Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gbar_A12

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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32

Warning! 3186644 characters in sequence are not A, C, G, or T


File 154 of 311

Found at i:52353522 original size:41 final size:40

Alignment explanation

Indices: 52353424--52353614 Score: 177 Period size: 43 Copynumber: 4.6 Consensus size: 40 52353414 TTTTATCAAA * * 52353424 TCACCGGCATTTAGCCTGCTAGGTTTTAAACCCGAATTCA- 1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCCGAA-TCAT ** * * * * 52353464 TCACCGGCATGAAGCCTGTTAGACTTTAAGTCTGAACTCAT 1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCCGAA-TCAT * * 52353505 TCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCATT 1 TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCCGA-ATCA-T *** * 52353547 TCACCGGCATTATAGCCTGCTAGGCCAGAAGCCCGATATTAT 1 TCACCGGCATT-TAGCCTGCTAGGCTTTAAGCCCGA-ATCAT 52353589 CTCACCGGCATTATAGCCTGCTAGGC 1 -TCACCGGCATT-TAGCCTGCTAGGC 52353615 CCGAAGCCCG Statistics Matches: 125, Mismatches: 21, Indels: 7 0.82 0.14 0.05 Matches are distributed among these distances: 40 31 0.25 41 30 0.24 42 14 0.11 43 50 0.40 ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27 Consensus pattern (40 bp): TCACCGGCATTTAGCCTGCTAGGCTTTAAGCCCGAATCAT Found at i:52353578 original size:43 final size:42 Alignment explanation

Indices: 52353504--52353674 Score: 186 Period size: 43 Copynumber: 4.0 Consensus size: 42 52353494 TCTGAACTCA * * 52353504 TTCACCGGCATT-TCGCCTGCTAGGCTTGAAGCCCGATATCAT 1 TTCACCGGCATTATAGCCTGCTAGGC-CGAAGCCCGATATCAT * 52353546 TTCACCGGCATTATAGCCTGCTAGGCCAGAAGCCCGATATTAT 1 TTCACCGGCATTATAGCCTGCTAGGCC-GAAGCCCGATATCAT * 52353589 CTCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATAAT-ATT 1 TTCACCGGCATTATAGCCTGCTAGG-CCGAAGCCCGAT-ATCA-T * * * * 52353633 ATTCACCAGC-TTAAAGCTTGCTAGGCCGAGGCCCGAATATCA 1 -TTCACCGGCATTATAGCCTGCTAGGCCGAAGCCCG-ATATCA 52353675 CATTTTGATA Statistics Matches: 112, Mismatches: 9, Indels: 14 0.83 0.07 0.10 Matches are distributed among these distances: 42 12 0.11 43 72 0.64 44 21 0.19 45 7 0.06 ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25 Consensus pattern (42 bp): TTCACCGGCATTATAGCCTGCTAGGCCGAAGCCCGATATCAT Found at i:52353667 original size:86 final size:85 Alignment explanation

Indices: 52353505--52353668 Score: 208 Period size: 86 Copynumber: 1.9 Consensus size: 85 52353495 CTGAACTCAT * ** * * 52353505 TCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTATAGCCTGCTAG 1 TCACCGGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCATTTCACCAGCATTAAAGCCTGCTAG 52353570 GCCAGAAGCCCGATATTATC 66 GCCAGAAGCCCGATATTATC * 52353590 TCACCGGCATTATAGCCTGCTAGGCCCGAAGCCCGATAAT-ATTATTCACCAGC-TTAAAGCTTG 1 TCACCGGCATT-TAGCCTGCTAGGCCCGAAGCCCGAT-ATCA-T-TTCACCAGCATTAAAGCCTG * 52353653 CTAGGCC-GAGGCCCGA 62 CTAGGCCAGAAGCCCGA 52353669 ATATCACATT Statistics Matches: 68, Mismatches: 7, Indels: 7 0.83 0.09 0.09 Matches are distributed among these distances: 85 11 0.16 86 31 0.46 87 18 0.26 88 8 0.12 ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24 Consensus pattern (85 bp): TCACCGGCATTTAGCCTGCTAGGCCCGAAGCCCGATATCATTTCACCAGCATTAAAGCCTGCTAG GCCAGAAGCCCGATATTATC Found at i:52355582 original size:14 final size:15 Alignment explanation

Indices: 52355553--52355582 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 52355543 CAAAATTTAG 52355553 ACATGATACTTTCAC 1 ACATGATACTTTCAC 52355568 ACATGATAC-TTCAC 1 ACATGATACTTTCAC 52355582 A 1 A 52355583 TATAATAAAC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.40 15 9 0.60 ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30 Consensus pattern (15 bp): ACATGATACTTTCAC Found at i:52357953 original size:31 final size:30 Alignment explanation

Indices: 52357918--52357987 Score: 106 Period size: 31 Copynumber: 2.3 Consensus size: 30 52357908 GAAACAAAGC * 52357918 AAAAAGAAAGTGAAAAATAAAAATGA-AATTG 1 AAAAAGAAAGTGAAAAATAAAAA-GAGAA-GG 52357949 AAAAAGAAAGTGAAAAATAAAAAGAGAAGG 1 AAAAAGAAAGTGAAAAATAAAAAGAGAAGG 52357979 AAAAAGAAA 1 AAAAAGAAA 52357988 AAAAGATCGA Statistics Matches: 37, Mismatches: 1, Indels: 3 0.90 0.02 0.07 Matches are distributed among these distances: 30 12 0.32 31 25 0.68 ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10 Consensus pattern (30 bp): AAAAAGAAAGTGAAAAATAAAAAGAGAAGG Found at i:52358357 original size:36 final size:36 Alignment explanation

Indices: 52358308--52358382 Score: 114 Period size: 36 Copynumber: 2.1 Consensus size: 36 52358298 CCAAAAGGTA * * * * 52358308 AGCAATGTCTGAGTTTTGAAGTTTTTAAAACATATC 1 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC 52358344 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC 1 AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC 52358380 AGC 1 AGC 52358383 CTCATTCGAT Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 36 35 1.00 ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35 Consensus pattern (36 bp): AGCAAGGTATGAGTTTTAAAGTTTTTAAAACACATC Found at i:52363394 original size:50 final size:50 Alignment explanation

Indices: 52363329--52363424 Score: 147 Period size: 50 Copynumber: 1.9 Consensus size: 50 52363319 ACCGAGGTTC * * 52363329 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA 1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAA * * * 52363379 TCTGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTGACCTA 1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTA 52363425 AACCCATCTT Statistics Matches: 41, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 50 41 1.00 ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27 Consensus pattern (50 bp): TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTATCAA Found at i:52364506 original size:69 final size:68 Alignment explanation

Indices: 52364326--52364516 Score: 238 Period size: 69 Copynumber: 2.8 Consensus size: 68 52364316 ATTTTTGGAA * * * * 52364326 AGCACATTAAGCATTTAAAATGGATGTAAATGAACACATTTTCAAGACAACAAATTAGCCCTTTA 1 AGCACATTAAGCATTT-AAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTA * 52364391 CAGC 65 CAAC * * * * 52364395 AGCACATTAAGCATCTAAAATTAATGTGAGTGAACACATTTTTAAGATAACAAATTAGCACTTTA 1 AGCACATTAAGCAT-TTAAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTA 52364460 CAAC 65 CAAC * * * * 52364464 ATCACATTAAGCATTTAAATCGAACGTAAATGAAGACATTTTTAATATAACAA 1 AGCACATTAAGCATTTAAAT-GAATGTAAATGAACACATTTTTAAGATAACAA 52364517 CTCATCAATT Statistics Matches: 103, Mismatches: 17, Indels: 4 0.83 0.14 0.03 Matches are distributed among these distances: 68 5 0.05 69 97 0.94 70 1 0.01 ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28 Consensus pattern (68 bp): AGCACATTAAGCATTTAAATGAATGTAAATGAACACATTTTTAAGATAACAAATTAGCACTTTAC AAC Found at i:52364844 original size:68 final size:68 Alignment explanation

Indices: 52364713--52364869 Score: 183 Period size: 68 Copynumber: 2.3 Consensus size: 68 52364703 TTAACTGTGA * * * * * 52364713 AATC-AACAGATTCGGACAACTACATTTACTAAATAAAACAACATATATGGTAGTGCATCGAACA 1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAGTGCATCGAACA 52364777 ATG 66 ATG * * ** * * 52364780 AATTTAACACATTCGGACAGCTACATTTACCAAATAAAATAGTATAAATGAT-GATGCTTTGAAC 1 AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAG-TGCATCGAAC 52364844 AATG 65 AATG * 52364848 AATCTAACACATTCGAACAGCT 1 AATCTAACACATTCGGACAGCT 52364870 TAATTTTAAG Statistics Matches: 75, Mismatches: 13, Indels: 3 0.82 0.14 0.03 Matches are distributed among these distances: 67 4 0.05 68 71 0.95 ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26 Consensus pattern (68 bp): AATCTAACACATTCGGACAGCTACATTTACCAAATAAAACAACATAAATGATAGTGCATCGAACA ATG Found at i:52379268 original size:43 final size:42 Alignment explanation

Indices: 52379202--52379319 Score: 146 Period size: 43 Copynumber: 2.8 Consensus size: 42 52379192 TCACATGTAT * * 52379202 CACATCCATTATGAACTCGGACCACTCAACGAGCTCGGATGC 1 CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC * * 52379244 TCGCATCCATAATGAACTCAGACCACTCAACGAGCTTGGATGC 1 -CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC ** * * * 52379287 CACATATATCACGAACCCAGACCACTCAACGAG 1 CACATCCATAATGAACTCAGACCACTCAACGAG 52379320 TTCAGGCTTT Statistics Matches: 65, Mismatches: 10, Indels: 1 0.86 0.13 0.01 Matches are distributed among these distances: 42 27 0.42 43 38 0.58 ACGTcount: A:0.32, C:0.33, G:0.17, T:0.18 Consensus pattern (42 bp): CACATCCATAATGAACTCAGACCACTCAACGAGCTCGGATGC Found at i:52384436 original size:32 final size:31 Alignment explanation

Indices: 52384316--52384446 Score: 88 Period size: 32 Copynumber: 3.9 Consensus size: 31 52384306 ACAAATTATG * * 52384316 TGCATGGGCTTTATTGTATGTAAAATATATTTATA 1 TGCAT-GG-TTTATTGTATATATAATATA--TATA * 52384351 TGCATGGACTTTATTATTATATATAATATATATA 1 TGCATGG--TTTATT-GTATATATAATATATATA * * 52384385 --CGTGGTTTTTGGTGTTATATATAATATATATA 1 TGCATGGTTTAT--TG-TATATATAATATATATA 52384417 TGCATGGTTCTATTGTATATAGT-ATATATA 1 TGCATGGTT-TATTGTATATA-TAATATATA 52384447 ATTATGGGTA Statistics Matches: 79, Mismatches: 8, Indels: 21 0.73 0.07 0.19 Matches are distributed among these distances: 30 4 0.05 32 35 0.44 33 3 0.04 34 12 0.15 35 14 0.18 36 11 0.14 ACGTcount: A:0.32, C:0.05, G:0.15, T:0.47 Consensus pattern (31 bp): TGCATGGTTTATTGTATATATAATATATATA Found at i:52384474 original size:31 final size:30 Alignment explanation

Indices: 52384402--52384485 Score: 82 Period size: 31 Copynumber: 2.8 Consensus size: 30 52384392 TTTGGTGTTA * * * 52384402 TATATAATATATAT-ATGCATGGTTCTATTG 1 TATATAATATATATAAT-TATGGGTATATTG * * 52384432 TATATAGTATATATAATTATGGGTATAGTTT 1 TATATAATATATATAATTATGGGTATA-TTG 52384463 TATATAATATATA-AATTTATGGG 1 TATATAATATATATAA-TTATGGG 52384486 ACTTTTAATG Statistics Matches: 45, Mismatches: 6, Indels: 5 0.80 0.11 0.09 Matches are distributed among these distances: 30 22 0.49 31 23 0.51 ACGTcount: A:0.37, C:0.02, G:0.14, T:0.46 Consensus pattern (30 bp): TATATAATATATATAATTATGGGTATATTG Found at i:52387010 original size:21 final size:21 Alignment explanation

Indices: 52386968--52387011 Score: 52 Period size: 21 Copynumber: 2.1 Consensus size: 21 52386958 GTAAAGTTTG ** 52386968 TAATTTTACATAATTAGGTGT 1 TAATTTTACATAATTACATGT * * 52386989 TAATTTTACATCATTTCATGT 1 TAATTTTACATAATTACATGT 52387010 TA 1 TA 52387012 TTATGCTACA Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50 Consensus pattern (21 bp): TAATTTTACATAATTACATGT Found at i:52392379 original size:47 final size:47 Alignment explanation

Indices: 52392310--52392429 Score: 213 Period size: 47 Copynumber: 2.6 Consensus size: 47 52392300 ATGCCAATGA 52392310 CATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCGATGC 1 CATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCGATGC * * 52392357 CATGTACCAAACATGGTCTTACACTGGCTTATCCATTAAGTCGATGC 1 CATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCGATGC * 52392404 CATGTCCCAGACATGGTCTTACACTG 1 CATGTCCCAAACATGGTCTTACACTG 52392430 ACTATCGAAA Statistics Matches: 69, Mismatches: 4, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 47 69 1.00 ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28 Consensus pattern (47 bp): CATGTCCCAAACATGGTCTTACACTGGCTCATCCATTAAGTCGATGC Found at i:52395577 original size:15 final size:15 Alignment explanation

Indices: 52395542--52395571 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 52395532 AGTGTTAATG * 52395542 GAATCTATTGGTTGT 1 GAATCTACTGGTTGT 52395557 GAATCTACTGGTTGT 1 GAATCTACTGGTTGT 52395572 ATATCTTACG Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43 Consensus pattern (15 bp): GAATCTACTGGTTGT Found at i:52399365 original size:49 final size:49 Alignment explanation

Indices: 52399278--52399408 Score: 145 Period size: 49 Copynumber: 2.7 Consensus size: 49 52399268 TATTGTGTGT * * * * * * 52399278 CAGTATAAGACTTGTCTAGGATATGGCATCGACATCGATAAATGAGAGC 1 CAGTGTAAGACCTGTCTAGGACACGACATCGACATCGATAAATGAAAGC * * * * ** 52399327 CAGTGTAAGACCTGTTTGGGACACGACATCGACCTCGATATATGAAATT 1 CAGTGTAAGACCTGTCTAGGACACGACATCGACATCGATAAATGAAAGC * 52399376 CAGTGTAAGACCTGTCTAGGACATGACATCGAC 1 CAGTGTAAGACCTGTCTAGGACACGACATCGAC 52399409 TTTGATGTGC Statistics Matches: 67, Mismatches: 15, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 49 67 1.00 ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24 Consensus pattern (49 bp): CAGTGTAAGACCTGTCTAGGACACGACATCGACATCGATAAATGAAAGC Found at i:52403391 original size:16 final size:17 Alignment explanation

Indices: 52403357--52403392 Score: 65 Period size: 17 Copynumber: 2.2 Consensus size: 17 52403347 ATAATAGCGA 52403357 AAACATAAATAGATAAG 1 AAACATAAATAGATAAG 52403374 AAACATAAATAG-TAAG 1 AAACATAAATAGATAAG 52403390 AAA 1 AAA 52403393 ATATATATAG Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 16 7 0.37 17 12 0.63 ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17 Consensus pattern (17 bp): AAACATAAATAGATAAG Found at i:52403402 original size:17 final size:16 Alignment explanation

Indices: 52403364--52403420 Score: 64 Period size: 16 Copynumber: 3.5 Consensus size: 16 52403354 CGAAAACATA 52403364 AATAGATAAGAAACATA- 1 AATAG-TAAGAAA-ATAT 52403381 AATAGTAAGAAAATAT 1 AATAGTAAGAAAATAT * 52403397 ATATAG-ATGAAAATAT 1 A-ATAGTAAGAAAATAT 52403413 AATAGTAA 1 AATAGTAA 52403421 TAATAATACG Statistics Matches: 35, Mismatches: 2, Indels: 7 0.80 0.05 0.16 Matches are distributed among these distances: 15 7 0.20 16 19 0.54 17 9 0.26 ACGTcount: A:0.61, C:0.02, G:0.12, T:0.25 Consensus pattern (16 bp): AATAGTAAGAAAATAT Found at i:52403557 original size:15 final size:15 Alignment explanation

Indices: 52403532--52403571 Score: 53 Period size: 15 Copynumber: 2.6 Consensus size: 15 52403522 TATTATATTG 52403532 ATAATAAATAAAAGGA 1 ATAA-AAATAAAAGGA * * 52403548 ATAAAAATAATAGTA 1 ATAAAAATAAAAGGA 52403563 ATAAAAATA 1 ATAAAAATA 52403572 TTAACAATAG Statistics Matches: 22, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 15 18 0.82 16 4 0.18 ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23 Consensus pattern (15 bp): ATAAAAATAAAAGGA Found at i:52403590 original size:3 final size:3 Alignment explanation

Indices: 52403547--52403867 Score: 156 Period size: 3 Copynumber: 105.7 Consensus size: 3 52403537 AAATAAAAGG * * * * * * * * 52403547 AAT AAA AAT AAT AGT AAT AAA AAT ATT AAC AAT AGT AAT AAT AAC GAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT * * 52403595 AAT -AT AAAT ACT AAT ATAT ACAT GAAT AAT AAT AAT AAT AGT AAT AAT 1 AAT AAT -AAT AAT AAT A-AT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT * * * 52403643 AAT AAT AAC AAT AAT AAT AAC AAT ACATT AAT ATAT GAT AAT -AT CAAT 1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT A-AT AAT AAT AAT -AAT * * * * * * 52403691 AAT ATT AGT AAGT AA- AAA AAGGG AAT AAT AAT AGT AGT AAT AAT AAT 1 AAT AAT AAT AA-T AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT * * * * * * 52403738 AAC AAT AGT AAG AAT AAT AAT GAT AAT -AT AAC AA- ACAT AGT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT * * ** * ** 52403782 -AT AAT CAAT AA- AAT -AT AAT AGT AAT AAA AAT AAT GCT AAC GGT 1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT * * 52403825 AAT AAT AAT AAT AAT GAT AGT AAT -AT AAT AAT AAT AAT AAT AA 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA 52403868 GTAAAATGAT Statistics Matches: 234, Mismatches: 63, Indels: 42 0.69 0.19 0.12 Matches are distributed among these distances: 2 17 0.07 3 190 0.81 4 22 0.09 5 5 0.02 ACGTcount: A:0.59, C:0.04, G:0.07, T:0.29 Consensus pattern (3 bp): AAT Found at i:52414002 original size:24 final size:24 Alignment explanation

Indices: 52413952--52414005 Score: 67 Period size: 24 Copynumber: 2.2 Consensus size: 24 52413942 AATCGAATTT * 52413952 GCACACATAGTGCTCGTCACACTC 1 GCACACATAGTGCTAGTCACACTC 52413976 GCACACATAGTGCCATAGT-ACAC-C 1 GCACACATAGTG-C-TAGTCACACTC 52414000 GCACAC 1 GCACAC 52414006 TCAGTGCATT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 24 19 0.70 25 5 0.19 26 3 0.11 ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17 Consensus pattern (24 bp): GCACACATAGTGCTAGTCACACTC Found at i:52421929 original size:24 final size:24 Alignment explanation

Indices: 52421879--52421932 Score: 67 Period size: 24 Copynumber: 2.2 Consensus size: 24 52421869 AATCGAATTT * 52421879 GCACACATAGTGCTCGTCACACTC 1 GCACACATAGTGCTAGTCACACTC 52421903 GCACACATAGTGCCATAGT-ACAC-C 1 GCACACATAGTG-C-TAGTCACACTC 52421927 GCACAC 1 GCACAC 52421933 TCAGTGCATT Statistics Matches: 27, Mismatches: 1, Indels: 4 0.84 0.03 0.12 Matches are distributed among these distances: 24 19 0.70 25 5 0.19 26 3 0.11 ACGTcount: A:0.30, C:0.37, G:0.17, T:0.17 Consensus pattern (24 bp): GCACACATAGTGCTAGTCACACTC Found at i:52426766 original size:48 final size:46 Alignment explanation

Indices: 52426636--52426806 Score: 175 Period size: 46 Copynumber: 3.7 Consensus size: 46 52426626 TCATCTCGTA * * * * 52426636 GCCGATTCATGTCCCAGACATGTCTCACACTGGCT-TACGTCTCGAG 1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATCTCAAG * * * * 52426682 GCCGATGCATGTCCTATACATGTCTTACACTAGCTCTCATCTCAAT 1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG * * * ** 52426728 GCTGATGCCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAT-GTG 1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCAT-CTCAAG 52426776 GCCGATGCATGTCCCAGACATGTCTTACACT 1 GCCGATGCATGTCCCAGACATGTCTTACACT 52426807 AGCCAACAAT Statistics Matches: 102, Mismatches: 19, Indels: 8 0.79 0.15 0.06 Matches are distributed among these distances: 46 51 0.50 47 27 0.26 48 23 0.23 49 1 0.01 ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29 Consensus pattern (46 bp): GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCAAG Found at i:52435949 original size:41 final size:43 Alignment explanation

Indices: 52435843--52435957 Score: 128 Period size: 42 Copynumber: 2.7 Consensus size: 43 52435833 ACGTATCAAT * * * * 52435843 GCCATACCCCAGATATGGTCTTACATGAAAT-ATCATATCGAC 1 GCCATATCCCAGATATGGTCTTATACGAAATCATCATACCGAC * * * * 52435885 GCCATGTCCCTGACATGGTCTTATACGAAATCA-CATACCGAT 1 GCCATATCCCAGATATGGTCTTATACGAAATCATCATACCGAC * 52435927 G-CATATCCCAGATATGGTCTTATACGGAATC 1 GCCATATCCCAGATATGGTCTTATACGAAATC 52435958 TCGGTAGTAC Statistics Matches: 60, Mismatches: 12, Indels: 3 0.80 0.16 0.04 Matches are distributed among these distances: 41 26 0.43 42 33 0.55 43 1 0.02 ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27 Consensus pattern (43 bp): GCCATATCCCAGATATGGTCTTATACGAAATCATCATACCGAC Found at i:52440294 original size:68 final size:67 Alignment explanation

Indices: 52440222--52440371 Score: 171 Period size: 67 Copynumber: 2.2 Consensus size: 67 52440212 CATCATGTGT * * * * 52440222 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC 1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC 52440284 ATGTAG 62 ATGTAG ** * * 52440290 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT 1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT 52440355 AG 66 AG 52440357 ACAAGAGAGCTACGA 1 ACAAGAGAGCTACGA 52440372 GATAAACTGG Statistics Matches: 70, Mismatches: 9, Indels: 7 0.81 0.10 0.08 Matches are distributed among these distances: 64 20 0.29 65 7 0.10 66 4 0.06 67 26 0.37 68 13 0.19 ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21 Consensus pattern (67 bp): ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT AG Found at i:52440327 original size:64 final size:64 Alignment explanation

Indices: 52440246--52440429 Score: 194 Period size: 67 Copynumber: 2.8 Consensus size: 64 52440236 AGACATTATG * * 52440246 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT 1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA * * * * * * 52440310 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT 1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT 52440375 AA 63 AA * * * * 52440377 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC 1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC 52440430 CGAACTATAT Statistics Matches: 98, Mismatches: 17, Indels: 11 0.78 0.13 0.09 Matches are distributed among these distances: 62 1 0.01 63 19 0.19 64 21 0.21 65 8 0.08 66 16 0.16 67 31 0.32 68 2 0.02 ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23 Consensus pattern (64 bp): ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA Found at i:52442761 original size:20 final size:20 Alignment explanation

Indices: 52442728--52442768 Score: 64 Period size: 20 Copynumber: 2.0 Consensus size: 20 52442718 AGCTCAATAC 52442728 ATAAGCTAGATGAATGGACA 1 ATAAGCTAGATGAATGGACA * * 52442748 ATAAGTTAGCTGAATGGACA 1 ATAAGCTAGATGAATGGACA 52442768 A 1 A 52442769 CTTGTGTTCA Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 20 19 1.00 ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22 Consensus pattern (20 bp): ATAAGCTAGATGAATGGACA Found at i:52443315 original size:40 final size:39 Alignment explanation

Indices: 52443260--52443337 Score: 129 Period size: 40 Copynumber: 2.0 Consensus size: 39 52443250 TTAACTCAAC * * 52443260 CAGCTAATTAAGTTGTAATGAGCTAAGACATACTTAAATT 1 CAGCTAATTAAGTTGTAATAAGCTAAGACA-AATTAAATT 52443300 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT 1 CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAAT 52443338 AGCTGTACTA Statistics Matches: 36, Mismatches: 2, Indels: 1 0.92 0.05 0.03 Matches are distributed among these distances: 39 7 0.19 40 29 0.81 ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31 Consensus pattern (39 bp): CAGCTAATTAAGTTGTAATAAGCTAAGACAAATTAAATT Found at i:52443395 original size:47 final size:46 Alignment explanation

Indices: 52443323--52443479 Score: 233 Period size: 47 Copynumber: 3.3 Consensus size: 46 52443313 TGTAATAAGC * * * 52443323 TAAGACAAATTAAATAGCTGTACTAACTAAAACATATTAAATTAACT 1 TAAGACAAATTAAATAGCTGAACTAA-TAGAACATATTAAATAAACT * 52443370 TAGGACAAATTAAATAGCTGAACTAATTAGAACATATTAAATAAACT 1 TAAGACAAATTAAATAGCTGAACTAA-TAGAACATATTAAATAAACT * * 52443417 TAAGACAAATTAAATTGCTGAACTAATCAGAACACATTAAATAAACT 1 TAAGACAAATTAAATAGCTGAACTAAT-AGAACATATTAAATAAACT 52443464 TAAGACAAATTAAATA 1 TAAGACAAATTAAATA 52443480 CTTAAGCTAA Statistics Matches: 100, Mismatches: 9, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 46 1 0.01 47 99 0.99 ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27 Consensus pattern (46 bp): TAAGACAAATTAAATAGCTGAACTAATAGAACATATTAAATAAACT Found at i:52446490 original size:49 final size:49 Alignment explanation

Indices: 52446430--52446606 Score: 180 Period size: 49 Copynumber: 3.6 Consensus size: 49 52446420 TGTTGTTTGT * 52446430 TAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAGAGC 1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGC * * * * 52446479 TAGTGTAAGACCTGCCTGTGACATGGCATCGACCTCGATATATGAAAG- 1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGC * * * * ** ** 52446527 TCAGTGTAAGACCTGTCTGAGACTTTGCATCGACTTTAAT-G-TGCTAGC 1 T-AGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGC * * 52446575 CAGTGTAAGACCATGTCTGGGACATGACATCG 1 TAGTGTAAGACC-TGTCTGGGACATGGCATCG 52446607 GCATTTTATC Statistics Matches: 105, Mismatches: 20, Indels: 7 0.80 0.15 0.05 Matches are distributed among these distances: 47 15 0.14 48 16 0.15 49 74 0.70 ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26 Consensus pattern (49 bp): TAGTGTAAGACCTGTCTGGGACATGGCATCGACATCGATAGATGAAAGC Found at i:52456568 original size:43 final size:43 Alignment explanation

Indices: 52456487--52456572 Score: 104 Period size: 43 Copynumber: 2.0 Consensus size: 43 52456477 AAATCATATA * ** 52456487 ATGCCAATGTCCTAGATGTGGTCTTACATGTAGCCACATATCG 1 ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG * 52456530 ATGCCACTGTCCCAGATAG-GGTCTTAC-TCGTAAACACATATCG 1 ATGCCAATGTCCCAGAT-GTGGTCTTACAT-GTAAACACATATCG 52456573 GAATCACAAA Statistics Matches: 37, Mismatches: 4, Indels: 4 0.82 0.09 0.09 Matches are distributed among these distances: 42 1 0.03 43 35 0.95 44 1 0.03 ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28 Consensus pattern (43 bp): ATGCCAATGTCCCAGATGTGGTCTTACATGTAAACACATATCG Found at i:52465121 original size:13 final size:13 Alignment explanation

Indices: 52465103--52465131 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 52465093 AATAGTTGTG 52465103 TGTTATTTAATTA 1 TGTTATTTAATTA 52465116 TGTTATTTAATTA 1 TGTTATTTAATTA 52465129 TGT 1 TGT 52465132 AGGTTAGCCG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62 Consensus pattern (13 bp): TGTTATTTAATTA Found at i:52469482 original size:10 final size:10 Alignment explanation

Indices: 52469469--52469514 Score: 56 Period size: 10 Copynumber: 4.5 Consensus size: 10 52469459 AGCTCACTTG 52469469 AGCTCGTTTT 1 AGCTCGTTTT * 52469479 AGCTCGTTTG 1 AGCTCGTTTT * 52469489 AGCTCGAATTT 1 AGCTCG-TTTT * 52469500 AGCTCGTTTC 1 AGCTCGTTTT 52469510 AGCTC 1 AGCTC 52469515 ATTCCTTTTT Statistics Matches: 30, Mismatches: 5, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 10 22 0.73 11 8 0.27 ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39 Consensus pattern (10 bp): AGCTCGTTTT Found at i:52469502 original size:21 final size:20 Alignment explanation

Indices: 52469466--52469514 Score: 71 Period size: 21 Copynumber: 2.4 Consensus size: 20 52469456 ATCAGCTCAC * 52469466 TTGAGCTCGTTTTAGCTCGT 1 TTGAGCTCGATTTAGCTCGT 52469486 TTGAGCTCGAATTTAGCTCGT 1 TTGAGCTCG-ATTTAGCTCGT * 52469507 TTCAGCTC 1 TTGAGCTC 52469515 ATTCCTTTTT Statistics Matches: 26, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 20 9 0.35 21 17 0.65 ACGTcount: A:0.14, C:0.22, G:0.22, T:0.41 Consensus pattern (20 bp): TTGAGCTCGATTTAGCTCGT Found at i:52469757 original size:13 final size:13 Alignment explanation

Indices: 52469739--52469767 Score: 58 Period size: 13 Copynumber: 2.2 Consensus size: 13 52469729 AATAGTTGTG 52469739 TGTTATTTAATTA 1 TGTTATTTAATTA 52469752 TGTTATTTAATTA 1 TGTTATTTAATTA 52469765 TGT 1 TGT 52469768 AGGTTAGCTG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62 Consensus pattern (13 bp): TGTTATTTAATTA Found at i:52472085 original size:46 final size:45 Alignment explanation

Indices: 52472029--52472196 Score: 180 Period size: 46 Copynumber: 3.6 Consensus size: 45 52472019 TGGTTGAGCA 52472029 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAA-G * ** * * 52472075 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAT-TTATG-GA-T-GCGAAG * * 52472122 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAA-G * 52472168 -CCCAAGCTCGTTGAGTTGAGTCCGAGTTC 1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTC 52472197 GCTTATGGGC Statistics Matches: 100, Mismatches: 14, Indels: 16 0.77 0.11 0.12 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 45 4 0.04 46 56 0.56 47 31 0.31 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAAG Found at i:52472185 original size:93 final size:93 Alignment explanation

Indices: 52472026--52472197 Score: 292 Period size: 93 Copynumber: 1.8 Consensus size: 93 52472016 GGATGGTTGA * * * 52472026 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT 52472091 TGAGTCCGAGTTCGTGAAATGTAACTAG 66 TGAGTCCGAGTTCGTGAAATGTAACTAG * 52472119 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCCAAGCTCGTTGAG 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAA-CTCGTTGAG 52472183 TTGAGTCCGAGTTCG 65 TTGAGTCCGAGTTCG 52472198 CTTATGGGCG Statistics Matches: 74, Mismatches: 4, Indels: 2 0.93 0.05 0.03 Matches are distributed among these distances: 92 4 0.05 93 70 0.95 ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCCAACTCGTTGAGT TGAGTCCGAGTTCGTGAAATGTAACTAG Found at i:52481005 original size:40 final size:39 Alignment explanation

Indices: 52480916--52481013 Score: 115 Period size: 40 Copynumber: 2.5 Consensus size: 39 52480906 CTAAGTCGGT * * 52480916 ACCGCACACTTAGTGCCCTCTATAGCCGAAGCTATGCCA 1 ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA * * * ** 52480955 ACTCGTACACTTAGTGCCATTTGTAGCCGAAGCTATATTAA 1 AC-CGCACACTTAGTGCCATCTATAGCCGAAGCTAT-GCAA 52480996 ACCGCACACTTAGTGCCA 1 ACCGCACACTTAGTGCCA 52481014 ATCATAGTCG Statistics Matches: 49, Mismatches: 8, Indels: 3 0.82 0.13 0.05 Matches are distributed among these distances: 39 2 0.04 40 44 0.90 41 3 0.06 ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24 Consensus pattern (39 bp): ACCGCACACTTAGTGCCATCTATAGCCGAAGCTATGCAA Found at i:52482931 original size:46 final size:46 Alignment explanation

Indices: 52482862--52482990 Score: 163 Period size: 46 Copynumber: 2.8 Consensus size: 46 52482852 GGTGGTAGGT * 52482862 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAT-CATGA 1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCA-ATACACGA * * * * * 52482908 GTGCTAGTGTAAGACATGTCTGGGATATGCTTCGG-CATTGAGACGA 1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAAT-ACACGA * 52482954 GAGCTAGTGTAATACATGTCTGGGACATGCATCGGCC 1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC 52482991 TCGGGATATA Statistics Matches: 70, Mismatches: 10, Indels: 5 0.82 0.12 0.06 Matches are distributed among these distances: 44 1 0.01 45 2 0.03 46 66 0.94 47 1 0.01 ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25 Consensus pattern (46 bp): GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAATACACGA Found at i:52483782 original size:21 final size:21 Alignment explanation

Indices: 52483735--52483775 Score: 55 Period size: 22 Copynumber: 1.9 Consensus size: 21 52483725 GGCTAATATT ** 52483735 AAAATTTTTTTTATGAATGCA 1 AAAATTTTTTCCATGAATGCA 52483756 AGAAATTTTTTCCATGAATG 1 A-AAATTTTTTCCATGAATG 52483776 TGAAAATGGT Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 21 1 0.06 22 16 0.94 ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44 Consensus pattern (21 bp): AAAATTTTTTCCATGAATGCA Found at i:52484406 original size:21 final size:20 Alignment explanation

Indices: 52484376--52484415 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 20 52484366 GTCATGATGG 52484376 CCACACGGGCGTGTTGCCCTT 1 CCACACGGGCGTGTT-CCCTT * 52484397 CCACATGGGCGTGTTCCCT 1 CCACACGGGCGTGTTCCCT 52484416 GCTTCAAGTG Statistics Matches: 18, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.10, C:0.38, G:0.28, T:0.25 Consensus pattern (20 bp): CCACACGGGCGTGTTCCCTT Found at i:52485967 original size:21 final size:22 Alignment explanation

Indices: 52485941--52485998 Score: 66 Period size: 23 Copynumber: 2.6 Consensus size: 22 52485931 CAGCTTGTCT 52485941 GAGCTTACTATT-AACTCGATA- 1 GAGCTTACTATTCAACTCG-TAC * 52485962 GAGCTTACCATTTCAACTCGTAC 1 GAGCTTACTA-TTCAACTCGTAC * 52485985 GAACTTACTATTCA 1 GAGCTTACTATTCA 52485999 TCAACTCAGG Statistics Matches: 31, Mismatches: 3, Indels: 5 0.79 0.08 0.13 Matches are distributed among these distances: 21 9 0.29 22 8 0.26 23 14 0.45 ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33 Consensus pattern (22 bp): GAGCTTACTATTCAACTCGTAC Found at i:52506713 original size:24 final size:25 Alignment explanation

Indices: 52506686--52506743 Score: 82 Period size: 24 Copynumber: 2.4 Consensus size: 25 52506676 AGCTCCCGTT * 52506686 ATATGGCTCTTTGTGAGCTTCCT-A 1 ATATGGCTCTTTGTGAACTTCCTGA * 52506710 ATATGGTTCTTTGTGAACTTCCTGA 1 ATATGGCTCTTTGTGAACTTCCTGA * 52506735 CTATGGCTC 1 ATATGGCTC 52506744 GTATGAGTTT Statistics Matches: 29, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 24 21 0.72 25 8 0.28 ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41 Consensus pattern (25 bp): ATATGGCTCTTTGTGAACTTCCTGA Found at i:52509015 original size:42 final size:44 Alignment explanation

Indices: 52508915--52509062 Score: 117 Period size: 42 Copynumber: 3.4 Consensus size: 44 52508905 TGCAATTTCA ** * * * 52508915 TGTAAGACCACATCTAGGACGTTGGCATCGATTTGAGATTTACG 1 TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG 52508959 TGTAAGACCATGTCTGGGACATCGGCATCGTATTT-A-ATTT-CG 1 TGTAAGACCATGTCTGGGACATCGGCATCG-ATTTGAGATTTACG * * * * * * * * 52509001 TGTATGGCCTTGTCTGGGATAGT-GGCATTGATATGTGA-TTACA 1 TGTAAGACCATGTCTGGGACA-TCGGCATCGATTTGAGATTTACG * 52509044 TGTAAGACCACGTCTGGGA 1 TGTAAGACCATGTCTGGGA 52509063 TGTTGGCATT Statistics Matches: 82, Mismatches: 17, Indels: 11 0.75 0.15 0.10 Matches are distributed among these distances: 41 3 0.04 42 27 0.33 43 22 0.27 44 26 0.32 45 4 0.05 ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32 Consensus pattern (44 bp): TGTAAGACCATGTCTGGGACATCGGCATCGATTTGAGATTTACG Found at i:52510389 original size:21 final size:20 Alignment explanation

Indices: 52510357--52510395 Score: 53 Period size: 19 Copynumber: 1.9 Consensus size: 20 52510347 CCTCTGTAAC 52510357 TTTGAAAATTTGT-TAAGTA 1 TTTGAAAATTTGTATAAGTA 52510376 TTTGAGAAATTTTGTATAAG 1 TTTGA-AAA-TTTGTATAAG 52510396 CTCGGTTTAG Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 19 5 0.29 20 3 0.18 21 5 0.29 22 4 0.24 ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46 Consensus pattern (20 bp): TTTGAAAATTTGTATAAGTA Found at i:52516630 original size:42 final size:41 Alignment explanation

Indices: 52516519--52516663 Score: 132 Period size: 42 Copynumber: 3.4 Consensus size: 41 52516509 TCCGATATGA * 52516519 AATTTCATGTAAGACCAC-GTCTGGGACATTGGCATC-AATTT 1 AATTTCATGTAAGACC-CTGTCTGGGACA-TGGCATCGTATTT * * * 52516560 GATATTTACGTGTAAGACCATGTTTGGGACATCGGCATCGTATTT 1 -A-ATTT-CATGTAAGACCCTGTCTGGGACAT-GGCATCGTATTT * * 52516605 AATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATTT 1 AATTTCATGTAAGACCCTGTCTGGGACA-TGGCATCG-TATTT * * 52516648 GATTACATGTAAGACC 1 AATTTCATGTAAGACC 52516664 AGGTCTAGGA Statistics Matches: 86, Mismatches: 10, Indels: 13 0.79 0.09 0.12 Matches are distributed among these distances: 42 28 0.33 43 28 0.33 44 26 0.30 45 4 0.05 ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33 Consensus pattern (41 bp): AATTTCATGTAAGACCCTGTCTGGGACATGGCATCGTATTT Found at i:52518547 original size:46 final size:46 Alignment explanation

Indices: 52518412--52518585 Score: 158 Period size: 46 Copynumber: 3.7 Consensus size: 46 52518402 GTTATTGTGA * * ** * 52518412 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCAC-ATTATAAGA 1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGA-GACGAGT * * * * * 52518458 GCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGAGACGAGT 1 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGACGAGT * 52518506 GCTAGTGTAAGACATGT-TTGGAACATGCATCGGCCTCGAGACGTAAGT 1 GCTAGTGTAAGACATGTCTAGG-ACATGCATCGGCCTCGAGACG--AGT * 52518554 -C-AGTGTAAGATATGTCTAGGACATGCATCGGC 1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGC 52518586 TATGAGATGT Statistics Matches: 104, Mismatches: 17, Indels: 14 0.77 0.13 0.10 Matches are distributed among these distances: 46 53 0.51 47 26 0.25 48 24 0.23 49 1 0.01 ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24 Consensus pattern (46 bp): GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACGAGT Found at i:52518628 original size:46 final size:45 Alignment explanation

Indices: 52518415--52518630 Score: 120 Period size: 46 Copynumber: 4.7 Consensus size: 45 52518405 ATTGTGAGCT * * * * * 52518415 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATAAG-AGC-C 1 AGTGTAAGACATGTCTGGGACAGGCATCGG-C-TATGAGAAGTA-CTC * * 52518461 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ATTGAGACGAGTGCT- 1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGGCTA-TGAGA--AGTACTC * * * * * * 52518509 AGTGTAAGACATGTTTGGAACATGCATCGGCCT-CGAGACGTAAGTC 1 AGTGTAAGACATGTCTGGGACAGGCATCGG-CTATGAGAAGT-ACTC * * * * 52518555 AGTGTAAGATATGTCTAGGACATGCATCGGCTATGAGATGT-CTC 1 AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC * 52518599 AGTGTAAGACCATGTTTGGGACACGGCATCGG 1 AGTGTAAGA-CATGTCTGGGACA-GGCATCGG 52518631 AACAGATATG Statistics Matches: 131, Mismatches: 25, Indels: 28 0.71 0.14 0.15 Matches are distributed among these distances: 44 13 0.10 45 14 0.11 46 61 0.47 47 25 0.19 48 18 0.14 ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24 Consensus pattern (45 bp): AGTGTAAGACATGTCTGGGACAGGCATCGGCTATGAGAAGTACTC Found at i:52530057 original size:38 final size:38 Alignment explanation

Indices: 52530006--52530081 Score: 134 Period size: 38 Copynumber: 2.0 Consensus size: 38 52529996 AGTGTTGTTG * 52530006 CTTTAATTGACCTGCGGTTGACATATTCATATATCTGT 1 CTTTAATTGACCTGCGGTCGACATATTCATATATCTGT * 52530044 CTTTAATTGACCTGGGGTCGACATATTCATATATCTGT 1 CTTTAATTGACCTGCGGTCGACATATTCATATATCTGT 52530082 ATGAGATTGG Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 38 36 1.00 ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41 Consensus pattern (38 bp): CTTTAATTGACCTGCGGTCGACATATTCATATATCTGT Found at i:52545890 original size:44 final size:44 Alignment explanation

Indices: 52545820--52546210 Score: 159 Period size: 44 Copynumber: 8.5 Consensus size: 44 52545810 TACTATGGCG * * 52545820 AATCTTATCTCCTTGAAGTT-TCAGTGGAGCAAGA-TAAAGCTACA 1 AATCTTATATCCCTGAAGTTGT-AGTGGAGC-AGATTAAAGCTACA * * * 52545864 AATCTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACA 1 AATCTTATATCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACA * * * * * * 52545908 ATTCATATACCCCTGAAGTTGCAGTGG-GTCAGAATGAAA-CTATGAGGGTA 1 AATCTTATATCCCTGAAGTTGTAGTGGAG-CAG-ATTAAAGC--T-A---CA * * * * 52545958 AATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA-TGAAGCTACA 1 AATCTTATATCCCTGAAGTTGTAGTGGAGC-AGATTAAAGCTACA * * ** ** * * 52546002 AATCTTATACCCCTAAAGTTACAGTGG-GTTGGAATAAAACTACGATAGCA 1 AATCTTATATCCCTGAAGTTGTAGTGGAG-CAG-AT-TAA--A-GCTA-CA * * ** * * 52546052 AATCTTATCTCCCTAAAGTTGTAGTAAAGTAAGA-TGAAGCTACA 1 AATCTTATATCCCTGAAGTTGTAGTGGAG-CAGATTAAAGCTACA * * * 52546096 AATCCTATACCCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGCA 1 AATCTTATATCCCTGAAGTTGTAGTGGAG-CAGATT-AA---AGC-TA-CA * * * 52546146 AATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACA 1 AATCTTATATCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACA ** 52546190 AATCTTATCCCCCTGAAGTTG 1 AATCTTATATCCCTGAAGTTG 52546211 CAGTAGGTTG Statistics Matches: 258, Mismatches: 59, Indels: 60 0.68 0.16 0.16 Matches are distributed among these distances: 43 11 0.04 44 128 0.50 45 11 0.04 46 5 0.02 47 2 0.01 48 5 0.02 49 8 0.03 50 79 0.31 51 9 0.03 ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29 Consensus pattern (44 bp): AATCTTATATCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACA Found at i:52545971 original size:94 final size:94 Alignment explanation

Indices: 52545862--52546402 Score: 550 Period size: 94 Copynumber: 5.8 Consensus size: 94 52545852 GATAAAGCTA * * * * 52545862 CAAATCTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT 1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT * ** 52545927 TGCAGTGGGTCAGAATGAAACTATGAGGG 66 TGCAGTGGGTCAGAATGAAACTACGATAG * ** * * 52545956 TAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA-TGAAGCTACAAATCTTATACCCCTAAAG 1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGC-AGATTGAAGCTACAAATCTTATACCCCTGAAG * ** * 52546020 TTACAGTGGGTTGGAATAAAACTACGATAG 65 TTGCAGTGGGTCAGAATGAAACTACGATAG ** * * 52546050 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA 1 CAAATCTTATCTCCCTGAAA-TTGTAGTGGAG-CAGATTGAAGCTACAAATCTTATACCCCTGAA * * * * * 52546113 GTTGTAGTGAGTCAGATTGAATCTACCATAG 64 GTTGCAGTGGGTCAGAATGAAACTACGATAG * * * 52546144 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT 1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT * ** * * * 52546209 TGCAGTAGGTTGGATTGAATCTACTATAG 66 TGCAGTGGGTCAGAATGAAACTACGATAG * ** ** 52546238 CAAATCTTATCTCCCTGAAATTGTAGTAGAGCAGATTGAAATTACAAATCTTATACATCTGAAGT 1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT ** ** 52546303 TGCAGTGGGTCA-AATTGATTCTAATATAG 66 TGCAGTGGGTCAGAA-TGAAACTACGATAG * * * * * * * * * 52546332 CAAACCTTATCTCCTTGAAGTTGCAATGGAGCAAATTAAACCTACAAATCTTATACCCTTGAAGT 1 CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT 52546397 TGCAGT 66 TGCAGT 52546403 AGATTAGATG Statistics Matches: 367, Mismatches: 74, Indels: 12 0.81 0.16 0.03 Matches are distributed among these distances: 93 5 0.01 94 357 0.97 95 5 0.01 ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30 Consensus pattern (94 bp): CAAATCTTATCTCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCTTATACCCCTGAAGT TGCAGTGGGTCAGAATGAAACTACGATAG Found at i:52546028 original size:138 final size:138 Alignment explanation

Indices: 52545775--52546028 Score: 350 Period size: 138 Copynumber: 1.8 Consensus size: 138 52545765 AAACAAATCC * * * * * * * 52545775 TATACCCTTGAAGTTGCAGTGGGTCGGATTGAACCTACTATGGCGAATCTTATCTCCTTGAAGTT 1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT * * ** 52545840 TCAGTGGAGCAAGATAAAGCTACAAATCTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCT 66 GCAGTGGAGCAAGATAAAGCTACAAATCTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT 52545905 ACAATTCA 131 ACAATTCA * * 52545913 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTA-TGAGGGTAAATCTTATCTCCCTGATGT 1 TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACT-AGGGCAAATCTTATCTCCCTGAAGT * 52545977 TGCAGTGGAGCAAGATGAAGCTACAAATCTTATACCCCT-AAAGTTACAGTGG 65 TGCAGTGGAGCAAGATAAAGCTACAAATCTTATACCCCTGAAA-TTACAGTGG 52546029 GTTGGAATAA Statistics Matches: 100, Mismatches: 14, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 137 4 0.04 138 96 0.96 ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29 Consensus pattern (138 bp): TATACCCCTGAAGTTGCAGTGGGTCAGAATGAAACTACTAGGGCAAATCTTATCTCCCTGAAGTT GCAGTGGAGCAAGATAAAGCTACAAATCTTATACCCCTGAAATTACAGTGGATCAGATTGAAGCT ACAATTCA Found at i:52546107 original size:188 final size:189 Alignment explanation

Indices: 52545862--52546404 Score: 643 Period size: 188 Copynumber: 2.9 Consensus size: 189 52545852 GATAAAGCTA * * * 52545862 CAAATCTTATATCCCTGAAATTGTAGTGGA-TCAGATTGAAGCTACAATTCATATACCCCTGAAG 1 CAAATCTTATCTCCCTGAAATTGTAGTAGAGTCAGATTGAAGCTACAAATCATATACCCCTGAAG * ** * * * 52545926 TTGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAG 66 TTGCAGTGGGTCAGAATGAATCTAT-ATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAG * 52545991 A-TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAG 130 ATTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG * * * 52546050 CAAATCTTATCTCCCT-AAAGTTGTAGTAAAGTAAGA-TGAAGCTACAAATCCTATACCCCTGAA 1 CAAATCTTATCTCCCTGAAA-TTGTAGTAGAGTCAGATTGAAGCTACAAATCATATACCCCTGAA * * * * * 52546113 GTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCTCCTTGAAGTTGTAGTGGAGC-A 65 GTTGCAGTGGGTCAGAATGAATCTA-TATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAA * * * * * * * 52546177 GATTGAAGCTACAAATCTTATCCCCCTGAAGTTGCAGTAGGTTGGATTGAATCTACTATAG 129 GATTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG ** * ** 52546238 CAAATCTTATCTCCCTGAAATTGTAGTAGAG-CAGATTGAAATTACAAATCTTATACATCTGAAG 1 CAAATCTTATCTCCCTGAAATTGTAGTAGAGTCAGATTGAAGCTACAAATCATATACCCCTGAAG * * * 52546302 TTGCAGTGGGTCA-AATTGATTCTAATATAGCAAACCTTATCTCCTTGAAGTTGCAATGGAGCAA 66 TTGCAGTGGGTCAGAA-TGAATCT-ATATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAA * * * * * 52546366 -ATTAAACCTACAAATCTTATACCCTTGAAGTTGCAGTAG 129 GATTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAG 52546405 ATTAGATGCA Statistics Matches: 302, Mismatches: 44, Indels: 18 0.83 0.12 0.05 Matches are distributed among these distances: 187 10 0.03 188 283 0.94 189 9 0.03 ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30 Consensus pattern (189 bp): CAAATCTTATCTCCCTGAAATTGTAGTAGAGTCAGATTGAAGCTACAAATCATATACCCCTGAAG TTGCAGTGGGTCAGAATGAATCTATATAGCAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGA TTGAAGCTACAAATCTTATACCCCTAAAGTTACAGTAGGTTGGAATAAAACTACGATAG Found at i:52546169 original size:50 final size:50 Alignment explanation

Indices: 52546106--52546277 Score: 182 Period size: 50 Copynumber: 3.6 Consensus size: 50 52546096 AATCCTATAC 52546106 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT 1 CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT * * * 52546156 CCTTGAAGTTGTAGTGGAG-CAGATTG-A---AGC-TA-CAAATCTTATCC 1 CCCTGAAGTTGTAGT-GAGTCAGATTGAATCTACCATAGCAAATCTTATCT * ** * 52546200 CCCTGAAGTTGCAGT-AGGTTGGATTGAATCTACTATAGCAAATCTTATCT 1 CCCTGAAGTTGTAGTGA-GTCAGATTGAATCTACCATAGCAAATCTTATCT * 52546250 CCCTGAAATTGTAGTAGAG-CAGATTGAA 1 CCCTGAAGTTGTAGT-GAGTCAGATTGAA 52546278 ATTACAAATC Statistics Matches: 97, Mismatches: 14, Indels: 22 0.73 0.11 0.17 Matches are distributed among these distances: 42 1 0.01 43 1 0.01 44 29 0.30 45 3 0.03 46 2 0.02 48 1 0.01 49 3 0.03 50 52 0.54 51 4 0.04 52 1 0.01 ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31 Consensus pattern (50 bp): CCCTGAAGTTGTAGTGAGTCAGATTGAATCTACCATAGCAAATCTTATCT Found at i:52546379 original size:282 final size:282 Alignment explanation

Indices: 52545862--52546398 Score: 614 Period size: 282 Copynumber: 1.9 Consensus size: 282 52545852 GATAAAGCTA * * 52545862 CAAATCTTATATCCCTGAAATTGTAGTGGATCAGATTGAAGCTACAATTCATATACCCCTGAAGT 1 CAAATCTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT * * * ** * 52545927 TGCAGTGGGTCAGAATGAAACTATGAGGGTAAATCTTATCTCCCTGATGTTGCAGTGGAGCAAGA 66 TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA * * ** * * 52545992 TGAAGCTACAAATCTTATACCCCTAAAGTTACAGTGGGTTGGAATAAAACTACGATAGCAAATCT 131 TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT * * * * * 52546057 TATCTCCCTAAAGTTGTAGTAAAGTAAGATGAAGCTACAAATCCTATACCCCTGAAGTTGTAGTG 196 TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG 52546122 AGTCAGATTGAATCTACCATAG 261 AGTCAGATTGAATCTACCATAG * * * * * 52546144 CAAATCTTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCCCCTGAAGT 1 CAAATCTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT ** * * * * 52546209 TGCAGTAGGTTGGATTGAATCTACT-ATAGCAAATCTTATCTCCCTGAAATTGTAGTAGAGC-AG 66 TGCAGTAGGTCAGAATGAAACTA-TGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAG * * * * * ** * 52546272 ATTGAAATTACAAATCTTATACATCTGAAGTTGCAGTGGG-TCAAATTGATTCTAATATAGCAAA 130 A-TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAA-TAAAACTAAGATAGCAAA * * ** * * 52546336 CCTTATCTCCTTGAAGTTGCAATGGAGCAA-ATTAAACCTACAAATCTTATACCCTTGAAGTTG 193 CCTTATCTCCCTAAAGTTGCAATAAAGCAAGA-TAAACCTACAAATCCTATACCCCTGAAGTTG 52546399 CAGTAGATTA Statistics Matches: 207, Mismatches: 44, Indels: 8 0.80 0.17 0.03 Matches are distributed among these distances: 281 7 0.03 282 199 0.96 283 1 0.00 ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30 Consensus pattern (282 bp): CAAATCTTATATCCCTGAAATTGTAGTGGAGCAGATTGAAGCTACAAATCATATACCCCTGAAGT TGCAGTAGGTCAGAATGAAACTATGAGAGCAAATCTTATCTCCCTGAAATTGCAGTAGAGCAAGA TGAAACTACAAATCTTATACACCTAAAGTTACAGTGGGTTCAAATAAAACTAAGATAGCAAACCT TATCTCCCTAAAGTTGCAATAAAGCAAGATAAACCTACAAATCCTATACCCCTGAAGTTGTAGTG AGTCAGATTGAATCTACCATAG Found at i:52548862 original size:40 final size:40 Alignment explanation

Indices: 52548786--52549000 Score: 328 Period size: 40 Copynumber: 5.4 Consensus size: 40 52548776 GATGACATCT * 52548786 GGGCTAAGTCCCGAAGGCA-TGGTGCTAGTGACTATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC * 52548825 GGGCTAAGTCCCGAAGGCAGTTGTGCTAGTGACTATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC * * 52548865 GGGCTAAGTCCCGAAGGCATTTGTGCTATTGACTATATTC 1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC * 52548905 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCT 1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC * 52548945 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CTATATCC 1 GGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACTATATCC * * 52548985 -GGCTAAATCCTGAAGG 1 GGGCTAAGTCCCGAAGG 52549001 TACTTGGGTT Statistics Matches: 163, Mismatches: 11, Indels: 4 0.92 0.06 0.02 Matches are distributed among these distances: 39 33 0.20 40 128 0.79 41 2 0.01 ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27 Consensus pattern (40 bp): GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCC Found at i:52553325 original size:14 final size:14 Alignment explanation

Indices: 52553306--52553332 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 52553296 AATTTTTATA 52553306 AAAAATTATTTTCT 1 AAAAATTATTTTCT 52553320 AAAAATTATTTTC 1 AAAAATTATTTTC 52553333 AATAAAACAA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48 Consensus pattern (14 bp): AAAAATTATTTTCT Found at i:52553339 original size:15 final size:14 Alignment explanation

Indices: 52553305--52553339 Score: 52 Period size: 14 Copynumber: 2.4 Consensus size: 14 52553295 CAATTTTTAT 52553305 AAAAAATTATTTTC 1 AAAAAATTATTTTC * 52553319 TAAAAATTATTTTC 1 AAAAAATTATTTTC 52553333 AATAAAA 1 AA-AAAA 52553340 CAATCATAAT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 14 14 0.78 15 4 0.22 ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40 Consensus pattern (14 bp): AAAAAATTATTTTC Found at i:52562564 original size:18 final size:19 Alignment explanation

Indices: 52562541--52562583 Score: 54 Period size: 18 Copynumber: 2.3 Consensus size: 19 52562531 CAACTAAAAT 52562541 TTTTAATATTT-TTAT-ACA 1 TTTTAAT-TTTATTATCACA 52562559 TTTTAATTTTATTATGCACA 1 TTTTAATTTTATTAT-CACA 52562579 TTTTA 1 TTTTA 52562584 TTATCTTCAT Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 17 3 0.14 18 11 0.50 20 8 0.36 ACGTcount: A:0.30, C:0.07, G:0.02, T:0.60 Consensus pattern (19 bp): TTTTAATTTTATTATCACA Found at i:52564944 original size:11 final size:9 Alignment explanation

Indices: 52564902--52564961 Score: 61 Period size: 9 Copynumber: 6.6 Consensus size: 9 52564892 GCCATCCTTC 52564902 TTTT-GTTT 1 TTTTAGTTT 52564910 TTTTAG-TT 1 TTTTAGTTT * * 52564918 TTTAACTTT 1 TTTTAGTTT 52564927 TTTTAGTTT 1 TTTTAGTTT 52564936 TATTATAGTTAT 1 T-TT-TAGTT-T 52564948 TTTTAGTTT 1 TTTTAGTTT 52564957 TTTTA 1 TTTTA 52564962 AAAATTTTTA Statistics Matches: 43, Mismatches: 4, Indels: 9 0.77 0.07 0.16 Matches are distributed among these distances: 8 10 0.23 9 17 0.40 10 7 0.16 11 7 0.16 12 2 0.05 ACGTcount: A:0.17, C:0.02, G:0.08, T:0.73 Consensus pattern (9 bp): TTTTAGTTT Found at i:52567041 original size:39 final size:40 Alignment explanation

Indices: 52566916--52567100 Score: 216 Period size: 40 Copynumber: 4.7 Consensus size: 40 52566906 GCTACTCGTT * 52566916 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA * 52566956 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA * * * * 52566996 CCAATGCCTTCGGG-CTTAGCCGGGAATTAGTAACTCACA 1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA * * * * * 52567035 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA 1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA 52567076 CAAA-GCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGACTTAGCCCGGA 52567101 CATCATTCGA Statistics Matches: 123, Mismatches: 17, Indels: 10 0.82 0.11 0.07 Matches are distributed among these distances: 38 2 0.02 39 31 0.25 40 78 0.63 41 12 0.10 ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA Found at i:52567060 original size:79 final size:80 Alignment explanation

Indices: 52566918--52567100 Score: 212 Period size: 79 Copynumber: 2.3 Consensus size: 80 52566908 TACTCGTTCA * * * 52566918 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT 1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT * * 52566983 TTAGTAAC-TCGCACC 66 ATAGTAACTTAGCA-C * ** 52566998 AATGCCTTCGGG-CTTAGCCGGGA-ATTAGTAACTCACACAAATGCCTTC-GGATCTTAGTCCGG 1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGG * * 52567060 ATATGGTCACTTAGCAC 64 ATATAGTAACTTAGCAC * 52567077 AAAGCCTTCGGGACTTAGCCCGGA 1 AATGCCTTCGGGACTTAGCCCGGA 52567101 CATCATTCGA Statistics Matches: 87, Mismatches: 12, Indels: 8 0.81 0.11 0.07 Matches are distributed among these distances: 78 4 0.05 79 57 0.66 80 26 0.30 ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24 Consensus pattern (80 bp): AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT ATAGTAACTTAGCAC Found at i:52574543 original size:90 final size:92 Alignment explanation

Indices: 52574343--52574556 Score: 290 Period size: 90 Copynumber: 2.3 Consensus size: 92 52574333 CGCTAAAAAG 52574343 AATGGCTCCACCAAATAAAATATTATTTTTATATTTAAATTAAAAAAAACAAGTTTACAAAAAAA 1 AATGGCTCCACCAAATAAAATATTATTTTTATATTTAAATTAAAAAAAACAAG-TTA-AAAAAAA * ** 52574408 ATGTACAATACACTTGTGGCACCATTCTT 64 AGGTACAATACACCAGTGGCACCATTCTT * * * 52574437 AATGTCTCCACAAAATAAAATATTATTTTTATATTTAAATT-AAAAAATCACA-TT-AAAAAAAA 1 AATGGCTCCACCAAATAAAATATTATTTTTATATTTAAATTAAAAAAAACA-AGTTAAAAAAAAA ** 52574499 GGTACAATACACCAGTGGTGCCATTCTT 65 GGTACAATACACCAGTGGCACCATTCTT * * 52574527 AATGGCTTCACCAAATAAAATATGATTTTT 1 AATGGCTCCACCAAATAAAATATTATTTTT 52574557 TTAATTTTTA Statistics Matches: 107, Mismatches: 12, Indels: 6 0.86 0.10 0.05 Matches are distributed among these distances: 90 57 0.53 92 2 0.02 93 8 0.07 94 40 0.37 ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33 Consensus pattern (92 bp): AATGGCTCCACCAAATAAAATATTATTTTTATATTTAAATTAAAAAAAACAAGTTAAAAAAAAAG GTACAATACACCAGTGGCACCATTCTT Found at i:52578542 original size:14 final size:13 Alignment explanation

Indices: 52578509--52578549 Score: 57 Period size: 12 Copynumber: 3.2 Consensus size: 13 52578499 TTTAAAACTC 52578509 CTTTAAAAGAAAA 1 CTTTAAAAGAAAA * 52578522 C-TTAAAAGAAATT 1 CTTTAAAAGAAA-A 52578535 CTTTAAAAGAAAA 1 CTTTAAAAGAAAA 52578548 CT 1 CT 52578550 CAAAGAGAAT Statistics Matches: 24, Mismatches: 2, Indels: 4 0.80 0.07 0.13 Matches are distributed among these distances: 12 10 0.42 13 4 0.17 14 10 0.42 ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27 Consensus pattern (13 bp): CTTTAAAAGAAAA Found at i:52581334 original size:40 final size:42 Alignment explanation

Indices: 52581290--52581384 Score: 106 Period size: 41 Copynumber: 2.3 Consensus size: 42 52581280 TTATAAATAG 52581290 CACTATGTGTGCGA-AATG-GAATAGCTTCAGCTATATGAGA- 1 CACTATGTGTGCGATAATGAG-ATAGCTTCAGCTATATGAGAT * * * * 52581330 CACTAGGTGTGCGATACTGAGGTAGCTTCAGCTATTTGAGATGT 1 CACTATGTGTGCGATAATGAGATAGCTTCAGCTATATGAGA--T 52581374 CACTATGTGTG 1 CACTATGTGTG 52581385 TGGAATCATT Statistics Matches: 45, Mismatches: 5, Indels: 6 0.80 0.09 0.11 Matches are distributed among these distances: 40 13 0.29 41 21 0.47 42 1 0.02 44 10 0.22 ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31 Consensus pattern (42 bp): CACTATGTGTGCGATAATGAGATAGCTTCAGCTATATGAGAT Found at i:52585888 original size:93 final size:93 Alignment explanation

Indices: 52585779--52585949 Score: 252 Period size: 93 Copynumber: 1.8 Consensus size: 93 52585769 GCCCCTAAGT ** * 52585779 GAACTCGAACTCAACTCAACAAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACAAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA 52585844 CGAGTTCGAATGCCTAGTTACATCTCAC 66 CGAGTTCGAATGCCTAGTTACATCTCAC * * * * * * 52585872 GAACTCGGACTCAACTCAACGAGTTTGAACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA 1 GAACTCGAACTCAACTCAACAAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA * 52585937 CGAGTTCGGATGC 66 CGAGTTCGAATGC 52585950 TCAACCATCC Statistics Matches: 68, Mismatches: 10, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 93 68 1.00 ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22 Consensus pattern (93 bp): GAACTCGAACTCAACTCAACAAGCTCGAACATTCGCATCCATAAATGAACTCGGACTCAACTCAA CGAGTTCGAATGCCTAGTTACATCTCAC Found at i:52585939 original size:46 final size:46 Alignment explanation

Indices: 52585774--52585944 Score: 168 Period size: 46 Copynumber: 3.7 Consensus size: 46 52585764 AACCCGCCCC * * * ** * * 52585774 TAAGTGAACTCGAACTCAACTCAACAAGCTCGGGCGTTCGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCA * * * 52585820 TAAATGAACTCGGACTCAACTCAACGAGTTCGAATGCCTAGTTACAT-C- 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAA---C-ATTTGCATCCA * * * 52585868 TCA-CGAACTCGGACTCAACTCAACGAGTTTGAACATTTGCATCCA 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCA 52585913 TAAGTGAACTCGGACTCAACTCAACGAGTTCG 1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG 52585945 GATGCTCAAC Statistics Matches: 100, Mismatches: 18, Indels: 14 0.76 0.14 0.11 Matches are distributed among these distances: 43 6 0.06 44 2 0.02 45 2 0.02 46 54 0.54 47 28 0.28 48 2 0.02 49 2 0.02 50 4 0.04 ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23 Consensus pattern (46 bp): TAAGTGAACTCGGACTCAACTCAACGAGTTCGAACATTTGCATCCA Found at i:52588384 original size:15 final size:15 Alignment explanation

Indices: 52588327--52588406 Score: 67 Period size: 15 Copynumber: 5.4 Consensus size: 15 52588317 CAAAGATAAC * 52588327 AAGAAAACC-GAATA 1 AAGAAATCCAGAATA 52588341 AAGAAATCCA-AGATA 1 AAGAAATCCAGA-ATA * * 52588356 GAGAAA-CCTGGAATA 1 AAGAAATCC-AGAATA * 52588371 AAGAAATTCAGAATA 1 AAGAAATCCAGAATA * * 52588386 AAGAGATCCAGGATA 1 AAGAAATCCAGAATA 52588401 AAGAAA 1 AAGAAA 52588407 CCCAAGATAC Statistics Matches: 51, Mismatches: 10, Indels: 9 0.73 0.14 0.13 Matches are distributed among these distances: 14 11 0.22 15 38 0.75 16 2 0.04 ACGTcount: A:0.57, C:0.11, G:0.19, T:0.12 Consensus pattern (15 bp): AAGAAATCCAGAATA Found at i:52588415 original size:15 final size:15 Alignment explanation

Indices: 52588338--52588415 Score: 61 Period size: 15 Copynumber: 5.2 Consensus size: 15 52588328 AGAAAACCGA 52588338 ATAAAGAAATCCAAG 1 ATAAAGAAATCCAAG * ** 52588353 ATAGAGAAA-CCTGG 1 ATAAAGAAATCCAAG * 52588367 AATAAAGAAATTC-AG 1 -ATAAAGAAATCCAAG * * 52588382 AATAAAGAGATCCAGG 1 -ATAAAGAAATCCAAG * 52588398 ATAAAGAAACCCAAG 1 ATAAAGAAATCCAAG 52588413 ATA 1 ATA 52588416 CGATACTATG Statistics Matches: 48, Mismatches: 12, Indels: 6 0.73 0.18 0.09 Matches are distributed among these distances: 14 3 0.06 15 43 0.90 16 2 0.04 ACGTcount: A:0.55, C:0.13, G:0.18, T:0.14 Consensus pattern (15 bp): ATAAAGAAATCCAAG Found at i:52601236 original size:18 final size:19 Alignment explanation

Indices: 52601213--52601248 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 52601203 AACTTGGCAC * 52601213 CATAA-TCATTTAATTTAA 1 CATAATTCAATTAATTTAA 52601231 CATAATTCAATTAATTTA 1 CATAATTCAATTAATTTA 52601249 CTAAATTTAA Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 5 0.31 19 11 0.69 ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44 Consensus pattern (19 bp): CATAATTCAATTAATTTAA Found at i:52605037 original size:42 final size:41 Alignment explanation

Indices: 52604874--52605038 Score: 123 Period size: 42 Copynumber: 3.9 Consensus size: 41 52604864 AATCATACCA ** * * * 52604874 ATGCCATATCCCAGATATGGTCTTTTATGGGATCTCATATCG 1 ATGCCATATCCCAGATATGGTCTTACA-CGAAACTCATATCG * * * * * ** 52604916 ATGCCAATAGCCTAGCTATAGTCTTACAAGATTCTCATATCG 1 ATGCC-ATATCCCAGATATGGTCTTACACGAAACTCATATCG * * * * * * 52604958 ACGCCATGTCCCAGACATGGTCCTACACAAAATCTCATAGCG 1 ATGCCATATCCCAGATATGGTCTTACACGAAA-CTCATATCG * 52605000 ATGCCATATCCCAGATATGGTCTTATACGTAAACTCATA 1 ATGCCATATCCCAGATATGGTCTTACACG-AAACTCATA 52605039 ACCCTAATAT Statistics Matches: 92, Mismatches: 28, Indels: 6 0.73 0.22 0.05 Matches are distributed among these distances: 41 16 0.17 42 57 0.62 43 19 0.21 ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29 Consensus pattern (41 bp): ATGCCATATCCCAGATATGGTCTTACACGAAACTCATATCG Found at i:52606911 original size:13 final size:13 Alignment explanation

Indices: 52606893--52606918 Score: 52 Period size: 13 Copynumber: 2.0 Consensus size: 13 52606883 TTAATACTTG 52606893 ACTGAAAATTGTT 1 ACTGAAAATTGTT 52606906 ACTGAAAATTGTT 1 ACTGAAAATTGTT 52606919 GTTATAGGCA Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 13 13 1.00 ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38 Consensus pattern (13 bp): ACTGAAAATTGTT Found at i:52620204 original size:42 final size:42 Alignment explanation

Indices: 52620051--52620215 Score: 158 Period size: 42 Copynumber: 3.9 Consensus size: 42 52620041 AATCATACCA * * ** 52620051 ATGCCATATCCCAGATATGGTTTTACATGGGATCTCATATCG 1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG * * * 52620093 ATGCCAATAGCGCAGCTATGGTCTTACA--AAATTCTCATATCG 1 ATGCC-ATATCCCAGATATGGTCTTACACGAAA-TCTCATATCG * * * * * 52620135 ATGCCATGTCCCAGACATGGTCCTACACGAAACCTCAT-TAGG 1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATAT-CG 52620177 ATGCCATATCCCAGATATGGTCTTACACGTAAA-CTCATA 1 ATGCCATATCCCAGATATGGTCTTACACG-AAATCTCATA 52620216 ACCCTAATGT Statistics Matches: 99, Mismatches: 17, Indels: 13 0.77 0.13 0.10 Matches are distributed among these distances: 41 18 0.18 42 57 0.58 43 24 0.24 ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28 Consensus pattern (42 bp): ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG Found at i:52622680 original size:20 final size:21 Alignment explanation

Indices: 52622655--52622694 Score: 55 Period size: 21 Copynumber: 2.0 Consensus size: 21 52622645 CTCTTGAAAC 52622655 AGGGC-ACACCCCCGTGTGGA 1 AGGGCAACACCCCCGTGTGGA * * 52622675 AGGGCAACACGCCTGTGTGG 1 AGGGCAACACCCCCGTGTGG 52622695 TTATTATAAC Statistics Matches: 17, Mismatches: 2, Indels: 1 0.85 0.10 0.05 Matches are distributed among these distances: 20 5 0.29 21 12 0.71 ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12 Consensus pattern (21 bp): AGGGCAACACCCCCGTGTGGA Found at i:52624017 original size:48 final size:46 Alignment explanation

Indices: 52623939--52624059 Score: 154 Period size: 48 Copynumber: 2.6 Consensus size: 46 52623929 CTCGTAGTCA * * 52623939 ATGCATGTCCTAGACATGTCTTACACTGGCTTACAT-TTGGAGGCCG 1 ATGCATGTCCCAGACATGTCTTACACTGGCTTACATAAT-GAGGCCG * * * * 52623985 ATGCCTTGTCCCAGACATGGTCTTACATTGGCTTTCATAATGTGGCCG 1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATAATGAGGCCG 52624033 ATGCATGTCCCAGACATGTCTTACACT 1 ATGCATGTCCCAGACATGTCTTACACT 52624060 AGCACACAAA Statistics Matches: 64, Mismatches: 8, Indels: 6 0.82 0.10 0.08 Matches are distributed among these distances: 46 12 0.19 47 25 0.39 48 26 0.41 49 1 0.02 ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31 Consensus pattern (46 bp): ATGCATGTCCCAGACATGTCTTACACTGGCTTACATAATGAGGCCG Found at i:52624055 original size:94 final size:92 Alignment explanation

Indices: 52623890--52624059 Score: 234 Period size: 92 Copynumber: 1.8 Consensus size: 92 52623880 CATATCCGTA * * 52623890 CCGATGCCATGTCCCAGACATGGTCTTACATTGACATATCTCGTAGTCAATGCATGTCCTAGACA 1 CCGATGCCATGTCCCAGACATGGTCTTACATTGACATATCTCGTAGCCAATGCATGTCCCAGACA 52623955 TGTCTTACACTGGCTTACATTTGGAGG 66 TGTCTTACACTGGCTTACATTTGGAGG * * * * * * 52623982 CCGATGCCTTGTCCCAGACATGGTCTTACATTGGC-TTTCATAATGTGGCCGATGCATGTCCCAG 1 CCGATGCCATGTCCCAGACATGGTCTTACATTGACATATC-T--CGTAGCCAATGCATGTCCCAG 52624046 ACATGTCTTACACT 63 ACATGTCTTACACT 52624060 AGCACACAAA Statistics Matches: 67, Mismatches: 8, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 91 3 0.04 92 34 0.51 94 30 0.45 ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31 Consensus pattern (92 bp): CCGATGCCATGTCCCAGACATGGTCTTACATTGACATATCTCGTAGCCAATGCATGTCCCAGACA TGTCTTACACTGGCTTACATTTGGAGG Found at i:52628633 original size:37 final size:37 Alignment explanation

Indices: 52628583--52628661 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 52628573 TTATTACGAA * * * 52628583 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG * 52628620 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG 52628657 GTCTT 1 GTCTT 52628662 TAGAGCTCGG Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG Found at i:52628883 original size:46 final size:47 Alignment explanation

Indices: 52628780--52628923 Score: 191 Period size: 47 Copynumber: 3.1 Consensus size: 47 52628770 CCCTTCGGGA * * * * * * * 52628780 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 52628827 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 52628873 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 52628920 CTTA 1 CTTA 52628924 CTATCATTTC Statistics Matches: 84, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 46 40 0.48 47 44 0.52 ACGTcount: A:0.26, C:0.31, G:0.10, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:52632825 original size:40 final size:40 Alignment explanation

Indices: 52632768--52632990 Score: 238 Period size: 40 Copynumber: 5.6 Consensus size: 40 52632758 CCAGCATGAT * * 52632768 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA * * * 52632808 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA * * 52632848 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA 1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA * * * * * * 52632888 TGCTCTTCAGGACTTAGCTCGGATTTAGTAACTCGCACCAA 1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACGAA * * 52632929 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA 1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACGAA * 52632969 AGC-CTTCGGGACTTAGCCCGGA 1 TGCTCTTCGGGACTTAGCCCGGA 52632991 CATCATTCGA Statistics Matches: 156, Mismatches: 22, Indels: 10 0.83 0.12 0.05 Matches are distributed among these distances: 39 3 0.02 40 133 0.85 41 20 0.13 ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26 Consensus pattern (40 bp): TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA Found at i:52632976 original size:120 final size:120 Alignment explanation

Indices: 52632755--52632990 Score: 289 Period size: 120 Copynumber: 2.0 Consensus size: 120 52632745 CGAATACACG * * * * * 52632755 TCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAA 1 TCACCAGCATGAATGCTCTTCAGGACTTAGCACGGATATATAACTAGCACCAATGCTCTTCGGAA * * 52632820 CTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA 66 CTTAGCCCGGATACATCACTAGCATCAAAGCTCTTCGGGACTTAGCCCGGATACA * * * * 52632875 TCACTAGCATGAATGCTCTTCAGGACTTAGCTCGGATTTAGTAACTCGCACCAATGC-CTTCGGA 1 TCACCAGCATGAATGCTCTTCAGGACTTAGCACGGATATA-TAACTAGCACCAATGCTCTTCGGA * * ** 52632939 TCTTAGTCCGGATATGGTCACTTAGCA-CAAAGC-CTTCGGGACTTAGCCCGGA 65 ACTTAGCCCGGATA-CATCAC-TAGCATCAAAGCTCTTCGGGACTTAGCCCGGA 52632991 CATCATTCGA Statistics Matches: 98, Mismatches: 15, Indels: 6 0.82 0.13 0.05 Matches are distributed among these distances: 120 72 0.73 121 21 0.21 122 5 0.05 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (120 bp): TCACCAGCATGAATGCTCTTCAGGACTTAGCACGGATATATAACTAGCACCAATGCTCTTCGGAA CTTAGCCCGGATACATCACTAGCATCAAAGCTCTTCGGGACTTAGCCCGGATACA Found at i:52633335 original size:29 final size:29 Alignment explanation

Indices: 52633296--52633374 Score: 106 Period size: 29 Copynumber: 2.7 Consensus size: 29 52633286 CTTAATAATC * 52633296 AACCACGCACACTTAGTGCCATGTACTTT-A 1 AACC-CGCACACTTAGTGCCATGCA-TTTCA * 52633326 AACTCGCACACTTAGTGCCATGCATTTCA 1 AACCCGCACACTTAGTGCCATGCATTTCA * 52633355 AGCCCGCACACTTAGTGCCA 1 AACCCGCACACTTAGTGCCA 52633375 ATCTCACAAC Statistics Matches: 44, Mismatches: 4, Indels: 3 0.86 0.08 0.06 Matches are distributed among these distances: 28 3 0.07 29 38 0.86 30 3 0.07 ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24 Consensus pattern (29 bp): AACCCGCACACTTAGTGCCATGCATTTCA Found at i:52633421 original size:43 final size:43 Alignment explanation

Indices: 52633356--52633501 Score: 274 Period size: 43 Copynumber: 3.4 Consensus size: 43 52633346 TGCATTTCAA 52633356 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * 52633399 GCCCGCACACTTAGTGCAAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT * 52633442 TCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT 52633485 GCCCGCACACTTAGTGC 1 GCCCGCACACTTAGTGC 52633502 TGAAAACCAA Statistics Matches: 99, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 43 99 1.00 ACGTcount: A:0.27, C:0.35, G:0.14, T:0.23 Consensus pattern (43 bp): GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT Found at i:52635406 original size:37 final size:37 Alignment explanation

Indices: 52635356--52635434 Score: 122 Period size: 37 Copynumber: 2.1 Consensus size: 37 52635346 TTATTACGAA * * * 52635356 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG * 52635393 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG 1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG 52635430 GTCTT 1 GTCTT 52635435 TAGAGCTCGG Statistics Matches: 38, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 37 38 1.00 ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24 Consensus pattern (37 bp): GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG Found at i:52635656 original size:46 final size:47 Alignment explanation

Indices: 52635553--52635696 Score: 191 Period size: 47 Copynumber: 3.1 Consensus size: 47 52635543 CCCTTCGGGA * * * * * * * 52635553 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * * 52635600 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC * 52635646 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC 1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC 52635693 CTTA 1 CTTA 52635697 CTATCATTTC Statistics Matches: 84, Mismatches: 12, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 46 40 0.48 47 44 0.52 ACGTcount: A:0.26, C:0.31, G:0.10, T:0.32 Consensus pattern (47 bp): CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC Found at i:52641459 original size:40 final size:40 Alignment explanation

Indices: 52641415--52641602 Score: 263 Period size: 40 Copynumber: 4.7 Consensus size: 40 52641405 GCTACTTGCT * 52641415 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAAGTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA 52641455 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA * ** * 52641495 CAAATGCCTTTGAAACTTAGCCCGGATATAGTAACTCGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA * * * ** 52641535 CAAATGCCTTCAGG-CTTAGCCCGG-AATTAGTCACGAGCA 1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA 52641574 CAAATGCCTTCGGGACTTAGCCCGGTTAT 1 CAAATGCCTTCGGGACTTAGCCCGGTTAT 52641603 CATCCGAATA Statistics Matches: 130, Mismatches: 15, Indels: 6 0.86 0.10 0.04 Matches are distributed among these distances: 38 1 0.01 39 32 0.25 40 96 0.74 41 1 0.01 ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24 Consensus pattern (40 bp): CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA Found at i:52651083 original size:49 final size:49 Alignment explanation

Indices: 52651019--52651193 Score: 244 Period size: 49 Copynumber: 3.5 Consensus size: 49 52651009 CTGGTACGCA * * * 52651019 TAGTAGCCTACACTTAGTACTATACATGCGACCAATTATCCGGTACACG 1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACG * * * * * 52651068 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCAGGTACGCA 1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCAGGTACACG 52651119 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-ATGGTACACG 1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCA-GGTACACG 52651168 TAGTAGCCTGCACTTAGTACTACACA 1 TAGTAGCCTGCACTTAGTACTACACA 52651194 CGTGACCTCA Statistics Matches: 110, Mismatches: 13, Indels: 6 0.85 0.10 0.05 Matches are distributed among these distances: 48 1 0.01 49 63 0.57 50 6 0.05 51 40 0.36 ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26 Consensus pattern (49 bp): TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCAGGTACACG Found at i:52651125 original size:51 final size:49 Alignment explanation

Indices: 52651006--52651200 Score: 239 Period size: 49 Copynumber: 3.9 Consensus size: 49 52650996 TAGCCGAAGC * * * * * 52651006 TATCTGGTACGCATAGTAGCCTACACTTAGTACTATACATGCGACCAAT 1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT * * * * 52651055 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT 1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T * * 52651106 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT 1 TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT * * 52651155 TAT-ATGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC 1 TATCA-GGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC 52651201 TCACAATAGC Statistics Matches: 125, Mismatches: 18, Indels: 6 0.84 0.12 0.04 Matches are distributed among these distances: 48 1 0.01 49 78 0.62 50 6 0.05 51 40 0.32 ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26 Consensus pattern (49 bp): TATCAGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT Found at i:52651173 original size:100 final size:100 Alignment explanation

Indices: 52651000--52651198 Score: 344 Period size: 100 Copynumber: 2.0 Consensus size: 100 52650990 CACTTGTAGC * * * 52651000 CGAAGCTATCTGGTACGCATAGTAGCCTACACTTAGTACTATACATGCGACCAATTATCCGGTAC 1 CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATACGGTAC 52651065 ACGTAGTAGCCTGCACTTAGTACTACACACGTGAT 66 ACGTAGTAGCCTGCACTTAGTACTACACACGTGAT * * * 52651100 CGAAGTTATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATATGGTAC 1 CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATACGGTAC 52651165 ACGTAGTAGCCTGCACTTAGTACTACACACGTGA 66 ACGTAGTAGCCTGCACTTAGTACTACACACGTGA 52651199 CCTCACAATA Statistics Matches: 93, Mismatches: 6, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 100 93 1.00 ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26 Consensus pattern (100 bp): CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATACGGTAC ACGTAGTAGCCTGCACTTAGTACTACACACGTGAT Found at i:52655370 original size:6 final size:6 Alignment explanation

Indices: 52655352--52655410 Score: 59 Period size: 6 Copynumber: 9.7 Consensus size: 6 52655342 AAGAAACATT * * 52655352 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATTAGA 1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA 52655401 ATCAGA ATCA 1 ATCAGA ATCA 52655411 ATATCAGGTA Statistics Matches: 44, Mismatches: 4, Indels: 10 0.76 0.07 0.17 Matches are distributed among these distances: 5 2 0.05 6 37 0.84 7 4 0.09 8 1 0.02 ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19 Consensus pattern (6 bp): ATCAGA Found at i:52655396 original size:31 final size:31 Alignment explanation

Indices: 52655361--52655439 Score: 97 Period size: 31 Copynumber: 2.5 Consensus size: 31 52655351 TATCAGAACT * 52655361 AGAATCAGAATCAGAATCAGA-ATCAGGTGAC 1 AGAATCAGAATCAGAATCA-ATATCAGGTAAC * * 52655392 AGAATTAGAATCAGAATCAATATCAGGTAAT 1 AGAATCAGAATCAGAATCAATATCAGGTAAC * * 52655423 AGAATCAAAACCAGAAT 1 AGAATCAGAATCAGAAT 52655440 GTGAATGCAA Statistics Matches: 41, Mismatches: 6, Indels: 2 0.84 0.12 0.04 Matches are distributed among these distances: 30 1 0.02 31 40 0.98 ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19 Consensus pattern (31 bp): AGAATCAGAATCAGAATCAATATCAGGTAAC Found at i:52655969 original size:27 final size:27 Alignment explanation

Indices: 52655833--52655975 Score: 178 Period size: 27 Copynumber: 5.3 Consensus size: 27 52655823 GGGGCAAAAT * * * * 52655833 GGTAATTTTACCCCACAAGGGTATCTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 52655860 AGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * * 52655887 GGTAATTATATCCTATAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * * 52655914 AGTAATTCTACCCATACAAGGGTATTTC 1 GGTAATTCTACCC-TACAGGGGTATTTC 52655942 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTCTACCCTACAGGGGTATTTC * 52655969 GATAATT 1 GGTAATT 52655976 TCACAAATTA Statistics Matches: 98, Mismatches: 17, Indels: 2 0.84 0.15 0.02 Matches are distributed among these distances: 27 74 0.76 28 24 0.24 ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34 Consensus pattern (27 bp): GGTAATTCTACCCTACAGGGGTATTTC Found at i:52655975 original size:55 final size:54 Alignment explanation

Indices: 52655833--52655968 Score: 191 Period size: 55 Copynumber: 2.5 Consensus size: 54 52655823 GGGGCAAAAT * * * * * 52655833 GGTAATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTATACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTC * * 52655887 GGTAATTATATCCTATAGGGGTATTTCAGTAATTCTACCCATACAAGGGTATTTC 1 GGTAATTATACCCTACAGGGGTATTTCAGTAATTCTACCC-TACAAGGGTATTTC * 52655942 GGTAATTCTACCCTACAGGGGTATTTC 1 GGTAATTATACCCTACAGGGGTATTTC 52655969 GATAATTTCA Statistics Matches: 71, Mismatches: 10, Indels: 1 0.87 0.12 0.01 Matches are distributed among these distances: 54 34 0.48 55 37 0.52 ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34 Consensus pattern (54 bp): GGTAATTATACCCTACAGGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTC Found at i:52656001 original size:82 final size:81 Alignment explanation

Indices: 52655832--52656002 Score: 220 Period size: 82 Copynumber: 2.1 Consensus size: 81 52655822 AGGGGCAAAA * * 52655832 TGGTAATTTTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGGTAATTATA 1 TGGTAATTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTATA ** 52655897 TCCTATAGGGGTATTT 66 TCAAATAGGGGTATTT ** * * * 52655913 CAGTAATTCTACCCATACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGATAATT-T 1 TGGTAATTCTACCC-CACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTAT 52655977 CA-CAAATTAGGGGTATTT 65 -ATCAAA-TAGGGGTATTT 52655995 TGGTAATT 1 TGGTAATT 52656003 TATTAATCGA Statistics Matches: 76, Mismatches: 11, Indels: 5 0.83 0.12 0.05 Matches are distributed among these distances: 81 14 0.18 82 62 0.82 ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36 Consensus pattern (81 bp): TGGTAATTCTACCCCACAAGGGTATCTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTATA TCAAATAGGGGTATTT Found at i:52656057 original size:27 final size:27 Alignment explanation

Indices: 52655987--52656264 Score: 144 Period size: 27 Copynumber: 10.6 Consensus size: 27 52655977 CACAAATTAG 52655987 GGGTATTTTGGTAA-TTTATTAATCGA 1 GGGTATTTTGGTAATTTTATTAATCGA * 52656013 GGGTATTTTGGTAATTTTATTGATCGA 1 GGGTATTTTGGTAATTTTATTAATCGA *** * * 52656040 GGGTATTTTGGTAATTTTGCAAACCAA 1 GGGTATTTTGGTAATTTTATTAATCGA ** * 52656067 GGGTATTTCAGTAATTTTATAAATCGA 1 GGGTATTTTGGTAATTTTATTAATCGA * *** * * * * 52656094 GAGTAAAATGGTAATTCTGTAAATTGA 1 GGGTATTTTGGTAATTTTATTAATCGA *** * * 52656121 GGGTAAAATGGTAATTCTATAAATCGA 1 GGGTATTTTGGTAATTTTATTAATCGA *** * 52656148 GGGTAAAATGGTAA--TT-CT-ATC-- 1 GGGTATTTTGGTAATTTTATTAATCGA * * ** 52656169 --TTATTTCGGTAATTTTACAAATCGA 1 GGGTATTTTGGTAATTTTATTAATCGA * * * * 52656194 GGATATTTGGGTAATTTTATAAATCGG 1 GGGTATTTTGGTAATTTTATTAATCGA * * 52656221 GGGTACTTTGGTAATTTTA-CAAGTCGA 1 GGGTATTTTGGTAATTTTATTAA-TCGA * 52656248 GGGTATTTTAGTAATTT 1 GGGTATTTTGGTAATTT 52656265 GATAAACTAA Statistics Matches: 197, Mismatches: 45, Indels: 19 0.75 0.17 0.07 Matches are distributed among these distances: 19 7 0.04 21 2 0.01 22 1 0.01 23 6 0.03 25 1 0.01 26 16 0.08 27 164 0.83 ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40 Consensus pattern (27 bp): GGGTATTTTGGTAATTTTATTAATCGA Found at i:52667008 original size:46 final size:45 Alignment explanation

Indices: 52666958--52667133 Score: 194 Period size: 46 Copynumber: 3.8 Consensus size: 45 52666948 TGGTTGAGCA 52666958 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G *** * * 52667004 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA- 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG * * 52667051 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G * * * 52667097 CCCGAGCTCGTTGAGTTGGGTCCGAGTTCACTTATGG 1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG 52667134 GCGGGTTACA Statistics Matches: 108, Mismatches: 15, Indels: 14 0.79 0.11 0.10 Matches are distributed among these distances: 43 1 0.01 44 3 0.03 45 1 0.01 46 67 0.62 47 31 0.29 48 1 0.01 49 3 0.03 50 1 0.01 ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29 Consensus pattern (45 bp): TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG Found at i:52667114 original size:93 final size:93 Alignment explanation

Indices: 52666955--52667125 Score: 288 Period size: 93 Copynumber: 1.8 Consensus size: 93 52666945 GGATGGTTGA * * 52666955 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT 52667020 TGAGTCCGAGTTCGAGAGATGTAACTAG 66 TGAGTCCGAGTTCGAGAGATGTAACTAG * * * 52667048 GCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT * 52667113 TGGGTCCGAGTTC 66 TGAGTCCGAGTTC 52667126 ACTTATGGGC Statistics Matches: 72, Mismatches: 6, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 93 72 1.00 ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT TGAGTCCGAGTTCGAGAGATGTAACTAG Found at i:52673224 original size:20 final size:20 Alignment explanation

Indices: 52673199--52673237 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 52673189 CAAATTTCAA 52673199 TTATTTCACACA-TTTACAAC 1 TTATTTCACA-ATTTTACAAC * 52673219 TTATTTTACAATTTTACAA 1 TTATTTCACAATTTTACAA 52673238 AATAGCCTTT Statistics Matches: 17, Mismatches: 1, Indels: 2 0.85 0.05 0.10 Matches are distributed among these distances: 19 1 0.06 20 16 0.94 ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46 Consensus pattern (20 bp): TTATTTCACAATTTTACAAC Found at i:52680302 original size:43 final size:43 Alignment explanation

Indices: 52680236--52680317 Score: 110 Period size: 43 Copynumber: 1.9 Consensus size: 43 52680226 CATGAATTGC * * * 52680236 ATCCATTATGAACCCGGACCTCTCAACAAGCTTGGATGCTCGT 1 ATCCATAATGAACCCGAACCTCTCAACAAGCTCGGATGCTCGT * * * 52680279 ATCCATAATGAACTCGAAGCTCTCAACGAGCTCGGATGC 1 ATCCATAATGAACCCGAACCTCTCAACAAGCTCGGATGC 52680318 CACATATATC Statistics Matches: 33, Mismatches: 6, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 43 33 1.00 ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23 Consensus pattern (43 bp): ATCCATAATGAACCCGAACCTCTCAACAAGCTCGGATGCTCGT Found at i:52682590 original size:72 final size:72 Alignment explanation

Indices: 52682441--52682617 Score: 198 Period size: 72 Copynumber: 2.5 Consensus size: 72 52682431 CGCATTTGAA * * * * 52682441 CTACTCACGGGTCTATACACAAAGTTAGCACCCGGACCCCAAAACATTATCATGTAATGGCCGTT 1 CTACTCACGGGTCTATACACAAAGTCAGCACCCGGAACCCAAAACATTAACATGTAATGGCCGCT * 52682506 CATTGAG 66 CAGTGAG * * * 52682513 CTACTCACGGGTTTATACACAAAGTCAGTACCCGGAACCCAAAGCATTAACATG-ATAT-GCTCG 1 CTACTCACGGGTCTATACACAAAGTCAGCACCCGGAACCCAAAACATTAACATGTA-ATGGC-CG 52682576 CTCAGTGAG 64 CTCAGTGAG * * * * 52682585 TTACTCACGGGCCTGAT-CACATAGTCAACACCC 1 CTACTCACGGGTCT-ATACACAAAGTCAGCACCC 52682618 AGACCCACAT Statistics Matches: 88, Mismatches: 14, Indels: 6 0.81 0.13 0.06 Matches are distributed among these distances: 71 3 0.03 72 83 0.94 73 2 0.02 ACGTcount: A:0.31, C:0.29, G:0.18, T:0.23 Consensus pattern (72 bp): CTACTCACGGGTCTATACACAAAGTCAGCACCCGGAACCCAAAACATTAACATGTAATGGCCGCT CAGTGAG Found at i:52692855 original size:27 final size:27 Alignment explanation

Indices: 52692825--52692886 Score: 83 Period size: 26 Copynumber: 2.3 Consensus size: 27 52692815 ATTTACTAAA 52692825 ATACCCCTAAGTATG-AAAATTACCATT 1 ATACCCCTAAG-ATGCAAAATTACCATT * 52692852 ATACCCCT-AGGTGCAAAATTACCATT 1 ATACCCCTAAGATGCAAAATTACCATT * 52692878 TTACCCCTA 1 ATACCCCTA 52692887 GGGTAAATTT Statistics Matches: 31, Mismatches: 2, Indels: 4 0.84 0.05 0.11 Matches are distributed among these distances: 25 2 0.06 26 21 0.68 27 8 0.26 ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29 Consensus pattern (27 bp): ATACCCCTAAGATGCAAAATTACCATT Found at i:52693030 original size:27 final size:27 Alignment explanation

Indices: 52692992--52693104 Score: 158 Period size: 27 Copynumber: 4.2 Consensus size: 27 52692982 GAGGAAGCAT * 52692992 TCTGATGGCTCTGCCACAAATATCTG-A 1 TCTGGTGGCTCTGCCAC-AATATCTGTA * 52693019 TCTGGTGGCTCTGCCACAAATATCTGTT 1 TCTGGTGGCTCTGCCAC-AATATCTGTA * 52693047 TCTAGTGGCTCTGCCACAATATCTGTA 1 TCTGGTGGCTCTGCCACAATATCTGTA * 52693074 TCTGGTGGCTCTGTCACAATATCTGT- 1 TCTGGTGGCTCTGCCACAATATCTGTA 52693100 TCTGG 1 TCTGG 52693105 AAGCCATGCT Statistics Matches: 79, Mismatches: 6, Indels: 3 0.90 0.07 0.03 Matches are distributed among these distances: 26 5 0.06 27 58 0.73 28 16 0.20 ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35 Consensus pattern (27 bp): TCTGGTGGCTCTGCCACAATATCTGTA Found at i:52693098 original size:54 final size:55 Alignment explanation

Indices: 52692997--52693100 Score: 176 Period size: 55 Copynumber: 1.9 Consensus size: 55 52692987 AGCATTCTGA 52692997 TGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGTTTCTAG 1 TGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGTTTCTAG * 52693052 TGGCTCTGCCAC-AATATCTGTATCTGGTGGCTCTGTCAC-AATATCTGTT 1 TGGCTCTGCCACAAATATCTG-ATCTGGTGGCTCTGCCACAAATATCTGTT 52693101 CTGGAAGCCA Statistics Matches: 47, Mismatches: 1, Indels: 3 0.92 0.02 0.06 Matches are distributed among these distances: 54 18 0.38 55 29 0.62 ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35 Consensus pattern (55 bp): TGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTGTTTCTAG Found at i:52699683 original size:40 final size:40 Alignment explanation

Indices: 52699613--52699869 Score: 358 Period size: 40 Copynumber: 6.5 Consensus size: 40 52699603 AAACCAAGTA * * * * 52699613 CCTTCGGAATTTAG-CCGGATATAGCT-ACTCGCTCAAATG 1 CCTTCGGGACTTAGCCCGGAAATAG-TAACTCGCACAAATG * ** 52699652 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG * 52699692 CCTTCGGGACTTAGCCCGGACATAGTAACTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG * * 52699732 CCTTCGGG-CTTAGCCTGGAAATAGTAACTCACACAAATG 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG * * 52699771 CCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATA 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG * * 52699811 CCTTCAGGACTTAGCCCGGAAATAGTAATTCGCACAAATG 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG 52699851 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 52699870 TTATCATCCG Statistics Matches: 195, Mismatches: 20, Indels: 5 0.89 0.09 0.02 Matches are distributed among these distances: 39 48 0.25 40 147 0.75 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23 Consensus pattern (40 bp): CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG Found at i:52699767 original size:79 final size:79 Alignment explanation

Indices: 52699613--52699869 Score: 347 Period size: 79 Copynumber: 3.2 Consensus size: 79 52699603 AAACCAAGTA * * * * * ** 52699613 CCTTCGGAATTTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGACTTGGCCCGGTTATA 1 CCTTCGGGACTTAGCCCGGAAATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAATA 52699676 GTAACTCGCACAAATG 64 GTAACTCGCACAAATG * * 52699692 CCTTCGGGACTTAGCCCGGACATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCTGGAAATAGT 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAATAGT * 52699757 AACTCACACAAATG 66 AACTCGCACAAATG * * * 52699771 CCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATACCTTCAGGACTTAGCCCGGAAATAG 1 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTC-GGGCTTAGCCCGGAAATAG * 52699836 TAATTCGCACAAATG 65 TAACTCGCACAAATG 52699851 CCTTCGGGACTTAGCCCGG 1 CCTTCGGGACTTAGCCCGG 52699870 TTATCATCCG Statistics Matches: 158, Mismatches: 17, Indels: 5 0.88 0.09 0.03 Matches are distributed among these distances: 79 81 0.51 80 77 0.49 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23 Consensus pattern (79 bp): CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAATAGT AACTCGCACAAATG Found at i:52699824 original size:119 final size:120 Alignment explanation

Indices: 52699646--52699866 Score: 363 Period size: 119 Copynumber: 1.9 Consensus size: 120 52699636 GCTACTCGCT * *** * * 52699646 CAAATGCCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG 1 CAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATACCTTCAGGACTTAGCCCGG * 52699711 ACATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCTGGAAATAGTAACTCACA 66 AAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCTGGAAATAGTAACTCACA 52699765 CAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATACCTTCAGGACTTAGCCCGG 1 CAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATACCTTCAGGACTTAGCCCGG * 52699830 AAATAGTAATTCGCACAAATGCCTTCGGGACTTAGCC 66 AAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCC 52699867 CGGTTATCAT Statistics Matches: 93, Mismatches: 8, Indels: 1 0.91 0.08 0.01 Matches are distributed among these distances: 119 86 0.92 120 7 0.08 ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22 Consensus pattern (120 bp): CAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATACCTTCAGGACTTAGCCCGG AAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCTGGAAATAGTAACTCACA Found at i:52707278 original size:40 final size:40 Alignment explanation

Indices: 52707185--52707430 Score: 374 Period size: 40 Copynumber: 6.2 Consensus size: 40 52707175 CCTTCAGAAT * * 52707185 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTC-GGAC 1 TTAGCCCGGAAATAG-TAACTCGCACAAATGCCTTCGGGAC ** 52707223 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC 1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC * * 52707263 TTAGCCCGGACATAGTAACTAGCACAAATGCCTTCGGG-C 1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC 52707302 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC 1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC * 52707342 TTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGAC 1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC * * 52707382 TTAGCCCGAAAATAGTAACTCGCACAAATGCCTTCGAGAC 1 TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC 52707422 TTAGCCCGG 1 TTAGCCCGG 52707431 TTATCATCCG Statistics Matches: 192, Mismatches: 12, Indels: 6 0.91 0.06 0.03 Matches are distributed among these distances: 38 5 0.03 39 63 0.33 40 124 0.65 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22 Consensus pattern (40 bp): TTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGAC Found at i:52707305 original size:79 final size:79 Alignment explanation

Indices: 52707208--52707430 Score: 367 Period size: 79 Copynumber: 2.8 Consensus size: 79 52707198 GCTACTCGCT * ** 52707208 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGCTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA 52707273 CA-TAGTAACTAGCA 66 -ATTAGTAACTAGCA 52707287 CAAATGCCTTCGGGCTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA 1 CAAATGCCTTCGGGCTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA * 52707352 ATTAGTAACTCGCA 66 ATTAGTAACTAGCA * * 52707366 CAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGG 1 CAAATGCCTTCGGG-CTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG 52707431 TTATCATCCG Statistics Matches: 136, Mismatches: 6, Indels: 3 0.94 0.04 0.02 Matches are distributed among these distances: 78 1 0.01 79 87 0.64 80 48 0.35 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22 Consensus pattern (79 bp): CAAATGCCTTCGGGCTTAGCCCGGAAATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA ATTAGTAACTAGCA Found at i:52707385 original size:119 final size:119 Alignment explanation

Indices: 52707185--52707430 Score: 374 Period size: 119 Copynumber: 2.1 Consensus size: 119 52707175 CCTTCAGAAT * * * 52707185 TTAG-CCGGATATAGCTACTCGCTCAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACA 1 TTAGCCCGGAAATAGCTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA * * * 52707249 AATGCCTTCGGGACTTAGCCCGGACATAGTAACTAGCACAAATGCCTTCG-GGC 66 AATGCCTTCGGGACTTAGCCCGAAAATAGTAACTAGCACAAATGCCTTCGAGAC 52707302 TTAGCCCGGAAATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGC 1 TTAGCCCGGAAATAGCT-ACTCGCACAAATGCCTTC-GGACTTAGCCCGGATA-TAGTAACTCGC * 52707365 ACAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTCGCACAAATGCCTTCGAGAC 63 ACAAATGCCTTCGGGACTTAGCCCGAAAATAGTAACTAGCACAAATGCCTTCGAGAC 52707422 TTAGCCCGG 1 TTAGCCCGG 52707431 TTATCATCCG Statistics Matches: 117, Mismatches: 7, Indels: 7 0.89 0.05 0.05 Matches are distributed among these distances: 117 5 0.04 118 27 0.23 119 74 0.63 120 11 0.09 ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22 Consensus pattern (119 bp): TTAGCCCGGAAATAGCTACTCGCACAAATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA AATGCCTTCGGGACTTAGCCCGAAAATAGTAACTAGCACAAATGCCTTCGAGAC Found at i:52712214 original size:79 final size:81 Alignment explanation

Indices: 52712078--52712260 Score: 223 Period size: 79 Copynumber: 2.3 Consensus size: 81 52712068 TCGAATGATG * * 52712078 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT 52712142 TGTGCGAGATACTA-A 66 TGTGCGAGATACTATA * * * ** 52712157 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA 1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA * 52712219 TTTGTGCGAGTTACTATA 64 TTTGTGCGAGATACTATA * * 52712237 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATT 52712261 TGAACGAGTA Statistics Matches: 89, Mismatches: 10, Indels: 8 0.83 0.09 0.07 Matches are distributed among these distances: 78 1 0.01 79 58 0.65 80 30 0.34 ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT TGTGCGAGATACTATA Found at i:52712276 original size:40 final size:40 Alignment explanation

Indices: 52712079--52712262 Score: 207 Period size: 40 Copynumber: 4.6 Consensus size: 40 52712069 CGAATGATGT * * * * 52712079 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT 1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA * * * 52712119 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT 1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A * 52712159 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA 1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA * 52712197 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA 1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA * 52712238 CCGGGCTATGTCCCGAAGGCATTTG 1 CCGGGCTAAGTCCCGAAGGCATTTG 52712263 AACGAGTAGC Statistics Matches: 124, Mismatches: 13, Indels: 14 0.82 0.09 0.09 Matches are distributed among these distances: 39 34 0.27 40 80 0.65 41 10 0.08 ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24 Consensus pattern (40 bp): CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA Found at i:52712284 original size:79 final size:79 Alignment explanation

Indices: 52712131--52712295 Score: 201 Period size: 79 Copynumber: 2.1 Consensus size: 79 52712121 GGACTAAGAT * ** 52712131 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA 1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA * 52712196 ATCCGGGTTAAGTC 66 ATCCGGGTTAAATC * * * 52712210 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC 1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C * * 52712273 TATATCC-GGTTAAATT 63 TAAATCCGGGTTAAATC 52712289 CCGAAGG 1 CCGAAGG 52712296 TACGTGATTT Statistics Matches: 74, Mismatches: 9, Indels: 6 0.83 0.10 0.07 Matches are distributed among these distances: 78 2 0.03 79 48 0.65 80 24 0.32 ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25 Consensus pattern (79 bp): CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA ATCCGGGTTAAATC Found at i:52719025 original size:40 final size:40 Alignment explanation

Indices: 52718981--52719111 Score: 192 Period size: 40 Copynumber: 3.3 Consensus size: 40 52718971 GGACTAAGAT * 52718981 CCGAAGGTATTTGTGCGAGTTATTAATTCCGGGTTAAGTC 1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC * * * 52719021 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC 1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC * * 52719061 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC 1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC 52719101 CCGAAGGCATT 1 CCGAAGGCATT 52719112 GAATGAGTTA Statistics Matches: 81, Mismatches: 9, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 39 1 0.01 40 80 0.99 ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29 Consensus pattern (40 bp): CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC Found at i:52719132 original size:39 final size:38 Alignment explanation

Indices: 52719009--52719158 Score: 131 Period size: 40 Copynumber: 3.8 Consensus size: 38 52718999 GTTATTAATT * ** * * 52719009 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT 1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A ** * 52719049 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA * 52719088 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA 1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA * * 52719128 CCGGGCTATGTCCCGAAGGCACTTGAACGAG 1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG 52719159 GAGCTATATC Statistics Matches: 93, Mismatches: 11, Indels: 12 0.80 0.09 0.10 Matches are distributed among these distances: 39 30 0.32 40 63 0.68 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (38 bp): CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA Found at i:52719166 original size:40 final size:39 Alignment explanation

Indices: 52719049--52719171 Score: 97 Period size: 40 Copynumber: 3.1 Consensus size: 39 52719039 GATACTAATT * ** ** * 52719049 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA 1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA * * * 52719088 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA 1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA * * 52719128 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT 1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA 52719168 CCGG 1 CCGG 52719172 TTAAATTCCG Statistics Matches: 69, Mismatches: 11, Indels: 6 0.80 0.13 0.07 Matches are distributed among these distances: 39 25 0.36 40 44 0.64 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24 Consensus pattern (39 bp): CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA Found at i:52726615 original size:40 final size:40 Alignment explanation

Indices: 52726531--52726714 Score: 196 Period size: 40 Copynumber: 4.6 Consensus size: 40 52726521 TTGAATGCTG * * * * 52726531 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT ** * 52726570 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT 1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT * * * 52726611 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT * * 52726651 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT 52726691 TCCGGGTTAAGTCCCGAAGGCATT 1 TCCGGGTTAAGTCCCGAAGGCATT 52726715 GAATGAGTTA Statistics Matches: 123, Mismatches: 16, Indels: 10 0.83 0.11 0.07 Matches are distributed among these distances: 39 2 0.02 40 111 0.90 41 10 0.08 ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28 Consensus pattern (40 bp): TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT Found at i:52726668 original size:80 final size:81 Alignment explanation

Indices: 52726531--52726711 Score: 221 Period size: 80 Copynumber: 2.3 Consensus size: 81 52726521 TTGAATGCTG * * * 52726531 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT * * 52726595 TGTGCGAGTTATT-AAT 66 CGTGCGAGTT-TTAAAA ** 52726611 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC 52726672 ATTCGTGCGAGTTTTAAAA 63 ATTCGTGCGAGTTTTAAAA 52726691 TCCGGGTTAAGTCCCGAAGGC 1 TCCGGGTTAAGTCCCGAAGGC 52726712 ATTGAATGAG Statistics Matches: 89, Mismatches: 7, Indels: 10 0.84 0.07 0.09 Matches are distributed among these distances: 79 4 0.04 80 76 0.85 81 9 0.10 ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28 Consensus pattern (81 bp): TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT CGTGCGAGTTTTAAAA Found at i:52726735 original size:39 final size:38 Alignment explanation

Indices: 52726612--52726761 Score: 131 Period size: 40 Copynumber: 3.8 Consensus size: 38 52726602 GTTATTAATT * ** * * 52726612 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT 1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A ** * 52726652 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA 1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA * 52726691 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA 1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA * * 52726731 CCGGGCTATGTCCCGAAGGCACTTGAACGAG 1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG 52726762 GAGCTAAATC Statistics Matches: 93, Mismatches: 11, Indels: 12 0.80 0.09 0.10 Matches are distributed among these distances: 39 30 0.32 40 63 0.68 ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25 Consensus pattern (38 bp): CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA Found at i:52730242 original size:22 final size:22 Alignment explanation

Indices: 52730207--52730258 Score: 72 Period size: 22 Copynumber: 2.4 Consensus size: 22 52730197 ATGCGTATTG * 52730207 AGTTA-TAATATGTAATG-CATT 1 AGTTAGTAAAATGT-ATGCCATT 52730228 AGTTAGTAAAATGTATGCCATT 1 AGTTAGTAAAATGTATGCCATT 52730250 AGTTAGTAA 1 AGTTAGTAA 52730259 TATATTATCT Statistics Matches: 28, Mismatches: 1, Indels: 3 0.88 0.03 0.09 Matches are distributed among these distances: 21 8 0.29 22 20 0.71 ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38 Consensus pattern (22 bp): AGTTAGTAAAATGTATGCCATT Found at i:52730509 original size:79 final size:81 Alignment explanation

Indices: 52730368--52730550 Score: 205 Period size: 79 Copynumber: 2.3 Consensus size: 81 52730358 TCGAATGATG * * 52730368 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT 52730432 TGTGCAAGATACTA-A 66 TGTGCAAGATACTATA * * * ** * 52730447 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGACGGCA 1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA * * 52730509 TTTGTGCGAGTTACTATA 64 TTTGTGCAAGATACTATA * * 52730527 ACCGGGCTATGTCCCGAAGGCATT 1 TCCGGGCTAAGTCCCGAAGGCATT 52730551 TGAACGAGTA Statistics Matches: 87, Mismatches: 12, Indels: 8 0.81 0.11 0.07 Matches are distributed among these distances: 78 1 0.01 79 56 0.64 80 30 0.34 ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25 Consensus pattern (81 bp): TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT TGTGCAAGATACTATA Found at i:52730559 original size:40 final size:40 Alignment explanation

Indices: 52730368--52730552 Score: 207 Period size: 40 Copynumber: 4.7 Consensus size: 40 52730358 TCGAATGATG * * * * 52730368 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA * * * * 52730408 TCCGGACTAAGAT-CCGAAGGCATTTGTGCAAGATACTAAT 1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA * 52730448 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA * * 52730487 TCCGGGTTAAGTCCCGACGGCATTTGTGCGAGTTACTATAA 1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA * 52730528 -CCGGGCTATGTCCCGAAGGCATTTG 1 TCCGGGCTAAGTCCCGAAGGCATTTG 52730553 AACGAGTAGC Statistics Matches: 123, Mismatches: 17, Indels: 10 0.82 0.11 0.07 Matches are distributed among these distances: 39 33 0.27 40 80 0.65 41 10 0.08 ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25 Consensus pattern (40 bp): TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA Done.