA-TTGTTACATGGTAAGG-GTCAATGGGTTATATTTTGA * * * * * * * * * * * 304755 AATGTCTGAAGATGTCCTATTACATCCATGAAAAAGTTTTTCTTTACCACACTAAACAATAGAGA 64 AATGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGA ** * * * * * 304820 TCTAAAAACTCATTAATT-GGGAGATTT-TCGGATGACCTTGACCATTGTCCTTTATGTCATTTT 129 TCTAAAAACTCATTAATTAACG-GATTTCT-GAATGATCTTGACCCTTGACCTTTATGTCAATTT * * * * * 304883 GTTCGGCCAAGATAAACGCTTCTATCCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAG 192 GTTCGGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAG * * * * * * * 304948 TTGGAAGTGATTTTATAGATATGTAGATAATTTCAAGGACAATAACTACTAGAAGGCGGG-CTCA 257 TTAGAAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGG-GGGCCTCA * * * * 305012 GATCCTTTCGGTATGAAAAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTCC 321 GATCTTTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCA * * * * * * 305077 AAGTTTA-TATCTCTTATGGTTTCA-GAGGAGAAGCGATAACAAGCTTTT 386 AAG-TCACTATCTTTTACGG-TTAATGAGGAGTAGCGATAACAAGCATTT 305125 TGTACACA-A-GGGCAATAACT 1 TGTACA-ATAGGGGCAATAACT 305145 TTGTAAGTTC Statistics Matches: 820, Mismatches: 58, Indels: 17 0.92 0.06 0.02 Matches are distributed among these distances: 432 16 0.02 433 790 0.96 434 14 0.02 ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30 Consensus pattern (433 bp): TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT Found at i:308122 original size:434 final size:432 Alignment explanation

Indices: 307276--308186 Score: 1253 Period size: 434 Copynumber: 2.1 Consensus size: 432 307266 AACGGTTAAT * * * * 307276 GAGGAGTAGCGATAACAAGCATTTTGTACAATA-GGGGCAATAACTTTATAATTGTTACATGGTA 1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTACAAGGTA * ** * 307340 ACGGTCAAAGGGTTATATTTTGAAATGTCCTAAGATGTCCTACTACATCCATGAAAAAGTGTTTC 66 AC-G-CAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTTTC * * * * 307405 TCTACCATCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAGATTCTCAGATGATCTTGAC 129 TCTACCACCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAAATTCTCAAATGACCTTGAC * * * 307470 CTTTGACCTTAATGTCATTTTGTTCGGCCAAAATAGACGCTTCCATCCCAAGTGGTCCGAAGTCT 194 CTTTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGAAGTCT * * * * * * 307535 CTATGATAAGTAATAAAAAAGTTAGAAGTGATTTTATGGAAATTTAAATTCTTTCAGGGGCAATA 259 CTATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGGCAATA * * * * 307600 ACTACTAGAAGGGGGCCTCAGATCATTTCATTATGAATAGATTGAAGAACCCTGTAAGTGTACTG 324 ACTAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTGTACTA 307665 AAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA 389 AAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA * * * 307709 GAGGAGTAGCGATAACAAGCATTTCGTACAAAAGGGGGTAATAACTCTGTAATTATT-CAAAGGC 1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTAC-AAGG- * * * * 307773 ATGAAC-CAAGGGGCTATATTTAAAAATGTCTTAAGATGGCCTACTATATCCATGAAAAAGTTTT 64 -T-AACGCAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTT ** * 307837 TCTCTACCACCCTTAA-CAAAAGAAAT-CTAAAAACTCATTAATTAAGAAATT-TCCAAATGACC 127 TCTCTACCACCCAAAACCAAAA-AAATAC-AAAAACTCATAAATTAAGAAATTCT-CAAATGACC * * ** 307899 TTGACCTTTGACCTTTATATCATTATGTTTGGCCAAGGTAGACGCTTCCATCCCAAGTAGTCCGA 189 TTGACCTTTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGA * * 307964 AGTCTCTATGACAAATAATAAAAAAGTTGGAAGGGGTTTTATAGAAATGTAAATACTTTCAGGGG 254 AGTCTCTATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGG * * * * 308029 CAATAACTAATAGAAGGGGGGCTCAGATCCTTTCGGTATGAATAGATTGGAGAACCCTCTAAGTG 319 CAATAACTAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTG 308094 TACTAAAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA 384 TACTAAAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA * * * 308143 GAGGAGTAGCGATAACAATCTTTTTGTACACAA--GGGCAATAACT 1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACT 308187 TTGTAAGTTC Statistics Matches: 420, Mismatches: 50, Indels: 17 0.86 0.10 0.03 Matches are distributed among these distances: 432 10 0.02 433 39 0.09 434 367 0.87 436 1 0.00 437 3 0.01 ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30 Consensus pattern (432 bp): GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTACAAGGTA ACGCAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTTTCTC TACCACCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAAATTCTCAAATGACCTTGACCT TTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGAAGTCTCT ATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAAC TAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTGTACTAAA GACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA Found at i:308319 original size:3 final size:3 Alignment explanation

Indices: 308313--308365 Score: 106 Period size: 3 Copynumber: 17.7 Consensus size: 3 308303 AAAAAAAGAG 308313 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT 308361 AAT AA 1 AAT AA 308366 AAAACATAAG Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 50 1.00 ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32 Consensus pattern (3 bp): AAT Found at i:309330 original size:433 final size:430 Alignment explanation

Indices: 308733--309726 Score: 1230 Period size: 433 Copynumber: 2.3 Consensus size: 430 308723 TACTTTGGAC * * * * * * * 308733 CCTTTCGGTATGAATAGACTGAAGAAATATCTTAGTGTACTGAATACATTAGTAAAAGTTTTAAG 1 CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG * * * * * 308798 TCTCTATCTCTAACGG-TTAATGAGGAGTAGCGATAACAAGCTTTTCGTAAATAGGGGCAGTAAC 66 TCTCTATCTCTTATGGTTTCA-GAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAAC ** * ** * * * 308862 TCTATAATTGTAACATGGTAAGGGTCAAAGGGTTATATTTTGAAATTTCATATGATGTCTTACTA 130 TC-ATAATTGTAACATAATAAGGGCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACTA * * * * * * 308927 CATCCTTGAAAAAGTTTTTTTCTACCACCCTAAGCAAAAGAGATCTTAAAACTCATTTAGTCTAT 194 CATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCA-TTAAT-TA- * * * 308992 A-GATTTCCCAATGACCATGACCTTTGACCTTTATGTTATTTTGTTCGGCCAAGGGCGACGCTTC 256 ACGATTTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTC * * 309056 CATCCAAAGTGGTCCGAAGTCTCTATGACAAATTATAAAAAAGTTGGAAGTGATTTTATAGATAT 321 CATCCAAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAAT * * 309121 GT-AAATAATTTCAGGGGCAA-AAATTACCAGAAGGGGGCCTCAGAT 386 -TCAAATAATTTCAGGGGCAATAAATGA-CAGAACGGGGCCTCAGAT * * * ** 309166 CCTTTTGGTATGAATAGGTTGAAGAACTCTCAAAGTGTTCTGAAGACATTGGTAAAAGTTCCAAG 1 CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG * 309231 TTTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTACAATAAGGGCAATAAC 66 TCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTA-AATAAGGGCAATAAC * * * * * * 309296 TC-T-GTTGTTATATAAATAAGGAGCCAAGGGGTTATATTTCAAAATGTCTTAAGATGTCCTATT 130 TCATAATTGTAACAT-AATAAGG-GCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACT * 309359 ACATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGTTCTAAAAACTCATTAATTAAC 193 ACATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCATTAATTAAC * * * * 309424 GGATTTCTAAATGACCTTGACCTTTGACCTTTATGTTTTTTTGGTCGGCCAAGGTAGACGCTTCC 258 -GATTTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTCC * * * * 309489 ATCCCAAGTGGTCCGAAGTCTCTATGATAAATAATAAAATAGTTGGAAGTGATTTTATGGAAATT 322 ATCCAAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAATT * * * * * 309554 CAAATACTTTCAGGGGCAATAACTGATAGAACGGGGTCTCGGAT 387 CAAATAATTTCAGGGGCAATAAATGACAGAACGGGGCCTCAGAT * * * * 309598 -CTTTTCGGTATTAGTAGATT-AAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAG 1 CCTTTT-GGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAA * * * 309661 GTCTCTGTCTCTTATGGTTTCAGAGAAGTAGCGATAACAAGCTTTTCGTAAACAAGGGCAATAAC 65 GTCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAAC 309726 T 130 T 309727 TTGTAAGTTC Statistics Matches: 480, Mismatches: 72, Indels: 21 0.84 0.13 0.04 Matches are distributed among these distances: 430 16 0.03 431 99 0.21 432 167 0.35 433 180 0.38 434 18 0.04 ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32 Consensus pattern (430 bp): CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG TCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAACT CATAATTGTAACATAATAAGGGCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACTACA TCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCATTAATTAACGAT TTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTCCATCC AAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAATTCAAA TAATTTCAGGGGCAATAAATGACAGAACGGGGCCTCAGAT Found at i:309930 original size:57 final size:57 Alignment explanation

Indices: 309867--310358 Score: 556 Period size: 50 Copynumber: 9.0 Consensus size: 57 309857 AAATAATAAG 309867 AATAATAAAAAACATAAAGAAA-ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT 1 AATAATAAAAAACAT-AAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * * 309924 AATAATAAAAATCATAAGAAATACAACAGGTCTTTCACCTGAAAGGTGGAAAGACC- 1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * 309980 -----T-AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC- 1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * 310030 -----T-AAAAACATAAGAAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCT 1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * 310081 AATAATAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACC- 1 AATAAT-AAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * 310138 --T--T--AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCT 1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * 310189 AATAAAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT 1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT * * * * * * * 310246 -A-AA-AATAAACAGAA-CAATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCT 1 AATAATAAAAAACATAAGAAATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCT * * * * 310298 AATAATAATACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCT 1 AATAAT-A-A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT 310358 A 1 A 310359 CATACAAAAG Statistics Matches: 380, Mismatches: 27, Indels: 53 0.83 0.06 0.12 Matches are distributed among these distances: 50 140 0.37 51 1 0.00 52 12 0.03 53 9 0.02 54 24 0.06 55 3 0.01 56 9 0.02 57 96 0.25 58 68 0.18 59 5 0.01 60 13 0.03 ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19 Consensus pattern (57 bp): AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT Found at i:310004 original size:107 final size:103 Alignment explanation

Indices: 309871--310250 Score: 502 Period size: 107 Copynumber: 3.6 Consensus size: 103 309861 AATAAGAATA 309871 ATAAAAAACATAA-AGAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAAAAA 1 ATAAAAAACATAAGA-AAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC---T--TAAAAA * 309935 TCATAAGAAATACAACAGGTCTTTCACCTGAAAGGTGGAAAGACC 60 -CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC 309980 -T-AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC-TAAAAACATAAG 1 ATAAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAACATAAG * 310042 AAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACC 66 AAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC * * 310080 TAATAATAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACCTT-AAAA 1 -----AT-AAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAA * 310144 CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACC 60 CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC * 310188 TAATAAAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC-TAAAAA 1 --AT---AAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAA 310251 TAAACAGAAC Statistics Matches: 251, Mismatches: 7, Indels: 28 0.88 0.02 0.10 Matches are distributed among these distances: 100 42 0.17 101 6 0.02 105 4 0.02 106 2 0.01 107 101 0.40 108 95 0.38 109 1 0.00 ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18 Consensus pattern (103 bp): ATAAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAACATAAG AAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC Found at i:310104 original size:58 final size:58 Alignment explanation

Indices: 310031--310358 Score: 375 Period size: 58 Copynumber: 5.9 Consensus size: 58 310021 GGAAAGACCT * 310031 AAAAACATAAGAAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA * 310089 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACC---T--T-- 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA * 310140 -AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCTAATAA-AA 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA 310196 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC---TAA-AA 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA * * * * * * * 310250 ATAAACAGAA-CAATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCTAATAATAA 1 AAAAACATAAGAAATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCTAATAATAA * * * * 310306 TACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCTA 1 -A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTA 310359 CATACAAAAG Statistics Matches: 231, Mismatches: 19, Indels: 38 0.80 0.07 0.13 Matches are distributed among these distances: 50 46 0.20 52 11 0.05 53 8 0.03 54 26 0.11 55 4 0.02 56 2 0.01 57 48 0.21 58 68 0.29 59 5 0.02 60 13 0.06 ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20 Consensus pattern (58 bp): AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA Found at i:310129 original size:108 final size:108 Alignment explanation

Indices: 309981--310358 Score: 530 Period size: 108 Copynumber: 3.5 Consensus size: 108 309971 GGAAAGACCT * 309981 AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT * 310046 ACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA 66 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA * * 310089 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACCTTAAAACATAAGAAAT 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT * 310154 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCTAATAA-AA 66 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA * * 310196 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAATAAACAGAAC 1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATA-AG-A- * * * * 310261 AATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCTAATAATAA 63 AATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCTAATAATAA * * * * 310306 TACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCTA 1 -A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTA 310359 CATACAAAAG Statistics Matches: 244, Mismatches: 18, Indels: 12 0.89 0.07 0.04 Matches are distributed among these distances: 107 57 0.23 108 102 0.42 109 17 0.07 110 8 0.03 111 14 0.06 112 46 0.19 ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19 Consensus pattern (108 bp): AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA Found at i:310746 original size:4 final size:4 Alignment explanation

Indices: 310737--310774 Score: 60 Period size: 4 Copynumber: 9.8 Consensus size: 4 310727 ACTGAAGTGG * 310737 GACA GACA GAGA GACA GACA GACA GACA GACA GA-A GAC 1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GAC 310775 GGACGGACGG Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 3 3 0.10 4 28 0.90 ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00 Consensus pattern (4 bp): GACA Found at i:314500 original size:22 final size:22 Alignment explanation

Indices: 314450--314502 Score: 61 Period size: 22 Copynumber: 2.4 Consensus size: 22 314440 TATATGTATT * 314450 GCTTAAAGGTGGCCTAAAGAAA 1 GCTTAAAGATGGCCTAAAGAAA * * ** 314472 GCGTAAAGATGGCTTAAAGGCA 1 GCTTAAAGATGGCCTAAAGAAA 314494 GCTTAAAGA 1 GCTTAAAGA 314503 CTATCTTTAA Statistics Matches: 25, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 25 1.00 ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19 Consensus pattern (22 bp): GCTTAAAGATGGCCTAAAGAAA Found at i:314584 original size:11 final size:11 Alignment explanation

Indices: 314567--314620 Score: 81 Period size: 11 Copynumber: 4.9 Consensus size: 11 314557 GTCCAAAATT 314567 CTTTAAGCCAC 1 CTTTAAGCCAC * * 314578 ATTTAAGCTAC 1 CTTTAAGCCAC * 314589 CTTTAAGCTAC 1 CTTTAAGCCAC 314600 CTTTAAGCCAC 1 CTTTAAGCCAC 314611 CTTTAAGCCA 1 CTTTAAGCCA 314621 TTAATAAAAA Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 11 39 1.00 ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:317253 original size:50 final size:50 Alignment explanation

Indices: 317198--317299 Score: 186 Period size: 50 Copynumber: 2.0 Consensus size: 50 317188 AAATAAGAAG * 317198 AAACAGTACGAAAACTATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT 1 AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT * 317248 AAACAGTACGCAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT 1 AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT 317298 AA 1 AA 317300 CCGGTGACGT Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 50 50 1.00 ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21 Consensus pattern (50 bp): AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT Done.