Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold7

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31

Warning! 349864 characters in sequence are not A, C, G, or T


File 22 of 37

Found at i:3846756 original size:38 final size:37

Alignment explanation

Indices: 3846682--3846757 Score: 118 Period size: 38 Copynumber: 2.0 Consensus size: 37 3846672 ATATGGCATA 3846682 GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC 1 GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC * 3846719 GGTTCAGAATAAAAATCACTATTCTT-ATCCGGTGGCAC 1 GGTT-AGAATAAAAATCACTATT-TTAATCCGATGGCAC 3846757 G 1 G 3846758 ACAAAACCAT Statistics Matches: 36, Mismatches: 1, Indels: 3 0.90 0.03 0.08 Matches are distributed among these distances: 37 4 0.11 38 30 0.83 39 2 0.06 ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29 Consensus pattern (37 bp): GGTTAGAATAAAAATCACTATTTTAATCCGATGGCAC Found at i:3846808 original size:31 final size:31 Alignment explanation

Indices: 3846729--3846837 Score: 148 Period size: 31 Copynumber: 3.5 Consensus size: 31 3846719 GGTTCAGAAT * 3846729 AAAAATCACTATTCTTATCCGGTGGCACGAC 1 AAAAACCACTATTCTTATCCGGTGGCACGAC * * * 3846760 -AAAACCATTATTATTATCTGGTGGCACGAC 1 AAAAACCACTATTCTTATCCGGTGGCACGAC ** 3846790 AAAAACCACTATTCTTATCCGGTGGCACGGT 1 AAAAACCACTATTCTTATCCGGTGGCACGAC * 3846821 AAAAATCACTATTCTTA 1 AAAAACCACTATTCTTA 3846838 ACTGATAGCA Statistics Matches: 67, Mismatches: 10, Indels: 2 0.85 0.13 0.03 Matches are distributed among these distances: 30 26 0.39 31 41 0.61 ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28 Consensus pattern (31 bp): AAAAACCACTATTCTTATCCGGTGGCACGAC Found at i:3849930 original size:21 final size:20 Alignment explanation

Indices: 3849906--3849972 Score: 68 Period size: 21 Copynumber: 3.5 Consensus size: 20 3849896 AAAAAATACA 3849906 TATAAATTTTTTAAAATTTT 1 TATAAATTTTTTAAAATTTT * * 3849926 GTATAAATTATTTATAATTTT 1 -TATAAATTTTTTAAAATTTT * 3849947 T-TTAATTTTTT--AATTTT 1 TATAAATTTTTTAAAATTTT * 3849964 TATATATTT 1 TATAAATTT 3849973 AAATAAAATG Statistics Matches: 39, Mismatches: 6, Indels: 5 0.78 0.12 0.10 Matches are distributed among these distances: 17 7 0.18 18 5 0.13 19 8 0.21 20 1 0.03 21 18 0.46 ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64 Consensus pattern (20 bp): TATAAATTTTTTAAAATTTT Found at i:3849941 original size:11 final size:10 Alignment explanation

Indices: 3849906--3849972 Score: 54 Period size: 10 Copynumber: 6.9 Consensus size: 10 3849896 AAAAAATACA 3849906 TATAAATTTT 1 TATAAATTTT 3849916 T-TAAAATTTT 1 TAT-AAATTTT 3849926 GTATAAATTATT 1 -TATAAATT-TT 3849938 TAT-AATTTT 1 TATAAATTTT * 3849947 T-TTAATTTT 1 TATAAATTTT 3849956 T-T-AATTTT 1 TATAAATTTT * 3849964 TATATATTT 1 TATAAATTT 3849973 AAATAAAATG Statistics Matches: 49, Mismatches: 1, Indels: 14 0.77 0.02 0.22 Matches are distributed among these distances: 8 8 0.16 9 13 0.27 10 16 0.33 11 9 0.18 12 3 0.06 ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64 Consensus pattern (10 bp): TATAAATTTT Found at i:3850855 original size:14 final size:14 Alignment explanation

Indices: 3850826--3850867 Score: 50 Period size: 14 Copynumber: 3.1 Consensus size: 14 3850816 TCACCCATTT * 3850826 TTTATTTTTAAT-A 1 TTTAATTTTAATAA * 3850839 TTTCATTTTAATAA 1 TTTAATTTTAATAA * 3850853 TTTAATATTAATAA 1 TTTAATTTTAATAA 3850867 T 1 T 3850868 CCTTATTTTT Statistics Matches: 24, Mismatches: 4, Indels: 1 0.83 0.14 0.03 Matches are distributed among these distances: 13 10 0.42 14 14 0.58 ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60 Consensus pattern (14 bp): TTTAATTTTAATAA Found at i:3853316 original size:20 final size:20 Alignment explanation

Indices: 3853291--3853344 Score: 81 Period size: 20 Copynumber: 2.7 Consensus size: 20 3853281 GTTTGAAGCA * * 3853291 ATGTATCGATACAATTTATC 1 ATGTATCGATACAATGTACC * 3853311 ATGTATCGATACAATGTGCC 1 ATGTATCGATACAATGTACC 3853331 ATGTATCGATACAA 1 ATGTATCGATACAA 3853345 ACAGTGGTAG Statistics Matches: 31, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 31 1.00 ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33 Consensus pattern (20 bp): ATGTATCGATACAATGTACC Found at i:3853417 original size:19 final size:20 Alignment explanation

Indices: 3853373--3853424 Score: 79 Period size: 19 Copynumber: 2.6 Consensus size: 20 3853363 CTGCCAGTTT ** 3853373 CATGTATCGATACAATTGTC 1 CATGTATCGATACAATTGAA 3853393 CATGTATCGATACAA-TGAA 1 CATGTATCGATACAATTGAA 3853412 CATGTATCGATAC 1 CATGTATCGATAC 3853425 CAAGCAAAAT Statistics Matches: 30, Mismatches: 2, Indels: 1 0.91 0.06 0.03 Matches are distributed among these distances: 19 15 0.50 20 15 0.50 ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31 Consensus pattern (20 bp): CATGTATCGATACAATTGAA Found at i:3853438 original size:20 final size:20 Alignment explanation

Indices: 3853394--3853444 Score: 61 Period size: 20 Copynumber: 2.6 Consensus size: 20 3853384 ACAATTGTCC * 3853394 ATGTATCGATA-CAATGAAC 1 ATGTATCGATACCAATGAAA 3853413 ATGTATCGATACCAA-GCAAA 1 ATGTATCGATACCAATG-AAA * 3853433 ATGTATCAATAC 1 ATGTATCGATAC 3853445 ATCTGGGTGT Statistics Matches: 28, Mismatches: 2, Indels: 3 0.85 0.06 0.09 Matches are distributed among these distances: 19 12 0.43 20 16 0.57 ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25 Consensus pattern (20 bp): ATGTATCGATACCAATGAAA Found at i:3855804 original size:22 final size:21 Alignment explanation

Indices: 3855769--3855818 Score: 59 Period size: 21 Copynumber: 2.4 Consensus size: 21 3855759 TTTGTTGATG * 3855769 ATTTTG-A-TGAAAAATGAAGT 1 ATTTTGAAGTGAAAAAT-AAGA 3855789 ATTTTGAAGTGAAAAATAAGA 1 ATTTTGAAGTGAAAAATAAGA * 3855810 AATTTGAAG 1 ATTTTGAAG 3855819 AAGATTTGAT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 20 6 0.23 21 12 0.46 22 8 0.31 ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32 Consensus pattern (21 bp): ATTTTGAAGTGAAAAATAAGA Found at i:3855815 original size:21 final size:22 Alignment explanation

Indices: 3855776--3855818 Score: 61 Period size: 21 Copynumber: 2.0 Consensus size: 22 3855766 ATGATTTTGA * * 3855776 TGAAAAATGAAGTATTTTGAAG 1 TGAAAAATGAAGAAATTTGAAG 3855798 TGAAAAAT-AAGAAATTTGAAG 1 TGAAAAATGAAGAAATTTGAAG 3855819 AAGATTTGAT Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 21 11 0.58 22 8 0.42 ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28 Consensus pattern (22 bp): TGAAAAATGAAGAAATTTGAAG Found at i:3862228 original size:20 final size:20 Alignment explanation

Indices: 3862203--3862260 Score: 66 Period size: 19 Copynumber: 3.0 Consensus size: 20 3862193 CTGCTAGTTT * 3862203 CATGTATCGATACAATTGTC 1 CATGTATCGATACAATTGTA * * 3862223 CATGTATTGATACAA-TGAA 1 CATGTATCGATACAATTGTA * 3862242 CATGTATCGTTAC-ATTGTA 1 CATGTATCGATACAATTGTA 3862261 TCAATAAAAA Statistics Matches: 31, Mismatches: 6, Indels: 3 0.77 0.15 0.08 Matches are distributed among these distances: 18 1 0.03 19 16 0.52 20 14 0.45 ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36 Consensus pattern (20 bp): CATGTATCGATACAATTGTA Found at i:3863767 original size:59 final size:58 Alignment explanation

Indices: 3863684--3863828 Score: 168 Period size: 59 Copynumber: 2.5 Consensus size: 58 3863674 CTCGATTTAT * * * ** * * 3863684 GACCATTTTAATAATTTTCGATGATTTAAGGGTTATTATG-TAATTTCAATGTATTTTAAA 1 GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCT-ATTTC-ATGCATTGT-AA * 3863744 GA-CATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAG 1 GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAA 3863801 GACCATTTTAGTCATTTTCTCATGATTT 1 GACCATTTTAGTCATTTTC-CATGATTT 3863829 TATGATTTTA Statistics Matches: 74, Mismatches: 8, Indels: 7 0.83 0.09 0.08 Matches are distributed among these distances: 57 3 0.04 58 23 0.31 59 45 0.61 60 3 0.04 ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46 Consensus pattern (58 bp): GACCATTTTAGTCATTTTCCATGATTTAAGGCCTATTATGCTATTTCATGCATTGTAA Found at i:3864097 original size:18 final size:18 Alignment explanation

Indices: 3864074--3864109 Score: 63 Period size: 18 Copynumber: 2.0 Consensus size: 18 3864064 ATGTTGCCTT 3864074 AAAATCAAGTCCTTAGGA 1 AAAATCAAGTCCTTAGGA * 3864092 AAAATCGAGTCCTTAGGA 1 AAAATCAAGTCCTTAGGA 3864110 TCATGTGAAA Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22 Consensus pattern (18 bp): AAAATCAAGTCCTTAGGA Found at i:3864311 original size:76 final size:76 Alignment explanation

Indices: 3864092--3864399 Score: 242 Period size: 75 Copynumber: 4.1 Consensus size: 76 3864082 GTCCTTAGGA ** * 3864092 AAAATCGAGTCCTTAGGATCATGTGA-AACTTTTGTGTCAAAACATGTCTC-TTAAA-GTAATTT 1 AAAATCGAGT-C-TAGGATCATGTGAGAACTTTCATGTCAAAACATGTC-CATTAAATGTATTTT * 3864154 AGGTTATAGTACCCTT 63 A-GTAATAGTA-CCTT * * * * * * ** * 3864170 AAAAT-GA-TTTTGGAATCATGTGGGAACATTCGTGTCGAAACATGT-CATT-AGGGTCATTTCA 1 AAAATCGAGTCTAGG-ATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGT-ATTTTA * 3864231 GTAATAATACCTT 64 GTAATAGTACCTT * * 3864244 AAAATCGAGTCTAGGATAATGTGAGAACTTTCATGTCAAAACATATCCATTAAATGTATTTTAGT 1 AAAATCGAGTCTAGGATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGTATTTTAGT 3864309 AATAGTACCTT 66 AATAGTACCTT * * * * * 3864320 AAAATTGATTCTAGAAGCATGTG-GAAACGTT-AGTGTC-AAACATGTCCATTAGAAT-TATTTT 1 AAAATCGAGTCTAGGATCATGTGAG-AACTTTCA-TGTCAAAACATGTCCATTA-AATGTATTTT * * 3864381 GGTAATAGTACCTC 63 AGTAATAGTACCTT 3864395 AAAAT 1 AAAAT 3864400 GGAAGCCCTA Statistics Matches: 186, Mismatches: 32, Indels: 27 0.76 0.13 0.11 Matches are distributed among these distances: 74 14 0.08 75 84 0.45 76 78 0.42 77 5 0.03 78 5 0.03 ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34 Consensus pattern (76 bp): AAAATCGAGTCTAGGATCATGTGAGAACTTTCATGTCAAAACATGTCCATTAAATGTATTTTAGT AATAGTACCTT Found at i:3864314 original size:151 final size:152 Alignment explanation

Indices: 3864092--3864371 Score: 365 Period size: 151 Copynumber: 1.8 Consensus size: 152 3864082 GTCCTTAGGA * ** * 3864092 AAAATCGAGTCCTTAGGATCATGTGAAACTTTTGTGTCAAAACATGTCTCTTAAAGTAATTTAGG 1 AAAATCGAGTCCTTAGGATAATGTGAAACTTTCATGTCAAAACATATCTCTTAAAGTAATTTAGG * * * * * * 3864157 TTATAGTACCCTTAAAA-TGATTTTGGAATCATGTGGGAACATTCGTGTCGAAACATGT-CATTA 66 TAATAGTA-CCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTC-AAACATGTCCATTA 3864220 GGGTCATTTCAGTAATAATACCTT 129 GGGTCATTTCAGTAATAATACCTT * 3864244 AAAATCGAGT-C-TAGGATAATGTGAGAACTTTCATGTCAAAACATATC-CATTAAATGTATTTT 1 AAAATCGAGTCCTTAGGATAATGTGA-AACTTTCATGTCAAAACATATCTC-TTAAA-GTAATTT * 3864306 A-GTAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACGTTAGTGTCAAACATGTCCATT 63 AGGTAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTCAAACATGTCCATT 3864370 AG 128 AG 3864372 AATTATTTTG Statistics Matches: 111, Mismatches: 12, Indels: 11 0.83 0.09 0.08 Matches are distributed among these distances: 150 29 0.26 151 65 0.59 152 17 0.15 ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34 Consensus pattern (152 bp): AAAATCGAGTCCTTAGGATAATGTGAAACTTTCATGTCAAAACATATCTCTTAAAGTAATTTAGG TAATAGTACCTTAAAATTGATTCTAGAAGCATGTGGAAACATTAGTGTCAAACATGTCCATTAGG GTCATTTCAGTAATAATACCTT Found at i:3866095 original size:79 final size:78 Alignment explanation

Indices: 3866012--3866291 Score: 325 Period size: 79 Copynumber: 3.6 Consensus size: 78 3866002 ACCCTCGATA * * 3866012 ATGAAAAATTTAATATTTTGGAAATAAAAACGGGGTTGGAGCAT-TCTGTCGGAAATAAAGGGGT 1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCT-TCGGAAATAAAGGGGT 3866076 TGAAGTATCCCCAAG 65 TGAAGTATCCCC-AG * * * * * * 3866091 ATGAAAAATTTAATATTTTTGAAAATAAAAACGGGATTGGAGTATCCCTTTGAAAATAATGGGGC 1 ATGAAAAATTTAATA-TTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGT * 3866156 TGGAGTA-CCCTCA- 65 TGAAGTATCCC-CAG * * * * 3866169 A-GAAAAATTTAATATTTTGGAAATAAAAATGGGGTTGGAGTATCTCTTCAGAAATAACGGGGTT 1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGTT * 3866233 GAAATATCCCCGAG 66 GAAGTATCCCC-AG * ** * 3866247 ATGAAAATTTTAATATTTTGAAAATAAAAGTGGGGTTAGAGTATC 1 ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATC 3866292 CCCAAAGATG Statistics Matches: 170, Mismatches: 24, Indels: 14 0.82 0.12 0.07 Matches are distributed among these distances: 76 46 0.27 77 17 0.10 78 2 0.01 79 58 0.34 80 45 0.26 81 2 0.01 ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29 Consensus pattern (78 bp): ATGAAAAATTTAATATTTTGAAAATAAAAACGGGGTTGGAGTATCTCTTCGGAAATAAAGGGGTT GAAGTATCCCCAG Found at i:3866948 original size:228 final size:228 Alignment explanation

Indices: 3866540--3866993 Score: 872 Period size: 228 Copynumber: 2.0 Consensus size: 228 3866530 AGGGGGTAAA 3866540 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA 1 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA 3866605 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG 66 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG * 3866670 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCTGATCGAGTTGCTAAAACCTCT 131 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT 3866735 ATACTTGAGTATGTTAATGTTCCCATGTCTAGG 196 ATACTTGAGTATGTTAATGTTCCCATGTCTAGG * * 3866768 CAAGGTACTGTTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA 1 CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA * 3866833 ATCACTTTCTAGGCAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG 66 ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG 3866898 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT 131 GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT 3866963 ATACTTGAGTATGTTAATGTTCCCATGTCTA 196 ATACTTGAGTATGTTAATGTTCCCATGTCTA 3866994 TGCTCAGTCA Statistics Matches: 222, Mismatches: 4, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 228 222 1.00 ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31 Consensus pattern (228 bp): CAAGCTACTATTAGAAAGGTGATTTAACAAAGATTAATGTAAAAATATTCCAAAAATCCTAGAAA ATCACTTTCTAGGAAAAATTAATTTTTGAAACTTGATCTCATTTTGACATTGGCAGCATATGCAG GGTAAAGGTGTGATGGACTTCGAAAAATCATGTGCAGATGTGCAGATCGAGTTGCTAAAACCTCT ATACTTGAGTATGTTAATGTTCCCATGTCTAGG Found at i:3868873 original size:11 final size:11 Alignment explanation

Indices: 3868859--3868893 Score: 54 Period size: 11 Copynumber: 3.3 Consensus size: 11 3868849 AACCAAAAAT 3868859 AAAAAAAATG- 1 AAAAAAAATGA 3868869 AAAAAAAATGA 1 AAAAAAAATGA * 3868880 AAAAAAAAAGA 1 AAAAAAAATGA 3868891 AAA 1 AAA 3868894 TTGATTGCAA Statistics Matches: 23, Mismatches: 1, Indels: 1 0.92 0.04 0.04 Matches are distributed among these distances: 10 10 0.43 11 13 0.57 ACGTcount: A:0.86, C:0.00, G:0.09, T:0.06 Consensus pattern (11 bp): AAAAAAAATGA Found at i:3868893 original size:9 final size:10 Alignment explanation

Indices: 3868853--3868886 Score: 61 Period size: 10 Copynumber: 3.5 Consensus size: 10 3868843 ATGTTAAACC 3868853 AAAAAT-AAA 1 AAAAATGAAA 3868862 AAAAATGAAA 1 AAAAATGAAA 3868872 AAAAATGAAA 1 AAAAATGAAA 3868882 AAAAA 1 AAAAA 3868887 AAGAAAATTG Statistics Matches: 24, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 9 6 0.25 10 18 0.75 ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09 Consensus pattern (10 bp): AAAAATGAAA Found at i:3873353 original size:45 final size:45 Alignment explanation

Indices: 3873289--3873431 Score: 189 Period size: 45 Copynumber: 3.1 Consensus size: 45 3873279 CCTTTTTACA * 3873289 AAACAATATTAAAAGTAAAACCCATGATCCTAATCTCCAAAAGAC 1 AAACAATATTAAAAATAAAACCCATGATCCTAATCTCCAAAAGAC * * 3873334 AAACAATATTAAAAATAAAATAAAATCCACGATCCTAATCTCCAAAAGAC 1 AAACAATATT----A-AAAATAAAACCCATGATCCTAATCTCCAAAAGAC * 3873384 AAACAATATTAAAAATAAAGCCCATGATCCTAATC-CTCAAAAGAC 1 AAACAATATTAAAAATAAAACCCATGATCCTAATCTC-CAAAAGAC 3873429 AAA 1 AAA 3873432 AAAAAAAAAT Statistics Matches: 86, Mismatches: 6, Indels: 12 0.83 0.06 0.12 Matches are distributed among these distances: 44 1 0.01 45 42 0.49 46 1 0.01 49 1 0.01 50 41 0.48 ACGTcount: A:0.54, C:0.21, G:0.06, T:0.20 Consensus pattern (45 bp): AAACAATATTAAAAATAAAACCCATGATCCTAATCTCCAAAAGAC Found at i:3873377 original size:50 final size:51 Alignment explanation

Indices: 3873298--3873402 Score: 185 Period size: 50 Copynumber: 2.1 Consensus size: 51 3873288 AAAACAATAT * 3873298 TAAAAGTAAAACCCATGATCCTAATCTCCAAAAGACAAACAATATTAAAAA 1 TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA * 3873349 TAAAA-TAAAATCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA 1 TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA 3873399 TAAA 1 TAAA 3873403 GCCCATGATC Statistics Matches: 52, Mismatches: 2, Indels: 1 0.95 0.04 0.02 Matches are distributed among these distances: 50 47 0.90 51 5 0.10 ACGTcount: A:0.56, C:0.19, G:0.05, T:0.20 Consensus pattern (51 bp): TAAAAGTAAAACCCACGATCCTAATCTCCAAAAGACAAACAATATTAAAAA Found at i:3877318 original size:20 final size:20 Alignment explanation

Indices: 3877293--3877346 Score: 74 Period size: 20 Copynumber: 2.7 Consensus size: 20 3877283 GTTACAAGCA * 3877293 ATGTATCGATACAAT-TCATC 1 ATGTATCGATACAATGT-ACC 3877313 ATGTATCGATACAATGTACC 1 ATGTATCGATACAATGTACC * 3877333 ATGTATTGATACAA 1 ATGTATCGATACAA 3877347 ACAGTGGTAG Statistics Matches: 31, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 20 30 0.97 21 1 0.03 ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33 Consensus pattern (20 bp): ATGTATCGATACAATGTACC Found at i:3877404 original size:20 final size:20 Alignment explanation

Indices: 3877375--3877468 Score: 129 Period size: 19 Copynumber: 4.8 Consensus size: 20 3877365 CTGCCAGTTT ** 3877375 CATGTATCGATACAATTGTC 1 CATGTATCGATACAATTGAA * 3877395 CATATATCGATACAA-TGAA 1 CATGTATCGATACAATTGAA ** 3877414 CATGTATCGATACAATTGTC 1 CATGTATCGATACAATTGAA 3877434 CATGTATCGATACAA-TGAA 1 CATGTATCGATACAATTGAA 3877453 CATGTATCGATACAAT 1 CATGTATCGATACAAT 3877469 GTATCGATAC Statistics Matches: 64, Mismatches: 8, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 19 33 0.52 20 31 0.48 ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31 Consensus pattern (20 bp): CATGTATCGATACAATTGAA Found at i:3877424 original size:39 final size:39 Alignment explanation

Indices: 3877375--3877468 Score: 179 Period size: 39 Copynumber: 2.4 Consensus size: 39 3877365 CTGCCAGTTT 3877375 CATGTATCGATACAATTGTCCATATATCGATACAATGAA 1 CATGTATCGATACAATTGTCCATATATCGATACAATGAA * 3877414 CATGTATCGATACAATTGTCCATGTATCGATACAATGAA 1 CATGTATCGATACAATTGTCCATATATCGATACAATGAA 3877453 CATGTATCGATACAAT 1 CATGTATCGATACAAT 3877469 GTATCGATAC Statistics Matches: 54, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 39 54 1.00 ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31 Consensus pattern (39 bp): CATGTATCGATACAATTGTCCATATATCGATACAATGAA Found at i:3877472 original size:13 final size:13 Alignment explanation

Indices: 3877454--3877480 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3877444 TACAATGAAC 3877454 ATGTATCGATACA 1 ATGTATCGATACA 3877467 ATGTATCGATACA 1 ATGTATCGATACA 3877480 A 1 A 3877481 AGCATAATGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3878106 original size:25 final size:25 Alignment explanation

Indices: 3878078--3878136 Score: 118 Period size: 25 Copynumber: 2.4 Consensus size: 25 3878068 TTTCCCTTAA 3878078 TCAAAGCAAAAATTTATTTTATTTT 1 TCAAAGCAAAAATTTATTTTATTTT 3878103 TCAAAGCAAAAATTTATTTTATTTT 1 TCAAAGCAAAAATTTATTTTATTTT 3878128 TCAAAGCAA 1 TCAAAGCAA 3878137 TATATATCTC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 34 1.00 ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42 Consensus pattern (25 bp): TCAAAGCAAAAATTTATTTTATTTT Found at i:3886176 original size:20 final size:20 Alignment explanation

Indices: 3886151--3886190 Score: 71 Period size: 20 Copynumber: 2.0 Consensus size: 20 3886141 GTTACAAGCA * 3886151 ATGTATCGATACAATTCATC 1 ATGTATCGATACAATGCATC 3886171 ATGTATCGATACAATGCATC 1 ATGTATCGATACAATGCATC 3886191 GATACAATGC Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33 Consensus pattern (20 bp): ATGTATCGATACAATGCATC Found at i:3886192 original size:33 final size:33 Alignment explanation

Indices: 3886149--3886214 Score: 105 Period size: 33 Copynumber: 2.0 Consensus size: 33 3886139 TTGTTACAAG * * * 3886149 CAATGTATCGATACAATTCATCATGTATCGATA 1 CAATGCATCGATACAATGCACCATGTATCGATA 3886182 CAATGCATCGATACAATGCACCATGTATCGATA 1 CAATGCATCGATACAATGCACCATGTATCGATA 3886215 TAAATAGTGG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29 Consensus pattern (33 bp): CAATGCATCGATACAATGCACCATGTATCGATA Found at i:3886193 original size:13 final size:13 Alignment explanation

Indices: 3886175--3886201 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3886165 TTCATCATGT 3886175 ATCGATACAATGC 1 ATCGATACAATGC 3886188 ATCGATACAATGC 1 ATCGATACAATGC 3886201 A 1 A 3886202 CCATGTATCG Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22 Consensus pattern (13 bp): ATCGATACAATGC Found at i:3886213 original size:20 final size:19 Alignment explanation

Indices: 3886143--3886214 Score: 61 Period size: 20 Copynumber: 4.1 Consensus size: 19 3886133 TTATAGTTGT 3886143 TACAA-GCA-ATGTATCGA 1 TACAATGCACATGTATCGA * 3886160 TACAATTCATCATGTATCGA 1 TACAATGCA-CATGTATCGA 3886180 TACAATG--C----ATCGA 1 TACAATGCACATGTATCGA 3886193 TACAATGCACCATGTATCGA 1 TACAATGCA-CATGTATCGA 3886213 TA 1 TA 3886215 TAAATAGTGG Statistics Matches: 43, Mismatches: 2, Indels: 17 0.69 0.03 0.27 Matches are distributed among these distances: 13 12 0.28 16 1 0.02 17 6 0.14 18 2 0.05 20 22 0.51 ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28 Consensus pattern (19 bp): TACAATGCACATGTATCGA Found at i:3886271 original size:20 final size:20 Alignment explanation

Indices: 3886246--3886321 Score: 102 Period size: 20 Copynumber: 3.8 Consensus size: 20 3886236 CTACCAGTTT 3886246 CATGTATCGATACAATTGTC 1 CATGTATCGATACAATTGTC 3886266 CATGTATCGATACAATTGTCC 1 CATGTATCGATACAATTGT-C ** 3886287 CATGTATCGATGA-AA-TGAA 1 CATGTATCGAT-ACAATTGTC 3886306 CATGTATCGATACAAT 1 CATGTATCGATACAAT 3886322 ATATCAATAC Statistics Matches: 50, Mismatches: 2, Indels: 8 0.83 0.03 0.13 Matches are distributed among these distances: 18 1 0.02 19 13 0.26 20 21 0.42 21 14 0.28 22 1 0.02 ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32 Consensus pattern (20 bp): CATGTATCGATACAATTGTC Found at i:3886416 original size:71 final size:71 Alignment explanation

Indices: 3886333--3886494 Score: 297 Period size: 71 Copynumber: 2.3 Consensus size: 71 3886323 TATCAATACA * * 3886333 AAGCATAATGTATCGATACATTTGGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC 1 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC 3886398 TAAGTC 66 TAAGTC 3886404 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC 1 AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC 3886469 TAAGTC 66 TAAGTC * 3886475 AACCATAATGTATCGATACA 1 AAGCATAATGTATCGATACA 3886495 AATTTTGTTG Statistics Matches: 88, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 71 88 1.00 ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35 Consensus pattern (71 bp): AAGCATAATGTATCGATACATCTAGGTATGTATTGATACATTCAAGGGTTTTGACCTTTGTAGCC TAAGTC Found at i:3902909 original size:11 final size:11 Alignment explanation

Indices: 3902889--3902962 Score: 89 Period size: 11 Copynumber: 6.6 Consensus size: 11 3902879 AGCGTCCTCC 3902889 ACAAAAAAAAA 1 ACAAAAAAAAA 3902900 ACAAATAAAAAA 1 ACAAA-AAAAAA * 3902912 AC-AAAAACAA 1 ACAAAAAAAAA 3902922 ACAAAAAAAAA 1 ACAAAAAAAAA 3902933 ACAAAAAATAAA 1 ACAAAAAA-AAA * 3902945 A-AAAAACAACA 1 ACAAAAA-AAAA 3902956 ACAAAAA 1 ACAAAAA 3902963 GGGTCCGGAT Statistics Matches: 55, Mismatches: 3, Indels: 9 0.82 0.04 0.13 Matches are distributed among these distances: 10 7 0.13 11 30 0.55 12 18 0.33 ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03 Consensus pattern (11 bp): ACAAAAAAAAA Found at i:3902911 original size:17 final size:17 Alignment explanation

Indices: 3902891--3902956 Score: 87 Period size: 18 Copynumber: 3.8 Consensus size: 17 3902881 CGTCCTCCAC 3902891 AAAAAAAAAACAAATAA 1 AAAAAAAAAACAAATAA * 3902908 AAAAACAAAAACAAACAA 1 AAAAA-AAAAACAAATAA * 3902926 AAAAAAAACAAAAAATAA 1 AAAAAAAA-AACAAATAA * 3902944 AAAAAAACAACAA 1 AAAAAAAAAACAA 3902957 CAAAAAGGGT Statistics Matches: 42, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 17 12 0.29 18 30 0.71 ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03 Consensus pattern (17 bp): AAAAAAAAAACAAATAA Found at i:3902917 original size:22 final size:21 Alignment explanation

Indices: 3902892--3902962 Score: 90 Period size: 20 Copynumber: 3.4 Consensus size: 21 3902882 GTCCTCCACA 3902892 AAAAAAAAACAAATAAAAAAAC 1 AAAAAAAAACAAA-AAAAAAAC * 3902914 AAAAACAAACAAAAAAAAAAC 1 AAAAAAAAACAAAAAAAAAAC * * 3902935 AAAAAATAA-AAAAAAACAAC 1 AAAAAAAAACAAAAAAAAAAC * 3902955 AACAAAAA 1 AAAAAAAA 3902963 GGGTCCGGAT Statistics Matches: 43, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 20 16 0.37 21 15 0.35 22 12 0.28 ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03 Consensus pattern (21 bp): AAAAAAAAACAAAAAAAAAAC Found at i:3902928 original size:32 final size:31 Alignment explanation

Indices: 3902889--3902962 Score: 105 Period size: 33 Copynumber: 2.3 Consensus size: 31 3902879 AGCGTCCTCC 3902889 ACAAAAAAAAAACAAATAAA-AAAACAAAAACAA 1 ACAAAAAAAAAACAAA-AAATAAAA-AAAAAC-A 3902922 ACAAAAAAAAAACAAAAAATAAAAAAAAACA 1 ACAAAAAAAAAACAAAAAATAAAAAAAAACA * 3902953 ACAACAAAAA 1 ACAAAAAAAA 3902963 GGGTCCGGAT Statistics Matches: 39, Mismatches: 1, Indels: 4 0.89 0.02 0.09 Matches are distributed among these distances: 31 10 0.26 32 9 0.23 33 20 0.51 ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03 Consensus pattern (31 bp): ACAAAAAAAAAACAAAAAATAAAAAAAAACA Found at i:3902948 original size:38 final size:35 Alignment explanation

Indices: 3902891--3902962 Score: 103 Period size: 35 Copynumber: 2.1 Consensus size: 35 3902881 CGTCCTCCAC * 3902891 AAAAAAAAAACAAATAAAAAAACAAAAACAAACAA 1 AAAAAAAAAAAAAATAAAAAAACAAAAACAAACAA * 3902926 AAAAAAAACAAAAAATAAAAAAA-AACAAC-AACAA 1 AAAAAAAA-AAAAAATAAAAAAACAAAAACAAACAA 3902960 AAA 1 AAA 3902963 GGGTCCGGAT Statistics Matches: 34, Mismatches: 2, Indels: 3 0.87 0.05 0.08 Matches are distributed among these distances: 34 8 0.24 35 13 0.38 36 13 0.38 ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03 Consensus pattern (35 bp): AAAAAAAAAAAAAATAAAAAAACAAAAACAAACAA Found at i:3902962 original size:1 final size:1 Alignment explanation

Indices: 3902891--3902950 Score: 57 Period size: 1 Copynumber: 60.0 Consensus size: 1 3902881 CGTCCTCCAC * * * * * * * 3902891 AAAAAAAAAACAAATAAAAAAACAAAAACAAACAAAAAAAAAACAAAAAATAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 3902951 CAACAACAAA Statistics Matches: 45, Mismatches: 14, Indels: 0 0.76 0.24 0.00 Matches are distributed among these distances: 1 45 1.00 ACGTcount: A:0.88, C:0.08, G:0.00, T:0.03 Consensus pattern (1 bp): A Found at i:3904491 original size:28 final size:28 Alignment explanation

Indices: 3904392--3904555 Score: 184 Period size: 28 Copynumber: 5.8 Consensus size: 28 3904382 CTTACCTCCC *** 3904392 AAAGCCCACAAGTCAGTGGCATGTTTTTCA 1 AAAGCCCACAAGTCAGTGGCA--ACCTTCA * * * * ** 3904422 AAAGGCCACAGGTCAGTGGCATCTTTTTT 1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA 3904451 AAAGCCCACAAGTCAGTGGCAACCTTCA 1 AAAGCCCACAAGTCAGTGGCAACCTTCA * * 3904479 AAAGCCCATAAGTTAGTGGCAACCTTCA 1 AAAGCCCACAAGTCAGTGGCAACCTTCA * 3904507 AAAGCCCATAAGTCAGTGGCAACCTTCA 1 AAAGCCCACAAGTCAGTGGCAACCTTCA * 3904535 AAAGCCCACAAGTCAATGGCA 1 AAAGCCCACAAGTCAGTGGCA 3904556 CATTTTTCCT Statistics Matches: 117, Mismatches: 16, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 28 75 0.64 29 23 0.20 30 19 0.16 ACGTcount: A:0.34, C:0.26, G:0.20, T:0.21 Consensus pattern (28 bp): AAAGCCCACAAGTCAGTGGCAACCTTCA Found at i:3904577 original size:33 final size:33 Alignment explanation

Indices: 3904551--3904860 Score: 304 Period size: 33 Copynumber: 9.3 Consensus size: 33 3904541 CACAAGTCAA * * * 3904551 TGGCACATTTTTCCTTTCAAGTCCACAACTCTG 1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG * * 3904584 TGGCATCTTTTTCCTTTTAAGTCCACAACTCCA 1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG * * * 3904617 CGGCACCTTGTTCCTTTTAAGTCCACAACTTCG 1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG * 3904650 TGGCACCTTTTT-CTTTTCAAAGTCCACAACTCTG 1 TGGCACCTTTTTCCTTTT--AAGTCCACAACTCCG * 3904684 TGGCA-CTTTGTTCCTTTTAAATCCACAACTCCG 1 TGGCACCTTT-TTCCTTTTAAGTCCACAACTCCG * * * ** 3904717 TGGCACCTTTTTCTTTTTAAAGCCCACAGCTTTG 1 TGGCACCTTTTTCCTTTT-AAGTCCACAACTCCG * * * * * 3904751 TGGCA-CATTTTCTTTTTAAGTCTACGACTCCA 1 TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG * * * * 3904783 TGGTACCCTTTTCTCTTTTAAGCCCACAACTCCA 1 TGGCACCTTTTTC-CTTTTAAGTCCACAACTCCG * 3904817 TGGCATCCCTTTTTCC-TATAAGTCCACAACTCCG 1 TGGCA--CCTTTTTCCTTTTAAGTCCACAACTCCG 3904851 TGGCACCTTT 1 TGGCACCTTT 3904861 AAGATCAATG Statistics Matches: 226, Mismatches: 41, Indels: 21 0.78 0.14 0.07 Matches are distributed among these distances: 32 22 0.10 33 112 0.50 34 79 0.35 35 6 0.03 36 7 0.03 ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37 Consensus pattern (33 bp): TGGCACCTTTTTCCTTTTAAGTCCACAACTCCG Found at i:3904712 original size:100 final size:99 Alignment explanation

Indices: 3904551--3904860 Score: 347 Period size: 100 Copynumber: 3.1 Consensus size: 99 3904541 CACAAGTCAA * * * 3904551 TGGCACATTTTTCCTTTCAAGTCCACAACTCTGTGGCATCTTTTTCCTTTTAAGTCCACAACTCC 1 TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACAACTCC * * 3904616 ACGGCACCTTGTTCCTTTTAAGTCCACAACTTCG 66 ATGGCACCTTTTTCCTTTTAAGTCCACAACTTCG * 3904650 TGGCACCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA-CTTTGTTCCTTTTAAATCCACAACT 1 TGGCACCTTTTTCTTTTC-AAGTCCACAACTCTGTGGCACCTTT-TTCCTTTTAAGTCCACAACT * * * * * 3904714 CCGTGGCACCTTTTTCTTTTTAAAGCCCACAGCTTTG 64 CCATGGCACCTTTTTCCTTTT-AAGTCCACAACTTCG * * * * ** * * * 3904751 TGGCA-CATTTTCTTTTTAAGTCTACGACTCCATGGTACCCTTTTCTCTTTTAAGCCCACAACTC 1 TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTC-CTTTTAAGTCCACAACTC * * 3904815 CATGGCATCCCTTTTTCC-TATAAGTCCACAACTCCG 65 CATGGCA--CCTTTTTCCTTTTAAGTCCACAACTTCG 3904851 TGGCACCTTT 1 TGGCACCTTT 3904861 AAGATCAATG Statistics Matches: 175, Mismatches: 28, Indels: 14 0.81 0.13 0.06 Matches are distributed among these distances: 99 38 0.22 100 107 0.61 101 22 0.13 102 8 0.05 ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37 Consensus pattern (99 bp): TGGCACCTTTTTCTTTTCAAGTCCACAACTCTGTGGCACCTTTTTCCTTTTAAGTCCACAACTCC ATGGCACCTTTTTCCTTTTAAGTCCACAACTTCG Found at i:3904921 original size:43 final size:43 Alignment explanation

Indices: 3904851--3905262 Score: 302 Period size: 43 Copynumber: 9.2 Consensus size: 43 3904841 CACAACTCCG * * 3904851 TGGCACCTTTAAGAT-CAATGTCGCTAGCCTTGAATCAGCACAT 1 TGGCACCTTTAAG-TCCAATATCGCTAGCCTTGAATCAGCATAT * * 3904894 TGGCACCTTTAAGTCCACTATCACTAGCCTTGAATCAGCATAT 1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * * * 3904937 TGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACAT 1 TGGCA-C-----CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * * * 3904986 TAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATAT 1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * 3905029 TGGCACCTTTACCATATTGAGTCCAATATCGCTAGCCTTGAATCAACATAT 1 TGGCACC-TT----TA---AGTCCAATATCGCTAGCCTTGAATCAGCATAT * * * * * 3905080 TGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTTGAATCAGCACAT 1 TGGCACC---T-T-TAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * * 3905128 TGGCA----TAAGCCCAATATCGCTGGCCTTGAATCAGCATAT 1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * * * * * 3905167 TGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACAT 1 TGGCACC-----TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT * * * 3905215 TGGCA-C---AAGCCCAATATTGCTGGCCTTGAATCAGCATAT 1 TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT 3905254 TGGCACCTT 1 TGGCACCTT 3905263 CATCTTTAAG Statistics Matches: 301, Mismatches: 38, Indels: 61 0.75 0.09 0.15 Matches are distributed among these distances: 39 70 0.23 40 1 0.00 42 1 0.00 43 80 0.27 44 3 0.01 47 1 0.00 48 69 0.23 49 36 0.12 51 38 0.13 53 1 0.00 54 1 0.00 ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29 Consensus pattern (43 bp): TGGCACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT Found at i:3904972 original size:49 final size:49 Alignment explanation

Indices: 3904857--3905643 Score: 568 Period size: 49 Copynumber: 16.9 Consensus size: 49 3904847 TCCGTGGCAC * * * 3904857 CTTTAAGATCAATGTCGCTAGCCTTGAATCAGCACATTGGCA----C-- 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * * * * 3904900 CTTTAAGTCCACTATCACTAGCCTTGAATCAGCATATTGGCACCTTTAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3904949 CTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATTAGCA----C-- 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * * * 3904992 CTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAC 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * * * * 3905041 CATATTGAGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-GT 1 C-T-TTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3905091 CTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG------CA- 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3905133 ---TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3905178 ATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGG------CA- 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3905220 C---AAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * ** * * 3905266 CTTTAAGACCGATGTCATTGGCCTTGAATCAACACATTAGCACCTTAACCAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT---CAT * * * * * 3905318 CTTTAAGTCCAATGTCG-TCAGCCTTGAATCAGTACATTGGCATCTTCAT 1 CTTTAAGACCAATATCGCT-GGCCTTGAATCAGCACATTGGCACCTTCAT * * * * * 3905367 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTAGCACCGTCAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * 3905416 CTTTAAGACCAATGTCGCTAGCCCTGAATCAGCACATTGG------CA- 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * ** 3905458 ---TGAG-CCTAATATCGCTAGCCTTGAATTAGCATGTTGGCACCTTCAT 1 CTTTAAGACC-AATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * * 3905504 CTTTAAGACCAATGTCGTTGGCCTTGAATCAACACATTGGCACGTTCAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * 3905553 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT * * * * 3905602 CTTTAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGGCA 1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA 3905644 TCTGTAACAT Statistics Matches: 586, Mismatches: 105, Indels: 100 0.74 0.13 0.13 Matches are distributed among these distances: 38 2 0.00 39 94 0.16 43 74 0.13 45 4 0.01 46 1 0.00 48 63 0.11 49 263 0.45 50 5 0.01 51 41 0.07 52 39 0.07 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30 Consensus pattern (49 bp): CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCAT Found at i:3905153 original size:39 final size:39 Alignment explanation

Indices: 3905094--3905258 Score: 159 Period size: 39 Copynumber: 4.0 Consensus size: 39 3905084 ACCTTGTCTC * * 3905094 TAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCA 1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA * * 3905133 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTA 1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG---C----A * * 3905179 TTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCA 1 --TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA * * * * 3905220 CAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCA 1 TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA 3905259 CCTTCATCTT Statistics Matches: 105, Mismatches: 12, Indels: 18 0.78 0.09 0.13 Matches are distributed among these distances: 39 68 0.65 41 1 0.01 42 1 0.01 45 1 0.01 46 1 0.01 48 33 0.31 ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27 Consensus pattern (39 bp): TAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA Found at i:3905173 original size:138 final size:140 Alignment explanation

Indices: 3904905--3905175 Score: 411 Period size: 138 Copynumber: 1.9 Consensus size: 140 3904895 GGCACCTTTA * * * * 3904905 AGTCCACTATCACTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAG 1 AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG * * 3904970 CCTTGAATCAGCACATTAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCAC 66 CCTTGAATCAGCACATTAGCA-C--TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC 3905035 CTTTACCATATTG 128 CTTTACCATATTG * * * 3905048 AGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACC-TTGTCTCTAAGACCAATGTCACTGG 1 AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG * 3905112 CCTTGAATCAGCACATTGGCA-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT 66 CCTTGAATCAGCACATTAGCACTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT 3905176 GTATTTAAGA Statistics Matches: 118, Mismatches: 10, Indels: 5 0.89 0.08 0.04 Matches are distributed among these distances: 138 41 0.35 142 41 0.35 143 36 0.31 ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30 Consensus pattern (140 bp): AGTCCAATATCACTAGCCTTGAATCAACATATTGGCACCTTTATCTCTAAGACCAATGTCACTAG CCTTGAATCAGCACATTAGCACTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT TACCATATTG Found at i:3905199 original size:87 final size:87 Alignment explanation

Indices: 3905051--3905308 Score: 390 Period size: 87 Copynumber: 3.0 Consensus size: 87 3905041 CATATTGAGT * * * 3905051 CCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACCAATGTCACTGGCCTT 1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT * 3905116 GAATCAGCACATTGGCATAAGC 66 GAATCAGCACATTGGCACAAGC * ** 3905138 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTT 1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT 3905203 GAATCAGCACATTGGCACAAGC 66 GAATCAGCACATTGGCACAAGC * * * * 3905225 CCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCATTGGCCT 1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCACTGGCCT * * 3905290 TGAATCAACACATTAGCAC 65 TGAATCAGCACATTGGCAC 3905309 CTTAACCATC Statistics Matches: 154, Mismatches: 16, Indels: 1 0.90 0.09 0.01 Matches are distributed among these distances: 87 117 0.76 88 37 0.24 ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28 Consensus pattern (87 bp): CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGGCCTT GAATCAGCACATTGGCACAAGC Found at i:3905506 original size:238 final size:229 Alignment explanation

Indices: 3904857--3905643 Score: 910 Period size: 238 Copynumber: 3.4 Consensus size: 229 3904847 TCCGTGGCAC * 3904857 CTTTAAGAT-CAATGTCGCTAGCCTTGAATCAGCACATTGGCAC-CTTTAAGTCC-ACTATCACT 1 CTTTAAG-TCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGA-TATCGCT * 3904919 AGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCAC 64 GGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCAC * * * * * 3904984 ATTAGCACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATATTGA 128 ATTGGCA----TAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-T-TTAA * * * * * * 3905049 GTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTT-GT 187 GACCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCAT * * * * * * 3905091 CTCTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG--CA---TAAGCCCAATATCGCTGG 1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGATATCGCTGG * * * * 3905151 CCTTGAATCAGCATATTGGCACCTTGTATTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATT 66 CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATT * * * * 3905216 GGCACAAGCCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGT 131 GGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGT * * 3905281 CATTGGCCTTGAATCAACACATTAGCACCTTAACCAT 196 CGTTGGCCTTGAATCAACACATTGGCACCTT---CAT * 3905318 CTTTAAGTCCAATGTCG-TCAGCCTTGAATCAGTACATTGGCATCTTCATCTTTAAGTCCGATAT 1 CTTTAAGTCCAATGTCGCT-AGCCTTGAATCAGCACATTGGCA----CA-CTTTAAGTCCGATAT * * * 3905382 CGCTGGCCTTGAATCAGCATATTAGCACCGTCATCTTTAAGACCAATGTCGCTAGCCCTGAATCA 60 CGCTGGCCTTGAATCAGCATATTGGCACC-TTATCTTTAAGACCAATGTCGCTAGCCTTGAATCA * * * * 3905447 GCACATTGGCATGAGCCTAATATCGCTAGCCTTGAATTAGCATGTTGGCACCTTCATCTTTAAGA 124 GCACATTGGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGA * 3905512 CCAATGTCGTTGGCCTTGAATCAACACATTGGCACGTTCAT 189 CCAATGTCGTTGGCCTTGAATCAACACATTGGCACCTTCAT * * * 3905553 CTTTAAGTCCGATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCGATATC 1 CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA----CA-CTTTAAGTCCGATATC * 3905618 GTTGGCCTTGAATCAGCATATTGGCA 61 GCTGGCCTTGAATCAGCATATTGGCA 3905644 TCTGTAACAT Statistics Matches: 473, Mismatches: 60, Indels: 39 0.83 0.10 0.07 Matches are distributed among these distances: 223 35 0.07 224 1 0.00 225 41 0.09 226 1 0.00 227 34 0.07 229 41 0.09 230 36 0.08 231 1 0.00 232 1 0.00 233 2 0.00 234 35 0.07 235 85 0.18 236 1 0.00 237 38 0.08 238 121 0.26 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30 Consensus pattern (229 bp): CTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACACTTTAAGTCCGATATCGCTGG CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACATT GGCATAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGT CGTTGGCCTTGAATCAACACATTGGCACCTTCAT Found at i:3911070 original size:20 final size:20 Alignment explanation

Indices: 3911045--3911098 Score: 74 Period size: 19 Copynumber: 2.8 Consensus size: 20 3911035 TGCCAATCTT ** 3911045 ATGTATCGATACAATTGTCC 1 ATGTATCGATACAATTGAAC * 3911065 ATGTATCGATAC-AGTGAAC 1 ATGTATCGATACAATTGAAC 3911084 ATGTATCGATACAAT 1 ATGTATCGATACAAT 3911099 GTATCGATAC Statistics Matches: 29, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 19 16 0.55 20 13 0.45 ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31 Consensus pattern (20 bp): ATGTATCGATACAATTGAAC Found at i:3911102 original size:13 final size:13 Alignment explanation

Indices: 3911084--3911109 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3911074 TACAGTGAAC 3911084 ATGTATCGATACA 1 ATGTATCGATACA 3911097 ATGTATCGATACA 1 ATGTATCGATACA 3911110 TCTGGGTGTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3912733 original size:45 final size:43 Alignment explanation

Indices: 3912614--3912733 Score: 105 Period size: 45 Copynumber: 2.7 Consensus size: 43 3912604 TAGATGTATT ** * * * 3912614 GAGTTTGACCAAGGCTAAACCTTTTGTCCAATGAAATAAAAAG 1 GAGTTTGACCAAGGCTAAACCTCATGTCAAAAGAAATAAAAAA * * * ** * 3912657 GAGTTTGACTAGGGCTAAGCCGTCACATCAAACAGAGATAAAAAA 1 GAGTTTGACCAAGGCTAAACC-TCATGTCAAA-AGAAATAAAAAA * 3912702 GAGTTTGACCAAGACTAAACCATCATGTCAAA 1 GAGTTTGACCAAGGCTAAACC-TCATGTCAAA 3912734 TGAAGTATGA Statistics Matches: 57, Mismatches: 18, Indels: 2 0.74 0.23 0.03 Matches are distributed among these distances: 43 18 0.32 44 5 0.09 45 34 0.60 ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22 Consensus pattern (43 bp): GAGTTTGACCAAGGCTAAACCTCATGTCAAAAGAAATAAAAAA Found at i:3912751 original size:45 final size:45 Alignment explanation

Indices: 3912702--3912867 Score: 149 Period size: 45 Copynumber: 3.7 Consensus size: 45 3912692 AGATAAAAAA * * 3912702 GAGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATGAAAG 1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG * ** * * * 3912747 GAGTTTGACTAGGGTTGAACCATTACGTCAAACGAAGGTGA-GAAA- 1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAA-GT-ATGAAAG * * * * 3912792 -AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAATAAAAG 1 GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG ** * * 3912836 GAGTTTGACCAGGGTTGAACTATCACGTCAAA 1 GAGTTTGACCAGGACTAAACCATCACGTCAAA 3912868 CAAGGGTGAT Statistics Matches: 95, Mismatches: 21, Indels: 10 0.75 0.17 0.08 Matches are distributed among these distances: 42 1 0.01 43 4 0.04 44 29 0.31 45 54 0.57 46 6 0.06 47 1 0.01 ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22 Consensus pattern (45 bp): GAGTTTGACCAGGACTAAACCATCACGTCAAATGAAGTATGAAAG Found at i:3912812 original size:89 final size:89 Alignment explanation

Indices: 3912703--3912893 Score: 267 Period size: 89 Copynumber: 2.1 Consensus size: 89 3912693 GATAAAAAAG * * * * 3912703 AGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATGAAAGGAGTTTGACTAGGGTTGAACC 1 AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC * 3912768 ATTACGTCAAACGAA-GGTGAGAAA 66 ATCACGTCAAAC-AAGGGTGAGAAA * * * * 3912792 AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAATAAAAGGAGTTTGACCAGGGTTGAACT 1 AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC * * 3912857 ATCACGTCAAACAAGGGTGATAAG 66 ATCACGTCAAACAAGGGTGAGAAA 3912881 AGTTTGACCAAGA 1 AGTTTGACCAAGA 3912894 TTAACGCCAA Statistics Matches: 88, Mismatches: 13, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 88 2 0.02 89 86 0.98 ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22 Consensus pattern (89 bp): AGTTTGACCAAGACTAAACCATCACGTCAAATGAAGAATAAAAGGAGTTTGACCAGGGTTGAACC ATCACGTCAAACAAGGGTGAGAAA Found at i:3912890 original size:44 final size:44 Alignment explanation

Indices: 3912698--3912934 Score: 142 Period size: 45 Copynumber: 5.3 Consensus size: 44 3912688 ACAGAGATAA * ** * * * ** 3912698 AAAAGAGTTTGACCAAGACTAAACCATCATGTCAAATGAAGTATG 1 AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAA-CAAGGGTG * * * 3912743 AAAGGAGTTTGACTAGGGTTGAACCATTACGTCAAACGAA-GGTG 1 AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAAC-AAGGGTG * ** * ** * 3912787 AGAAA-AGTTTGACTAGGACTAAACCATCACGTCAAATGAGGAAT- 1 A-AAAGAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGG-GTG * 3912831 AAAAGGAGTTTGACCAGGGTTGAACTATCACGTCAAACAAGGGTG 1 AAAA-GAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGGGTG * * * * * 3912876 ATAAGAGTTTGACCAAGATT-AACGCCAATTTA-GTCAAACAATGGTG 1 AAAAGAGTTTGACCAGGGTTGAA--CC-A-TCACGTCAAACAAGGGTG 3912922 AAAAGAGTTTGAC 1 AAAAGAGTTTGAC 3912935 TAAGACTAAT Statistics Matches: 147, Mismatches: 34, Indels: 21 0.73 0.17 0.10 Matches are distributed among these distances: 43 6 0.04 44 47 0.32 45 66 0.45 46 26 0.18 47 2 0.01 ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22 Consensus pattern (44 bp): AAAAGAGTTTGACCAGGGTTGAACCATCACGTCAAACAAGGGTG Found at i:3913138 original size:47 final size:47 Alignment explanation

Indices: 3912862--3913496 Score: 386 Period size: 47 Copynumber: 13.6 Consensus size: 47 3912852 GAACTATCAC * * * * * ** 3912862 GTCAAACAAGGGTGATAAGAGTTTGACCAAGAT-TAACGCCAATTTA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * * * 3912908 GTCAAACAATGGTGAAAAGAGTTTGACTAAG-ACTAATGCCAATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * ** * 3912954 GTCAAACAAAGGTAAAAAAAGGTTTAACTAGGCCCTTACGCCAATACA 1 GTCAAACAAGGGTAAAAAGA-GTTTGACTAGGTTCTAACGCCAATACA * ** ** * * * * * * * 3913002 ATCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAACACTAATATA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * * * 3913049 GTCAAACGAGGATAAAAA-AGTTTAACTAGGTCCTAATGCCAATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * * 3913095 GGT-AAACAAGGGAAAAAAGAGTTTGACGAGGTTCTAACACCAATATA 1 -GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * * 3913142 GTCAAACAAGTGTAAAAAGAGTTTGACCAGG-TCTTAACGTCAATAAA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTC-TAACGCCAATACA * ** * * 3913189 ATCAAATGAGGGTAAAAAGAGTTTGACTAGGTCCTAATGCCAATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * 3913236 GTCAAACAAGGGTAAAAAGAGTTTGACTAGG-TCATAATGCCAATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTC-TAACGCCAATACA * ** ** * * * * * 3913283 GTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * ** * * * * ** 3913330 ATCAAATGA-GGTATGAAAAGAGTTTGACCAAG-ACTAATGCCAATATT 1 GTCAAACAAGGGTA--AAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * * * * 3913377 GTCAAACAAGGGTAAAAAGAGTATGACCAAGTCCTAATGCCAATACA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA * * ** * * * * * 3913424 GTCAAACGAGAGTGGAAAGAGTTTGACCAGGTCCTAATGCTAATATA 1 GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA ** * * 3913471 GTCAAATGATGGTGAAAAGAGTTTGA 1 GTCAAACAAGGGTAAAAAGAGTTTGA 3913497 GCATGTTTTA Statistics Matches: 464, Mismatches: 111, Indels: 27 0.77 0.18 0.04 Matches are distributed among these distances: 46 112 0.24 47 308 0.66 48 44 0.09 ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23 Consensus pattern (47 bp): GTCAAACAAGGGTAAAAAGAGTTTGACTAGGTTCTAACGCCAATACA Found at i:3913461 original size:94 final size:93 Alignment explanation

Indices: 3912907--3913496 Score: 443 Period size: 94 Copynumber: 6.3 Consensus size: 93 3912897 ACGCCAATTT * * * * * * 3912907 AGTCAAACAATGGTGAAAAGAGTTTGACTAAG-ACTAATGCCAATACAGTCAAACAAAGGTAAAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAAC-GAGGTAAAA * * * * * * 3912971 AAAGGTTTAACTAGGCCCTTACGCCAATACA 65 AGA-GTTTGACCAGGTCCTAATGCCAATA-A ** ** * * ** * * 3913002 A-TCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAACACTAATATAGTCAAACGAGGATAAAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGG-TAAAA * * 3913066 A-AGTTTAACTAGGTCCTAATGCCAATACA 65 AGAGTTTGACCAGGTCCTAATGCCAATA-A * * * * ** * * 3913095 GGT-AAACAAGGGAAAAAAGAGTTTGACGAGGTTCTAACACCAATATAGTCAAACAAGTGTAAAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAG-GTAAAA * * * 3913159 AGAGTTTGACCAGGTCTTAACGTCAATAA 65 AGAGTTTGACCAGGTCCTAATGCCAATAA * ** * * 3913188 AATCAAATGAGGGTAAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGA-GGTAAAA * * * 3913253 AGAGTTTGACTAGGTCATAATGCCAATAC 65 AGAGTTTGACCAGGTCCTAATGCCAATAA * ** ** * * * * * * 3913282 AGTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACAATCAAATGAGGTATGAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGGTA--AA * * * 3913347 AAGAGTTTGACCAAG-ACTAATGCCAATAT 64 AAGAGTTTGACCAGGTCCTAATGCCAATAA * * * ** 3913376 TGTCAAACAAGGGTAAAAAGAGTATGACCAAGTCCTAATGCCAATACAGTCAAACGAGAGTGGAA 1 AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAG-GTAAAA * * 3913441 AGAGTTTGACCAGGTCCTAATGCTAATAT 65 AGAGTTTGACCAGGTCCTAATGCCAATAA ** * * 3913470 AGTCAAATGATGGTGAAAAGAGTTTGA 1 AGTCAAACAAGGGTAAAAAGAGTTTGA 3913497 GCATGTTTTA Statistics Matches: 397, Mismatches: 87, Indels: 23 0.78 0.17 0.05 Matches are distributed among these distances: 93 94 0.24 94 261 0.66 95 42 0.11 ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23 Consensus pattern (93 bp): AGTCAAACAAGGGTAAAAAGAGTTTGACCAGGTCCTAATGCCAATACAGTCAAACGAGGTAAAAA GAGTTTGACCAGGTCCTAATGCCAATAA Found at i:3913523 original size:141 final size:141 Alignment explanation

Indices: 3912920--3913496 Score: 565 Period size: 141 Copynumber: 4.1 Consensus size: 141 3912910 CAAACAATGG * * * * * * 3912920 TGAAAAGAGTTTGACTAAG-ACTAATGCCAATACAGTCAAACAAAGGTAAAAAAAGGTTTAACTA 1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGA-GTTTGACCA * * * * * * ** * * * 3912984 GGCCCTTACGCCAATACAATCAAATGAGGGTGGACAGAGTTTGACCAAGTCCTAAC-ACTAATAT 65 GGTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTC-AATAT * * 3913048 AGTCAAACGAGGA 129 AATCAAATGAGGA * * * * 3913061 T-AAAAAAGTTTAACTAGGTCCTAATGCCAATACAGGT-AAACAAGGGAAAAAAGAGTTTGACGA 1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACA-GTCAAACAAGGGTAAAAAGAGTTTGACCA * ** * * * * 3913124 GGTTCTAACACCAATATAGTCAAACAAGTGTAAAAAGAGTTTGACCAGGTCTTAACGTCAATAAA 65 GGTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATA * 3913189 ATCAAATGAGGG 130 ATCAAATGAGGA * * 3913201 TAAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACTAG 1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG * * * * * * * * * 3913266 GTCATAATGCCAATACAGTTAAATGACTGTAAAAAGAGTTTAACTAGGTCCTAATGTCGATACAA 66 GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATAA 3913331 TCAAATGAGGTA 131 TCAAATGAGG-A * * * ** * * 3913343 TGAAAAGAGTTTGACCAAG-ACTAATGCCAATATTGTCAAACAAGGGTAAAAAGAGTATGACCAA 1 TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG * ** * 3913407 GTCCTAATGCCAATACAGTCAAACGAGAGTGGAAAGAGTTTGACCAGGTCCTAATG-CTAATATA 66 GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTC-AATATA * 3913471 GTCAAATGATGG- 130 ATCAAATGA-GGA 3913483 TGAAAAGAGTTTGA 1 TGAAAAGAGTTTGA 3913497 GCATGTTTTA Statistics Matches: 359, Mismatches: 69, Indels: 17 0.81 0.16 0.04 Matches are distributed among these distances: 140 95 0.26 141 244 0.68 142 20 0.06 ACGTcount: A:0.42, C:0.15, G:0.21, T:0.23 Consensus pattern (141 bp): TGAAAAGAGTTTGACTAGGTCCTAATGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAG GTCCTAATGCCAATACAGTCAAACGAGTGTAAAAAGAGTTTGACCAGGTCCTAACGTCAATATAA TCAAATGAGGA Found at i:3914647 original size:17 final size:16 Alignment explanation

Indices: 3914627--3914694 Score: 64 Period size: 17 Copynumber: 4.1 Consensus size: 16 3914617 TCTCTCTCTC * * 3914627 TTTTGTTTTTTTTCTT 1 TTTTTTTTTTTTTGTT * 3914643 TTTTTTTGGTTTTTGTT 1 TTTTTTT-TTTTTTGTT * * 3914660 CTTCTTTCTTTTTTGTT 1 -TTTTTTTTTTTTTGTT 3914677 TTTTTTGTTTTTTTGTT 1 TTTTTT-TTTTTTTGTT 3914694 T 1 T 3914695 GCCCCCTCAT Statistics Matches: 41, Mismatches: 8, Indels: 5 0.76 0.15 0.09 Matches are distributed among these distances: 16 11 0.27 17 25 0.61 18 5 0.12 ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84 Consensus pattern (16 bp): TTTTTTTTTTTTTGTT Found at i:3914656 original size:43 final size:43 Alignment explanation

Indices: 3914610--3914690 Score: 119 Period size: 43 Copynumber: 1.9 Consensus size: 43 3914600 TATTATCTAT * * 3914610 TTTTTTTTC-TCTCTCTCTTTTGTTTTTTTTCTTTTTTTTTGG 1 TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTTTTGG * * 3914652 TTTTTGTTCTTCTTTCTTTTTTGTTTTTTTTGTTTTTTT 1 TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTT 3914691 GTTTGCCCCC Statistics Matches: 34, Mismatches: 4, Indels: 1 0.87 0.10 0.03 Matches are distributed among these distances: 42 8 0.24 43 26 0.76 ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81 Consensus pattern (43 bp): TTTTTGTTCTTCTTTCTCTTTTGTTTTTTTTCTTTTTTTTTGG Found at i:3915674 original size:13 final size:13 Alignment explanation

Indices: 3915656--3915681 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3915646 TACACCAAGT 3915656 ATGTATCGATACA 1 ATGTATCGATACA 3915669 ATGTATCGATACA 1 ATGTATCGATACA 3915682 CAAAAAATTG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3915679 original size:32 final size:33 Alignment explanation

Indices: 3915638--3915701 Score: 94 Period size: 32 Copynumber: 2.0 Consensus size: 33 3915628 TAGCCAAACT * ** 3915638 TGTATCGATACACCAAGTA-TGTATCGATACAA 1 TGTATCGATACACAAAAAATTGTATCGATACAA 3915670 TGTATCGATACACAAAAAATTGTATCGATACA 1 TGTATCGATACACAAAAAATTGTATCGATACA 3915702 TTGGCTTGTA Statistics Matches: 28, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 32 16 0.57 33 12 0.43 ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28 Consensus pattern (33 bp): TGTATCGATACACAAAAAATTGTATCGATACAA Found at i:3921944 original size:73 final size:75 Alignment explanation

Indices: 3921854--3922004 Score: 198 Period size: 73 Copynumber: 2.0 Consensus size: 75 3921844 ACCCTAGAGA * * * 3921854 ACTCAAAAAGGATAAAAACCAACCTATTTC-AATTCCTACCTGCGACATGGAAGTAGACCGA-TA 1 ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA * 3921917 GTTTTATAGG 66 GTTTTATAAG * * * * * 3921927 ACTCAGAAAGGATAAAAACCAACCAATTCCTAATTCTTACCTTCGGCATAGAAGTAGACCTAGTA 1 ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA * 3921992 TTTTTATAAG 66 GTTTTATAAG 3922002 ACT 1 ACT 3922005 AGGTTTCAAG Statistics Matches: 66, Mismatches: 10, Indels: 2 0.85 0.13 0.03 Matches are distributed among these distances: 73 27 0.41 74 26 0.39 75 13 0.20 ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26 Consensus pattern (75 bp): ACTCAAAAAGGATAAAAACCAACCAATTCCTAATTCCTACCTGCGACATAGAAGTAGACCGAGTA GTTTTATAAG Found at i:3922654 original size:141 final size:142 Alignment explanation

Indices: 3922365--3923301 Score: 1107 Period size: 141 Copynumber: 6.6 Consensus size: 142 3922355 AGGGGATATG * * * * 3922365 AAAAA-TTTTGAAAATTTCTGTACTCCTACGAAAAACCATAAG-A-ATTAGAAATCTTGAAAAAT 1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT * ** * ** * * * 3922427 TAAGACAATAATTTTTAATTAAAATTTTTTTATTTCCAA-AAATATTTATTTCATACATAAATGG 66 TAAGATAATAATTTTT-ATT-TGA-TTTTTAATTTTTAAGAAA-ATTCATTTCATACCTTAATGG * 3922491 AGAAACGAAAAGATAC 127 AGAACCGAAAAGATAC * * * 3922507 AAAAAGTTTTGAAGATTTCTATACCTCTACGGAAAACCATAAGAATATTAGAAATCCTAAAAAAT 1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT * * 3922572 TAAGATAATAA-TTTTATTTGATTTTTCATTTTTAAGAAAATTCATTTCGTACCTTAATGGAGAA 66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA 3922636 CCGAAAAGATAC 131 CCGAAAAGATAC * * * * 3922648 AAAAAGTTTTGAAGATTTTTATACCCCCACAAGAAAACCATAAGAATATTAGAAATCTTAAAAAA 1 AAAAAGTTTTGAAGATTTCTATACCCCTAC-GGAAAACCATAAGAATATTAGAAATCTTGAAAAA * * * 3922713 TTAAAATAATAATTTTTGTTTGATTTGTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGA 65 TTAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGA 3922778 ACCGAAAAGATAC 130 ACCGAAAAGATAC * * * * * * * * 3922791 GAAAAGTTTTGAAAAGATTTCTATACCCCTATGAAAAACTATAGGAGTATTACAAATTTTGAAAA 1 AAAAAGTTTTG--AAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAA * * * * * 3922856 CTTAAGAAAATAATTTTTATTTGATTTTTAATTTTTAAAAAAATTTATTTCGTACCTTAATGGAG 64 ATTAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAG * * * 3922921 AATCGAAAATATAT 129 AACCGAAAAGATAC * * * 3922935 GAAAAGTTTTGAAGATTTTTATACCCCTACGGAAAACCATAGGAATATTAGAAATCTTGAAAAAT 1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT * ** 3923000 TAAAATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCCGACCTTAATGGAGAA 66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA * * * * 3923065 TCAAAAAGACAT 131 CCGAAAAGATAC * * ** * * * 3923077 AAAAA-TTTTGAAGATTTCTATACTCATACAAAAAACCATAGGAATAATAAAAATCTTGAAAAAT 1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT * * * * 3923141 TAAGATAATAACTTTTATTTGATTTTTAATTTTTAAAAAAATTCATTTCACACCTCAATGGAGAA 66 TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA * * 3923206 CC-AAAAAATAT 131 CCGAAAAGATAC * * * * 3923217 GAAAAGTTTTGAAGATTTTTATACCCCTACGGAAAACTATAAGAATATTA-ATAATTTTGAAAAA 1 AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGA-AATCTTGAAAAA * * 3923281 TTAAGAAAATAAGTTTTATTT 65 TTAAGATAATAATTTTTATTT 3923302 TGGGATAAAA Statistics Matches: 688, Mismatches: 97, Indels: 21 0.85 0.12 0.03 Matches are distributed among these distances: 140 12 0.02 141 248 0.36 142 170 0.25 143 106 0.15 144 109 0.16 145 43 0.06 ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35 Consensus pattern (142 bp): AAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAAGAATATTAGAAATCTTGAAAAAT TAAGATAATAATTTTTATTTGATTTTTAATTTTTAAGAAAATTCATTTCATACCTTAATGGAGAA CCGAAAAGATAC Found at i:3924606 original size:19 final size:18 Alignment explanation

Indices: 3924560--3924645 Score: 65 Period size: 19 Copynumber: 4.8 Consensus size: 18 3924550 TTCAACTAAT * 3924560 TTGTATCGATACAAACTG 1 TTGTATCGATACAAAGTG 3924578 TAACTGTATCGATACATAAGTG 1 T---TGTATCGATACA-AAGTG 3924600 TTGTATCGATAC-AA--- 1 TTGTATCGATACAAAGTG * * 3924614 -TATATCGATACATAAGTT 1 TTGTATCGATACA-AAGTG 3924632 TTGTATCGATACAA 1 TTGTATCGATACAA 3924646 TGTATCACTA Statistics Matches: 55, Mismatches: 3, Indels: 20 0.71 0.04 0.26 Matches are distributed among these distances: 13 10 0.18 15 2 0.04 17 2 0.04 18 2 0.04 19 22 0.40 21 12 0.22 22 5 0.09 ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35 Consensus pattern (18 bp): TTGTATCGATACAAAGTG Found at i:3924625 original size:32 final size:32 Alignment explanation

Indices: 3924584--3924651 Score: 118 Period size: 32 Copynumber: 2.1 Consensus size: 32 3924574 ACTGTAACTG 3924584 TATCGATACATAAGTGTTGTATCGATACAATA 1 TATCGATACATAAGTGTTGTATCGATACAATA * * 3924616 TATCGATACATAAGTTTTGTATCGATACAATG 1 TATCGATACATAAGTGTTGTATCGATACAATA 3924648 TATC 1 TATC 3924652 ACTACGAAGC Statistics Matches: 34, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 32 34 1.00 ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37 Consensus pattern (32 bp): TATCGATACATAAGTGTTGTATCGATACAATA Found at i:3924715 original size:13 final size:13 Alignment explanation

Indices: 3924697--3924724 Score: 56 Period size: 13 Copynumber: 2.2 Consensus size: 13 3924687 ATTACTCAAA 3924697 TGTATCGATACAT 1 TGTATCGATACAT 3924710 TGTATCGATACAT 1 TGTATCGATACAT 3924723 TG 1 TG 3924725 ACCTTTGTAT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 15 1.00 ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3928488 original size:167 final size:161 Alignment explanation

Indices: 3928258--3928845 Score: 547 Period size: 167 Copynumber: 3.5 Consensus size: 161 3928248 AAATTTCATG * * * * 3928258 AAATAAATTGAATTTTCTAAAACTGATATACTATGAGTGTAATGAA-AATATTAGATGAATTTTA 1 AAATAAATT-AATTTT-TGAAACTGAT-TA-TATGAAT-TAAT-AATGATATTTGATGAATTTTA * * * 3928322 AAAATTTTAAACCGAGAAAAATCCCCCCGAAAACATTTATTGAATAAAAAATTTGATTTTTCGAA 60 AAAATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATTT-ATTTTTCGAA * * 3928387 AACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCATGA 124 AATAGAGAAATTTCAAGGAAAA-AATGAAAAACTTATGA * 3928426 AAATAAATTAATTTTTCGAAATTGACTTACTATGAATTGAATAATGATATTTGATGAATTTTAAA 1 AAATAAATTAATTTTT-GAAACTGA-TTA-TATGAATT-AATAATGATATTTGATGAATTTTAAA ** * * * * 3928491 AATTATAAACTGAGAAAAATCCTCCCGAAAACTTTTATAGAGTAGAAAATTCTATTTTTC-AACA 62 AATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATT-TATTTTTCGAA-A * * * * 3928555 ATAG-GAAAATTTCTAGGAAAAAATTAAAATCTTAGGA 125 ATAGAG-AAATTTCAAGGAAAAAATGAAAAACTTATGA * * * * * 3928592 ATATAAATTAATTTTTGAAAACAGATTTATTATAAATTAATGATGATATTTGATGAATTTTGAAA 1 AAATAAATTAATTTTTG-AAACTGA-TTA-TATGAATTAATAATGATATTTGATGAATTTTAAAA * * * * * 3928657 ATTATAAATCAAGAAAAATTCTCTCGAAAACATTTA-TGAAGTAGAAAATTTCATATTTTAG-AA 63 ATTATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAA-TAGAAAATTT-AT-TTTTCGAAA * * 3928720 ATAGAGAAATTTCAAGAAAAAAATGAAAAATTTATGA 125 ATAGAGAAATTTCAAGGAAAAAATGAAAAACTTATGA * * * * * * 3928757 AAATAAATAAATTTTTTAAAGCTGATTAAATGGTGATTAGATAATAATATTTGATGAAATTTTGA 1 AAATAAATTAATTTTTGAAA-CTGATTATAT-G-AATTA-ATAATGATATTTGATG-AATTTTAA * * 3928822 AAATTTTAAACAAAGAAAAATCCC 61 AAATTATAAACCAAGAAAAATCCC 3928846 TATAAAATCA Statistics Matches: 347, Mismatches: 55, Indels: 37 0.79 0.13 0.08 Matches are distributed among these distances: 163 2 0.01 164 9 0.03 165 118 0.34 166 69 0.20 167 138 0.40 168 11 0.03 ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33 Consensus pattern (161 bp): AAATAAATTAATTTTTGAAACTGATTATATGAATTAATAATGATATTTGATGAATTTTAAAAATT ATAAACCAAGAAAAATCCCCCCGAAAACATTTATTGAATAGAAAATTTATTTTTCGAAAATAGAG AAATTTCAAGGAAAAAATGAAAAACTTATGA Found at i:3928687 original size:165 final size:165 Alignment explanation

Indices: 3928305--3928772 Score: 495 Period size: 165 Copynumber: 2.8 Consensus size: 165 3928295 TGTAATGAAA * * * * * 3928305 ATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAATCCCCCCGAAAACATTTATTGAATAAA 1 ATATTTGATGAATTTTAAAAATTATAAA-CGAGAAAAATCCTCCCGAAAACATTTA-TGAGTAGA * 3928370 AAATT-TGATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCATGAAAATAAAT 64 AAATTCT-ATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAAT ** * 3928434 TAATTTTTCGAAATTGACTTACTATGAATTGAATAATG 128 TAATTTTTCGAAACAGACTTACTATAAATTGAATAATG * 3928472 ATATTTGATGAATTTTAAAAATTATAAACTGAGAAAAATCCTCCCGAAAACTTTTATAGAGTAGA 1 ATATTTGATGAATTTTAAAAATTATAAAC-GAGAAAAATCCTCCCGAAAACATTTAT-GAGTAGA * * * * * * 3928537 AAATTCTATTTTTC-AACAATAG-GAAAATTTCTAGGAAAA-AATTAAAATCTTAGGAATATAAA 64 AAATTCTATTTTTCGAA-AACAGAG-AAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAA * * * 3928599 TTAATTTTT-GAAAACAGATTTATTATAAATT-AATGATG 127 TTAATTTTTCG-AAACAGACTTACTATAAATTGAATAATG * * * * 3928637 ATATTTGATGAATTTTGAAAATTATAAATCAAGAAAAATTCTCTCGAAAACATTTATGAAGTAGA 1 ATATTTGATGAATTTTAAAAATTATAAA-CGAGAAAAATCCTCCCGAAAACATTTATG-AGTAGA * * * * * * 3928702 AAATT-TCATATTTTAG-AAATAGAGAAATTTCAA-GAAAAAAATGAAAAATTTATGAAAATAAA 64 AAATTCT-AT-TTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAA * 3928764 TAAATTTTT 127 TTAATTTTT 3928773 TAAAGCTGAT Statistics Matches: 256, Mismatches: 32, Indels: 28 0.81 0.10 0.09 Matches are distributed among these distances: 164 7 0.03 165 109 0.43 166 54 0.21 167 85 0.33 168 1 0.00 ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33 Consensus pattern (165 bp): ATATTTGATGAATTTTAAAAATTATAAACGAGAAAAATCCTCCCGAAAACATTTATGAGTAGAAA ATTCTATTTTTCGAAAACAGAGAAATTTCAAGGAAAAGAATGAAAAACTCAGGAAAATAAATTAA TTTTTCGAAACAGACTTACTATAAATTGAATAATG Found at i:3938294 original size:24 final size:24 Alignment explanation

Indices: 3938267--3938313 Score: 67 Period size: 24 Copynumber: 2.0 Consensus size: 24 3938257 AAATGCATGG * ** 3938267 GAAATAAAAATGGCATGGAAAAAT 1 GAAAAAAAAATGAAATGGAAAAAT 3938291 GAAAAAAAAATGAAATGGAAAAA 1 GAAAAAAAAATGAAATGGAAAAA 3938314 AAATGGCCAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 24 20 1.00 ACGTcount: A:0.66, C:0.02, G:0.19, T:0.13 Consensus pattern (24 bp): GAAAAAAAAATGAAATGGAAAAAT Found at i:3938312 original size:16 final size:16 Alignment explanation

Indices: 3938287--3938318 Score: 55 Period size: 16 Copynumber: 2.0 Consensus size: 16 3938277 TGGCATGGAA 3938287 AAATGAAAAAAAAATG 1 AAATGAAAAAAAAATG * 3938303 AAATGGAAAAAAAATG 1 AAATGAAAAAAAAATG 3938319 GCCATTTAGC Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 15 1.00 ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12 Consensus pattern (16 bp): AAATGAAAAAAAAATG Found at i:3939563 original size:141 final size:141 Alignment explanation

Indices: 3939354--3939619 Score: 331 Period size: 141 Copynumber: 1.9 Consensus size: 141 3939344 TAATAATAAA * * * * 3939354 TTTTCAAGATTTTTAGTATTCCTATGGTTTTTCGTAGGAGTATAGAAATCTTCAAAAATTTTCAT 1 TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGTAGGAGTACAGAAATCTTCAAAAATTTTCAT * * * 3939419 ATCTTTT-TTACTCTCCATTAAGGTAAAAAATGA-ATTTTTAAAAAATTAAAAATTAAATAAAAA 66 ATCTTTTATT--TCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATAAAAA 3939482 TTATTATCTTAAT 129 TTATTATCTTAAT * * * ** 3939495 TTTTCAATATTTCTAATATTCTTATAGTTTTTCGTAAGG-GTACAGAAATCTTCAAAACTTTTTG 1 TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGT-AGGAGTACAGAAATCTTCAAAAATTTTCA ** ** 3939559 TATCTTTTCATTTCTCCATTAAAGTATGAAATGAGATTTTCAAAACTTTAAAAATAAAATA 65 TATCTTTT-ATTTCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATA 3939620 TTACATTATT Statistics Matches: 105, Mismatches: 16, Indels: 7 0.82 0.12 0.05 Matches are distributed among these distances: 141 78 0.74 142 25 0.24 143 2 0.02 ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43 Consensus pattern (141 bp): TTTTCAAGATTTCTAATATTCCTATAGTTTTTCGTAGGAGTACAGAAATCTTCAAAAATTTTCAT ATCTTTTATTTCTCCATTAAAGTAAAAAATGAGATTTTCAAAAAATTAAAAATAAAATAAAAATT ATTATCTTAAT Found at i:3941417 original size:13 final size:13 Alignment explanation

Indices: 3941399--3941429 Score: 53 Period size: 13 Copynumber: 2.4 Consensus size: 13 3941389 ACAATTCATC 3941399 ATGTATCGATACA 1 ATGTATCGATACA 3941412 ATGTATCGATACA 1 ATGTATCGATACA * 3941425 TTGTA 1 ATGTA 3941430 CCATGTATCG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 17 1.00 ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3941417 original size:33 final size:33 Alignment explanation

Indices: 3941378--3941442 Score: 96 Period size: 33 Copynumber: 2.0 Consensus size: 33 3941368 CGTTACAAGT * 3941378 AATGTATCGATACAATT-CATCATGTATCGATAC 1 AATGTATCGATAC-ATTGCACCATGTATCGATAC * 3941411 AATGTATCGATACATTGTACCATGTATCGATA 1 AATGTATCGATACATTGCACCATGTATCGATA 3941443 TAAACAGTGG Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 32 3 0.10 33 26 0.90 ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34 Consensus pattern (33 bp): AATGTATCGATACATTGCACCATGTATCGATAC Found at i:3941532 original size:13 final size:13 Alignment explanation

Indices: 3941514--3941572 Score: 67 Period size: 13 Copynumber: 5.0 Consensus size: 13 3941504 TACAATGAAC 3941514 ATGTATCGATACA 1 ATGTATCGATACA 3941527 ATGTATCGATACA 1 ATGTATCGATACA * 3941540 A---AGC-AT--A 1 ATGTATCGATACA 3941547 ATGTATCGATACA 1 ATGTATCGATACA 3941560 ATGTATCGATACA 1 ATGTATCGATACA 3941573 TTATCTGGGT Statistics Matches: 38, Mismatches: 2, Indels: 12 0.73 0.04 0.23 Matches are distributed among these distances: 7 2 0.05 9 2 0.05 10 4 0.11 11 2 0.05 13 28 0.74 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3941556 original size:33 final size:32 Alignment explanation

Indices: 3941495--3941572 Score: 122 Period size: 33 Copynumber: 2.4 Consensus size: 32 3941485 ATAATTGTCC * 3941495 ATGTATCGATACAATGAACATGTATCGATACA 1 ATGTATCGATACAAAGAACATGTATCGATACA 3941527 ATGTATCGATACAAAGCATA-ATGTATCGATACA 1 ATGTATCGATACAAAG-A-ACATGTATCGATACA 3941560 ATGTATCGATACA 1 ATGTATCGATACA 3941573 TTATCTGGGT Statistics Matches: 43, Mismatches: 1, Indels: 3 0.91 0.02 0.06 Matches are distributed among these distances: 32 15 0.35 33 27 0.63 34 1 0.02 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28 Consensus pattern (32 bp): ATGTATCGATACAAAGAACATGTATCGATACA Found at i:3942127 original size:22 final size:22 Alignment explanation

Indices: 3942100--3942179 Score: 97 Period size: 22 Copynumber: 3.5 Consensus size: 22 3942090 AGTTTTCATT 3942100 TTTCTCCCCCTTAATTAAAGAA 1 TTTCTCCCCCTTAATTAAAGAA * 3942122 TTTCTCCCCCTTAATTAAAAAAAA 1 TTTCTCCCCCTTAATT--AAAGAA * * * 3942146 ATTCTCCCCCTTAATCAAAGCA 1 TTTCTCCCCCTTAATTAAAGAA * 3942168 TTTCTCTCCCTT 1 TTTCTCCCCCTT 3942180 TGTCAAATCT Statistics Matches: 49, Mismatches: 7, Indels: 4 0.82 0.12 0.07 Matches are distributed among these distances: 22 30 0.61 24 19 0.39 ACGTcount: A:0.30, C:0.31, G:0.03, T:0.36 Consensus pattern (22 bp): TTTCTCCCCCTTAATTAAAGAA Found at i:3942155 original size:24 final size:22 Alignment explanation

Indices: 3942101--3942160 Score: 84 Period size: 24 Copynumber: 2.6 Consensus size: 22 3942091 GTTTTCATTT * * 3942101 TTCTCCCCCTTAATTAAAGAAT 1 TTCTCCCCCTTAATTAAAAAAA 3942123 TTCTCCCCCTTAATTAAAAAAAAA 1 TTCTCCCCCTTAATT--AAAAAAA 3942147 TTCTCCCCCTTAAT 1 TTCTCCCCCTTAAT 3942161 CAAAGCATTT Statistics Matches: 34, Mismatches: 2, Indels: 2 0.89 0.05 0.05 Matches are distributed among these distances: 22 15 0.44 24 19 0.56 ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35 Consensus pattern (22 bp): TTCTCCCCCTTAATTAAAAAAA Found at i:3948721 original size:13 final size:13 Alignment explanation

Indices: 3948703--3948727 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3948693 CATAAAGTGT 3948703 TGTATCGATACAA 1 TGTATCGATACAA 3948716 TGTATCGATACA 1 TGTATCGATACA 3948728 TATTTTTTTG 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:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3948725 original size:33 final size:33 Alignment explanation

Indices: 3948683--3948749 Score: 98 Period size: 33 Copynumber: 2.0 Consensus size: 33 3948673 TTCAACGATT 3948683 TGTATCGATACATAAAGTGTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA *** * 3948716 TGTATCGATACATATTTTTTTGTATCGATACAA 1 TGTATCGATACATAAAGTGTTGTATCGATACAA 3948749 T 1 T 3948750 TTAAGCTACT Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40 Consensus pattern (33 bp): TGTATCGATACATAAAGTGTTGTATCGATACAA Found at i:3948808 original size:13 final size:13 Alignment explanation

Indices: 3948790--3948814 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3948780 ATCACTTAAA 3948790 TGTATCGATACAT 1 TGTATCGATACAT 3948803 TGTATCGATACA 1 TGTATCGATACA 3948815 CTGATCTTTG 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:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3948867 original size:52 final size:51 Alignment explanation

Indices: 3948803--3948951 Score: 244 Period size: 52 Copynumber: 2.9 Consensus size: 51 3948793 ATCGATACAT ** 3948803 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA 1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA * 3948855 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA 1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA 3948907 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT 1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT 3948952 TCATATTTCG Statistics Matches: 91, Mismatches: 4, Indels: 4 0.92 0.04 0.04 Matches are distributed among these distances: 51 2 0.02 52 88 0.97 53 1 0.01 ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30 Consensus pattern (51 bp): TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA Found at i:3956607 original size:13 final size:13 Alignment explanation

Indices: 3956589--3956613 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3956579 AAAACTCAGA 3956589 TGTATCGATACAG 1 TGTATCGATACAG 3956602 TGTATCGATACA 1 TGTATCGATACA 3956614 AAGGGTTTAT 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:0.32, C:0.16, G:0.20, T:0.32 Consensus pattern (13 bp): TGTATCGATACAG Found at i:3959023 original size:13 final size:13 Alignment explanation

Indices: 3959005--3959029 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 3958995 ATAATGCACA 3959005 GTATCGATACATT 1 GTATCGATACATT 3959018 GTATCGATACAT 1 GTATCGATACAT 3959030 GACCACTATA 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:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): GTATCGATACATT Found at i:3959139 original size:32 final size:33 Alignment explanation

Indices: 3959098--3959161 Score: 105 Period size: 32 Copynumber: 2.0 Consensus size: 33 3959088 CCTTAACTGT 3959098 TTGTATCGATACAT-A-CAAGATGTATCGATACC 1 TTGTATCGATACATGACCAA-ATGTATCGATACC 3959130 TTGTATCGATACATGACCAAATGTATCGATAC 1 TTGTATCGATACATGACCAAATGTATCGATAC 3959162 ATTGGCTTGT Statistics Matches: 30, Mismatches: 0, Indels: 3 0.91 0.00 0.09 Matches are distributed among these distances: 32 14 0.47 33 13 0.43 34 3 0.10 ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31 Consensus pattern (33 bp): TTGTATCGATACATGACCAAATGTATCGATACC Found at i:3962603 original size:21 final size:21 Alignment explanation

Indices: 3962559--3962604 Score: 58 Period size: 21 Copynumber: 2.2 Consensus size: 21 3962549 TTTTTGCCAA * * 3962559 AATGTGTCGATACATGCCCTT 1 AATGTATCGATACAGGCCCTT 3962580 AATGTATCGATACAAGGCCC-T 1 AATGTATCGATAC-AGGCCCTT 3962601 AATG 1 AATG 3962605 GTCAAAAATT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 21 17 0.77 22 5 0.23 ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28 Consensus pattern (21 bp): AATGTATCGATACAGGCCCTT Found at i:3965000 original size:51 final size:51 Alignment explanation

Indices: 3964920--3965088 Score: 162 Period size: 51 Copynumber: 3.3 Consensus size: 51 3964910 ATTTTTCATC ** 3964920 TCGGGGATACTCCAA-TCCCGATTCCATTTCCAAAACATCAATTTTTCTTAA 1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTTCTTAA * * * * *** ** 3964971 TCGGGGATATTCCAACTCCGATTTTATTTCTAAAGCATTAATTAACCGCAA 1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA * * * 3965022 TCGGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAA-TTTTCTATAA 1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCT-TAA ** 3965073 TTAGGGATACTCCAAC 1 TCGGGGATACTCCAAC 3965089 CCTGTTATTT Statistics Matches: 90, Mismatches: 26, Indels: 4 0.75 0.22 0.03 Matches are distributed among these distances: 50 2 0.02 51 87 0.97 52 1 0.01 ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33 Consensus pattern (51 bp): TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA Found at i:3965158 original size:79 final size:79 Alignment explanation

Indices: 3965024--3965244 Score: 318 Period size: 79 Copynumber: 2.8 Consensus size: 79 3965014 AACCGCAATC * * * * 3965024 GGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATTAGGGATACTCCAAC 1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC 3965089 CCTGTTATTTCCGA 66 CCTGTTATTTCCGA * * 3965103 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATCAGGGATACTCCAAT 1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC ** 3965168 CCTGTTATTTTTGA 66 CCTGTTATTTCCGA * * * * 3965182 GTGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTT-TCATAAACGGGGATACTCCA 1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCT-ATAATCAGGGATACTCCA 3965245 GCCCCGTTGT Statistics Matches: 128, Mismatches: 13, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 78 1 0.01 79 127 0.99 ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33 Consensus pattern (79 bp): GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC CCTGTTATTTCCGA Found at i:3967693 original size:19 final size:19 Alignment explanation

Indices: 3967647--3967701 Score: 74 Period size: 19 Copynumber: 2.8 Consensus size: 19 3967637 TGCCAATTTT ** 3967647 ATGTATCGATACAATTGTCC 1 ATGTATCGATACAA-TGAAC * 3967667 ACGTATCGATACAATGAAC 1 ATGTATCGATACAATGAAC 3967686 ATGTATCGATACAATG 1 ATGTATCGATACAATG 3967702 TATCGATACA Statistics Matches: 31, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 19 18 0.58 20 13 0.42 ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29 Consensus pattern (19 bp): ATGTATCGATACAATGAAC Found at i:3967704 original size:13 final size:13 Alignment explanation

Indices: 3967686--3967712 Score: 54 Period size: 13 Copynumber: 2.1 Consensus size: 13 3967676 TACAATGAAC 3967686 ATGTATCGATACA 1 ATGTATCGATACA 3967699 ATGTATCGATACA 1 ATGTATCGATACA 3967712 A 1 A 3967713 GGCATAATGT Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 14 1.00 ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30 Consensus pattern (13 bp): ATGTATCGATACA Found at i:3969401 original size:20 final size:19 Alignment explanation

Indices: 3969376--3969466 Score: 85 Period size: 20 Copynumber: 4.6 Consensus size: 19 3969366 ACCCTAGAAA 3969376 GTATCGATACATATCCAGAT 1 GTATCGATACATATCCA-AT * ** 3969396 GTATCGATACATTATGCTTT 1 GTATCGATACA-TATCCAAT * * * 3969416 GTATCGATACATGTTCATT 1 GTATCGATACATATCCAAT 3969435 GTATCGATACATA-CTCAATT 1 GTATCGATACATATC-CAA-T 3969455 GTATCGATACAT 1 GTATCGATACAT 3969467 GAAACTGGCA Statistics Matches: 59, Mismatches: 9, Indels: 6 0.80 0.12 0.08 Matches are distributed among these distances: 19 19 0.32 20 36 0.61 21 4 0.07 ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37 Consensus pattern (19 bp): GTATCGATACATATCCAAT Found at i:3969445 original size:39 final size:40 Alignment explanation

Indices: 3969376--3969467 Score: 109 Period size: 39 Copynumber: 2.3 Consensus size: 40 3969366 ACCCTAGAAA * * 3969376 GTATCGATACATATCCAGATGTATCGATACATTA-TGC-TTT 1 GTATCGATACATGTCCAGATGTATCGATACA-TACT-CAATT * * 3969416 GTATCGATACATGTTCA-TTGTATCGATACATACTCAATT 1 GTATCGATACATGTCCAGATGTATCGATACATACTCAATT 3969455 GTATCGATACATG 1 GTATCGATACATG 3969468 AAACTGGCAG Statistics Matches: 46, Mismatches: 4, Indels: 5 0.84 0.07 0.09 Matches are distributed among these distances: 38 3 0.07 39 28 0.61 40 15 0.33 ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37 Consensus pattern (40 bp): GTATCGATACATGTCCAGATGTATCGATACATACTCAATT Found at i:3970563 original size:33 final size:33 Alignment explanation

Indices: 3970519--3970587 Score: 95 Period size: 33 Copynumber: 2.1 Consensus size: 33 3970509 CTACCACTGT * 3970519 TTGTATCGATACAT-AGGACATTGTATCGTTACA 1 TTGTATCGATACATGAGGA-ATTGTATCGATACA * * 3970552 TTGTATTGATACATGATGAATTGTATCGATACA 1 TTGTATCGATACATGAGGAATTGTATCGATACA 3970585 TTG 1 TTG 3970588 CTTGTAACGG Statistics Matches: 32, Mismatches: 3, Indels: 2 0.86 0.08 0.05 Matches are distributed among these distances: 33 29 0.91 34 3 0.09 ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39 Consensus pattern (33 bp): TTGTATCGATACATGAGGAATTGTATCGATACA Found at i:3976714 original size:21 final size:19 Alignment explanation

Indices: 3976690--3976737 Score: 51 Period size: 21 Copynumber: 2.4 Consensus size: 19 3976680 TAAATCCTTT * 3976690 TCAAAATTCATCATTTTCACA 1 TCAAAATACAT-ATTTT-ACA * 3976711 TCAAAACTACATATTTTTCA 1 TCAAAA-TACATATTTTACA 3976731 TCAAAAT 1 TCAAAAT 3976738 CTTCATCAAA Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 19 1 0.04 20 8 0.33 21 11 0.46 22 4 0.17 ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38 Consensus pattern (19 bp): TCAAAATACATATTTTACA Found at i:3978165 original size:15 final size:15 Alignment explanation

Indices: 3978145--3978175 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 3978135 TTACTTTTCC * 3978145 TCTAGTGATGATGAG 1 TCTAGTGACGATGAG 3978160 TCTAGTGACGATGAG 1 TCTAGTGACGATGAG 3978175 T 1 T 3978176 AATAGGGTTA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32 Consensus pattern (15 bp): TCTAGTGACGATGAG Found at i:3979139 original size:13 final size:13 Alignment explanation

Indices: 3979121--3979180 Score: 51 Period size: 13 Copynumber: 5.1 Consensus size: 13 3979111 ACATTATGCT 3979121 TTGTATCGATACA 1 TTGTATCGATACA * 3979134 TTGTATCAATACA 1 TTGTATCGATACA * 3979147 -TG---GGA--CA 1 TTGTATCGATACA 3979154 TTGTATCGATACA 1 TTGTATCGATACA * 3979167 TTGTATAGATACA 1 TTGTATCGATACA 3979180 T 1 T 3979181 GGTAAAAAGT Statistics Matches: 36, Mismatches: 5, Indels: 12 0.68 0.09 0.23 Matches are distributed among these distances: 7 2 0.06 8 2 0.06 9 1 0.03 11 2 0.06 12 2 0.06 13 27 0.75 ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37 Consensus pattern (13 bp): TTGTATCGATACA Found at i:3979146 original size:33 final size:34 Alignment explanation

Indices: 3979102--3979180 Score: 92 Period size: 33 Copynumber: 2.4 Consensus size: 34 3979092 CATATCTAGA * * * 3979102 TGTATCGATACATTATG-CTTTGTATCGATACAT 1 TGTATCAATACATTAGGACATTGTATCGATACAT * 3979135 TGTATCAATACA-TGGGACATTGTATCGATACAT 1 TGTATCAATACATTAGGACATTGTATCGATACAT 3979168 TGTAT-AGATACAT 1 TGTATCA-ATACAT 3979181 GGTAAAAAGT Statistics Matches: 39, Mismatches: 4, Indels: 5 0.81 0.08 0.10 Matches are distributed among these distances: 32 3 0.08 33 36 0.92 ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38 Consensus pattern (34 bp): TGTATCAATACATTAGGACATTGTATCGATACAT Found at i:3979181 original size:33 final size:33 Alignment explanation

Indices: 3979121--3979201 Score: 110 Period size: 33 Copynumber: 2.5 Consensus size: 33 3979111 ACATTATGCT * 3979121 TTGTATCGATACATTGTATCAATACATGGGACA 1 TTGTATCGATACATTGTATCAATACATGGGAAA * 3979154 TTGTATCGATACATTGTAT-AGATACATGGTAAA 1 TTGTATCGATACATTGTATCA-ATACATGGGAAA ** 3979187 AAGTATCGATACATT 1 TTGTATCGATACATT 3979202 ATGCCCAACG Statistics Matches: 43, Mismatches: 4, Indels: 2 0.88 0.08 0.04 Matches are distributed among these distances: 32 1 0.02 33 42 0.98 ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35 Consensus pattern (33 bp): TTGTATCGATACATTGTATCAATACATGGGAAA Found at i:3984930 original size:50 final size:51 Alignment explanation

Indices: 3984816--3984930 Score: 162 Period size: 50 Copynumber: 2.3 Consensus size: 51 3984806 TACATTGAAG * * 3984816 AATGTATCGATACATTTGGATCAAAAACCTAGAATGTGTCAATATAATAAGA 1 AATGTATCGATACATTTGGATC-AAAACCTAGAATGTATCAATATAATAAAA * * 3984868 AATGTATTGATACATTTGGATC-AAACCTAGAATGTATCGATATAATGAAAA 1 AATGTATCGATACATTTGGATCAAAACCTAGAATGTATCAATATAAT-AAAA 3984919 AAT-TATCGATAC 1 AATGTATCGATAC 3984931 CTTTTCTTTT Statistics Matches: 57, Mismatches: 5, Indels: 4 0.86 0.08 0.06 Matches are distributed among these distances: 50 30 0.53 51 6 0.11 52 21 0.37 ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30 Consensus pattern (51 bp): AATGTATCGATACATTTGGATCAAAACCTAGAATGTATCAATATAATAAAA Found at i:3985522 original size:20 final size:20 Alignment explanation

Indices: 3985497--3985535 Score: 69 Period size: 20 Copynumber: 1.9 Consensus size: 20 3985487 GCACTTTGAA 3985497 AAGTAAATGTATCAATATAT 1 AAGTAAATGTATCAATATAT * 3985517 AAGTAAATGTATCGATATA 1 AAGTAAATGTATCAATATA 3985536 CTTACTGTTT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 20 18 1.00 ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33 Consensus pattern (20 bp): AAGTAAATGTATCAATATAT Found at i:3989196 original size:12 final size:12 Alignment explanation

Indices: 3989166--3989210 Score: 51 Period size: 12 Copynumber: 3.9 Consensus size: 12 3989156 GCAAAAGCGT * 3989166 AAAAGGAAAATG 1 AAAAGAAAAATG 3989178 -AAA-AAAAATG 1 AAAAGAAAAATG 3989188 AAAAGAAAAA-G 1 AAAAGAAAAATG 3989199 AAAAAGAAAAAT 1 -AAAAGAAAAAT 3989211 AAAGTGAAAA Statistics Matches: 28, Mismatches: 1, Indels: 7 0.78 0.03 0.19 Matches are distributed among these distances: 10 6 0.21 11 7 0.25 12 15 0.54 ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07 Consensus pattern (12 bp): AAAAGAAAAATG Found at i:3991935 original size:155 final size:153 Alignment explanation

Indices: 3991639--3992017 Score: 413 Period size: 155 Copynumber: 2.4 Consensus size: 153 3991629 CTAAGTTCAA * * ** * ** 3991639 GAAAAATTACGAAAATGCTCTTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAAA 1 GAAAAATTATGAAAATGC-CCTAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA * * * * * 3991704 CTTAAAAAAGATAATAGATGAGATGAACCTATCATTAATATCTACCTTCGGCATAAAAGCAGACC 64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC * 3991769 CAATGATAACCTAGGACGT-AATTCT 129 CAATGACAACCTAGGAC-TCAATTCT * * 3991794 GAAAAATTATGAAATTGCCCATAAGGGACATTTTCGACGTAAAAGTACCCGATATCCCTAAAGGA 1 GAAAAATTATGAAAATGCCC-TAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA * * * * 3991859 CTTAAAAAGGATAACATATGAGATGAGCCTATCCTAAATATCTACCTCCGACATAAAAGCAAACC 64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC ** * * 3991924 CGGTGACAACCTAGGACTCGATTTT 129 CAATGACAACCTAGGACTCAATTCT * * * * 3991949 AAAAAATTATGAAAATGACCCT-AGAGG-ATTACTTCAATGTAAAAGTACCCAATACCCCTAAAG 1 GAAAAATTATGAAAATG-CCCTAAG-GGAATT--TTCGACGTAAAAGTACCCGATACCCCTAAAG 3992012 GACTTA 62 GACTTA 3992018 GGATAATGCT Statistics Matches: 188, Mismatches: 30, Indels: 12 0.82 0.13 0.05 Matches are distributed among these distances: 153 3 0.02 154 4 0.02 155 178 0.95 156 3 0.02 ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23 Consensus pattern (153 bp): GAAAAATTATGAAAATGCCCTAAGGGAATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGACT TAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACCCA ATGACAACCTAGGACTCAATTCT Found at i:3993480 original size:13 final size:13 Alignment explanation

Indices: 3993462--3993487 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 3993452 CAATTTTTTG 3993462 TGTATCGATACAT 1 TGTATCGATACAT 3993475 TGTATCGATACAT 1 TGTATCGATACAT 3993488 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:3993572 original size:20 final size:20 Alignment explanation

Indices: 3993547--3993619 Score: 92 Period size: 20 Copynumber: 3.6 Consensus size: 20 3993537 CAACTTTTTT 3993547 ATGTATCGATACATTACAAC 1 ATGTATCGATACATTACAAC **** 3993567 ATGTATCGATACATCTTTTTC 1 ATGTATCGATACAT-TACAAC * 3993588 ATGTATCGATACATTGCAAC 1 ATGTATCGATACATTACAAC 3993608 ATGTATCGATAC 1 ATGTATCGATAC 3993620 TTTGAATTGT Statistics Matches: 44, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 20 28 0.64 21 16 0.36 ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36 Consensus pattern (20 bp): ATGTATCGATACATTACAAC Found at i:3993585 original size:41 final size:41 Alignment explanation

Indices: 3993526--3993619 Score: 161 Period size: 41 Copynumber: 2.3 Consensus size: 41 3993516 CTGCCAAGAA * 3993526 ATGTATCGATACAACTTTTTTATGTATCGATACATTACAAC 1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC * * 3993567 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC 1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC 3993608 ATGTATCGATAC 1 ATGTATCGATAC 3993620 TTTGAATTGT Statistics Matches: 50, Mismatches: 3, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 41 50 1.00 ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38 Consensus pattern (41 bp): ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC Found at i:3993601 original size:21 final size:21 Alignment explanation

Indices: 3993526--3993601 Score: 91 Period size: 21 Copynumber: 3.7 Consensus size: 21 3993516 CTGCCAAGAA * * 3993526 ATGTATCGATACAACTTTTTT 1 ATGTATCGATACATCTTTTTC **** 3993547 ATGTATCGATACAT-TACAAC 1 ATGTATCGATACATCTTTTTC 3993567 ATGTATCGATACATCTTTTTC 1 ATGTATCGATACATCTTTTTC 3993588 ATGTATCGATACAT 1 ATGTATCGATACAT 3993602 TGCAACATGT Statistics Matches: 44, Mismatches: 10, Indels: 2 0.79 0.18 0.04 Matches are distributed among these distances: 20 15 0.34 21 29 0.66 ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41 Consensus pattern (21 bp): ATGTATCGATACATCTTTTTC Found at i:3994353 original size:100 final size:100 Alignment explanation

Indices: 3994180--3994381 Score: 404 Period size: 100 Copynumber: 2.0 Consensus size: 100 3994170 TACGAATTCG 3994180 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA 1 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA 3994245 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT 66 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT 3994280 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA 1 TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA 3994345 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT 66 ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT 3994380 TA 1 TA 3994382 TTTTCACTTT Statistics Matches: 102, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 100 102 1.00 ACGTcount: A:0.28, C:0.29, G:0.06, T:0.37 Consensus pattern (100 bp): TACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTGTCTCCCCCGTTTATTAATAA ATCTCCCCCTTAATCAAGTAATTCATATCAAAATT Found at i:3996180 original size:13 final size:13 Alignment explanation

Indices: 3996162--3996200 Score: 69 Period size: 13 Copynumber: 3.0 Consensus size: 13 3996152 ATAATCACCC * 3996162 TGTATCGATACAG 1 TGTATCGATACAA 3996175 TGTATCGATACAA 1 TGTATCGATACAA 3996188 TGTATCGATACAA 1 TGTATCGATACAA 3996201 AGAAAAATGT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31 Consensus pattern (13 bp): TGTATCGATACAA Found at i:3996211 original size:20 final size:20 Alignment explanation

Indices: 3996186--3996264 Score: 70 Period size: 20 Copynumber: 3.7 Consensus size: 20 3996176 GTATCGATAC 3996186 AATGTATCGATACAAAGAAA 1 AATGTATCGATACAAAGAAA * 3996206 AATGTATCGATACATAGAATTTCCA 1 AATGTATCGATACAAAGAA-----A * 3996231 GATGTATCGATACACAA-AAA 1 AATGTATCGATACA-AAGAAA * 3996251 CATGTATCGATACA 1 AATGTATCGATACA 3996265 TTTTGGACAT Statistics Matches: 49, Mismatches: 4, Indels: 12 0.75 0.06 0.18 Matches are distributed among these distances: 20 32 0.65 25 16 0.33 26 1 0.02 ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25 Consensus pattern (20 bp): AATGTATCGATACAAAGAAA Found at i:3998297 original size:15 final size:15 Alignment explanation

Indices: 3998277--3998307 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 3998267 ATTTCGTTTG * 3998277 GAGCTTCTTCATTTT 1 GAGCTTCCTCATTTT 3998292 GAGCTTCCTCATTTT 1 GAGCTTCCTCATTTT 3998307 G 1 G 3998308 GACATTTTTA Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48 Consensus pattern (15 bp): GAGCTTCCTCATTTT Found at i:4000140 original size:21 final size:21 Alignment explanation

Indices: 4000111--4000155 Score: 56 Period size: 21 Copynumber: 2.1 Consensus size: 21 4000101 AAGTTTTCAT * 4000111 TTTTCTTAGCTAAC-TCATTA 1 TTTTCTTAGCCAACTTCATTA * 4000131 TTTTCATTAGCCAACTTCTTTA 1 TTTTC-TTAGCCAACTTCATTA 4000153 TTT 1 TTT 4000156 CAACTTGCAA Statistics Matches: 21, Mismatches: 2, Indels: 2 0.84 0.08 0.08 Matches are distributed among these distances: 20 5 0.24 21 8 0.38 22 8 0.38 ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53 Consensus pattern (21 bp): TTTTCTTAGCCAACTTCATTA Found at i:4002373 original size:13 final size:13 Alignment explanation

Indices: 4002355--4002380 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 4002345 CAATTTTTTG 4002355 TGTATCGATACAT 1 TGTATCGATACAT 4002368 TGTATCGATACAT 1 TGTATCGATACAT 4002381 ACTTGCTGTA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4002466 original size:20 final size:20 Alignment explanation

Indices: 4002441--4002513 Score: 101 Period size: 20 Copynumber: 3.6 Consensus size: 20 4002431 AACTTTTTTT 4002441 ATGTATCGATACATTGCAAC 1 ATGTATCGATACATTGCAAC **** 4002461 ATGTATCGATACATCTTTTTC 1 ATGTATCGATACAT-TGCAAC 4002482 ATGTATCGATACATTGCAAC 1 ATGTATCGATACATTGCAAC 4002502 ATGTATCGATAC 1 ATGTATCGATAC 4002514 TTTGAATTGT Statistics Matches: 44, Mismatches: 8, Indels: 2 0.81 0.15 0.04 Matches are distributed among these distances: 20 28 0.64 21 16 0.36 ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36 Consensus pattern (20 bp): ATGTATCGATACATTGCAAC Found at i:4002492 original size:41 final size:42 Alignment explanation

Indices: 4002419--4002513 Score: 165 Period size: 41 Copynumber: 2.3 Consensus size: 42 4002409 CTGCCAAGAA * 4002419 ATGTATCGATACAACTTTTTTTATGTATCGATACATTGCAAC 1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC * 4002461 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC 1 ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC 4002502 ATGTATCGATAC 1 ATGTATCGATAC 4002514 TTTGAATTGT Statistics Matches: 51, Mismatches: 2, Indels: 1 0.94 0.04 0.02 Matches are distributed among these distances: 41 37 0.73 42 14 0.27 ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39 Consensus pattern (42 bp): ATGTATCGATACAACTTTTTTCATGTATCGATACATTGCAAC Found at i:4004487 original size:168 final size:166 Alignment explanation

Indices: 4004094--4004547 Score: 546 Period size: 168 Copynumber: 2.7 Consensus size: 166 4004084 ATATACAAAA * * * * ** * * 4004094 AAAATTAATG-AAATAAATTAAAATTTTCAAAACTGA-ATTAATGAGAGTTTAATTACAATATTA 1 AAAACTAATGAAAATAAATT-AATTTTTCAAAACT-ATTTTAATGAGAATTCCATGACATTATTA * * * * * ** * * 4004157 GATGCATTTTAAAAGTTTTAGACCAAAGAAAATCCCTTCGGAAATATTTATCGAATAGAAAACTT 64 GATACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCCAAAAATATTTATGGATTAGAAAACTT * * * * 4004222 TGTTTGTCGAGAAAAAGGGGATTGTAAAGAAAAAATTT 129 TGTTTGTCGAGAAAAAAGAGATTGTAAAGAAAAAAATC 4004260 AAAACTAATGAAAATAAATTAATTTTTCAAAACCT-TTTTAATG-GAAATTCCATGACATTATTA 1 AAAACTAATGAAAATAAATTAATTTTTCAAAA-CTATTTTAATGAG-AATTCCATGACATTATTA 4004323 GATACATTTTAAAAATTTTAAATCAAAGAAAATCACC-CCAAAAATATTTATGGATTAGAAAAC- 64 GATACATTTTAAAAATTTTAAATCAAAGAAAATC-CCTCCAAAAATATTTATGGATTAGAAAACT * * 4004386 TTGATTTTTCGGGAAAAAAAGAGATT-TCAAAGAAAAAAAATC 128 TTG-TTTGTCGAG-AAAAAAGAGATTGT-AAAG-AAAAAAATC * 4004428 AAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA 1 AAAACTAATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA 4004493 TACATTTTAAAAATTTTAAATCAAAGAAAA-CCCTCCTAAAAATATTTATGGATTA 66 TACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCC-AAAAATATTTATGGATTA 4004548 AAGAACTCGA Statistics Matches: 251, Mismatches: 24, Indels: 24 0.84 0.08 0.08 Matches are distributed among these distances: 165 4 0.02 166 100 0.40 167 32 0.13 168 114 0.45 169 1 0.00 ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32 Consensus pattern (166 bp): AAAACTAATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATTAGA TACATTTTAAAAATTTTAAATCAAAGAAAATCCCTCCAAAAATATTTATGGATTAGAAAACTTTG TTTGTCGAGAAAAAAGAGATTGTAAAGAAAAAAATC Found at i:4004643 original size:131 final size:132 Alignment explanation

Indices: 4004425--4004689 Score: 423 Period size: 131 Copynumber: 2.0 Consensus size: 132 4004415 AAGAAAAAAA * * 4004425 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAGAATTCCATGACATTATT 1 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT * 4004490 AGATACATTTTAAAAATTTT-AAATCAAAGAAAA-C-CCTCCTAAAAATATTTATGGATTA-AAG 66 AGATACATTTTAAAAATTTTAAAAT-AAAGAAAATCACC-CC-AAAAATAGTTATGGATTAGAA- 4004551 AACTCG 127 AACTCG * 4004557 ATCAAAACTCATGAAAATAAATTAATTTTTTAAAACTATTTTAAT-AAAATTCCACGACATTATT 1 ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT 4004621 AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT 66 AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT 4004686 CG 131 CG 4004688 AT 1 AT 4004690 TTTTTGGGGG Statistics Matches: 125, Mismatches: 4, Indels: 9 0.91 0.03 0.07 Matches are distributed among these distances: 131 70 0.56 132 53 0.42 133 2 0.02 ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33 Consensus pattern (132 bp): ATCAAAACTCATGAAAATAAATTAATTTTTCAAAACTATTTTAATGAAAATTCCACGACATTATT AGATACATTTTAAAAATTTTAAAATAAAGAAAATCACCCCAAAAATAGTTATGGATTAGAAAACT CG Found at i:4005156 original size:165 final size:167 Alignment explanation

Indices: 4004718--4005175 Score: 466 Period size: 165 Copynumber: 2.8 Consensus size: 167 4004708 ATTCCAAAGA * * * * * * * *** 4004718 AAAAAAATT-AAAAGCTCATGAAAATGAAAGAATTTCTCAAAACTGATTCAATCCAAAATAAATA 1 AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA * * * 4004782 ATAATATTTG-TGGAATTTAAAAAAATTTTACACCCATGAAAATCT-TCCCAAAAAAATTTACGG 66 ATAATATTTGAT-GAA-TTATAAAAATTTTAAACCCATGAAAATCTCT-CCAAAAAAATTTACGA * ** * 4004845 AGTAAAAAATTTTATATTTCAAAAACAATGAAATTTTAAG 128 AGTAAAAAACTGCATATTTCAAAAACAATGAAATTTCAAG * * * 4004885 GAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTGAAAACTAATTTAATATGGAATAAATA 1 AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA * * * * * * * 4004950 GTAATATTTGATGAATTTTAAAAA-TTAAAAACTAAGAAAATCTCTCCAAAAAAA-TTATGAAGT 66 ATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAATCTCTCCAAAAAAATTTACGAAGT * * * 4005013 AGAAAACTGCGTATTTCGAAAACAGA-GAAATTTCAAG 131 AAAAAACTGCATATTTCAAAAACA-ATGAAATTTCAAG * * * * 4005050 AAAAAAATAT-AGAAACTCATGAAAATGAAT-AATTTTTTAAAAACTAATTTACTATGAAATAAG 1 AAAAAAAT-TCAAAAACCCATGAAAATGAATGAA-TTTTTAAAAACTAATTTAATATGAAATAAA * * 4005113 TAATAATATTTGATGAA-TATAAAAATTTTAAACCCATGAAAATCCTCCCCAAAAAATTTTACG 64 TAATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAAT-CTCTCCAAAAAAATTTACG 4005176 GTGAAAAAAA Statistics Matches: 237, Mismatches: 45, Indels: 18 0.79 0.15 0.06 Matches are distributed among these distances: 164 9 0.04 165 115 0.49 166 36 0.15 167 20 0.08 168 56 0.24 169 1 0.00 ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29 Consensus pattern (167 bp): AAAAAAATTCAAAAACCCATGAAAATGAATGAATTTTTAAAAACTAATTTAATATGAAATAAATA ATAATATTTGATGAATTATAAAAATTTTAAACCCATGAAAATCTCTCCAAAAAAATTTACGAAGT AAAAAACTGCATATTTCAAAAACAATGAAATTTCAAG Found at i:4006773 original size:33 final size:33 Alignment explanation

Indices: 4006736--4006805 Score: 104 Period size: 33 Copynumber: 2.1 Consensus size: 33 4006726 TTCAACGATT 4006736 TGTATCGATACATAAAATGTTGTATCGATACAA 1 TGTATCGATACATAAAATGTTGTATCGATACAA *** * 4006769 TGTATCGATACATATTTTTTTGTATCGATACAA 1 TGTATCGATACATAAAATGTTGTATCGATACAA 4006802 TGTA 1 TGTA 4006806 AGCTACTGCC Statistics Matches: 33, Mismatches: 4, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 33 33 1.00 ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40 Consensus pattern (33 bp): TGTATCGATACATAAAATGTTGTATCGATACAA Found at i:4006774 original size:13 final size:13 Alignment explanation

Indices: 4006756--4006780 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4006746 CATAAAATGT 4006756 TGTATCGATACAA 1 TGTATCGATACAA 4006769 TGTATCGATACA 1 TGTATCGATACA 4006781 TATTTTTTTG 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:0.36, C:0.16, G:0.16, T:0.32 Consensus pattern (13 bp): TGTATCGATACAA Found at i:4006863 original size:13 final size:13 Alignment explanation

Indices: 4006845--4006869 Score: 50 Period size: 13 Copynumber: 1.9 Consensus size: 13 4006835 ATTACTCACA 4006845 TGTATCGATACAT 1 TGTATCGATACAT 4006858 TGTATCGATACA 1 TGTATCGATACA 4006870 CTGATCTTTG 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:0.32, C:0.16, G:0.16, T:0.36 Consensus pattern (13 bp): TGTATCGATACAT Found at i:4006934 original size:52 final size:52 Alignment explanation

Indices: 4006878--4007006 Score: 206 Period size: 52 Copynumber: 2.5 Consensus size: 52 4006868 CACTGATCTT * 4006878 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACATTA-TAAA 1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA * 4006929 CTGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA 1 -TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA * * 4006982 TGTATCGATACATGCAAATAAATTT 1 TGTATCGATACATGCAGACAAATTT 4007007 TCATATTTCG Statistics Matches: 71, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 52 67 0.94 53 4 0.06 ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30 Consensus pattern (52 bp): TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATTAAA Found at i:4010162 original size:60 final size:59 Alignment explanation

Indices: 4010081--4010195 Score: 151 Period size: 59 Copynumber: 1.9 Consensus size: 59 4010071 CACCTATATT * * * 4010081 GAGAGTAAAGTCCAATATAGCTAGC-CCTATGGCAAGCCTAGTGAAGTTGCCCTATATAAA 1 GAGAGTAAAGCCCAATATAGCTA-CTAC-ATGGCAAGCCTAGTGAAATTGCCCTATATAAA * * * 4010141 GAGAGTCAAGCCCAATGTAGCTACTACATGGTAAGCCTAGTGAAATTGCCCTATA 1 GAGAGTAAAGCCCAATATAGCTACTACATGGCAAGCCTAGTGAAATTGCCCTATA 4010196 CCAAGAGTCA Statistics Matches: 48, Mismatches: 6, Indels: 3 0.84 0.11 0.05 Matches are distributed among these distances: 59 27 0.56 60 21 0.44 ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23 Consensus pattern (59 bp): GAGAGTAAAGCCCAATATAGCTACTACATGGCAAGCCTAGTGAAATTGCCCTATATAAA Done.