Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 514 of 770

Found at i:159438961 original size:40 final size:40

Alignment explanation

Indices: 159438878--159439085 Score: 184 Period size: 40 Copynumber: 5.2 Consensus size: 40 159438868 CGGGATTTAA * * * * * * 159438878 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACCTAGC 1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC * ** * * * 159438918 CCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAAC 1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC * * * * * 159438958 CCGGATTTGGTAACTTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC * 159438998 CCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC *** * * * 159439038 CCGGATATAATTACTAGCA-TAATTGCCTTCGGGACTTAGC 1 CCGGATATAGCAACTCGCACGAA-TGCCTTCGGGTCTTAGC 159439078 CCGGATAT 1 CCGGATAT 159439086 CATTCCAATG Statistics Matches: 139, Mismatches: 28, Indels: 2 0.82 0.17 0.01 Matches are distributed among these distances: 39 2 0.01 40 137 0.99 ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28 Consensus pattern (40 bp): CCGGATATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC Found at i:159438998 original size:80 final size:80 Alignment explanation

Indices: 159438904--159439085 Score: 220 Period size: 80 Copynumber: 2.3 Consensus size: 80 159438894 GCTCGATTGT * * *** * * * ** 159438904 CTTCGGGACCTAGCCCGGTTATAGTGATTCGCACGATTGCCTTCGGGTCTTAACCCGGATTTGGT 1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT * 159438969 AACTTGCACAAATGC 66 AACTAGCACAAATGC * * 159438984 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAAT 1 CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT * * * 159439049 TACTAGCATAATTGC 66 AACTAGCACAAATGC 159439064 CTTCGGGACTTAGCCCGGATAT 1 CTTCGGGACTTAGCCCGGATAT 159439086 CATTCCAATG Statistics Matches: 85, Mismatches: 17, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 80 85 1.00 ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28 Consensus pattern (80 bp): CTTCGGGACTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAACCCGGATATAAT AACTAGCACAAATGC Found at i:159442238 original size:40 final size:40 Alignment explanation

Indices: 159442179--159442365 Score: 180 Period size: 40 Copynumber: 4.7 Consensus size: 40 159442169 CATTGGAATG * * * * 159442179 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT * * 159442219 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGTTATT * ** 159442259 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT * * * * * 159442299 AAATCCGGGTTAAGACCCGAAGGCAATCGTGCGAA-TCACT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTATT * * * * 159442339 ATAACCGGGCTAGGTCCCGAAGACAAT 1 ATATCCGGGCTAAGACCCGAAGGCAAT 159442366 CGAGCGAGTC Statistics Matches: 122, Mismatches: 22, Indels: 6 0.81 0.15 0.04 Matches are distributed among these distances: 39 3 0.02 40 115 0.94 41 4 0.03 ACGTcount: A:0.29, C:0.24, G:0.26, T:0.22 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTATT Found at i:159442281 original size:80 final size:80 Alignment explanation

Indices: 159442179--159442332 Score: 218 Period size: 80 Copynumber: 1.9 Consensus size: 80 159442169 CATTGGAATG * * ** * 159442179 ATATCCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA * 159442244 TTCGTGCGAGTTGTT 66 ATCGTGCGAGTTGTT * * * * 159442259 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA 159442324 ATCGTGCGA 66 ATCGTGCGA 159442333 ATCACTATAA Statistics Matches: 64, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 80 64 1.00 ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23 Consensus pattern (80 bp): ATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCA ATCGTGCGAGTTGTT Found at i:159442347 original size:80 final size:80 Alignment explanation

Indices: 159442183--159442365 Score: 213 Period size: 80 Copynumber: 2.3 Consensus size: 80 159442173 GGAATGATAT * ** * * 159442183 CCGGGCTAAGTCCCGAAGGCAATTATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCG 1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG * *** * 159442248 TGCGAGTTGTTATAT 66 TGCGAATCACTATAA * * * * * 159442263 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATCG 1 CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG 159442328 TGCGAATCACTATAA 66 TGCGAATCACTATAA * * 159442343 CCGGGCTAGGTCCCGAAGACAAT 1 CCGGGCTAAGTCCCGAAGGCAAT 159442366 CGAGCGAGTC Statistics Matches: 84, Mismatches: 19, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 80 84 1.00 ACGTcount: A:0.28, C:0.24, G:0.26, T:0.21 Consensus pattern (80 bp): CCGGGCTAAGTCCCGAAGGCAATTATGCAAGTAACCAAATCCGGGCTAAGACCCGAAGGCAATCG TGCGAATCACTATAA Found at i:159442385 original size:80 final size:80 Alignment explanation

Indices: 159442183--159442400 Score: 181 Period size: 80 Copynumber: 2.7 Consensus size: 80 159442173 GGAATGATAT * * * * * * * * 159442183 CCGGGCTAAGTCCCGAAGGCAAT-TATGCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTC 1 CCGGGCTAAGACCCGAAGACAATCGA-GCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATC * *** * 159442247 GTGCGAGTTGTTATAT 65 GTGCGAATCACTATAA * * * * * * * 159442263 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCCGGGTTAAGACCCGAAGGCAATCG 1 CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATCG 159442328 TGCGAATCACTATAA 66 TGCGAATCACTATAA * * * * 159442343 CCGGGCTAGGTCCCGAAGACAATCGAGCGAGTCGCTATATCC-GGTTAA-ATCCCGAAGG 1 CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGA-CCCGAAGG 159442401 TACGTGATTC Statistics Matches: 109, Mismatches: 27, Indels: 5 0.77 0.19 0.04 Matches are distributed among these distances: 78 1 0.01 79 14 0.13 80 94 0.86 ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21 Consensus pattern (80 bp): CCGGGCTAAGACCCGAAGACAATCGAGCAAGTCACTATATCCGGGTTAAGACCCGAAGGCAATCG TGCGAATCACTATAA Found at i:159455371 original size:30 final size:29 Alignment explanation

Indices: 159455315--159455471 Score: 214 Period size: 30 Copynumber: 5.5 Consensus size: 29 159455305 ATAGTGAATC 159455315 CGCACACTTAGTGCTATATA-TTTCAGCT 1 CGCACACTTAGTGCTATATATTTTCAGCT 159455343 CGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATAT-ATTTTCAGCT 159455373 CGCACACTTAGTGCTATATATTTTCAG-T 1 CGCACACTTAGTGCTATATATTTTCAGCT * 159455401 CGCACACTTAGTGCT-TATA-TTTCAGTT 1 CGCACACTTAGTGCTATATATTTTCAGCT * * * * * 159455428 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATA-TATTTTCAGCT 159455458 CGCACACTTAGTGC 1 CGCACACTTAGTGC 159455472 CAATCTTGTC Statistics Matches: 118, Mismatches: 5, Indels: 10 0.89 0.04 0.08 Matches are distributed among these distances: 26 6 0.05 27 20 0.17 28 37 0.31 29 10 0.08 30 45 0.38 ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35 Consensus pattern (29 bp): CGCACACTTAGTGCTATATATTTTCAGCT Found at i:159455405 original size:58 final size:55 Alignment explanation

Indices: 159455315--159455442 Score: 204 Period size: 58 Copynumber: 2.3 Consensus size: 55 159455305 ATAGTGAATC 159455315 CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCT-TAT-A-TTTCAGCT * 159455373 CGCACACTTAGTGCTATATATTTTCAG-TCGCACACTTAGTGCTTATATTTCAGTT 1 CGCACACTTAGTGCTATATA-TTTCAGCTCGCACACTTAGTGCTTATATTTCAGCT 159455428 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 159455443 GTACAATTTT Statistics Matches: 68, Mismatches: 1, Indels: 5 0.92 0.01 0.07 Matches are distributed among these distances: 55 22 0.32 56 1 0.01 57 3 0.04 58 36 0.53 59 6 0.09 ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37 Consensus pattern (55 bp): CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTTATATTTCAGCT Found at i:159455451 original size:85 final size:86 Alignment explanation

Indices: 159455315--159455471 Score: 253 Period size: 85 Copynumber: 1.8 Consensus size: 86 159455305 ATAGTGAATC * * * * 159455315 CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCTCGCACAC 1 CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATACAATTTTAAACCCGCACAC 159455380 TTAGTGCTATATATTTTCAGT 66 TTAGTGCTATATATTTTCAGT * * 159455401 CGCACACTTAGTGCT-TATATTTCAGTTCGCACACTTAGTGCTGTACAATTTTAAACCCGCACAC 1 CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATACAATTTTAAACCCGCACAC 159455465 TTAGTGC 66 TTAGTGC 159455472 CAATCTTGTC Statistics Matches: 65, Mismatches: 6, Indels: 1 0.90 0.08 0.01 Matches are distributed among these distances: 85 50 0.77 86 15 0.23 ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35 Consensus pattern (86 bp): CGCACACTTAGTGCTATATATTTCAGCTCGCACACTTAGTGCTATACAATTTTAAACCCGCACAC TTAGTGCTATATATTTTCAGT Found at i:159463184 original size:29 final size:29 Alignment explanation

Indices: 159463152--159463283 Score: 237 Period size: 29 Copynumber: 4.5 Consensus size: 29 159463142 ATAGTGAATC 159463152 CGCACACTTAGTGCTATATATTTTCAGCT 1 CGCACACTTAGTGCTATATATTTTCAGCT 159463181 CGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATAT-ATTTTCAGCT * 159463211 CGCACACTTAGTGCTATATATTTTCAGTT 1 CGCACACTTAGTGCTATATATTTTCAGCT * 159463240 CGCACACTTAGTGCTATATATTTTCAGTT 1 CGCACACTTAGTGCTATATATTTTCAGCT 159463269 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 159463284 GTACAATTTT Statistics Matches: 101, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 29 72 0.71 30 29 0.29 ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38 Consensus pattern (29 bp): CGCACACTTAGTGCTATATATTTTCAGCT Found at i:159463293 original size:59 final size:59 Alignment explanation

Indices: 159463152--159463283 Score: 239 Period size: 59 Copynumber: 2.3 Consensus size: 59 159463142 ATAGTGAATC 159463152 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT 1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT * * 159463211 CGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTATAT-ATTTTCAGTT 1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT 159463269 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 159463284 GTACAATTTT Statistics Matches: 71, Mismatches: 2, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 58 24 0.34 59 47 0.66 ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38 Consensus pattern (59 bp): CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGCT Found at i:159465248 original size:17 final size:17 Alignment explanation

Indices: 159465226--159465260 Score: 52 Period size: 17 Copynumber: 2.1 Consensus size: 17 159465216 ACATATGCTC 159465226 TCTTTTTCTCTCTTTTT 1 TCTTTTTCTCTCTTTTT * * 159465243 TCTTTTTTTTTCTTTTT 1 TCTTTTTCTCTCTTTTT 159465260 T 1 T 159465261 TTTCACGAGC Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83 Consensus pattern (17 bp): TCTTTTTCTCTCTTTTT Found at i:159465261 original size:10 final size:10 Alignment explanation

Indices: 159465228--159465264 Score: 56 Period size: 10 Copynumber: 3.6 Consensus size: 10 159465218 ATATGCTCTC * 159465228 TTTTTCTCTCT 1 TTTTTCT-TTT 159465239 TTTTTCTTTT 1 TTTTTCTTTT 159465249 TTTTTCTTTT 1 TTTTTCTTTT 159465259 TTTTTC 1 TTTTTC 159465265 ACGAGCATTT Statistics Matches: 25, Mismatches: 1, Indels: 1 0.93 0.04 0.04 Matches are distributed among these distances: 10 18 0.72 11 7 0.28 ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84 Consensus pattern (10 bp): TTTTTCTTTT Found at i:159476670 original size:42 final size:43 Alignment explanation

Indices: 159476623--159476766 Score: 132 Period size: 42 Copynumber: 3.4 Consensus size: 43 159476613 TCCTAAATAG * 159476623 GGTCTTACACG-AAATTAGATATGATGCCGATGTCCCAGACAT 1 GGTCTTACACGTAAATTAGATATGATGCCAATGTCCCAGACAT * * ** ** * * 159476665 AGTCTTATACGTAAATTTCA-ATCGCGGCCTATGTCCCAGACAC 1 GGTCTTACACGTAAATTAGATAT-GATGCCAATGTCCCAGACAT * * * * 159476708 GGTCTTACATG-AAATCAGATACGATGCCAATGTCCCAAACAT 1 GGTCTTACACGTAAATTAGATATGATGCCAATGTCCCAGACAT * 159476750 GGTCTTATACGTAAATT 1 GGTCTTACACGTAAATT 159476767 TCAATAGAGG Statistics Matches: 75, Mismatches: 23, Indels: 7 0.71 0.22 0.07 Matches are distributed among these distances: 42 40 0.53 43 35 0.47 ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28 Consensus pattern (43 bp): GGTCTTACACGTAAATTAGATATGATGCCAATGTCCCAGACAT Found at i:159476699 original size:43 final size:43 Alignment explanation

Indices: 159476652--159476799 Score: 149 Period size: 43 Copynumber: 3.5 Consensus size: 43 159476642 TATGATGCCG * * 159476652 ATGTCCCAGACATAGTCTTATACGTAAATTTCAATCGCGGCCT 1 ATGTCCCAGACATGGTCTTATACGTAAATTTCAATCGAGGCCT * * * * * 159476695 ATGTCCCAGACACGGTCTTACATG-AAA--TCAGATACGATGCCA 1 ATGTCCCAGACATGGTCTTATACGTAAATTTCA-AT-CGAGGCCT * * 159476737 ATGTCCCAAACATGGTCTTATACGTAAATTTCAATAGAGGCCT 1 ATGTCCCAGACATGGTCTTATACGTAAATTTCAATCGAGGCCT * * * 159476780 GTGTCTCAGACACGGTCTTA 1 ATGTCCCAGACATGGTCTTA 159476800 CACAAAATCA Statistics Matches: 82, Mismatches: 18, Indels: 10 0.75 0.16 0.09 Matches are distributed among these distances: 40 3 0.04 41 2 0.02 42 28 0.34 43 44 0.54 44 2 0.02 45 3 0.04 ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28 Consensus pattern (43 bp): ATGTCCCAGACATGGTCTTATACGTAAATTTCAATCGAGGCCT Found at i:159476728 original size:85 final size:85 Alignment explanation

Indices: 159476623--159476822 Score: 292 Period size: 85 Copynumber: 2.4 Consensus size: 85 159476613 TCCTAAATAG * * * * * 159476623 GGTCTTACACGAAATTAGATATGATGCCGATGTCCCAGACATAGTCTTATACGTAAATTTCAATC 1 GGTCTTACACGAAATCAGATACGATGCCAATGTCCCAAACATAGTCTTATACGTAAATTTCAATA * 159476688 GCGGCCTATGTCCCAGACAC 66 GAGGCCTATGTCCCAGACAC * * 159476708 GGTCTTACATGAAATCAGATACGATGCCAATGTCCCAAACATGGTCTTATACGTAAATTTCAATA 1 GGTCTTACACGAAATCAGATACGATGCCAATGTCCCAAACATAGTCTTATACGTAAATTTCAATA * * 159476773 GAGGCCTGTGTCTCAGACAC 66 GAGGCCTATGTCCCAGACAC * * 159476793 GGTCTTACACAAAATCAAATACGATGCCAA 1 GGTCTTACACGAAATCAGATACGATGCCAA 159476823 CTTTTCTTAG Statistics Matches: 102, Mismatches: 13, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 85 102 1.00 ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26 Consensus pattern (85 bp): GGTCTTACACGAAATCAGATACGATGCCAATGTCCCAAACATAGTCTTATACGTAAATTTCAATA GAGGCCTATGTCCCAGACAC Found at i:159483671 original size:39 final size:40 Alignment explanation

Indices: 159483549--159483712 Score: 217 Period size: 40 Copynumber: 4.2 Consensus size: 40 159483539 GGACTAAGAT * * 159483549 CCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTC 1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC * * * * 159483589 CCGAAGGCATTTATGCTAG-TGATTATATCCGGGCTAAGAC 1 CCGAAGGCATTTGTGCGAGTTG-CTATATCCGGGCTAAGTC * 159483629 CCGAAGGCATTTGTGCGAGTTGCTAT-TCCGGGCTAAGGC 1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC * * 159483668 CCGAAGGCATTTGTGCGAGTTGTTATATCC-GGCTAAATC 1 CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC 159483707 CCGAAG 1 CCGAAG 159483713 ATACTTGGAT Statistics Matches: 108, Mismatches: 13, Indels: 7 0.84 0.10 0.05 Matches are distributed among these distances: 39 52 0.48 40 54 0.50 41 2 0.02 ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27 Consensus pattern (40 bp): CCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTC Found at i:159487772 original size:40 final size:40 Alignment explanation

Indices: 159487727--159487856 Score: 172 Period size: 40 Copynumber: 3.2 Consensus size: 40 159487717 CGGAATATAA 159487727 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACT-TGCACAAATGCCTTCGGGTCTTAGC * ** * * 159487767 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC * * * 159487807 CCGGATATAGCCACTTGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC 159487847 CCGGATATAA 1 CCGGATATAA 159487857 TTTCCAGCAT Statistics Matches: 75, Mismatches: 14, Indels: 2 0.82 0.15 0.02 Matches are distributed among these distances: 40 74 0.99 41 1 0.01 ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAACCACTTGCACAAATGCCTTCGGGTCTTAGC Found at i:159487871 original size:40 final size:39 Alignment explanation

Indices: 159487743--159487893 Score: 153 Period size: 40 Copynumber: 3.8 Consensus size: 39 159487733 ATAACCATGT * * * 159487743 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-C ** * 159487783 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCACTT 1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-C * ** 159487823 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCC 1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACC * * 159487862 AGCATAATTGTCTTCGGG-CTTAGCCCGGATAT 1 -GCACAATTGCCTTCGGGTCTTAGCCCGGATAT 159487894 CATTCAATTT Statistics Matches: 94, Mismatches: 14, Indels: 7 0.82 0.12 0.06 Matches are distributed among these distances: 39 15 0.16 40 77 0.82 41 2 0.02 ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27 Consensus pattern (39 bp): GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACC Found at i:159487877 original size:80 final size:79 Alignment explanation

Indices: 159487727--159487893 Score: 205 Period size: 80 Copynumber: 2.1 Consensus size: 79 159487717 CGGAATATAA * 159487727 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATG 1 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATG 159487792 CCTTCGGGTCTTAGC 66 CCTTCGGG-CTTAGC * * * ** * 159487807 CCGGATATAGCCACT-TGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA 1 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA * 159487869 TTGTCTTCGGGCTTAGC 64 -TGCCTTCGGGCTTAGC 159487886 CCGGATAT 1 CCGGATAT 159487894 CATTCAATTT Statistics Matches: 76, Mismatches: 8, Indels: 7 0.84 0.09 0.08 Matches are distributed among these distances: 79 17 0.22 80 58 0.76 81 1 0.01 ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27 Consensus pattern (79 bp): CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATG CCTTCGGGCTTAGC Found at i:159495737 original size:40 final size:40 Alignment explanation

Indices: 159495692--159495780 Score: 117 Period size: 40 Copynumber: 2.2 Consensus size: 40 159495682 CGGAATATAA * 159495692 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACT-CGCACAAATGCCTTCGGGTCTTAGC * ** * 159495732 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCACTCGCACAAATGCCTTCGGGTCTTAGC 159495772 CCGGATATA 1 CCGGATATA 159495781 GCCAGCACAA Statistics Matches: 42, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 40 41 0.98 41 1 0.02 ACGTcount: A:0.25, C:0.27, G:0.25, T:0.24 Consensus pattern (40 bp): CCGGATATAACCACTCGCACAAATGCCTTCGGGTCTTAGC Found at i:159495803 original size:13 final size:13 Alignment explanation

Indices: 159495785--159495810 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 159495775 GATATAGCCA 159495785 GCACAATTGCCTT 1 GCACAATTGCCTT 159495798 GCACAATTGCCTT 1 GCACAATTGCCTT 159495811 CGGGTCTTAA 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:0.23, C:0.31, G:0.15, T:0.31 Consensus pattern (13 bp): GCACAATTGCCTT Found at i:159500647 original size:40 final size:40 Alignment explanation

Indices: 159500541--159500724 Score: 140 Period size: 40 Copynumber: 4.6 Consensus size: 40 159500531 TGCTGGAAAT * * * * * ** 159500541 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * 159500581 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * * * * 159500621 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * * * * * * 159500659 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGC-AGGTTAC 1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTCAC * * * 159500700 CATATCCGGGCTATGTCCCGAAGGC 1 TATATCCGGGCTAAGACCCGAAGGC 159500725 GTTTGAACGA Statistics Matches: 116, Mismatches: 25, Indels: 6 0.79 0.17 0.04 Matches are distributed among these distances: 38 1 0.01 39 30 0.26 40 85 0.73 ACGTcount: A:0.23, C:0.24, G:0.29, T:0.23 Consensus pattern (40 bp): TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC Found at i:159505811 original size:39 final size:39 Alignment explanation

Indices: 159505767--159506041 Score: 444 Period size: 39 Copynumber: 7.1 Consensus size: 39 159505757 ATTATATTAT * * 159505767 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC * * 159505806 CAGCACGAAGCCTGCGGGACTTTGGTCCGGATACATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC * * * 159505845 CAGCATGAAGCCTGCGGGACTTTGGCCCGGATATATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC * 159505884 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATAAATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC * * 159505923 CAGCAC-AAGCCTGCGGGACTTTGGCCCGGATATATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC * 159505961 TAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC 159506000 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC 1 CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC 159506039 CAG 1 CAG 159506042 TGTCTTGCAT Statistics Matches: 219, Mismatches: 16, Indels: 2 0.92 0.07 0.01 Matches are distributed among these distances: 38 35 0.16 39 184 0.84 ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22 Consensus pattern (39 bp): CAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTC Found at i:159505989 original size:116 final size:117 Alignment explanation

Indices: 159505759--159506041 Score: 462 Period size: 116 Copynumber: 2.4 Consensus size: 117 159505749 AACCCGAAAT * * 159505759 TATATTAT-CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTCCAGCACGAAGCCTGCGG 1 TATATT-TCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGG * * * 159505823 GACTTTGGTCCGGATACATTTCCAGCATGAAGCCTGCGGGACTTTGGCCCGGA 65 GACTTTGGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA * 159505876 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAAATTTCCAGCAC-AAGCCTGCGGG 1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGG * * 159505940 ACTTTGGCCCGGATATATTTCTAGCACGAAGCCTGCGGGACTTTAGCCCGGA 66 ACTTTGGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA * 159505992 TACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAG 1 TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAG 159506042 TGTCTTGCAT Statistics Matches: 155, Mismatches: 10, Indels: 3 0.92 0.06 0.02 Matches are distributed among these distances: 116 107 0.69 117 48 0.31 ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23 Consensus pattern (117 bp): TATATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTTCCAGCACGAAGCCTGCGGG ACTTTGGCCCGGATACATTTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGA Found at i:159510451 original size:15 final size:15 Alignment explanation

Indices: 159510428--159510458 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 159510418 TCAAAAATTC 159510428 CAATACAAAACATAT 1 CAATACAAAACATAT * 159510443 CAATCCAAAACATAT 1 CAATACAAAACATAT 159510458 C 1 C 159510459 TTTCATATTT 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:0.55, C:0.26, G:0.00, T:0.19 Consensus pattern (15 bp): CAATACAAAACATAT Found at i:159518711 original size:42 final size:42 Alignment explanation

Indices: 159518664--159518747 Score: 168 Period size: 42 Copynumber: 2.0 Consensus size: 42 159518654 CAGGATCCAT 159518664 TACTATATTAAAATAAAACACAGTTTAGAATAATCAGGAATC 1 TACTATATTAAAATAAAACACAGTTTAGAATAATCAGGAATC 159518706 TACTATATTAAAATAAAACACAGTTTAGAATAATCAGGAATC 1 TACTATATTAAAATAAAACACAGTTTAGAATAATCAGGAATC 159518748 ACCACACTAT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 42 42 1.00 ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29 Consensus pattern (42 bp): TACTATATTAAAATAAAACACAGTTTAGAATAATCAGGAATC Found at i:159523665 original size:27 final size:28 Alignment explanation

Indices: 159523635--159523734 Score: 121 Period size: 27 Copynumber: 3.5 Consensus size: 28 159523625 ATAGTGAGTC 159523635 CGCACACTTAGTGCTATAAAATC-AACT 1 CGCACACTTAGTGCTATAAAATCAAACT * * 159523662 CGCACACCTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATAAAATCAAACT * * * 159523690 CGCACACTTAGTGCTGTACAAATTTAAAACC 1 CGCACACTTAGTGCTATA-AAA--TCAAACT 159523721 CGCACACTTAGTGC 1 CGCACACTTAGTGC 159523735 AATCTCATGA Statistics Matches: 62, Mismatches: 7, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 27 21 0.34 28 20 0.32 29 2 0.03 31 19 0.31 ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25 Consensus pattern (28 bp): CGCACACTTAGTGCTATAAAATCAAACT Found at i:159524586 original size:7 final size:7 Alignment explanation

Indices: 159524576--159524600 Score: 50 Period size: 7 Copynumber: 3.6 Consensus size: 7 159524566 TCATCACCAC 159524576 AACATCA 1 AACATCA 159524583 AACATCA 1 AACATCA 159524590 AACATCA 1 AACATCA 159524597 AACA 1 AACA 159524601 AGAAGACAAC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 7 18 1.00 ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12 Consensus pattern (7 bp): AACATCA Found at i:159534072 original size:25 final size:25 Alignment explanation

Indices: 159534043--159534090 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 159534033 TTATAATATG * * * 159534043 AAAATGACCGTTTTGCCCCTAGGTA 1 AAAATGACCATTATACCCCTAGGTA 159534068 AAAATGACCATTATACCCCTAGG 1 AAAATGACCATTATACCCCTAGG 159534091 GTTTATGTAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25 Consensus pattern (25 bp): AAAATGACCATTATACCCCTAGGTA Found at i:159534159 original size:20 final size:20 Alignment explanation

Indices: 159534134--159534192 Score: 100 Period size: 20 Copynumber: 3.0 Consensus size: 20 159534124 TAAATATGGT 159534134 ATGTATGATATGCACATGAA 1 ATGTATGATATGCACATGAA * * 159534154 ATGTATGATACGCACATGAT 1 ATGTATGATATGCACATGAA 159534174 ATGTATGATATGCACATGA 1 ATGTATGATATGCACATGA 159534193 GGTAATCATA Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 36 1.00 ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31 Consensus pattern (20 bp): ATGTATGATATGCACATGAA Found at i:159534312 original size:47 final size:48 Alignment explanation

Indices: 159534243--159534361 Score: 172 Period size: 47 Copynumber: 2.5 Consensus size: 48 159534233 GAGGAAGTGA 159534243 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTAT-GCCCCAGTTA-T 1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTT-TGGCCCCAGTTATT * 159534290 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTGGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT * 159534338 AAAAGAGGC-TAGGCCTCCAGTTAT 1 AAAAG-GGCTTATGCC-CCAGTTAT 159534362 ATGATAAAGC Statistics Matches: 66, Mismatches: 2, Indels: 6 0.89 0.03 0.08 Matches are distributed among these distances: 46 1 0.02 47 43 0.65 48 11 0.17 49 11 0.17 ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26 Consensus pattern (48 bp): AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT Found at i:159534337 original size:24 final size:24 Alignment explanation

Indices: 159534243--159534361 Score: 154 Period size: 24 Copynumber: 5.0 Consensus size: 24 159534233 GAGGAAGTGA * 159534243 AAAAGGGCTTATGCCCCAGTTATC 1 AAAAGGGCTTATGCCCCAGTTATT * 159534267 GAAAGGGCTTATGCCCCAGTTA-T 1 AAAAGGGCTTATGCCCCAGTTATT 159534290 AAAAGGGCTTATGCCCCAGTTATT 1 AAAAGGGCTTATGCCCCAGTTATT * 159534314 GAAAGGGCTT-TGGCCCCAGTTATT 1 AAAAGGGCTTAT-GCCCCAGTTATT * 159534338 AAAAGAGGC-TAGGCCTCCAGTTAT 1 AAAAG-GGCTTATGCC-CCAGTTAT 159534362 ATGATAAAGC Statistics Matches: 84, Mismatches: 6, Indels: 9 0.85 0.06 0.09 Matches are distributed among these distances: 23 22 0.26 24 51 0.61 25 11 0.13 ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26 Consensus pattern (24 bp): AAAAGGGCTTATGCCCCAGTTATT Found at i:159534588 original size:31 final size:31 Alignment explanation

Indices: 159534553--159534654 Score: 123 Period size: 31 Copynumber: 3.1 Consensus size: 31 159534543 CGTTTACAGT 159534553 AAAGGCTTCGGCCCAGTAATATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA * 159534584 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA 1 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA * 159534622 AAAGGCTTCGGCCCAGTATTATGAAATATGA 1 AAAGGCTTCGGCCCAGTAATATGAAATATGA 159534653 AA 1 AA 159534655 TATGAAAAGG Statistics Matches: 61, Mismatches: 3, Indels: 14 0.78 0.04 0.18 Matches are distributed among these distances: 31 30 0.49 33 1 0.02 36 1 0.02 38 29 0.48 ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTAATATGAAATATGA Found at i:159534622 original size:38 final size:38 Alignment explanation

Indices: 159534570--159534677 Score: 189 Period size: 38 Copynumber: 2.8 Consensus size: 38 159534560 TCGGCCCAGT 159534570 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA 1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA * 159534608 AATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGA 1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA * 159534646 AATATGAAATATGAAAAGGGCTACGGCCCAGT 1 AATATGAAATATGAAAA-GGCTTCGGCCCAGT 159534678 GCATGATTGA Statistics Matches: 66, Mismatches: 3, Indels: 1 0.94 0.04 0.01 Matches are distributed among these distances: 38 53 0.80 39 13 0.20 ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23 Consensus pattern (38 bp): AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA Found at i:159542376 original size:25 final size:25 Alignment explanation

Indices: 159542347--159542394 Score: 69 Period size: 25 Copynumber: 1.9 Consensus size: 25 159542337 TTATAATATG * * * 159542347 AAAATGACCGTTTTGCCCCTAGGTA 1 AAAATGACCATTATACCCCTAGGTA 159542372 AAAATGACCATTATACCCCTAGG 1 AAAATGACCATTATACCCCTAGG 159542395 GTTTATGTAT Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 25 20 1.00 ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25 Consensus pattern (25 bp): AAAATGACCATTATACCCCTAGGTA Found at i:159542463 original size:20 final size:20 Alignment explanation

Indices: 159542438--159542496 Score: 100 Period size: 20 Copynumber: 3.0 Consensus size: 20 159542428 TAAATATGGT 159542438 ATGTATGATATGCACATGAA 1 ATGTATGATATGCACATGAA * * 159542458 ATGTATGATACGCACATGAT 1 ATGTATGATATGCACATGAA 159542478 ATGTATGATATGCACATGA 1 ATGTATGATATGCACATGA 159542497 GGTAATCATA Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 36 1.00 ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31 Consensus pattern (20 bp): ATGTATGATATGCACATGAA Found at i:159542576 original size:22 final size:22 Alignment explanation

Indices: 159542548--159542591 Score: 88 Period size: 22 Copynumber: 2.0 Consensus size: 22 159542538 AGGAAGTGAA 159542548 AAAGGGCTTATGCCCCAGTTAT 1 AAAGGGCTTATGCCCCAGTTAT 159542570 AAAGGGCTTATGCCCCAGTTAT 1 AAAGGGCTTATGCCCCAGTTAT 159542592 TTGAAGAAAG Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 22 22 1.00 ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27 Consensus pattern (22 bp): AAAGGGCTTATGCCCCAGTTAT Found at i:159542626 original size:28 final size:28 Alignment explanation

Indices: 159542548--159542626 Score: 82 Period size: 28 Copynumber: 3.0 Consensus size: 28 159542538 AGGAAGTGAA 159542548 AAAGGGCTTATGCCCCAGTTA-T----- 1 AAAGGGCTTATGCCCCAGTTATTAAAAG ** 159542570 AAAGGGCTTATGCCCCAGTTATTTGAAG 1 AAAGGGCTTATGCCCCAGTTATTAAAAG 159542598 AAAGGGCTT-TGGCCCCAGTTATTAAAAG 1 AAAGGGCTTAT-GCCCCAGTTATTAAAAG 159542626 A 1 A 159542627 GGCTAGGCCT Statistics Matches: 48, Mismatches: 2, Indels: 8 0.83 0.03 0.14 Matches are distributed among these distances: 22 21 0.44 23 1 0.02 27 1 0.02 28 25 0.52 ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27 Consensus pattern (28 bp): AAAGGGCTTATGCCCCAGTTATTAAAAG Found at i:159542892 original size:31 final size:31 Alignment explanation

Indices: 159542836--159542936 Score: 132 Period size: 38 Copynumber: 3.1 Consensus size: 31 159542826 CGTTTACAGT 159542836 AAAGGCTTCGGCCCAGTA-TATGAAATATGA 1 AAAGGCTTCGGCCCAGTATTATGAAATATGA 159542866 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA 1 AAAGGCTTCGGCCCAGTATTATG-AA-AT-----ATGA 159542904 AAAGGCTTCGGCCCAGTATTATGAAATATGA 1 AAAGGCTTCGGCCCAGTATTATGAAATATGA 159542935 AA 1 AA 159542937 TATGAAAAGG Statistics Matches: 63, Mismatches: 0, Indels: 15 0.81 0.00 0.19 Matches are distributed among these distances: 30 18 0.29 31 10 0.16 32 2 0.03 33 2 0.03 36 2 0.03 37 2 0.03 38 27 0.43 ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24 Consensus pattern (31 bp): AAAGGCTTCGGCCCAGTATTATGAAATATGA Found at i:159542904 original size:38 final size:38 Alignment explanation

Indices: 159542853--159542959 Score: 187 Period size: 38 Copynumber: 2.8 Consensus size: 38 159542843 TCGGCCCAGT 159542853 ATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGAA 1 ATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGAA * 159542891 ATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGAA 1 ATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGAA * 159542929 ATATGAAATATGAAAAGGGCTACGGCCCAGT 1 ATATGAAATATGAAAA-GGCTTCGGCCCAGT 159542960 GCATGATTGA Statistics Matches: 65, Mismatches: 3, Indels: 1 0.94 0.04 0.01 Matches are distributed among these distances: 38 52 0.80 39 13 0.20 ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23 Consensus pattern (38 bp): ATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGAA Found at i:159549090 original size:40 final size:39 Alignment explanation

Indices: 159549045--159549252 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 159549035 CGGAATACAA * 159549045 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 159549085 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 159549125 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 159549165 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 159549205 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 159549245 CCGGATAT 1 CCGGATAT 159549253 CATTCAATTG Statistics Matches: 141, Mismatches: 24, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 39 4 0.03 40 134 0.95 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:159549185 original size:80 final size:80 Alignment explanation

Indices: 159549045--159549251 Score: 238 Period size: 80 Copynumber: 2.6 Consensus size: 80 159549035 CGGAATACAA * * * 159549045 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 159549109 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 159549125 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 159549189 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 159549205 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 159549252 TCATTCAATT Statistics Matches: 107, Mismatches: 18, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 79 3 0.03 80 102 0.95 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:159557004 original size:40 final size:39 Alignment explanation

Indices: 159556959--159557163 Score: 200 Period size: 40 Copynumber: 5.2 Consensus size: 39 159556949 CGGAATACAA * 159556959 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 159556999 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 159557039 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * * 159557079 CCGGATGT-AGCACTAGCAC-AATGCCTTCGGGTCTCAAC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC ** * * * 159557117 CC-GATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 159557156 CCGGATAT 1 CCGGATAT 159557164 CATTCAATTG Statistics Matches: 138, Mismatches: 23, Indels: 8 0.82 0.14 0.05 Matches are distributed among these distances: 37 4 0.03 38 28 0.20 39 24 0.17 40 82 0.59 ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:159559056 original size:24 final size:24 Alignment explanation

Indices: 159559019--159559099 Score: 128 Period size: 24 Copynumber: 3.4 Consensus size: 24 159559009 CTAGAGGCCT * * 159559019 AGCCTCTTTGAATAACTGGGGCAAA 1 AGCC-CTTTTAATAACTGGGGCATA 159559044 AGCCCTTTTAATAACTGGGGCATA 1 AGCCCTTTTAATAACTGGGGCATA 159559068 AGCCC-TTTAATAACTGGGGCATA 1 AGCCCTTTTAATAACTGGGGCATA 159559091 AGCCCTTTT 1 AGCCCTTTT 159559100 TCACTTCCTC Statistics Matches: 53, Mismatches: 2, Indels: 3 0.91 0.03 0.05 Matches are distributed among these distances: 23 23 0.43 24 26 0.49 25 4 0.08 ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28 Consensus pattern (24 bp): AGCCCTTTTAATAACTGGGGCATA Found at i:159559080 original size:23 final size:23 Alignment explanation

Indices: 159559019--159559098 Score: 124 Period size: 23 Copynumber: 3.3 Consensus size: 23 159559009 CTAGAGGCCT * 159559019 AGCCTCTTTGAATAACTGGGGCAAA 1 AGCC-CTTT-AATAACTGGGGCATA 159559044 AGCCCTTTTAATAACTGGGGCATA 1 AGCCC-TTTAATAACTGGGGCATA 159559068 AGCCCTTTAATAACTGGGGCATA 1 AGCCCTTTAATAACTGGGGCATA 159559091 AGCCCTTT 1 AGCCCTTT 159559099 TTCACTTCCT Statistics Matches: 53, Mismatches: 1, Indels: 4 0.91 0.02 0.07 Matches are distributed among these distances: 23 26 0.49 24 20 0.38 25 7 0.13 ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28 Consensus pattern (23 bp): AGCCCTTTAATAACTGGGGCATA Found at i:159559216 original size:20 final size:20 Alignment explanation

Indices: 159559149--159559215 Score: 107 Period size: 20 Copynumber: 3.4 Consensus size: 20 159559139 TTATGATTAC 159559149 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT 159559169 ATCATGTGCATATCATACAT 1 ATCATGTGCATATCATACAT * * 159559189 GTCATGTTCATATCATACAT 1 ATCATGTGCATATCATACAT * 159559209 ACCATGT 1 ATCATGT 159559216 TTATCAAAAT Statistics Matches: 43, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 20 43 1.00 ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36 Consensus pattern (20 bp): ATCATGTGCATATCATACAT Found at i:159566866 original size:31 final size:31 Alignment explanation

Indices: 159566828--159566891 Score: 101 Period size: 31 Copynumber: 2.1 Consensus size: 31 159566818 CCATTTCATA 159566828 TTTCATATTTCATAACACTAGGCCGAAGCCT 1 TTTCATATTTCATAACACTAGGCCGAAGCCT ** * 159566859 TTTCATATTTCATATTACTGGGCCGAAGCCT 1 TTTCATATTTCATAACACTAGGCCGAAGCCT 159566890 TT 1 TT 159566892 ACTATAAACG Statistics Matches: 30, Mismatches: 3, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38 Consensus pattern (31 bp): TTTCATATTTCATAACACTAGGCCGAAGCCT Found at i:159573165 original size:19 final size:19 Alignment explanation

Indices: 159573128--159573165 Score: 51 Period size: 19 Copynumber: 2.0 Consensus size: 19 159573118 TTTAAAAGGT * 159573128 TAAAAGTGTAATAAGTAAA 1 TAAAAGTGTAATAAATAAA 159573147 TAAAAGT-TAATATAATAAA 1 TAAAAGTGTAATA-AATAAA 159573166 AACAAAAGAA Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 18 5 0.29 19 12 0.71 ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29 Consensus pattern (19 bp): TAAAAGTGTAATAAATAAA Found at i:159573949 original size:41 final size:41 Alignment explanation

Indices: 159573904--159574074 Score: 198 Period size: 41 Copynumber: 4.2 Consensus size: 41 159573894 TTTGTGATTA * * * 159573904 CCTGTTTGTACTTTGGTACCCCTGAATCGCACATACATGCC 1 CCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTGCC ** * 159573945 CCTGTTTGTACTTTAGTACCCCTGAATTGCACATACTTGCC 1 CCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTGCC * * * * * * 159573986 CTTGTTTGTACTTCGGTATCCCTAAATTGCATATATGTACC 1 CCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTGCC * * * * 159574027 CCTGTTTGTACTTCGATACCTCTGAATTGCATATATGTGCC 1 CCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTGCC 159574068 CCTGTTT 1 CCTGTTT 159574075 ACACTCAGAT Statistics Matches: 112, Mismatches: 18, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 41 112 1.00 ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38 Consensus pattern (41 bp): CCTGTTTGTACTTCGGTACCCCTGAATTGCACATACGTGCC Found at i:159576329 original size:8 final size:8 Alignment explanation

Indices: 159576316--159576348 Score: 50 Period size: 8 Copynumber: 4.2 Consensus size: 8 159576306 TGCAAGTTAA 159576316 TATTATTT 1 TATTATTT 159576324 TATTATTT 1 TATTATTT 159576332 TATTA-TT 1 TATTATTT * 159576339 TATTAATT 1 TATTATTT 159576347 TA 1 TA 159576349 CTTTTTCTTT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 7 7 0.29 8 17 0.71 ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70 Consensus pattern (8 bp): TATTATTT Found at i:159580235 original size:40 final size:40 Alignment explanation

Indices: 159580109--159580237 Score: 145 Period size: 40 Copynumber: 3.2 Consensus size: 40 159580099 ATGCTGGAAA * * * 159580109 TTATATCCGGGTTAAGA-CCGAAGGCAATTGTGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * * * * ** 159580148 CTACATCCAGGCTAAGACCCGAAGGCATTCGTGCGAGTCA 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG * 159580188 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG 159580228 TTATATCCGG 1 TTATATCCGG 159580238 TTATATTCCG Statistics Matches: 71, Mismatches: 17, Indels: 3 0.78 0.19 0.03 Matches are distributed among these distances: 39 14 0.20 40 57 0.80 ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG Found at i:159588767 original size:28 final size:28 Alignment explanation

Indices: 159588702--159588802 Score: 114 Period size: 28 Copynumber: 3.5 Consensus size: 28 159588692 ATAGTGAATC * 159588702 CGCACACTTAGTGCTATATGTATTC-AACT 1 CGCACACTTAGTGCTATA--TAATCAAACT 159588731 CGCACACTTAGTGCTATATAATCAAACT 1 CGCACACTTAGTGCTATATAATCAAACT * * * * 159588759 CGCACACTTAGTGCTGTACAATTTTAAACC 1 CGCACACTTAGTGCTATATAA--TCAAACT 159588789 CGCACACTTAGTGC 1 CGCACACTTAGTGC 159588803 CAATCTTGTC Statistics Matches: 64, Mismatches: 5, Indels: 5 0.86 0.07 0.07 Matches are distributed among these distances: 27 4 0.06 28 23 0.36 29 18 0.28 30 19 0.30 ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30 Consensus pattern (28 bp): CGCACACTTAGTGCTATATAATCAAACT Found at i:159592640 original size:41 final size:41 Alignment explanation

Indices: 159592595--159592712 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 159592585 TGAAAGATAA 159592595 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 159592636 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 159592666 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 159592707 ATGTAG 1 ATGTAG 159592713 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:159592651 original size:71 final size:71 Alignment explanation

Indices: 159592563--159592726 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 159592553 GAGATGTATC 159592563 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 159592628 AGGACA 66 AGGACA 159592634 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 159592699 AGGACA 66 AGGACA 159592705 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 159592727 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:159600215 original size:41 final size:41 Alignment explanation

Indices: 159600170--159600287 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 159600160 TGAAAGATAA 159600170 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 159600211 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 159600241 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 159600282 ATGTAG 1 ATGTAG 159600288 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:159600226 original size:71 final size:71 Alignment explanation

Indices: 159600138--159600301 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 159600128 GAGATGTATC 159600138 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 159600203 AGGACA 66 AGGACA 159600209 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 159600274 AGGACA 66 AGGACA 159600280 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 159600302 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:159607196 original size:40 final size:40 Alignment explanation

Indices: 159607147--159607394 Score: 142 Period size: 40 Copynumber: 6.2 Consensus size: 40 159607137 TCGAATTTAA * * * 159607147 CCGGATATAGCGACTCGCTCGATTGTCTTCGGGACA-TAGC 1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGA-ATTAGC * * * 159607187 CCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTAGC 1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC * * ** * * * * 159607227 CCGTATTTAGTAACTCACACAAATGCCTTCGGGACTTAAC 1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC * * * ** * * * 159607267 CCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACTTAAC 1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC * * * ** * 159607307 CCGGTTTTGGTAACTCGCACAAATGCCTTCGGGAATT-GAC 1 CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAG-C * * ** * 159607347 CCGGATTTAGTC-ACTTAGCACAAAAGCCTTCGGGACTTAGC 1 CCGGATATAG-CGAC-TCGCACAATTGCCTTCGGGAATTAGC 159607388 CCGGATA 1 CCGGATA 159607395 CCATTCGAAT Statistics Matches: 175, Mismatches: 28, Indels: 9 0.83 0.13 0.04 Matches are distributed among these distances: 39 1 0.01 40 146 0.83 41 27 0.15 42 1 0.01 ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27 Consensus pattern (40 bp): CCGGATATAGCGACTCGCACAATTGCCTTCGGGAATTAGC Found at i:159607285 original size:80 final size:79 Alignment explanation

Indices: 159607173--159607390 Score: 256 Period size: 80 Copynumber: 2.7 Consensus size: 79 159607163 GCTCGATTGT * * * * * * * 159607173 CTTCGGGACATAGCCCGGTTATAGTGATTCGCACAATTGCCTTCGGGAATTAGCCCGTATTTAGT 1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGT-TTTAGT 159607238 AACTCACACAAATGC 65 AACTCACACAAATGC * * * 159607253 CTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGTTTTGGT 1 CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-GTTTTAGT * 159607318 AACTCGCACAAATGC 65 AACTCACACAAATGC * * * * * * 159607333 CTTCGGGAATTGACCCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCG 1 CTTCGGGACTTAACCCGGTTTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG 159607391 GATACCATTC Statistics Matches: 117, Mismatches: 19, Indels: 4 0.84 0.14 0.03 Matches are distributed among these distances: 80 90 0.77 81 27 0.23 ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27 Consensus pattern (79 bp): CTTCGGGACTTAACCCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGTTTTAGTA ACTCACACAAATGC Found at i:159609281 original size:40 final size:40 Alignment explanation

Indices: 159609236--159609347 Score: 118 Period size: 40 Copynumber: 2.8 Consensus size: 40 159609226 ATTATGTTCG ** 159609236 GCACTAAGTGTGCAATTTGAAATAGCTTCGTTTATAAATA 1 GCACTAAGTGTGCAATTTGAAATAGCTTCGGCTATAAATA * ** * 159609276 GCACTAAGTGTGCGAATTAG-AATAGCTTCGGCTATATGTG 1 GCACTAAGTGTGC-AATTTGAAATAGCTTCGGCTATAAATA * * * 159609316 GCACTAAGTGTGAAATATTGAGATAGTTTCGG 1 GCACTAAGTGTGCAAT-TTGAAATAGCTTCGG 159609348 TTCAATATGA Statistics Matches: 59, Mismatches: 10, Indels: 5 0.80 0.14 0.07 Matches are distributed among these distances: 39 3 0.05 40 42 0.71 41 14 0.24 ACGTcount: A:0.31, C:0.12, G:0.24, T:0.32 Consensus pattern (40 bp): GCACTAAGTGTGCAATTTGAAATAGCTTCGGCTATAAATA Found at i:159609378 original size:44 final size:41 Alignment explanation

Indices: 159609277--159609391 Score: 101 Period size: 44 Copynumber: 2.8 Consensus size: 41 159609267 TTATAAATAG * * 159609277 CACTAAGTGTGCGA-ATTAGAATAGCTTCGGCTATATGTGG 1 CACTAAGTGTGCGATATTAGAATAGCTTCGGCAATATGTGA ** * 159609317 CACTAAGTGTGAAATATT-GAGATAGTTTCGGTTCAATATGATGA 1 CACTAAGTGTGCGATATTAGA-ATAGCTTCGG--CAATATG-TGA * ** 159609361 CATTAAGTGTGCGATATT-TTATAGCTTCGGC 1 CACTAAGTGTGCGATATTAGAATAGCTTCGGC 159609392 TAGATTATTG Statistics Matches: 59, Mismatches: 11, Indels: 9 0.75 0.14 0.11 Matches are distributed among these distances: 40 14 0.24 41 13 0.22 43 15 0.25 44 17 0.29 ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34 Consensus pattern (41 bp): CACTAAGTGTGCGATATTAGAATAGCTTCGGCAATATGTGA Found at i:159613577 original size:5 final size:5 Alignment explanation

Indices: 159613567--159613692 Score: 109 Period size: 5 Copynumber: 25.4 Consensus size: 5 159613557 GGTTGTTACT * * * 159613567 ATATG ATATG ATATG ATATG ATATG ATATG TTAGG ATATG ATATA ATATG 1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG * * *** 159613617 ATATG AT-TCA ATATG ATATG ATAT- AGTGTG ATATG -TCCA ATATG AT-TCG 1 ATATG ATAT-G ATATG ATATG ATATG A-TATG ATATG ATATG ATATG ATAT-G 159613666 ATATG ATATG ATAT- AGTATG ATATG AT 1 ATATG ATATG ATATG A-TATG ATATG AT 159613693 CCGATACGTT Statistics Matches: 96, Mismatches: 16, Indels: 18 0.74 0.12 0.14 Matches are distributed among these distances: 4 5 0.05 5 87 0.91 6 4 0.04 ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40 Consensus pattern (5 bp): ATATG Found at i:159615554 original size:20 final size:20 Alignment explanation

Indices: 159615525--159615614 Score: 53 Period size: 20 Copynumber: 4.5 Consensus size: 20 159615515 AGCTGTGCCC * 159615525 CTATTCGCACTTCGGTGTCT 1 CTATTTGCACTTCGGTGTCT * * 159615545 CTATTTGCACGTCTGTG-CT 1 CTATTTGCACTTCGGTGTCT * * 159615564 CCTGTTCGCAC-TCTGGTGTC- 1 -CTATTTGCACTTC-GGTGTCT * * 159615584 CT-TGTATACACTTTGGTGTCT 1 CTAT-T-TGCACTTCGGTGTCT 159615605 CTATTTGCAC 1 CTATTTGCAC 159615615 ATTTATGCTC Statistics Matches: 52, Mismatches: 10, Indels: 16 0.67 0.13 0.21 Matches are distributed among these distances: 18 1 0.02 19 7 0.13 20 38 0.73 21 5 0.10 22 1 0.02 ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41 Consensus pattern (20 bp): CTATTTGCACTTCGGTGTCT Found at i:159615585 original size:19 final size:19 Alignment explanation

Indices: 159615524--159615585 Score: 56 Period size: 20 Copynumber: 3.2 Consensus size: 19 159615514 TAGCTGTGCC 159615524 CCTATTCGCACT-TCGGTGT 1 CCTATTCGCACTCT-GGTGT * 159615543 CTCTATTTGCACGTCT-GTGCT 1 C-CTATTCGCAC-TCTGGTG-T * 159615564 CCTGTTCGCACTCTGGTGT 1 CCTATTCGCACTCTGGTGT 159615583 CCT 1 CCT 159615586 TGTATACACT Statistics Matches: 35, Mismatches: 3, Indels: 10 0.73 0.06 0.21 Matches are distributed among these distances: 19 8 0.23 20 23 0.66 21 3 0.09 22 1 0.03 ACGTcount: A:0.08, C:0.32, G:0.21, T:0.39 Consensus pattern (19 bp): CCTATTCGCACTCTGGTGT Found at i:159615605 original size:60 final size:60 Alignment explanation

Indices: 159615532--159615707 Score: 217 Period size: 60 Copynumber: 2.9 Consensus size: 60 159615522 CCCCTATTCG * * * * * 159615532 CACTTCGGTGTCTCTATTTGCACGTCTGTGCTCCTGTTCGCACTCTGGTGTCCTTGTATA 1 CACTTTGGTGTCTCTATTTGCACATTTGTGCTCCTGTTCGCACTCTGGTGCCCCTGTATA * * * * 159615592 CACTTTGGTGTCTCTATTTGCACATTTATGCTCCTATTCACACTCTAGTGCCCCTGTATA 1 CACTTTGGTGTCTCTATTTGCACATTTGTGCTCCTGTTCGCACTCTGGTGCCCCTGTATA * * * * * * 159615652 CACTTTGGTGTCCCTGTTTGCACATTTGTTCCCCTGTTGGCACTTTGGTGCCCCTG 1 CACTTTGGTGTCTCTATTTGCACATTTGTGCTCCTGTTCGCACTCTGGTGCCCCTG 159615708 ACTGTATGTA Statistics Matches: 97, Mismatches: 19, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 60 97 1.00 ACGTcount: A:0.12, C:0.29, G:0.19, T:0.40 Consensus pattern (60 bp): CACTTTGGTGTCTCTATTTGCACATTTGTGCTCCTGTTCGCACTCTGGTGCCCCTGTATA Found at i:159615705 original size:20 final size:19 Alignment explanation

Indices: 159615639--159615707 Score: 68 Period size: 20 Copynumber: 3.5 Consensus size: 19 159615629 TCACACTCTA * 159615639 GTGCCCCTGTATACACTTTG 1 GTGCCCCTGT-TGCACTTTG * 159615659 GTGTCCCTGTTTGCACATTT- 1 GTGCCCCTG-TTGCAC-TTTG * 159615679 GTTCCCCTGTTGGCACTTTG 1 GTGCCCCTGTT-GCACTTTG 159615699 GTGCCCCTG 1 GTGCCCCTG 159615708 ACTGTATGTA Statistics Matches: 40, Mismatches: 5, Indels: 8 0.75 0.09 0.15 Matches are distributed among these distances: 19 5 0.12 20 31 0.77 21 4 0.10 ACGTcount: A:0.09, C:0.30, G:0.23, T:0.38 Consensus pattern (19 bp): GTGCCCCTGTTGCACTTTG Found at i:159619852 original size:21 final size:22 Alignment explanation

Indices: 159619826--159619866 Score: 66 Period size: 22 Copynumber: 1.9 Consensus size: 22 159619816 TAGAATAATT 159619826 ACTAAA-CACATCATTTTGTAA 1 ACTAAAGCACATCATTTTGTAA * 159619847 ACTAAAGCACATTATTTTGT 1 ACTAAAGCACATCATTTTGT 159619867 TAATCCTTTC Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 21 6 0.33 22 12 0.67 ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37 Consensus pattern (22 bp): ACTAAAGCACATCATTTTGTAA Found at i:159621388 original size:44 final size:44 Alignment explanation

Indices: 159621282--159621393 Score: 122 Period size: 44 Copynumber: 2.6 Consensus size: 44 159621272 CGTACAACGA *** * * 159621282 CAACGTCCCAGACGTGGTCTTACA-TGTAATCACATATCGATGC 1 CAACGTCCCAGACGTGGTCTTACACAAAAATCACAAATCGACGC * 159621325 C-ACTGTCCCAGACAG-GGTCTTACACAAAAATTACAAATCGACGC 1 CAAC-GTCCCAGAC-GTGGTCTTACACAAAAATCACAAATCGACGC * 159621369 CAACGTCCTAGACGTGGTCTTACAC 1 CAACGTCCCAGACGTGGTCTTACAC 159621394 GAATCACATA Statistics Matches: 57, Mismatches: 7, Indels: 9 0.78 0.10 0.12 Matches are distributed among these distances: 42 2 0.04 43 20 0.35 44 33 0.58 45 2 0.04 ACGTcount: A:0.30, C:0.29, G:0.18, T:0.22 Consensus pattern (44 bp): CAACGTCCCAGACGTGGTCTTACACAAAAATCACAAATCGACGC Found at i:159627444 original size:40 final size:40 Alignment explanation

Indices: 159627378--159627544 Score: 169 Period size: 40 Copynumber: 4.2 Consensus size: 40 159627368 AAATTGAATG * * * 159627378 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 159627417 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * 159627457 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * ** * 159627497 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT 159627537 ATATCCGG 1 ATATCCGG 159627545 TTATATTCCG Statistics Matches: 105, Mismatches: 18, Indels: 9 0.80 0.14 0.07 Matches are distributed among these distances: 39 16 0.15 40 87 0.83 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:159635446 original size:40 final size:40 Alignment explanation

Indices: 159635380--159635546 Score: 169 Period size: 40 Copynumber: 4.2 Consensus size: 40 159635370 AAATTGAATG * * * 159635380 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 159635419 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * 159635459 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * ** * 159635499 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT 159635539 ATATCCGG 1 ATATCCGG 159635547 TTATATTCCG Statistics Matches: 105, Mismatches: 18, Indels: 9 0.80 0.14 0.07 Matches are distributed among these distances: 39 16 0.15 40 87 0.83 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:159642998 original size:40 final size:40 Alignment explanation

Indices: 159642953--159643120 Score: 185 Period size: 40 Copynumber: 4.2 Consensus size: 40 159642943 CGGAATATAA 159642953 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC * * * * 159642993 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * 159643033 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC ** * * * * * 159643073 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC 159643113 CCGGATAT 1 CCGGATAT 159643121 CATTCAATTT Statistics Matches: 107, Mismatches: 20, Indels: 2 0.83 0.16 0.02 Matches are distributed among these distances: 39 1 0.01 40 106 0.99 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (40 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC Found at i:159646761 original size:40 final size:40 Alignment explanation

Indices: 159646703--159646987 Score: 282 Period size: 40 Copynumber: 7.2 Consensus size: 40 159646693 TTCGGAATTT * * * * * 159646703 ACCCGGATATAGCT-ACTCGTTCAAACGCCTTTGGGACATA 1 ACCCGGATTTAG-TAACTCGCTCAAATGCCTTCGGGACTTA * 159646743 GCCCGG-TTATAGTAACTCGCAT-AAATGCCTTCGGGACTTA 1 ACCCGGATT-TAGTAACTCGC-TCAAATGCCTTCGGGACTTA * 159646783 ACCCGGATTTAGTAACTCG-TATAAATGCCTTCGGGACTTA 1 ACCCGGATTTAGTAACTCGCT-CAAATGCCTTCGGGACTTA * 159646823 ACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTA 1 ACCCGGATTTAGTAACTCGCTCAAATGCCTTCGGGACTTA * 159646863 ACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTA 1 ACCCGGATTTAGTAACTCGCTCAAATGCCTTCGGGACTTA * * 159646902 GCCCGGGA-TTAGTAACTCGCACAAATGCCTTC-GGATCTTA 1 ACCC-GGATTTAGTAACTCGCTCAAATGCCTTCGGGA-CTTA ** * * * * 159646942 GTCCGGATATAGTCACTTAGCACAAA-GCCTTC-GGACTTA 1 ACCCGGATTTAGTAAC-TCGCTCAAATGCCTTCGGGACTTA * 159646981 GCCCGGA 1 ACCCGGA 159646988 CATCATTCGA Statistics Matches: 218, Mismatches: 15, Indels: 25 0.84 0.06 0.10 Matches are distributed among these distances: 38 3 0.01 39 46 0.21 40 158 0.72 41 11 0.05 ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26 Consensus pattern (40 bp): ACCCGGATTTAGTAACTCGCTCAAATGCCTTCGGGACTTA Found at i:159646836 original size:80 final size:80 Alignment explanation

Indices: 159646703--159646987 Score: 325 Period size: 80 Copynumber: 3.6 Consensus size: 80 159646693 TTCGGAATTT * * * * * 159646703 ACCCGGATATAGCT-ACTCGT-TCAAACGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCAT 1 ACCCGGATTTAG-TAACTCGTAT-AAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCAC 159646765 AAATGCCTTCGGGACTTA 63 AAATGCCTTCGGGACTTA * 159646783 ACCCGGATTTAGTAACTCGTATAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAA 1 ACCCGGATTTAGTAACTCGTATAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA 159646848 TGCCTTCGGGACTTA 66 TGCCTTCGGGACTTA * * 159646863 ACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGGA-TTAGTAACTCGCACAA 1 ACCCGGATTTAGTAACTCGTATAAATGCCTTCGGGACTTAGCCC-GGATTTAGTAACTCGCACAA 159646926 ATGCCTTC-GGATCTTA 65 ATGCCTTCGGGA-CTTA ** * * * * * 159646942 GTCCGGATATAGTCACTTAGCACAAA-GCCTTC-GGACTTAGCCCGGA 1 ACCCGGATTTAGTAAC-TCGTATAAATGCCTTCGGGACTTAGCCCGGA 159646988 CATCATTCGA Statistics Matches: 184, Mismatches: 14, Indels: 16 0.86 0.07 0.07 Matches are distributed among these distances: 78 8 0.04 79 62 0.34 80 111 0.60 81 3 0.02 ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26 Consensus pattern (80 bp): ACCCGGATTTAGTAACTCGTATAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAA TGCCTTCGGGACTTA Found at i:159649993 original size:244 final size:244 Alignment explanation

Indices: 159649644--159650132 Score: 951 Period size: 244 Copynumber: 2.0 Consensus size: 244 159649634 GCATCAATAC 159649644 GCAACCTAACCCAAGTAGGGAGGCGTCACTATAGATGACAAACTCTTTGCCTGATTCGGGCTACA 1 GCAACCTAACCCAAGTAGGGAGGCGTCACTATAGATGACAAACTCTTTGCCTGATTCGGGCTACA 159649709 CTAAGATTGGAGCTTCAGTCAAATAAGTTTTCAGTTGATCAAAACTTTTCTGACATTTTTCCGTC 66 CTAAGATTGGAGCTTCAGTCAAATAAGTTTTCAGTTGATCAAAACTTTTCTGACATTTTTCCGTC 159649774 CATTCGAACTTAACATCTTTTTGAAGTAGCTTCGTCATGGGTGTGGCTATCATCGAGAAACCTTT 131 CATTCGAACTTAACATCTTTTTGAAGTAGCTTCGTCATGGGTGTGGCTATCATCGAGAAACCTTT * 159649839 TACAAACCGTCGGTAGTAACTGGCAAGTCCCAAAAAGCTCCGAACCTCA 196 TACAAACCGTCGGTAGTAACCGGCAAGTCCCAAAAAGCTCCGAACCTCA * 159649888 GCAACCTAACCCAAGTAGGGAGGCGTCACTATAGATGACAAACTCTTTGCCTGATTCGGGCTGCA 1 GCAACCTAACCCAAGTAGGGAGGCGTCACTATAGATGACAAACTCTTTGCCTGATTCGGGCTACA 159649953 CTAAGATTGGAGCTTCAGTCAAATAAGTTTTCAGTTGATCAAAACTTTTCTGACATTTTTCCGTC 66 CTAAGATTGGAGCTTCAGTCAAATAAGTTTTCAGTTGATCAAAACTTTTCTGACATTTTTCCGTC 159650018 CATTCGAACTTAACATCTTTTTGAAGTAGCTTCGTCATGGGTGTGGCTATCATCGAGAAACCTTT 131 CATTCGAACTTAACATCTTTTTGAAGTAGCTTCGTCATGGGTGTGGCTATCATCGAGAAACCTTT * 159650083 TACAAACCGTCGGTAGTAACCGGCAAGTCCCAAAAAGCTTCGAACCTCA 196 TACAAACCGTCGGTAGTAACCGGCAAGTCCCAAAAAGCTCCGAACCTCA 159650132 G 1 G 159650133 TAATATTTCT Statistics Matches: 242, Mismatches: 3, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 244 242 1.00 ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29 Consensus pattern (244 bp): GCAACCTAACCCAAGTAGGGAGGCGTCACTATAGATGACAAACTCTTTGCCTGATTCGGGCTACA CTAAGATTGGAGCTTCAGTCAAATAAGTTTTCAGTTGATCAAAACTTTTCTGACATTTTTCCGTC CATTCGAACTTAACATCTTTTTGAAGTAGCTTCGTCATGGGTGTGGCTATCATCGAGAAACCTTT TACAAACCGTCGGTAGTAACCGGCAAGTCCCAAAAAGCTCCGAACCTCA Found at i:159655790 original size:47 final size:47 Alignment explanation

Indices: 159655710--159655867 Score: 167 Period size: 47 Copynumber: 3.4 Consensus size: 47 159655700 ATTGTCTAAG * * * * * 159655710 CTTATGACACATTAAGTAGCTGTATTAACTAGAACACATTAAATAAA 1 CTTAAGACATATTAAATAGCTGTACTAATTAGAACACATTAAATAAA * * 159655757 CTTAAGACATATTAAATGGCTGTACTAATTAGAACACATT-AATTAA 1 CTTAAGACATATTAAATAGCTGTACTAATTAGAACACATTAAATAAA * * * * * 159655803 CTTAAGACATATTAATTA-CCGAATCTAATTAGAACATATTAAATAGA 1 CTTAAGACATATTAAATAGCTGTA-CTAATTAGAACACATTAAATAAA * * 159655850 CTCAAGGCATATTAAATA 1 CTTAAGACATATTAAATA 159655868 CTTAAACTAA Statistics Matches: 92, Mismatches: 17, Indels: 4 0.81 0.15 0.04 Matches are distributed among these distances: 45 3 0.03 46 36 0.39 47 53 0.58 ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31 Consensus pattern (47 bp): CTTAAGACATATTAAATAGCTGTACTAATTAGAACACATTAAATAAA Found at i:159655831 original size:46 final size:45 Alignment explanation

Indices: 159655739--159655864 Score: 135 Period size: 46 Copynumber: 2.7 Consensus size: 45 159655729 CTGTATTAAC * * * * 159655739 TAGAACACATTAAATAAACTTAAGACATATTAAATGGCTGTACTAAT 1 TAGAACACATT-AATTAACTTAAGACATATT-AATGACCGAACTAAT * 159655786 TAGAACACATTAATTAACTTAAGACATATTAATTACCGAATCTAAT 1 TAGAACACATTAATTAACTTAAGACATATTAATGACCGAA-CTAAT * * * * 159655832 TAGAACATATTAAATAGACTCAAGGCATATTAA 1 TAGAACACATTAATTA-ACTTAAGACATATTAA 159655865 ATACTTAAAC Statistics Matches: 68, Mismatches: 9, Indels: 4 0.84 0.11 0.05 Matches are distributed among these distances: 45 6 0.09 46 37 0.54 47 25 0.37 ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30 Consensus pattern (45 bp): TAGAACACATTAATTAACTTAAGACATATTAATGACCGAACTAAT Found at i:159658417 original size:28 final size:28 Alignment explanation

Indices: 159658329--159658418 Score: 101 Period size: 28 Copynumber: 3.2 Consensus size: 28 159658319 CTACAAAGGT * 159658329 TTCCTTATCCAAAGATTGCCAAAATGGC 1 TTCCTTATCCAAAGATTTCCAAAATGGC * * * 159658357 TTCATTATCCAGAGATTT-CAACAAAGGC 1 TTCCTTATCCAAAGATTTCCAA-AATGGC * * 159658385 TTCCTTATCTAAAGATTTCCATAATGGC 1 TTCCTTATCCAAAGATTTCCAAAATGGC * 159658413 GTCCTT 1 TTCCTT 159658419 TTCATTAAGT Statistics Matches: 50, Mismatches: 10, Indels: 4 0.78 0.16 0.06 Matches are distributed among these distances: 27 3 0.06 28 45 0.90 29 2 0.04 ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33 Consensus pattern (28 bp): TTCCTTATCCAAAGATTTCCAAAATGGC Found at i:159658543 original size:57 final size:57 Alignment explanation

Indices: 159658476--159658638 Score: 173 Period size: 57 Copynumber: 2.9 Consensus size: 57 159658466 AAAGGCGTCA * * * * * * 159658476 TTTAAGAGGTTCACCGCAAAGGCTTACCTTTCCAGATTTTTTCTACAAAAGCTATCC 1 TTTAACAGGTTCACCACAAAGGCTTGCCTTTCCAGAGTTTTGCAACAAAAGCTATCC * * * * * * 159658533 TTTAATAGGTTCACCATAAAGGCTTGCCTTTCTAGAGTTTTGCAACAAAGGTTGTCC 1 TTTAACAGGTTCACCACAAAGGCTTGCCTTTCCAGAGTTTTGCAACAAAAGCTATCC * * * * * 159658590 TTTAGCAGGTCCGCCACAAAGGCTTGCCTTTCCAAAGTTTTGCCACAAA 1 TTTAACAGGTTCACCACAAAGGCTTGCCTTTCCAGAGTTTTGCAACAAA 159658639 GGATTTTTTT Statistics Matches: 87, Mismatches: 19, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 57 87 1.00 ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32 Consensus pattern (57 bp): TTTAACAGGTTCACCACAAAGGCTTGCCTTTCCAGAGTTTTGCAACAAAAGCTATCC Found at i:159658583 original size:29 final size:29 Alignment explanation

Indices: 159658550--159658640 Score: 89 Period size: 29 Copynumber: 3.2 Consensus size: 29 159658540 GGTTCACCAT * 159658550 AAAGGCTTGCCTTTCTAGAGTTTTGCAAC 1 AAAGGCTTGCCTTTCTAGAGTTTTGCCAC * ** 159658579 AAAGG-TTGTCC-TT-TAGCAGGTCCGCCAC 1 AAAGGCTTG-CCTTTCTAG-AGTTTTGCCAC * * 159658607 AAAGGCTTGCCTTTCCAAAGTTTTGCCAC 1 AAAGGCTTGCCTTTCTAGAGTTTTGCCAC 159658636 AAAGG 1 AAAGG 159658641 ATTTTTTTCT Statistics Matches: 48, Mismatches: 9, Indels: 10 0.72 0.13 0.15 Matches are distributed among these distances: 27 3 0.06 28 19 0.40 29 25 0.52 30 1 0.02 ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29 Consensus pattern (29 bp): AAAGGCTTGCCTTTCTAGAGTTTTGCCAC Found at i:159663894 original size:15 final size:16 Alignment explanation

Indices: 159663869--159663898 Score: 53 Period size: 15 Copynumber: 1.9 Consensus size: 16 159663859 GACATGTCAC 159663869 TATGCTGATTATGTGT 1 TATGCTGATTATGTGT 159663885 TATG-TGATTATGTG 1 TATGCTGATTATGTG 159663899 ATTTGAGTGC Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 15 10 0.71 16 4 0.29 ACGTcount: A:0.20, C:0.03, G:0.27, T:0.50 Consensus pattern (16 bp): TATGCTGATTATGTGT Found at i:159663897 original size:8 final size:8 Alignment explanation

Indices: 159663869--159663901 Score: 50 Period size: 8 Copynumber: 4.1 Consensus size: 8 159663859 GACATGTCAC 159663869 TATGCTGAT 1 TATG-TGAT 159663878 TATGTG-T 1 TATGTGAT 159663885 TATGTGAT 1 TATGTGAT 159663893 TATGTGAT 1 TATGTGAT 159663901 T 1 T 159663902 TGAGTGCTGG Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 7 7 0.30 8 12 0.52 9 4 0.17 ACGTcount: A:0.21, C:0.03, G:0.24, T:0.52 Consensus pattern (8 bp): TATGTGAT Found at i:159670216 original size:40 final size:40 Alignment explanation

Indices: 159670161--159670368 Score: 303 Period size: 40 Copynumber: 5.2 Consensus size: 40 159670151 TGAATGATAC * * 159670161 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATAT * 159670201 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT 159670241 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT * * * 159670281 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAC 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT * * * * 159670321 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT 159670361 CC-GGCTAA 1 CCGGGCTAA 159670369 ATTCGAAGAA Statistics Matches: 152, Mismatches: 15, Indels: 3 0.89 0.09 0.02 Matches are distributed among these distances: 39 5 0.03 40 145 0.95 41 2 0.01 ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTTGTTATAT Found at i:159673734 original size:40 final size:40 Alignment explanation

Indices: 159673628--159673799 Score: 141 Period size: 40 Copynumber: 4.3 Consensus size: 40 159673618 TGCTGGAAAT * * * * * ** 159673628 TATAACCGGGTTAAGACCCGAAGGCAATGGTGCTAGTGGC 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * 159673668 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAT 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * * * * 159673708 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATC-G 1 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * * * * * * * 159673746 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC 1 T-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC * 159673787 CATATCCGGGCTA 1 TATATCCGGGCTA 159673800 TGTCCCAAAG Statistics Matches: 105, Mismatches: 24, Indels: 6 0.78 0.18 0.04 Matches are distributed among these distances: 38 1 0.01 39 29 0.28 40 75 0.71 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24 Consensus pattern (40 bp): TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCAC Found at i:159681521 original size:39 final size:39 Alignment explanation

Indices: 159681398--159681603 Score: 132 Period size: 39 Copynumber: 5.2 Consensus size: 39 159681388 TGCTGGAAAT * * * * * 159681398 TATAACCGGGTTAAGACCCGAAGGCA-ATGTGCTAGTGG 1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTCG * * 159681436 CTATATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTCAT 1 -TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTC-G * * 159681476 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-AATCG 1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTCG * * * * * * 159681514 TGATATCCGGGTTAAGTCCCGTAGGCCTTGGTGCGGGTTAC- 1 T-ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAG-T-CG * * * * ** * 159681555 CATATCCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAG 1 TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTCG 159681594 CTATATCCGG 1 -TATATCCGG 159681604 TTAAGCTCCG Statistics Matches: 128, Mismatches: 30, Indels: 17 0.73 0.17 0.10 Matches are distributed among these distances: 38 10 0.08 39 66 0.52 40 50 0.39 41 1 0.01 42 1 0.01 ACGTcount: A:0.23, C:0.23, G:0.30, T:0.24 Consensus pattern (39 bp): TATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTCG Found at i:159685452 original size:80 final size:80 Alignment explanation

Indices: 159685368--159685516 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 159685358 TATGGTAACC * * * * 159685368 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG 1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA 159685432 CCCGGATAGAATGACT 65 CCCGGATAGAATGACT * * * * * * * 159685448 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC 159685513 CCGG 66 CCGG 159685517 TTATAATTTC Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22 Consensus pattern (80 bp): CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC CCGGATAGAATGACT Found at i:159685458 original size:40 final size:38 Alignment explanation

Indices: 159685409--159685516 Score: 128 Period size: 40 Copynumber: 2.7 Consensus size: 38 159685399 ATCACGATTT * 159685409 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA * 159685449 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA * 159685489 GCACAATTGCCTTCGGGTCTTAACCCGG 1 GCACAA-TGCCTTCGGGTCTTAGCCCGG 159685517 TTATAATTTC Statistics Matches: 61, Mismatches: 4, Indels: 6 0.86 0.06 0.08 Matches are distributed among these distances: 38 1 0.02 39 4 0.07 40 56 0.92 ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23 Consensus pattern (38 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA Found at i:159693569 original size:80 final size:80 Alignment explanation

Indices: 159693485--159693633 Score: 183 Period size: 80 Copynumber: 1.9 Consensus size: 80 159693475 TATGGTAACC * * * * 159693485 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG 1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA 159693549 CCCGGATAGAATGACT 65 CCCGGATAGAATGACT * * * * * * * 159693565 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC 159693630 CCGG 66 CCGG 159693634 TTATAATTTC Statistics Matches: 57, Mismatches: 11, Indels: 2 0.81 0.16 0.03 Matches are distributed among these distances: 79 1 0.02 80 56 0.98 ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22 Consensus pattern (80 bp): CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC CCGGATAGAATGACT Found at i:159693575 original size:40 final size:38 Alignment explanation

Indices: 159693526--159693633 Score: 128 Period size: 40 Copynumber: 2.7 Consensus size: 38 159693516 ATCACGATTT * 159693526 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA * 159693566 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA * 159693606 GCACAATTGCCTTCGGGTCTTAACCCGG 1 GCACAA-TGCCTTCGGGTCTTAGCCCGG 159693634 TTATAATTTC Statistics Matches: 61, Mismatches: 4, Indels: 6 0.86 0.06 0.08 Matches are distributed among these distances: 38 1 0.02 39 4 0.07 40 56 0.92 ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23 Consensus pattern (38 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA Found at i:159704376 original size:20 final size:20 Alignment explanation

Indices: 159704341--159704463 Score: 108 Period size: 20 Copynumber: 6.1 Consensus size: 20 159704331 GCATCATAGA * * 159704341 TGCATAACAAGGGCACCGAAG 1 TGCA-AACAGGGGCACCAAAG * 159704362 TGCAGACAGGGGCA-CAAATG 1 TGCAAACAGGGGCACCAAA-G 159704382 TGCAAACAGGGGCACCATAGAG 1 TGCAAACAGGGGCACCA-A-AG * 159704404 TG--AACAGGGACACCAAAG 1 TGCAAACAGGGGCACCAAAG * * * 159704422 TGTATACAGGGGCACCGAAG 1 TGCAAACAGGGGCACCAAAG * * 159704442 TGCAAACAGAGGTACCAAAG 1 TGCAAACAGGGGCACCAAAG 159704462 TG 1 TG 159704464 AAAATCTCAT Statistics Matches: 83, Mismatches: 13, Indels: 13 0.76 0.12 0.12 Matches are distributed among these distances: 18 4 0.05 19 4 0.05 20 64 0.77 21 6 0.07 22 4 0.05 23 1 0.01 ACGTcount: A:0.37, C:0.21, G:0.31, T:0.11 Consensus pattern (20 bp): TGCAAACAGGGGCACCAAAG Found at i:159709993 original size:40 final size:39 Alignment explanation

Indices: 159709828--159710011 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 159709818 AAATTGAATG * * * 159709828 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 159709868 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 159709908 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 159709948 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 159709987 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 159710012 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:159710036 original size:80 final size:81 Alignment explanation

Indices: 159709868--159710056 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 159709858 GCTGGAAATT * * * * 159709868 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 159709933 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 159709949 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 159710012 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 159710028 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 159710057 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:159718101 original size:40 final size:39 Alignment explanation

Indices: 159717936--159718119 Score: 138 Period size: 40 Copynumber: 4.6 Consensus size: 39 159717926 AAATTGAATG * * * 159717936 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T 1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT * * * * * * 159717976 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T * * * * * 159718016 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT * 159718056 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT * * * 159718095 GATATCCGGGTTAAGTCCCGTAGGC 1 -ATATCCGGGCTAAGACCCGAAGGC 159718120 CTTGGTGCGG Statistics Matches: 113, Mismatches: 26, Indels: 10 0.76 0.17 0.07 Matches are distributed among these distances: 37 4 0.04 38 2 0.02 39 3 0.03 40 104 0.92 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (39 bp): ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT Found at i:159718144 original size:80 final size:81 Alignment explanation

Indices: 159717976--159718164 Score: 186 Period size: 80 Copynumber: 2.4 Consensus size: 81 159717966 GCTGGAAATT * * * * 159717976 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA * 159718041 TTCGTGCGAGTCATTC 66 TTCGTGCGAGTCATCC * * * * * * 159718057 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC 1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC * * * * 159718120 CTTGGTGCGGGTTA-CC 65 ATTCGTGCGAGTCATCC * * * 159718136 ATAACCGGGCTATGTCCCGAAGGCGATTG 1 ATAACCGGGCTAAGACCCGAAGGCAATTG 159718165 ATCGAGTAGC Statistics Matches: 86, Mismatches: 20, Indels: 5 0.77 0.18 0.05 Matches are distributed among these distances: 79 2 0.02 80 84 0.98 ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23 Consensus pattern (81 bp): ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA TTCGTGCGAGTCATCC Found at i:159720869 original size:37 final size:37 Alignment explanation

Indices: 159720814--159720940 Score: 229 Period size: 37 Copynumber: 3.4 Consensus size: 37 159720804 TTATTACGAA 159720814 GTCTTACCC-GACATAATCTCCACACGTAGTCATCGG 1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 159720850 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 159720887 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG 1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG * 159720924 GTCTCACCCGGAACATA 1 GTCTTACCCGG-ACATA 159720941 TTTCCAAGTT Statistics Matches: 88, Mismatches: 1, Indels: 2 0.97 0.01 0.02 Matches are distributed among these distances: 36 9 0.10 37 74 0.84 38 5 0.06 ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG Found at i:159721038 original size:48 final size:48 Alignment explanation

Indices: 159720980--159721131 Score: 277 Period size: 48 Copynumber: 3.2 Consensus size: 48 159720970 TGTTACAACA * 159720980 TTCACATTAGCCATTCGGCTTTACCACACATACATATCACACATATAT 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT * 159721028 TTCACATTAGCCATTCGGCTTTTCCACATATACATATCACACATATAT 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT * 159721076 TTCACATTAGCCCTTCGGCTTTACCACATATACATATCACACATATAT 1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT 159721124 TTCACATT 1 TTCACATT 159721132 CATCACATCG Statistics Matches: 100, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 48 100 1.00 ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34 Consensus pattern (48 bp): TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT Found at i:159721180 original size:49 final size:49 Alignment explanation

Indices: 159721123--159721407 Score: 470 Period size: 49 Copynumber: 5.9 Consensus size: 49 159721113 CACACATATA * 159721123 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * * * 159721172 CTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACTC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 159721219 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACTC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 159721266 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATGTATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 159721315 TTTCACGTTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC * 159721364 TTTCACATTCATCACATTGGCCATTAGGCCATATCACATATATA 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATA 159721408 CATCTCATAC Statistics Matches: 224, Mismatches: 10, Indels: 4 0.94 0.04 0.02 Matches are distributed among these distances: 47 91 0.41 49 133 0.59 ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34 Consensus pattern (49 bp): TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC Found at i:159721223 original size:96 final size:96 Alignment explanation

Indices: 159721123--159721409 Score: 479 Period size: 96 Copynumber: 3.0 Consensus size: 96 159721113 CACACATATA * * 159721123 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACCTTCACATTCATCACA 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA * * 159721188 TCGGCCATTAGGCCTTATCACATATATACTC 66 TTGGCCATTAGGCCTTATCACATATATACAC * 159721219 TTTCACATTCATCACATTGGCCATTAGGCCTTATCAC--ATATATACTCTTTCACATTCATCACA 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA 159721282 TTGGCCATTAGGCCTTATCACATGTATATACAC 66 TTGGCCATTAGGCCTTATCACA--TATATACAC * 159721315 TTTCACGTTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA 1 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA * 159721380 TTGGCCATTAGGCCATATCACATATATACA 66 TTGGCCATTAGGCCTTATCACATATATACA 159721410 TCTCATACAT Statistics Matches: 179, Mismatches: 8, Indels: 8 0.92 0.04 0.04 Matches are distributed among these distances: 94 45 0.25 96 88 0.49 98 46 0.26 ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34 Consensus pattern (96 bp): TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA TTGGCCATTAGGCCTTATCACATATATACAC Found at i:159728672 original size:15 final size:15 Alignment explanation

Indices: 159728652--159728699 Score: 55 Period size: 15 Copynumber: 3.3 Consensus size: 15 159728642 AAAATTTATT 159728652 AAAAATAATAATGTA 1 AAAAATAATAATGTA * 159728667 AAAAATAAATAATAT- 1 AAAAAT-AATAATGTA * 159728682 AAAAAT-ATATTGTA 1 AAAAATAATAATGTA 159728696 AAAA 1 AAAA 159728700 TTTATAAATA Statistics Matches: 28, Mismatches: 3, Indels: 5 0.78 0.08 0.14 Matches are distributed among these distances: 13 5 0.18 14 4 0.14 15 12 0.43 16 7 0.25 ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27 Consensus pattern (15 bp): AAAAATAATAATGTA Found at i:159728677 original size:16 final size:15 Alignment explanation

Indices: 159728652--159728686 Score: 52 Period size: 16 Copynumber: 2.3 Consensus size: 15 159728642 AAAATTTATT * 159728652 AAAAATAATAATGTA 1 AAAAATAATAATATA 159728667 AAAAATAAATAATATA 1 AAAAAT-AATAATATA 159728683 AAAA 1 AAAA 159728687 TATATTGTAA Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 6 0.33 16 12 0.67 ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23 Consensus pattern (15 bp): AAAAATAATAATATA Found at i:159731154 original size:39 final size:38 Alignment explanation

Indices: 159731096--159731270 Score: 124 Period size: 39 Copynumber: 4.5 Consensus size: 38 159731086 AAATTGAATG * 159731096 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGAAAT-T 1 ATATCCGGGCTAAGACCCGAAGACAATTATGCT--AATCT * * * * 159731135 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGCT 1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAAT-CT * * * 159731174 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AAGTTGT 1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAA--TCT * * * * * 159731213 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT 1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAATC-T * 159731252 GATATCCGGG-TAAGTCCCG 1 -ATATCCGGGCTAAGACCCG 159731271 TTAGGCCTTG Statistics Matches: 114, Mismatches: 13, Indels: 18 0.79 0.09 0.12 Matches are distributed among these distances: 37 2 0.02 38 5 0.04 39 94 0.82 40 13 0.11 ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24 Consensus pattern (38 bp): ATATCCGGGCTAAGACCCGAAGACAATTATGCTAATCT Found at i:159739287 original size:40 final size:39 Alignment explanation

Indices: 159739119--159739289 Score: 159 Period size: 40 Copynumber: 4.3 Consensus size: 39 159739109 AGAAATTGAA * * 159739119 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT- 1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG * * * * * 159739159 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G * * 159739199 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG 1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG * * 159739239 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG 1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G 159739279 TGATATCCGGG 1 TGATATCCGGG 159739290 TAAAGTCCCG Statistics Matches: 107, Mismatches: 17, Indels: 14 0.78 0.12 0.10 Matches are distributed among these distances: 37 2 0.02 38 4 0.04 39 4 0.04 40 95 0.89 41 2 0.02 ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24 Consensus pattern (39 bp): TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG Found at i:159746266 original size:27 final size:27 Alignment explanation

Indices: 159746242--159746340 Score: 90 Period size: 27 Copynumber: 3.6 Consensus size: 27 159746232 ACCATACAGA * * 159746242 GGTATTACGGTCATTTTGCTCTACAAG 1 GGTATTACGGTCATTTTACACTACAAG * * * 159746269 GGTATTTCGATAATTTTACACTACAAG 1 GGTATTACGGTCATTTTACACTACAAG * * * * * 159746296 GGTATTTCGGTCATTTTCCCCTATAGG 1 GGTATTACGGTCATTTTACACTACAAG * 159746323 GGCATTACGGTCAATTTT 1 GGTATTACGGTC-ATTTT 159746341 CAAACTATGG Statistics Matches: 58, Mismatches: 13, Indels: 1 0.81 0.18 0.01 Matches are distributed among these distances: 27 53 0.91 28 5 0.09 ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38 Consensus pattern (27 bp): GGTATTACGGTCATTTTACACTACAAG Found at i:159749658 original size:63 final size:62 Alignment explanation

Indices: 159749454--159749721 Score: 249 Period size: 63 Copynumber: 4.3 Consensus size: 62 159749444 ATGTTACATG ** * * 159749454 TAAATAAATTATGGACTTCCAGAGGTTCGGTGGATGAGTAC-GAGAATCAGAATTGAAAATCGA 1 TAAATAAATTATGG-CTTTAAGAGATTCGGTGGATGAGTACAG-GAATCAAAATTGAAAATCGA * * * * * * 159749517 TAAATAAATTATTGCTTT-TGAAATTTCGGTGGATGAGTACAGTAATCAAAATT-TAAATCAA 1 TAAATAAATTATGGCTTTAAGAGA-TTCGGTGGATGAGTACAGGAATCAAAATTGAAAATCGA * * * * * 159749578 TGAATAAATTATGGCTTTAAGGAGATTCGGTGTACGTGTAC-GGAGATCAAAATTGAAAATTGA 1 TAAATAAATTATGGCTTTAA-GAGATTCGGTGGATGAGTACAGGA-ATCAAAATTGAAAATCGA * * * * * 159749641 TAAATAAATTATGGCTTTGCAA-AGGTTTGGTGGATGAATACAGGAATCAAAACTGAAAATTGA 1 TAAATAAATTATGGCTTT--AAGAGATTCGGTGGATGAGTACAGGAATCAAAATTGAAAATCGA * 159749704 TAAATAAATCATGGCTTT 1 TAAATAAATTATGGCTTT 159749722 GTAGAGGGTC Statistics Matches: 167, Mismatches: 29, Indels: 18 0.78 0.14 0.08 Matches are distributed among these distances: 61 26 0.16 62 50 0.30 63 86 0.51 64 3 0.02 65 2 0.01 ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31 Consensus pattern (62 bp): TAAATAAATTATGGCTTTAAGAGATTCGGTGGATGAGTACAGGAATCAAAATTGAAAATCGA Found at i:159749750 original size:63 final size:63 Alignment explanation

Indices: 159749623--159749743 Score: 170 Period size: 63 Copynumber: 1.9 Consensus size: 63 159749613 GTGTACGGAG * * * *** 159749623 ATCAAAATTGAAAATTGATAAATAAATTATGGCTTTGCAAAGGTTTGGTGGATGAATACAGGA 1 ATCAAAACTGAAAATTGATAAATAAATCATGGCTTTGCAAAGGGTCAATGGATGAATACAGGA * * 159749686 ATCAAAACTGAAAATTGATAAATAAATCATGGCTTTGTAGAGGGTCAATGGATGAATA 1 ATCAAAACTGAAAATTGATAAATAAATCATGGCTTTGCAAAGGGTCAATGGATGAATA 159749744 TGGGAATTAA Statistics Matches: 50, Mismatches: 8, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 63 50 1.00 ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29 Consensus pattern (63 bp): ATCAAAACTGAAAATTGATAAATAAATCATGGCTTTGCAAAGGGTCAATGGATGAATACAGGA Found at i:159766546 original size:39 final size:40 Alignment explanation

Indices: 159766490--159766681 Score: 266 Period size: 39 Copynumber: 4.8 Consensus size: 40 159766480 CATGAGCATT * 159766490 TGAATGATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG 1 TGAAT-ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG 159766531 TGAATATA-CCGGGCTAAGTCCCGAAGGCATTTATGCTAG 1 TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG 159766570 TG-ATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG 1 TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG * * ** * 159766609 TGATTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAG 1 TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG * 159766649 TTG--TCATATCCGGGCTAAGACCCGAAGGCATTT 1 -TGAAT-ATATCCGGGCTAAGTCCCGAAGGCATTT 159766682 GTGCAAGATA Statistics Matches: 141, Mismatches: 6, Indels: 9 0.90 0.04 0.06 Matches are distributed among these distances: 38 5 0.04 39 67 0.48 40 62 0.44 41 7 0.05 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26 Consensus pattern (40 bp): TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG Found at i:159766633 original size:40 final size:40 Alignment explanation

Indices: 159766500--159766745 Score: 277 Period size: 40 Copynumber: 6.2 Consensus size: 40 159766490 TGAATGATAC * * 159766500 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATA- 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT * 159766539 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGA-TATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT * 159766578 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT ** * * 159766618 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TCATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT * * ** * 159766658 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT * * * * * 159766698 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT 159766738 CC-GGCTAA 1 CCGGGCTAA 159766746 ATTCCGAAGA Statistics Matches: 183, Mismatches: 19, Indels: 10 0.86 0.09 0.05 Matches are distributed among these distances: 38 4 0.02 39 74 0.40 40 103 0.56 41 2 0.01 ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT Found at i:159774690 original size:40 final size:40 Alignment explanation

Indices: 159774623--159774844 Score: 229 Period size: 40 Copynumber: 5.6 Consensus size: 40 159774613 AAGTAAGCAT * 159774623 TGCTAGTGAATATA-CCGGGCTAAGTCCCGAAGGCATTTA 1 TGCTAGTGAATATATCCGGGCTAAGACCCGAAGGCATTTA * 159774662 TGCTAGTGAATATATCCGGGCTAAGTCCCGAAGGCATTTA 1 TGCTAGTGAATATATCCGGGCTAAGACCCGAAGGCATTTA * ** 159774702 TGCTAGTGATTATATCCGGGCTAAGACCCGAAGGCATTCG 1 TGCTAGTGAATATATCCGGGCTAAGACCCGAAGGCATTTA * * 159774742 TGCGAGTTG--TCATATCCGGGCTAAGACCCGAAGGCATTTG 1 TGCTAG-TGAAT-ATATCCGGGCTAAGACCCGAAGGCATTTA * ** * * * * 159774782 TGCAAGAT-ACCAAATCCGGGTTAAGACCCGAAGGCAATTG 1 TGCTAG-TGAATATATCCGGGCTAAGACCCGAAGGCATTTA * ** 159774822 TGCTTGTGGTTATATCC-GGCTAA 1 TGCTAGTGAATATATCCGGGCTAA 159774845 ATTCTGAAGA Statistics Matches: 158, Mismatches: 19, Indels: 12 0.84 0.10 0.06 Matches are distributed among these distances: 39 21 0.13 40 135 0.85 41 2 0.01 ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26 Consensus pattern (40 bp): TGCTAGTGAATATATCCGGGCTAAGACCCGAAGGCATTTA Found at i:159777909 original size:93 final size:93 Alignment explanation

Indices: 159777797--159777968 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 159777787 GCCCATAAGT * * 159777797 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 159777862 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 159777890 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 159777955 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 159777969 CAAATATCCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:159777964 original size:46 final size:46 Alignment explanation

Indices: 159777789--159777964 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 159777779 TGTAACCCGC * * * 159777789 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 159777835 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 159777885 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 159777928 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 159777965 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:159780391 original size:30 final size:30 Alignment explanation

Indices: 159780347--159780435 Score: 101 Period size: 30 Copynumber: 3.0 Consensus size: 30 159780337 CAAAGATAAC 159780347 AAGAAAACC-GAATAAAGAAATCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA * * 159780376 GAGAAACCCAGAATAAAGAAATCC-AGAATA 1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA * * * * 159780406 AAGAGATCCAGGATAAAGAAACCCAAGATA 1 AAGAAAACCAGAATAAAGAAATCCAAGATA 159780436 CGATACTATG Statistics Matches: 50, Mismatches: 7, Indels: 5 0.81 0.11 0.08 Matches are distributed among these distances: 29 9 0.18 30 39 0.78 31 2 0.04 ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10 Consensus pattern (30 bp): AAGAAAACCAGAATAAAGAAATCCAAGATA Found at i:159780395 original size:15 final size:15 Alignment explanation

Indices: 159780347--159780426 Score: 92 Period size: 15 Copynumber: 5.4 Consensus size: 15 159780337 CAAAGATAAC * 159780347 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 159780361 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 159780376 GAGAAACCCAGAATA 1 AAGAAATCCAGAATA 159780391 AAGAAATCCAGAATA 1 AAGAAATCCAGAATA * * 159780406 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 159780421 AAGAAA 1 AAGAAA 159780427 CCCAAGATAC Statistics Matches: 55, Mismatches: 8, Indels: 5 0.81 0.12 0.07 Matches are distributed among these distances: 14 9 0.16 15 45 0.82 16 1 0.02 ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:159780435 original size:15 final size:15 Alignment explanation

Indices: 159780358--159780435 Score: 79 Period size: 15 Copynumber: 5.2 Consensus size: 15 159780348 AGAAAACCGA 159780358 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * * 159780373 ATAGAGAAA-CCCAG 1 ATAAAGAAATCCAAG 159780387 AATAAAGAAATCC-AG 1 -ATAAAGAAATCCAAG * * 159780402 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 159780418 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 159780433 ATA 1 ATA 159780436 CGATACTATG Statistics Matches: 52, Mismatches: 8, Indels: 6 0.79 0.12 0.09 Matches are distributed among these distances: 14 4 0.08 15 45 0.87 16 3 0.06 ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:159783496 original size:93 final size:93 Alignment explanation

Indices: 159783384--159783555 Score: 317 Period size: 93 Copynumber: 1.8 Consensus size: 93 159783374 GCCCATAAGT * * 159783384 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 159783449 CGAGTTCGGATGCCTAGTTACATCTCAC 66 CGAGTTCGGATGCCTAGTTACATCTCAC * 159783477 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA 159783542 CGAGTTCGGATGCC 66 CGAGTTCGGATGCC 159783556 CAAATATCCC Statistics Matches: 76, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 93 76 1.00 ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20 Consensus pattern (93 bp): GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA CGAGTTCGGATGCCTAGTTACATCTCAC Found at i:159783551 original size:46 final size:46 Alignment explanation

Indices: 159783376--159783551 Score: 232 Period size: 46 Copynumber: 3.8 Consensus size: 46 159783366 TGTAACCCGC * * * 159783376 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT * * 159783422 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT * * 159783472 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT 159783515 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA 159783552 TGCCCAAATA Statistics Matches: 112, Mismatches: 11, Indels: 14 0.82 0.08 0.10 Matches are distributed among these distances: 43 3 0.03 44 1 0.01 45 2 0.02 46 68 0.61 47 32 0.29 48 2 0.02 49 1 0.01 50 3 0.03 ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20 Consensus pattern (46 bp): CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT Found at i:159788065 original size:12 final size:12 Alignment explanation

Indices: 159788046--159788080 Score: 61 Period size: 12 Copynumber: 2.8 Consensus size: 12 159788036 ATACAAGTTT 159788046 GAAAAAAAAATTC 1 GAAAAAAAAA-TC 159788059 GAAAAAAAAATC 1 GAAAAAAAAATC 159788071 GAAAAAAAAA 1 GAAAAAAAAA 159788081 AGTGATTTAT Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 12 12 0.55 13 10 0.45 ACGTcount: A:0.77, C:0.06, G:0.09, T:0.09 Consensus pattern (12 bp): GAAAAAAAAATC Found at i:159790236 original size:16 final size:15 Alignment explanation

Indices: 159790168--159790236 Score: 50 Period size: 17 Copynumber: 4.2 Consensus size: 15 159790158 AGCAAATGAG 159790168 AGAAAAAGAAAAAAA 1 AGAAAAAGAAAAAAA ** 159790183 AGAAAGTTGTAAAAAAA 1 AGAAA-AAG-AAAAAAA 159790200 TA-AAAGAAGAGAAAAATA 1 -AGAAA-AAGA-AAAAA-A 159790218 AGAAAAAGAAAACAAA 1 AGAAAAAGAAAA-AAA 159790234 AGA 1 AGA 159790237 GAGTGACAAG Statistics Matches: 43, Mismatches: 4, Indels: 13 0.72 0.07 0.22 Matches are distributed among these distances: 15 5 0.12 16 9 0.21 17 24 0.56 18 5 0.12 ACGTcount: A:0.75, C:0.01, G:0.16, T:0.07 Consensus pattern (15 bp): AGAAAAAGAAAAAAA Found at i:159795311 original size:30 final size:30 Alignment explanation

Indices: 159795277--159795359 Score: 103 Period size: 30 Copynumber: 2.8 Consensus size: 30 159795267 TAAACTAAAA * 159795277 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT * * * * * * 159795307 TGAGCTGAGGTTAAACTCCTAAGCTGAAGT 1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT 159795337 TGAGCTAAGGTTTAGCTCGTGAG 1 TGAGCTAAGGTTTAGCTCGTGAG 159795360 TTGAAAGTGA Statistics Matches: 41, Mismatches: 12, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 30 41 1.00 ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29 Consensus pattern (30 bp): TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT Found at i:159797353 original size:40 final size:40 Alignment explanation

Indices: 159797298--159797547 Score: 385 Period size: 40 Copynumber: 6.2 Consensus size: 40 159797288 AACATTGGAA 159797298 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159797338 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159797378 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159797418 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * * * * 159797458 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * * * * * * 159797497 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG 1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * 159797538 CTATATCCGG 1 ATATATCCGG 159797548 TTAAATCCCG Statistics Matches: 191, Mismatches: 17, Indels: 4 0.90 0.08 0.02 Matches are distributed among these distances: 39 2 0.01 40 189 0.99 ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22 Consensus pattern (40 bp): ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG Found at i:159805529 original size:40 final size:40 Alignment explanation

Indices: 159805474--159805723 Score: 385 Period size: 40 Copynumber: 6.2 Consensus size: 40 159805464 AACATTGGAA 159805474 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159805514 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159805554 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 159805594 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * * * * 159805634 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC 1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * * * * * * 159805673 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG 1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG * 159805714 CTATATCCGG 1 ATATATCCGG 159805724 TTAAATCCCG Statistics Matches: 191, Mismatches: 17, Indels: 4 0.90 0.08 0.02 Matches are distributed among these distances: 39 2 0.01 40 189 0.99 ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22 Consensus pattern (40 bp): ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG Found at i:159811892 original size:30 final size:30 Alignment explanation

Indices: 159811858--159811940 Score: 85 Period size: 30 Copynumber: 2.8 Consensus size: 30 159811848 TAAACTAAAA * * 159811858 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT 1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC * * * * * * 159811888 TGAGCTGAGATTAAACTCCTAAGCTGAAGC 1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC * 159811918 TGAGCTAAGGTTTAGCTCGTGAG 1 TGAGCTAAGATTTAGCTCGTGAG 159811941 ATGAATATGA Statistics Matches: 39, Mismatches: 14, Indels: 0 0.74 0.26 0.00 Matches are distributed among these distances: 30 39 1.00 ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28 Consensus pattern (30 bp): TGAGCTAAGATTTAGCTCGTGAGCTAAAGC Done.