Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold1024

Parameters: 2 7 7 80 10 50 500

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

Length: 1774716
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 201941 characters in sequence are not A, C, G, or T


File 3 of 5

Found at i:463100 original size:27 final size:27

Alignment explanation

Indices: 463069--463168 Score: 121 Period size: 27 Copynumber: 3.7 Consensus size: 27 463059 ATATCATGAC * * 463069 TTACAAGTTGATAAGCCTAATAATAAT 1 TTACAAGTTGATAAGGCTAATCATAAT * * 463096 TTACAATTTGATAAGGCTAATCAT-TT 1 TTACAAGTTGATAAGGCTAATCATAAT * * 463122 CTTACATGTTGATAAGGCTAATCATAAC 1 -TTACAAGTTGATAAGGCTAATCATAAT * 463150 TTACAAGTTGATATGGCTA 1 TTACAAGTTGATAAGGCTA 463169 CTCCTTGGAA Statistics Matches: 61, Mismatches: 10, Indels: 4 0.81 0.13 0.05 Matches are distributed among these distances: 26 1 0.02 27 60 0.98 ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36 Consensus pattern (27 bp): TTACAAGTTGATAAGGCTAATCATAAT Found at i:464611 original size:4 final size:4 Alignment explanation

Indices: 464602--464661 Score: 63 Period size: 4 Copynumber: 15.0 Consensus size: 4 464592 TACCCTTGTG * 464602 TGTC TGTC TGTT TGTC TGTCC T-TC TGTC TGT- TCGTC TGTCC T-TC TGTC 1 TGTC TGTC TGTC TGTC TGT-C TGTC TGTC TGTC T-GTC TGT-C TGTC TGTC 464650 TGTC TGTC TGTC 1 TGTC TGTC TGTC 464662 CGTCCGTAAC Statistics Matches: 48, Mismatches: 2, Indels: 12 0.77 0.03 0.19 Matches are distributed among these distances: 3 5 0.10 4 38 0.79 5 5 0.10 ACGTcount: A:0.00, C:0.27, G:0.22, T:0.52 Consensus pattern (4 bp): TGTC Found at i:464629 original size:20 final size:20 Alignment explanation

Indices: 464604--464662 Score: 100 Period size: 20 Copynumber: 3.0 Consensus size: 20 464594 CCCTTGTGTG 464604 TCTGTCTGTTTGTCTGTCCT 1 TCTGTCTGTTTGTCTGTCCT * 464624 TCTGTCTGTTCGTCTGTCCT 1 TCTGTCTGTTTGTCTGTCCT * 464644 TCTGTCTGTCTGTCTGTCC 1 TCTGTCTGTTTGTCTGTCC 464663 GTCCGTAACA Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 36 1.00 ACGTcount: A:0.00, C:0.29, G:0.20, T:0.51 Consensus pattern (20 bp): TCTGTCTGTTTGTCTGTCCT Found at i:465486 original size:166 final size:166 Alignment explanation

Indices: 464692--465486 Score: 1117 Period size: 166 Copynumber: 4.8 Consensus size: 166 464682 GTCGCATTTA * * * * 464692 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTTAAGGCAAGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT * * * 464757 CGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACAACTTTGCTTATTTT 66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTA-TTT * * 464822 TTAACCAAAATTTTCAAACAAATTTTTGTCAAAGATT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * * 464859 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTTACACAATATTTGTATGGGTATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT * ** 464924 TGTGGGATATATTTTTGTACCAATCGGGCGTCAATTTCCTGTTAAATGACGACTTTGTTTATTTT 66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT * * 464989 TAGCAAAAATTTTCAAACAAATTTTTGTCAAAG-TAT 131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGAT-T * * * * 465025 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT * * * 465090 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTTAATGA-GTACTTTGTTTATTT 66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACG-ACTTTGTTTATTT * * * 465154 TTAGCCAAAATTTTCAAACAAATTTCCGTCAATGAAT 130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 465191 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT ** * * * * 465256 TGTGGGATATATTTTTGTGTCAATCGGACGTCACCTTCCTGTTAGATAATGACTTTGTTTATTTT 66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT 465321 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 465357 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT * *** * * * * * 465422 TGTGGGATATATTTCTGTACCAATCGGATACCAGCTTTCTGTTCAATGTCTACTTTGCTTATTTT 66 TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT 465487 GCATATTCAT Statistics Matches: 560, Mismatches: 64, Indels: 9 0.88 0.10 0.01 Matches are distributed among these distances: 165 2 0.00 166 445 0.79 167 113 0.20 ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40 Consensus pattern (166 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACACTATTTGTTTAGGCATGCCATAT TGTGGGATATATTTTTGTACCAATCGGACGTCAGCTTCCTGTTAAATGACGACTTTGTTTATTTT TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT Found at i:469683 original size:15 final size:15 Alignment explanation

Indices: 469663--469692 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 469653 GTTTTTTTTC 469663 ATTATTATTATTATA 1 ATTATTATTATTATA 469678 ATTATTATTATTATA 1 ATTATTATTATTATA 469693 GGAAATACTC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60 Consensus pattern (15 bp): ATTATTATTATTATA Found at i:473425 original size:2 final size:2 Alignment explanation

Indices: 473418--473448 Score: 62 Period size: 2 Copynumber: 15.5 Consensus size: 2 473408 GCATACACAA 473418 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A 473449 TCTTCACCAT Statistics Matches: 29, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00 Consensus pattern (2 bp): AG Found at i:480570 original size:25 final size:25 Alignment explanation

Indices: 480542--480594 Score: 70 Period size: 25 Copynumber: 2.1 Consensus size: 25 480532 TTATAAAAAC * * * 480542 ATCACATTGCTATTTATTGAATACT 1 ATCACATTGATATTAATTAAATACT * 480567 ATCACATTGATATTAATTAAATGCT 1 ATCACATTGATATTAATTAAATACT 480592 ATC 1 ATC 480595 CAGACTTTAC Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 25 24 1.00 ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42 Consensus pattern (25 bp): ATCACATTGATATTAATTAAATACT Found at i:481268 original size:163 final size:160 Alignment explanation

Indices: 480949--481444 Score: 655 Period size: 163 Copynumber: 3.1 Consensus size: 160 480939 TGTACCAACT * * * * * 480949 GTTTCCGTTCATTTTCTTCGCAA-AGTATGCACAAAATGAAATGAAATTTAGTATACAGATTTAT 1 GTTTCCGTTCATTTTTTTCG-AAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTAT * * * * * * * 481013 C--AATA-ATATAGGTCAAGTTCGATTTTGGGTGAGATCGAGCAATTTTCGATAGAGTTGTGCCC 65 CATAATATATCTAGGTCAACTTTGATTTTGAGTGCGATCGAGCAATTTTCGACAGAGTTATGCCC 481075 CTTGGACGTAGAAAAATTCCAATTATTTGCA 130 CTTGGACGTAGAAAAATTCCAATTATTTGCA * * 481106 GTTTCCATTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTGGTATACAGGTTTATC 1 GTTTCCGTTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTATC * * 481171 ATAATAGTATCTAGGTCAACTTTGATTTTGAGTGCG-TCGGGGAGCAATTTTCAACAGAGCTATG 66 ATAATA-TATCTAGGTCAACTTTGATTTTGAGTGCGATC---GAGCAATTTTCGACAGAGTTATG 481235 CCCCTTGGACGTAGAAAAATTCCAATTATTTGCA 127 CCCCTTGGACGTAGAAAAATTCCAATTATTTGCA * * 481269 GTTTCCGTTCATTTTCTTT-GCAGAGGATGCACATATTAAAATGAAATTTAGTATACAGGTTTAT 1 GTTTCCGTTCATTTT-TTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTAT * * 481333 CATAATAATATCTAGGTCAACTTTGATTTTCGA-TACGATCGAGCAATTTTCGACAGAGTTATGT 65 CATAAT-ATATCTAGGTCAACTTTGATTTT-GAGTGCGATCGAGCAATTTTCGACAGAGTTATGC * * * 481397 GCCTTGGACTTAGAAAAATTCCAATTATTTGTA 128 CCCTTGGACGTAGAAAAATTCCAATTATTTGCA * 481430 GGTTCCGTTCATTTT 1 GTTTCCGTTCATTTT 481445 CTATGGAGAT Statistics Matches: 299, Mismatches: 28, Indels: 20 0.86 0.08 0.06 Matches are distributed among these distances: 156 2 0.01 157 55 0.18 159 4 0.01 160 2 0.01 161 88 0.29 163 140 0.47 164 8 0.03 ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36 Consensus pattern (160 bp): GTTTCCGTTCATTTTTTTCGAAGAGGATGCACATATTGAAATGAAATTTAGTATACAGGTTTATC ATAATATATCTAGGTCAACTTTGATTTTGAGTGCGATCGAGCAATTTTCGACAGAGTTATGCCCC TTGGACGTAGAAAAATTCCAATTATTTGCA Found at i:487695 original size:166 final size:166 Alignment explanation

Indices: 487485--488184 Score: 1025 Period size: 166 Copynumber: 4.2 Consensus size: 166 487475 TTTTTAAAAA * * 487485 AAAAATCTTCTTCTCAAGAATCATAA--AGTCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA 1 AAAAATCTTCTTCTC-AGAAAC-TAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCA * * * 487548 GGTAGTGTAGATTAAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGTGGCCACAA-TGGGG 64 GGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGG * 487612 GCTCGAAGTTTTACATAGGAAAATATAGAGTAAATCTTT 129 G-TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT * 487651 AAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG ** 487716 TAGTGTAGATTCAAAGTTGTGAAAATTGTGACCCCCGGGGGTAGGGTGGGGCCACAA-TGGGGGA 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGG- * 487780 TCGAAGTTTTACATAGGAATATATAGAGTAAATTTTT 130 TCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT * * 487817 AAAAATCCTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGGAACTTGTGTGGAAGCATCCTCAGG 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG * ** * * 487882 TAGTGTAGATTCCAAGTTGTGAAAATCATGA-CCATGGGGGTAGGATGGGGCCACAATTGGGGGT 66 TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGGT 487946 CGAAGTTTTACATAGGAATATATAGAGTAAAT-TTT 131 CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT * * * * * * 487981 AAAAAATCCTCTTCTCGGAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGTATCCTTAG 1 -AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAG * * 488046 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGTGGGAAGGGTGGGGCCACCATAGTGGG 65 GTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCA-CA-AGTGGG * ** * 488111 TGTTAAAGTTTTACATAGGAATGTATAGAGTAAATCTTT 128 GGTCGAAGTTTTACATAGGAATATATAGAGTAAATCTTT * 488150 TAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAA 1 AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAA 488185 TGAAACTCAT Statistics Matches: 485, Mismatches: 41, Indels: 14 0.90 0.08 0.03 Matches are distributed among these distances: 164 6 0.01 165 148 0.31 166 259 0.53 167 2 0.00 168 67 0.14 169 3 0.01 ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26 Consensus pattern (166 bp): AAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGG TAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAAGTGGGGGT CGAAGTTTTACATAGGAATATATAGAGTAAATCTTT Found at i:488095 original size:331 final size:334 Alignment explanation

Indices: 487514--488184 Score: 1032 Period size: 331 Copynumber: 2.0 Consensus size: 334 487504 ATCATAAAGT * 487514 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAATTCAT 1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT * * * 487579 GACCCCCGGGGGTAGGGTGTGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA 66 GACCCACGGGGGTAGGATGGGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA * * * 487644 AATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCAT 131 AATCTTTAAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGCAT ** * 487709 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATTGTGACCCCCGGGGGTAGGGTGGGGCCA-CA- 196 CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACCAT * 487772 A-TGGGGGATCGAAGTTTTACATAGGAATATATAGAGTAAAT-TTTTAAAAATCCTCTTCTCAGA 261 AGTGGGGG-TCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTT-AAAATCCTCTTCTCAGA 487835 AACTAATCAGC 324 AACTAATCAGC * ** 487846 CAGGAAAGCTGGAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCCAAGTTGTGAAAATCAT 1 CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT * * 487911 GA-CCATGGGGGTAGGATGGGGCCACAATTGGGGG-TCGAAGTTTTACATAGGAATATATAGAGT 66 GACCCACGGGGGTAGGATGGGGCCACAA-TGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGT ** * 487974 AAAT-TTTAAAAAATCCTCTTCTCGGAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGT 130 AAATCTTT-AAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGC * * 488038 ATCCTTAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGTGGGAAGGGTGGGGCCACC 194 ATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACC * * * * 488103 ATAGTGGGTGTTAAAGTTTTACATAGGAATGTATAGAGTAAATCTTTTAAAATCTTCTTCTCAGA 259 ATAGTGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTTAAAATCCTCTTCTCAGA 488168 AACTAATCAGC 324 AACTAATCAGC 488179 CAGGAA 1 CAGGAA 488185 TGAAACTCAT Statistics Matches: 308, Mismatches: 25, Indels: 11 0.90 0.07 0.03 Matches are distributed among these distances: 330 3 0.01 331 161 0.52 332 71 0.23 333 64 0.21 334 9 0.03 ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26 Consensus pattern (334 bp): CAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTAAAAGTTGTGAAAATCAT GACCCACGGGGGTAGGATGGGGCCACAATGGGGGCTCGAAGTTTTACATAGGAAAATATAGAGTA AATCTTTAAAAATCCTCTTCTCAAAAACGAATCAGCCAGGAAAGCTGAAACTTGTGTAGAAGCAT CCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGAAGGGTGGGGCCACCAT AGTGGGGGTCAAAGTTTTACATAGGAATATATAGAGTAAATCTTTTAAAATCCTCTTCTCAGAAA CTAATCAGC Found at i:493205 original size:16 final size:16 Alignment explanation

Indices: 493174--493213 Score: 55 Period size: 16 Copynumber: 2.6 Consensus size: 16 493164 CACATTTTTT 493174 TCTGTC-GTCAGGCCG 1 TCTGTCTGTCAGGCCG * * 493189 TGTGTCTGTCAGTCCG 1 TCTGTCTGTCAGGCCG 493205 TCTGTCTGT 1 TCTGTCTGT 493214 AAACTTTTTA Statistics Matches: 21, Mismatches: 3, Indels: 1 0.84 0.12 0.04 Matches are distributed among these distances: 15 5 0.24 16 16 0.76 ACGTcount: A:0.05, C:0.28, G:0.30, T:0.38 Consensus pattern (16 bp): TCTGTCTGTCAGGCCG Found at i:494493 original size:15 final size:16 Alignment explanation

Indices: 494475--494512 Score: 51 Period size: 17 Copynumber: 2.4 Consensus size: 16 494465 CACTCGATGG 494475 CTCGAACTTC-GATCT 1 CTCGAACTTCTGATCT * 494490 CTCGAAGTTCTTGATCT 1 CTCGAACTTC-TGATCT 494507 CTCGAA 1 CTCGAA 494513 GTGAACTCGC Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 15 9 0.45 17 11 0.55 ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34 Consensus pattern (16 bp): CTCGAACTTCTGATCT Found at i:502770 original size:53 final size:54 Alignment explanation

Indices: 502665--502775 Score: 143 Period size: 53 Copynumber: 2.0 Consensus size: 54 502655 AGCTTAGATT * * 502665 CTGTAAGAAGACCCTATTTTGTAATTATGTACAATATCAATACACATGTACATCGAA 1 CTGTAAGAAGACACTATTTTG--A-TATGTACAATACCAATACACATGTACATCGAA * * * 502722 CTGTAAGAAGACACTATTTTG-TATGTATAATACCAATACACATTTACATTGAA 1 CTGTAAGAAGACACTATTTTGATATGTACAATACCAATACACATGTACATCGAA 502775 C 1 C 502776 ACATGGACAG Statistics Matches: 49, Mismatches: 5, Indels: 4 0.84 0.09 0.07 Matches are distributed among these distances: 53 29 0.59 57 20 0.41 ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32 Consensus pattern (54 bp): CTGTAAGAAGACACTATTTTGATATGTACAATACCAATACACATGTACATCGAA Found at i:503061 original size:23 final size:23 Alignment explanation

Indices: 503030--503079 Score: 73 Period size: 23 Copynumber: 2.2 Consensus size: 23 503020 TTGAGCCAAT * * 503030 AAAATATTCACTCACAAAAAAAA 1 AAAATATTCACCCAAAAAAAAAA * 503053 AAAANATTCACCCAAAAAAAAAA 1 AAAATATTCACCCAAAAAAAAAA 503076 AAAA 1 AAAA 503080 AAAAAAAAAA Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 23 24 1.00 ACGTcount: A:0.70, C:0.16, G:0.00, T:0.12 Consensus pattern (23 bp): AAAATATTCACCCAAAAAAAAAA Found at i:503070 original size:1 final size:1 Alignment explanation

Indices: 503066--503094 Score: 58 Period size: 1 Copynumber: 29.0 Consensus size: 1 503056 ANATTCACCC 503066 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA 503095 TCATTCAGTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 28 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:509789 original size:2 final size:2 Alignment explanation

Indices: 509782--509838 Score: 114 Period size: 2 Copynumber: 28.5 Consensus size: 2 509772 CAAGACTGAG 509782 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 509824 CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT C 509839 GCACGTACGC Statistics Matches: 55, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 55 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:509869 original size:14 final size:14 Alignment explanation

Indices: 509848--509887 Score: 53 Period size: 14 Copynumber: 2.9 Consensus size: 14 509838 CGCACGTACG * 509848 CACAAACACACGCA 1 CACAAACACACACA * 509862 CGCAAACACACACA 1 CACAAACACACACA * 509876 CACACACACACA 1 CACAAACACACA 509888 TATTTAATAT Statistics Matches: 22, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 14 22 1.00 ACGTcount: A:0.50, C:0.45, G:0.05, T:0.00 Consensus pattern (14 bp): CACAAACACACACA Found at i:510144 original size:16 final size:16 Alignment explanation

Indices: 510125--510155 Score: 53 Period size: 16 Copynumber: 1.9 Consensus size: 16 510115 CACTGCGACA 510125 AGGCATCACCTTTATG 1 AGGCATCACCTTTATG * 510141 AGGCGTCACCTTTAT 1 AGGCATCACCTTTAT 510156 AAGACCACCT Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 16 14 1.00 ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32 Consensus pattern (16 bp): AGGCATCACCTTTATG Found at i:510338 original size:17 final size:17 Alignment explanation

Indices: 510318--510352 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 510308 AAAATATACA 510318 ATATTGAATCCTATGAT 1 ATATTGAATCCTATGAT 510335 ATATTGAATCCTATGAT 1 ATATTGAATCCTATGAT 510352 A 1 A 510353 CTTACAATAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40 Consensus pattern (17 bp): ATATTGAATCCTATGAT Found at i:515907 original size:12 final size:12 Alignment explanation

Indices: 515890--515925 Score: 63 Period size: 12 Copynumber: 3.0 Consensus size: 12 515880 TTCAATTAAG 515890 GTTTTTTTTTTT 1 GTTTTTTTTTTT * 515902 GTTTTTGTTTTT 1 GTTTTTTTTTTT 515914 GTTTTTTTTTTT 1 GTTTTTTTTTTT 515926 TGCAAAATAA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89 Consensus pattern (12 bp): GTTTTTTTTTTT Found at i:515926 original size:6 final size:6 Alignment explanation

Indices: 515890--515924 Score: 54 Period size: 6 Copynumber: 6.0 Consensus size: 6 515880 TTCAATTAAG * 515890 GTTTTT TTTTTT GTTTTT GTTTTT GTTTTT -TTTTT 1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT 515925 TTGCAAAATA Statistics Matches: 27, Mismatches: 2, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 5 5 0.19 6 22 0.81 ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89 Consensus pattern (6 bp): GTTTTT Found at i:516673 original size:18 final size:18 Alignment explanation

Indices: 516630--516664 Score: 61 Period size: 18 Copynumber: 1.9 Consensus size: 18 516620 ATGTAAAGTT * 516630 ACATATACATATATATAA 1 ACATATACAAATATATAA 516648 ACATATACAAATATATA 1 ACATATACAAATATATA 516665 CGCATATACC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31 Consensus pattern (18 bp): ACATATACAAATATATAA Found at i:523238 original size:10 final size:11 Alignment explanation

Indices: 523205--523244 Score: 55 Period size: 11 Copynumber: 3.6 Consensus size: 11 523195 GGATACCCTA 523205 TTTTAAGACAAC 1 TTTTAA-ACAAC 523217 TTTTAAACAAC 1 TTTTAAACAAC * 523228 TTTT-TACAAC 1 TTTTAAACAAC 523238 TTTTAAA 1 TTTTAAA 523245 AATATGCAAG Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 10 9 0.36 11 10 0.40 12 6 0.24 ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42 Consensus pattern (11 bp): TTTTAAACAAC Found at i:523620 original size:30 final size:30 Alignment explanation

Indices: 523586--523648 Score: 90 Period size: 30 Copynumber: 2.1 Consensus size: 30 523576 AGTTATTCAG * * * 523586 AAAATGGGAAGGTGGAATTCGGATGCTTTT 1 AAAATGAGAAGATGGAATTCAGATGCTTTT * 523616 AAAATGAGAAGATGGAATTTAGATGCTTTT 1 AAAATGAGAAGATGGAATTCAGATGCTTTT 523646 AAA 1 AAA 523649 CACTACATTT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 30 29 1.00 ACGTcount: A:0.38, C:0.05, G:0.27, T:0.30 Consensus pattern (30 bp): AAAATGAGAAGATGGAATTCAGATGCTTTT Found at i:556635 original size:177 final size:176 Alignment explanation

Indices: 556433--556799 Score: 506 Period size: 177 Copynumber: 2.1 Consensus size: 176 556423 GGGTCCTCAA * ** * 556433 TTTCAGATGCTTGAGAAGGTTAAGGTTTTTGGAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTTT 1 TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT * * 556498 GATAGCA-ATATCTAAG-TAACTGCTGGT-TCTAACTTCACCAAACTTGCATGGATGGTGTGTCA 66 GAT-G-ATATATCTAAGCT-ACTACTGGTCT-TAACTTCACCAAACTTGCATGGATGGTGCGTCA * * 556560 TATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCTATGGG 127 TATGATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG * * * * 556610 TTTCGGATGCTGGAGGAGGTTAAGGTTTTTAAAGCTGGTTAAAGTTTTTGTTGCAGGTGCCCTCT 1 TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT * * * 556675 GATGATTATATCTTAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGTTGGTGCGTCTTAT 66 GATGA-TATATCTAAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGATGGTGCGTCATAT * * 556740 GATACTGATGCTCGAGACAGGCTTGAATGCTGAATCTGAGCCATAGG 130 GATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG * 556787 TTTCAGAGGCTGG 1 TTTCAGATGCTGG 556800 TTGAGGTAAA Statistics Matches: 167, Mismatches: 19, Indels: 8 0.86 0.10 0.04 Matches are distributed among these distances: 175 1 0.01 176 1 0.01 177 163 0.98 178 2 0.01 ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33 Consensus pattern (176 bp): TTTCAGATGCTGGAGAAGGTTAAGGTTTTTAAAGCAGGGTAAAGTTTTTGTTGCAGGTGCCCTCT GATGATATATCTAAGCTACTACTGGTCTTAACTTCACCAAACTTGCATGGATGGTGCGTCATATG ATACTGATGCACCAGACAGGCTTGAATGCTGAATCTGAGCCATAGG Found at i:557736 original size:15 final size:15 Alignment explanation

Indices: 557718--557777 Score: 51 Period size: 15 Copynumber: 4.3 Consensus size: 15 557708 TATTTTACTA 557718 TATCACATTATATTG 1 TATCACATTATATTG * 557733 TATCA-TTTGATA-TG 1 TATCACATT-ATATTG 557747 -AT-ACA--ATATTG 1 TATCACATTATATTG * 557758 TATCAAATTATATTG 1 TATCACATTATATTG 557773 TATCA 1 TATCA 557778 TATGATACAA Statistics Matches: 35, Mismatches: 3, Indels: 14 0.67 0.06 0.27 Matches are distributed among these distances: 10 3 0.09 11 2 0.06 12 3 0.09 13 4 0.11 14 4 0.11 15 19 0.54 ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45 Consensus pattern (15 bp): TATCACATTATATTG Found at i:558278 original size:16 final size:16 Alignment explanation

Indices: 558257--558290 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 558247 TAAAGGTGGT * 558257 CTAATAAAGGTGATGC 1 CTAATAAAAGTGATGC 558273 CTAATAAAAGTGATGC 1 CTAATAAAAGTGATGC 558289 CT 1 CT 558291 CGTCTCGGTG Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26 Consensus pattern (16 bp): CTAATAAAAGTGATGC Found at i:560426 original size:46 final size:46 Alignment explanation

Indices: 560345--560464 Score: 215 Period size: 46 Copynumber: 2.6 Consensus size: 46 560335 ACCATTAACT 560345 ATATAAAAGGACTATA-TTTTGGCGGAACTAATTAAAAAATTATCC 1 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC * * 560390 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAACAATTATCT 1 ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC 560436 ATATAAAAGGACTATATTTTTGGCGGAAC 1 ATATAAAAGGACTATATTTTTGGCGGAAC 560465 ATTGACGTAG Statistics Matches: 72, Mismatches: 2, Indels: 1 0.96 0.03 0.01 Matches are distributed among these distances: 45 16 0.22 46 56 0.78 ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33 Consensus pattern (46 bp): ATATAAAAGGACTATATTTTTGGCGGAACTAATTAAAAAATTATCC Found at i:563738 original size:2 final size:2 Alignment explanation

Indices: 563731--563783 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 563721 CTTCACCCAC 563731 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 563773 AG AG AG AG AG A 1 AG AG AG AG AG A 563784 TAAGGTCATG Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:567483 original size:21 final size:20 Alignment explanation

Indices: 567455--567494 Score: 71 Period size: 21 Copynumber: 1.9 Consensus size: 20 567445 GTACATAAAT 567455 GTACATACATTCTGTTGATA 1 GTACATACATTCTGTTGATA 567475 GTACGATACATTCTGTTGAT 1 GTAC-ATACATTCTGTTGAT 567495 TATTTAATTT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 4 0.21 21 15 0.79 ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40 Consensus pattern (20 bp): GTACATACATTCTGTTGATA Found at i:570277 original size:12 final size:12 Alignment explanation

Indices: 570260--570285 Score: 52 Period size: 12 Copynumber: 2.2 Consensus size: 12 570250 CCCGTTGTCC 570260 GTCCGTCCGTCT 1 GTCCGTCCGTCT 570272 GTCCGTCCGTCT 1 GTCCGTCCGTCT 570284 GT 1 GT 570286 AAACTTTTCA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 14 1.00 ACGTcount: A:0.00, C:0.38, G:0.27, T:0.35 Consensus pattern (12 bp): GTCCGTCCGTCT Found at i:570738 original size:166 final size:167 Alignment explanation

Indices: 570435--570775 Score: 495 Period size: 166 Copynumber: 2.0 Consensus size: 167 570425 AATAGGGTGC * * 570435 ATGTCTTTAAAAATCTTTTTCTCAAGAACCACTGCACCAGAAATGCAAATTTTTACACAAAAGCT 1 ATGT-TTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCT * * * 570500 TGTATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCGGACCAAAACTGGGGCCCCAG 65 TGCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAG * 570565 ACGGGGTTCAAAGTTAAACATAGAAATACAT-AGGAAA 130 ACGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA * * 570602 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCCAACTTTTATACAAAAGCTT 1 ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCTT * * * * ** * 570667 GCATATATTGTGAAGATTCTAAATTGTAAAAATCGTGATCCTCATACCACTACTGGGCCCCCAGG 66 GCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAGA **** 570732 CGGGGTTCAAAGTTTTTTATAGAAATACATAAGAAAA 131 CGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA 570769 ATGTTTT 1 ATGTTTT 570776 CATGACTTTT Statistics Matches: 154, Mismatches: 19, Indels: 2 0.88 0.11 0.01 Matches are distributed among these distances: 166 138 0.90 167 16 0.10 ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28 Consensus pattern (167 bp): ATGTTTTAAAAATCTTCTTCTCAAGAACCACTGCACCAGAAATGCAAACTTTTACACAAAAGCTT GCATATATAGTGAAGATTCTAAATTATAAAAATCGTGACCCTCAGACCAAAACTGGGCCCCCAGA CGGGGTTCAAAGTTAAACATAGAAATACATAAGAAAA Found at i:572407 original size:165 final size:165 Alignment explanation

Indices: 572157--572564 Score: 439 Period size: 165 Copynumber: 2.5 Consensus size: 165 572147 CGGTATATAT * * * * * * 572157 GGAAAATGTTTAAAAATCTTCTTT-TCGAGAACTACAATGCATCAATTTGTCAGATAACTACGTA 1 GGAAAATGTTTAAAAATCTT-TTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCA * * * * 572221 AGCACCCTCAAATAGTGTAGATTCGAAATTA-TAAAAGCCGTGA-C-CTCAATCTAATACTGGGG 65 AGCATCCTCAAATAATGTAGATTCCAAATAATTAAAA--CGTGAGCACTCAA-CTAATACTGGGG * * * * 572283 CCCCAAGAGGTGTTCAAAGTTTAGCATAGAAATATAGAG 127 CCCCAAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG * * * * 572322 GGAAAATGTTGAAAAATCTTTTTCTAGGGAACTATAATGCTTCAGCTTGTGAGATAACTATGCAA 1 GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA * * * ** * 572387 GCATCCTTAAATAATGTAGATTCCAAATAATTAAAACTTTAGCACTGGACTAATACTGTGGCCCC 66 GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACGTGAGCACTCAACTAATACTGGGGCCCC * * 572452 AAAAGGGGTTCAAAGTTTAACATAGAAAGATATAT 131 AAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG * * * * * 572487 TGAAAATGTTTTTAAAAA-GTTCTTCTCGAGAACTATAATGCTACAGTTTGTGAGATTACTATGC 1 GGAAAATG--TTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGC * 572551 AAGGATCCTCAAAT 64 AAGCATCCTCAAAT 572565 TGTGTAAACT Statistics Matches: 200, Mismatches: 37, Indels: 11 0.81 0.15 0.04 Matches are distributed among these distances: 164 6 0.03 165 128 0.64 166 59 0.29 167 7 0.04 ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30 Consensus pattern (165 bp): GGAAAATGTTTAAAAATCTTTTTCTCGAGAACTATAATGCTTCAGTTTGTGAGATAACTATGCAA GCATCCTCAAATAATGTAGATTCCAAATAATTAAAACGTGAGCACTCAACTAATACTGGGGCCCC AAAAGGGGTTCAAAGTTTAACATAGAAAGATAGAG Found at i:573309 original size:2 final size:2 Alignment explanation

Indices: 573302--573343 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 573292 CTCCCCCTCC 573302 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 573344 ACCTCTACCT Statistics Matches: 40, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 40 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:573349 original size:12 final size:11 Alignment explanation

Indices: 573301--573349 Score: 66 Period size: 10 Copynumber: 4.5 Consensus size: 11 573291 CCTCCCCCTC 573301 CCTCTCTCTCT 1 CCTCTCTCTCT 573312 -CTCTCTCTCT 1 CCTCTCTCTCT 573322 -CTCTCTCTCT 1 CCTCTCTCTCT 573332 CTCTCTCTCTCT 1 C-CTCTCTCTCT 573344 ACCTCT 1 -CCTCT 573350 ACCTCTACCT Statistics Matches: 35, Mismatches: 0, Indels: 5 0.88 0.00 0.12 Matches are distributed among these distances: 10 20 0.57 12 14 0.40 13 1 0.03 ACGTcount: A:0.02, C:0.51, G:0.00, T:0.47 Consensus pattern (11 bp): CCTCTCTCTCT Found at i:574536 original size:11 final size:11 Alignment explanation

Indices: 574506--574539 Score: 52 Period size: 11 Copynumber: 3.1 Consensus size: 11 574496 AGGTGTGTCT 574506 TAAAA-AAGGG 1 TAAAACAAGGG 574516 TAACAACAAGGG 1 TAA-AACAAGGG 574528 TAAAACAAGGG 1 TAAAACAAGGG 574539 T 1 T 574540 TTTAGGGTTC Statistics Matches: 22, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 10 3 0.14 11 11 0.50 12 8 0.36 ACGTcount: A:0.53, C:0.09, G:0.26, T:0.12 Consensus pattern (11 bp): TAAAACAAGGG Found at i:576699 original size:15 final size:16 Alignment explanation

Indices: 576671--576701 Score: 55 Period size: 15 Copynumber: 2.0 Consensus size: 16 576661 GTCAACACAG 576671 TCAATCAGTTAAATCA 1 TCAATCAGTTAAATCA 576687 TCAATCA-TTAAATCA 1 TCAATCAGTTAAATCA 576702 ATGGTCTCTC Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 15 8 0.53 16 7 0.47 ACGTcount: A:0.45, C:0.19, G:0.03, T:0.32 Consensus pattern (16 bp): TCAATCAGTTAAATCA Found at i:576975 original size:24 final size:24 Alignment explanation

Indices: 576942--576987 Score: 65 Period size: 24 Copynumber: 1.9 Consensus size: 24 576932 TTTACTTCGT * 576942 TATAATAGTAATTCGCTATATCGG 1 TATAAGAGTAATTCGCTATATCGG * * 576966 TATAAGAGTAATTTGTTATATC 1 TATAAGAGTAATTCGCTATATC 576988 AGTCAAGTTT Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 24 19 1.00 ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41 Consensus pattern (24 bp): TATAAGAGTAATTCGCTATATCGG Found at i:577307 original size:65 final size:65 Alignment explanation

Indices: 577225--577541 Score: 431 Period size: 65 Copynumber: 4.9 Consensus size: 65 577215 CGGGCCATTC * 577225 ACCTCGCGCCTCAAAACCATCCTCAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT 1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT * * * * 577290 ACCTCGCACCTCAAAACCATCATAAACACCATCAAATACCTAACTAGTGTAAGTAAATGATCGTT 1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT * * * 577355 ACCTCGCACCTCAAAACCATCATAAACACCATCAAATACCTAACTAGT-TAAGTAAACGATCGTT 1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT * * * * * 577419 ACCTCGCGCCTCAAAACTATCCTCAACACCATCAAATACATACCCAGTGTAAGAAAACGA-CTGT 1 ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATC-GT 577483 T 65 T * * * ** * 577484 CACCTCACGCCTCAAATCCATCCTTAACACCATCAGGTACCTATCCAGTGTAAGTAAA 1 -ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAA 577542 AAACCAGTCA Statistics Matches: 226, Mismatches: 23, Indels: 5 0.89 0.09 0.02 Matches are distributed among these distances: 64 57 0.25 65 121 0.54 66 48 0.21 ACGTcount: A:0.37, C:0.32, G:0.10, T:0.21 Consensus pattern (65 bp): ACCTCGCGCCTCAAAACCATCCTAAACACCATCAAATACCTAACCAGTGTAAGTAAACGATCGTT Found at i:577908 original size:16 final size:16 Alignment explanation

Indices: 577887--577920 Score: 68 Period size: 16 Copynumber: 2.1 Consensus size: 16 577877 TATATAGAGG 577887 GTTATTTTTGCCCTGT 1 GTTATTTTTGCCCTGT 577903 GTTATTTTTGCCCTGT 1 GTTATTTTTGCCCTGT 577919 GT 1 GT 577921 AAACTTTTGC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.06, C:0.18, G:0.21, T:0.56 Consensus pattern (16 bp): GTTATTTTTGCCCTGT Found at i:577928 original size:17 final size:16 Alignment explanation

Indices: 577892--577933 Score: 57 Period size: 16 Copynumber: 2.6 Consensus size: 16 577882 AGAGGGTTAT * * 577892 TTTTGCCCTGTGTTAT 1 TTTTGCCCTGTGTAAC 577908 TTTTGCCCTGTGTAAAC 1 TTTTGCCCTGTGT-AAC 577925 TTTTGCCCT 1 TTTTGCCCT 577934 TCTACACTTG Statistics Matches: 23, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 16 13 0.57 17 10 0.43 ACGTcount: A:0.10, C:0.24, G:0.17, T:0.50 Consensus pattern (16 bp): TTTTGCCCTGTGTAAC Found at i:579454 original size:16 final size:16 Alignment explanation

Indices: 579430--579466 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 579420 AGAGGTCAGG * * 579430 GACAGCCTCATTCTGA 1 GACAACCTCATTCTAA 579446 GACAACCTCATTCTAA 1 GACAACCTCATTCTAA 579462 GACAA 1 GACAA 579467 AGTCCTTAAT Statistics Matches: 19, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 16 19 1.00 ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22 Consensus pattern (16 bp): GACAACCTCATTCTAA Found at i:582147 original size:2 final size:2 Alignment explanation

Indices: 582140--582205 Score: 125 Period size: 2 Copynumber: 33.5 Consensus size: 2 582130 GTTTAACAAC 582140 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 582182 AG AG AG AG AG AG -G AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG A 582206 ACCATATGTA Statistics Matches: 63, Mismatches: 0, Indels: 2 0.97 0.00 0.03 Matches are distributed among these distances: 1 1 0.02 2 62 0.98 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:583728 original size:37 final size:39 Alignment explanation

Indices: 583654--583730 Score: 104 Period size: 37 Copynumber: 1.9 Consensus size: 39 583644 CGCACCTGTT * 583654 ACAGTCAGGTGGGTATACAGTAAATCTGTGTGGTTAACGTTC 1 ACAGTCAGGTGGGTATA-AG--AATCTGTGTGATTAACGTTC 583696 ACAGTCAGGTGGGTAT-AG-ATCTGTGTGATTAACGT 1 ACAGTCAGGTGGGTATAAGAATCTGTGTGATTAACGT 583731 CCCCAACACA Statistics Matches: 34, Mismatches: 1, Indels: 5 0.85 0.03 0.12 Matches are distributed among these distances: 37 16 0.47 40 2 0.06 42 16 0.47 ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31 Consensus pattern (39 bp): ACAGTCAGGTGGGTATAAGAATCTGTGTGATTAACGTTC Found at i:583914 original size:67 final size:67 Alignment explanation

Indices: 583801--583964 Score: 204 Period size: 67 Copynumber: 2.4 Consensus size: 67 583791 AAGGCAACGC * * * * * * 583801 GCCTGTTACAGTCAGGTGGGTATAAATCTACTGTAAACAATGAATTTAGCAATGTACTGTACAAC 1 GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC 583866 AT 66 AT * * 583868 GCCTATTACAATCTGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAT 1 GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC * 583933 GT 66 AT * * * 583935 GCCTGTTACAGTCATGTG-GATATAAATCTA 1 GCCTATTACAATCAGGTGAG-TATAAATCTA 583965 GTACATATAC Statistics Matches: 83, Mismatches: 13, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 66 1 0.01 67 82 0.99 ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31 Consensus pattern (67 bp): GCCTATTACAATCAGGTGAGTATAAATCTACTGTAAACAATAAATTTAGAAAAGTACTGTACAAC AT Found at i:587652 original size:18 final size:18 Alignment explanation

Indices: 587631--587672 Score: 66 Period size: 18 Copynumber: 2.3 Consensus size: 18 587621 CTCTTGATTT 587631 AGCTATATAGCTTGAAAA 1 AGCTATATAGCTTGAAAA * * 587649 AGCTATATAGCTTTATAA 1 AGCTATATAGCTTGAAAA 587667 AGCTAT 1 AGCTAT 587673 TCAAAATAGC Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 18 22 1.00 ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33 Consensus pattern (18 bp): AGCTATATAGCTTGAAAA Found at i:588235 original size:18 final size:18 Alignment explanation

Indices: 588211--588252 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 588201 GCTACTCTGA 588211 ATAGCTTAATAAAGCTAT 1 ATAGCTTAATAAAGCTAT * * * 588229 TTAGCTTATTCAAGCTAT 1 ATAGCTTAATAAAGCTAT 588247 ATAGCT 1 ATAGCT 588253 AAATCTGGAG Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38 Consensus pattern (18 bp): ATAGCTTAATAAAGCTAT Found at i:589951 original size:2 final size:2 Alignment explanation

Indices: 589938--590689 Score: 390 Period size: 2 Copynumber: 355.5 Consensus size: 2 589928 GGATTGTCTC * ** ** * * 589938 AG AG AA AG AG AG AG AG AG AG AG AG AG CTC TC AA AG AA AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG * ** ** 589981 AG AG AG AG AG CG AG CTC AG AG AG AG AG CTC AG AG AG AG AG AG A- 1 AG AG AG AG AG AG AG -AG AG AG AG AG AG -AG AG AG AG AG AG AG AG ** 590024 AG AG AG AG AG AG AG AG AG AG AG AG AG CTT ATG CAG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG -AG A-G -AG AG AG AG AG ** ** 590067 CTC AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG CTC AG AG AG AG 1 -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG ** * * * 590111 AG AG AG AG AG AG AG AG AG CTC TG AG AG AT AG AG AG AG CTG AG AG 1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG AG ** ** * 590155 AG AG AG AG AG AG AG AG CTC AG AG AG AG AG AG AG AG CTC TG AG AG 1 AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG AG AG * * * 590199 AG AG AG AG AG AG AG CTG AG AG AG AG AG AG AG TG GG AG AG AG AG 1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * ** * ** 590242 AG AG TG GG AG AG AG AG AG AG CTC AG AG AG AT AG AG AG AG CTC AG 1 AG AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG -AG AG * ** * * ** 590286 AG AG AG AG AG AG AG CTG CTC AG AG AG GG GG AG AG AG CTC AG AG 1 AG AG AG AG AG AG AG -AG -AG AG AG AG AG AG AG AG AG -AG AG AG ** ** ** 590329 AG AG AG AG AG AG CTC ATG CAG AG AG AG CTC AG AG AG AG AG AG CTC 1 AG AG AG AG AG AG -AG A-G -AG AG AG AG -AG AG AG AG AG AG AG -AG ** 590374 ATG CAG AG AG AG AG AG AG CTC AG AG AG AG AG AG AG AG AG AG AG 1 A-G -AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG ** * 590417 ATG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG CTC AG AG AG GG 1 A-G AG AG AG AG AG AG AG AG AG AG AG AG AG A-G -AG AG AG AG AG * ** ** 590460 GG AG AG AG CTC AG AG AG AG AG AG AG AG AG AG AG CTC ATG CAG AG 1 AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG -AG A-G -AG AG * * 590504 AG AG AG AG AG AG AG AG AG AA AG AG AG AG ATC AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG ** * * ** 590547 AG AG AG AG AG TAG CTC AG AG AG GG GG AG AG AG CTC AG AG AG AG 1 AG AG AG AG AG -AG -AG AG AG AG AG AG AG AG AG -AG AG AG AG AG ** ** 590590 AG AG AG AG AG CTC ATG CAG AG AG AG AG AG AG AG CTC AG AG AG AG 1 AG AG AG AG AG -AG A-G -AG AG AG AG AG AG AG AG -AG AG AG AG AG * ** * * * 590634 AG AG GG AG AG AG AG CTC AG AG AG AG AG TG GG AG AG AG AG AA AG 1 AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG * * 590677 GG AA AG AG AG AG A 1 AG AG AG AG AG AG A 590690 ATTATCTTGT Statistics Matches: 566, Mismatches: 143, Indels: 82 0.72 0.18 0.10 Matches are distributed among these distances: 1 1 0.00 2 544 0.96 3 16 0.03 4 5 0.01 ACGTcount: A:0.42, C:0.08, G:0.44, T:0.06 Consensus pattern (2 bp): AG Found at i:589975 original size:31 final size:31 Alignment explanation

Indices: 589934--589997 Score: 110 Period size: 31 Copynumber: 2.1 Consensus size: 31 589924 GGTAGGATTG * 589934 TCTCAGAGAAAGAGAGAGAGAGAGAGAGAGC 1 TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC * 589965 TCTCAAAGAAAGAGAGAGAGAGAGAGCGAGC 1 TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC 589996 TC 1 TC 589998 AGAGAGAGAG Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 31 31 1.00 ACGTcount: A:0.44, C:0.12, G:0.36, T:0.08 Consensus pattern (31 bp): TCTCAAAGAAAGAGAGAGAGAGAGAGAGAGC Found at i:590003 original size:13 final size:13 Alignment explanation

Indices: 589985--590660 Score: 117 Period size: 13 Copynumber: 56.8 Consensus size: 13 589975 AGAGAGAGAG * 589985 AGAGAGCGAGCTC 1 AGAGAGAGAGCTC 589998 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590011 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590021 AGA-AGAGAG--- 1 AGAGAGAGAGCTC 590030 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590040 AGAGAGAGAGCTTATGC 1 AGAGAGAGAGC---T-C 590057 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590070 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590080 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590090 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC *** 590103 AGAGAGAGAGAGAGAG 1 --AGAGAGAGAG-CTC 590119 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC * 590132 TGAGAGATAGAGAGAGCTG 1 ----AG--AGAGAGAGCTC 590151 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590161 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590174 ----AGAGAG--- 1 AGAGAGAGAGCTC 590180 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC * 590193 TGAGAGAGAG--- 1 AGAGAGAGAGCTC * 590203 AGAGAGAGAGCTG 1 AGAGAGAGAGCTC 590216 AGAGAGAGAG--- 1 AGAGAGAGAGCTC * * ** 590226 AGAGTGGGAG-AG 1 AGAGAGAGAGCTC * *** 590238 AGAGAGAGTGGGAG 1 AGAGAGAG-AGCTC 590252 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590265 --AGAGAGA--T- 1 AGAGAGAGAGCTC 590273 --AGAGAGAGCTC 1 AGAGAGAGAGCTC 590284 AGAGAGAGAG--- 1 AGAGAGAGAGCTC ** 590294 AGAGAG-CTGCTC 1 AGAGAGAGAGCTC ** 590306 AGAGAG-G-G-GG 1 AGAGAGAGAGCTC ** 590316 AGAGAGCTCAGAG-AG 1 AGAGAG---AGAGCTC 590331 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590344 ATGCAGAGAGAGCTC 1 A-G-AGAGAGAGCTC 590359 AGAGAGAGAGAGCTC 1 --AGAGAGAGAGCTC * * 590374 A-TG-CAGAG--- 1 AGAGAGAGAGCTC 590382 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC ** 590395 AGAGAGAGAG-AG 1 AGAGAGAGAGCTC * 590407 AGAGAGAGAGAT- 1 AGAGAGAGAGCTC 590419 -GAGAGAGAG--- 1 AGAGAGAGAGCTC 590428 AGAGAGAGAG--- 1 AGAGAGAGAGCTC 590438 AGAGAGAGATGCTC 1 AGAGAGAGA-GCTC 590452 AGAGAG-G-G--- 1 AGAGAGAGAGCTC 590460 -G-GAGAGAGCTC 1 AGAGAGAGAGCTC ** 590471 AGAGAGAGAG-AG 1 AGAGAGAGAGCTC 590483 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC ** 590496 ATGCAGAGAGAG-AG 1 A-G-AGAGAGAGCTC ** 590510 AGAGAGAGAG-AG 1 AGAGAGAGAGCTC * * 590522 AAAGAGAGAGATC 1 AGAGAGAGAGCTC *** 590535 AGAGAGAGAGAGAG 1 AGAGAGAGAG-CTC 590549 AGAGAGAGTAGCTC 1 AGAGAGAG-AGCTC 590563 AGAGAG-G-G--- 1 AGAGAGAGAGCTC 590571 -G-GAGAGAGCTC 1 AGAGAGAGAGCTC 590582 --AGAGAGAG--- 1 AGAGAGAGAGCTC 590590 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC * 590603 ATG-CAGAGAG--- 1 A-GAGAGAGAGCTC 590613 AGAGAGAGAGCTC 1 AGAGAGAGAGCTC ** 590626 AGAGAGAGAG-AG 1 AGAGAGAGAGCTC * 590638 GGAGAGAGAGCTC 1 AGAGAGAGAGCTC 590651 AGAGAGAGAG 1 AGAGAGAGAG 590661 TGGGAGAGAG Statistics Matches: 509, Mismatches: 58, Indels: 192 0.67 0.08 0.25 Matches are distributed among these distances: 6 6 0.01 7 4 0.01 8 10 0.02 9 19 0.04 10 122 0.24 11 31 0.06 12 66 0.13 13 128 0.25 14 46 0.09 15 52 0.10 16 1 0.00 17 14 0.03 19 10 0.02 ACGTcount: A:0.41, C:0.08, G:0.44, T:0.06 Consensus pattern (13 bp): AGAGAGAGAGCTC Found at i:590656 original size:19 final size:19 Alignment explanation

Indices: 589979--590637 Score: 463 Period size: 19 Copynumber: 35.6 Consensus size: 19 589969 AAAGAAAGAG * 589979 AGAGAGAGAGAGCGAGCTC 1 AGAGAGAGAGAGAGAGCTC 589998 AGAGAGAGAGCTCAGAGAG--- 1 AGAGAGAGAG---AGAGAGCTC 590017 AGAGAGAAGAGAGAGAG--- 1 AGAGAG-AGAGAGAGAGCTC * 590034 AGAGAGAGAGAGAGAGCTT 1 AGAGAGAGAGAGAGAGCTC * * 590053 A-TG-CAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590070 --AGAGAGAGAGAGAG--- 1 AGAGAGAGAGAGAGAGCTC 590084 AGAGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590103 AGAGAGAGAGAGAGAG--- 1 AGAGAGAGAGAGAGAGCTC * * 590119 AGAGAGAGAGCTCTGAGAGAT- 1 AGAGAGAGAG---AGAGAGCTC ** 590140 AGAGAGAG-CTGAGAG--- 1 AGAGAGAGAGAGAGAGCTC 590155 AGAGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590174 AGAGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC ** 590193 TGAGAGAGAGAGAGAGAGAGC 1 --AGAGAGAGAGAGAGAGCTC * 590214 TGAGAGAGAGAGAGAG-T- 1 AGAGAGAGAGAGAGAGCTC * 590231 -GGGAGAGAGAGAGAG-T- 1 AGAGAGAGAGAGAGAGCTC * 590247 -GGGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC * 590265 AGAGAGATAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590284 AGAGAGAGAGAGAGAGCTGCTC 1 AGAGAGAGAGAGAGA---GCTC * * 590306 AGAGAGGGGGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590325 AGAGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC * * 590344 --A-TG-CAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590359 ----AGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590374 ATGCAGAGAGAGAGAGAGCTC 1 A-G-AGAGAGAGAGAGAGCTC ** 590395 AGAGAGAGAGAGAGAG-AG 1 AGAGAGAGAGAGAGAGCTC ** 590413 AGAGATGAGAGAGAGAG-AG 1 AGAGA-GAGAGAGAGAGCTC 590432 AGAGAGAGAGAGAGATGCTC 1 AGAGAGAGAGAGAGA-GCTC * * 590452 AGAGAGGGGGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590471 AGAGAGAGAGAGAGAG--- 1 AGAGAGAGAGAGAGAGCTC ** 590487 AGAGAGCTCATGCAGAGAG--- 1 AGAGAG-AGA-G-AGAGAGCTC ** 590506 AGAGAGAGAGAGAGAG-AA 1 AGAGAGAGAGAGAGAGCTC * ** 590524 AGAGAGAGATCAGAGAG-AG 1 AGAGAGAGA-GAGAGAGCTC 590543 AGAGAGAGAGAGAGTAGCTC 1 AGAGAGAGAGAGAG-AGCTC * * 590563 AGAGAGGGGGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590582 AGAGAGAGAGAGAGAGAGCTCATGC 1 --AGAGAGAGAGAGAGAG--C-T-C 590607 AGAGAGAGAGAGAGAGCTC 1 AGAGAGAGAGAGAGAGCTC 590626 AGAGAGAGAGAG 1 AGAGAGAGAGAG 590638 GGAGAGAGAG Statistics Matches: 539, Mismatches: 47, Indels: 108 0.78 0.07 0.16 Matches are distributed among these distances: 14 1 0.00 15 30 0.06 16 83 0.15 17 44 0.08 18 31 0.06 19 222 0.41 20 31 0.06 21 56 0.10 22 22 0.04 23 17 0.03 24 1 0.00 25 1 0.00 ACGTcount: A:0.41, C:0.08, G:0.44, T:0.06 Consensus pattern (19 bp): AGAGAGAGAGAGAGAGCTC Found at i:590665 original size:25 final size:24 Alignment explanation

Indices: 589999--590672 Score: 235 Period size: 25 Copynumber: 29.4 Consensus size: 24 589989 AGCGAGCTCA * 589999 GAGAGAGAGCTCAGAGAGAGA-GA 1 GAGAGAGAGCTCAGAGAGAGAGGG * 590022 GA-AGAGAG---AGAGAGAGA-GA 1 GAGAGAGAGCTCAGAGAGAGAGGG ** 590041 GAGAGAGAGCTTATGCAGAGAGAGAGCT 1 GAGAGAGAGC---T-CAGAGAGAGAGGG * * 590069 CAGAGAGAG---AGAGAGAGAGAGA 1 GAGAGAGAGCTCAGAGAGAGAG-GG 590091 GAGAGAGAGCTCAGAGAGAGAGAGAGAG 1 GAGAGAGAGCTC--AGAGAGAGAG-G-G * 590119 AGAGAGAGAGCTC--TGAGAGA--- 1 -GAGAGAGAGCTCAGAGAGAGAGGG * * * 590139 TAGAGAGAGCTGAGAGAGAGA-GA 1 GAGAGAGAGCTCAGAGAGAGAGGG 590162 GAGAGAGAGCTC--AGAGAGA--- 1 GAGAGAGAGCTCAGAGAGAGAGGG * * 590181 GAGAGAGAGCTCTGAGAGAGA-GA 1 GAGAGAGAGCTCAGAGAGAGAGGG * 590204 GAGAGAGAGCTGAGAGAGAGAGAGAG 1 GAGAGAGAGCTCAGAGAGAGAG-G-G * * 590230 TGGGAGAGAG---AGAGAGTG-GGAG 1 -GAGAGAGAGCTCAGAGAGAGAGG-G 590252 AGAGAGAGAGCTC--AGAGAGA--- 1 -GAGAGAGAGCTCAGAGAGAGAGGG * 590272 TAGAGAGAGCTCAGAGAGAGA--- 1 GAGAGAGAGCTCAGAGAGAGAGGG * 590293 GAGAGAGCTGCTC----AGAGAGGG 1 GAGAGAG-AGCTCAGAGAGAGAGGG 590314 G-GAGAGAGCTC--AGAGAGA--- 1 GAGAGAGAGCTCAGAGAGAGAGGG * 590332 GAGAGAGAGCTCATGCAGAGAGAGCTCAGA 1 GAGAGAGAGCTCA-G-AGAGAGAG----GG * 590362 GAGAGAGAGCTCATG-CAGAGA--- 1 GAGAGAGAGCTCA-GAGAGAGAGGG * 590383 GAGAGAGAGCTCAGAGAGAGAGAGA 1 GAGAGAGAGCTCAGAGAGAGAG-GG * * * 590408 GAGAGAGAGATGAGAGAGAGAGAGA 1 GAGAGAGAGCTCAGAGAGAGAG-GG ** 590433 GAGAGAGAG-AGAGATGCTCAGAGAGGG 1 GAGAGAGAGCTCAGA-G---AGAGAGGG * 590460 G-GAGAGAGCTCAGAGAGAGAGAGA 1 GAGAGAGAGCTCAGAGAGAGAG-GG * 590484 GAGAGAGAGCTCATGCAGAGAGA-GA 1 GAGAGAGAGCTCA-G-AGAGAGAGGG * * 590509 GAGAGAGAG---AGAGAAAGAGAGA 1 GAGAGAGAGCTCAGAGAGAGAG-GG * * 590531 GATCAGAGAG---AGAGAGAGA-GA 1 GA-GAGAGAGCTCAGAGAGAGAGGG * 590552 GAGAG-TAGCTC--AGA--GAGGG 1 GAGAGAGAGCTCAGAGAGAGAGGG 590571 G-GAGAGAGCTCAGAGAGAGA--- 1 GAGAGAGAGCTCAGAGAGAGAGGG 590591 GAGAGAGAGCTCATGCAGAGAGA--- 1 GAGAGAGAGCTCA-G-AGAGAGAGGG 590614 GAGAGAGAGCTCAGAGAGAGAGAGG 1 GAGAGAGAGCTCAGAGAGAGAG-GG 590639 GAGAGAGAGCTCAGAGAGAGAGTGG 1 GAGAGAGAGCTCAGAGAGAGAG-GG 590664 GAGAGAGAG 1 GAGAGAGAG 590673 AAAGGGAAAG Statistics Matches: 523, Mismatches: 42, Indels: 170 0.71 0.06 0.23 Matches are distributed among these distances: 18 11 0.02 19 69 0.13 20 24 0.05 21 93 0.18 22 36 0.07 23 86 0.16 24 13 0.02 25 95 0.18 26 9 0.02 27 41 0.08 28 19 0.04 29 12 0.02 30 15 0.03 ACGTcount: A:0.41, C:0.08, G:0.45, T:0.06 Consensus pattern (24 bp): GAGAGAGAGCTCAGAGAGAGAGGG Found at i:591123 original size:75 final size:75 Alignment explanation

Indices: 591000--591146 Score: 294 Period size: 75 Copynumber: 2.0 Consensus size: 75 590990 TGAAAATTAA 591000 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG 1 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG 591065 TATCCTTATT 66 TATCCTTATT 591075 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG 1 AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG 591140 TATCCTT 66 TATCCTT 591147 GAAACTTTGT Statistics Matches: 72, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 75 72 1.00 ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38 Consensus pattern (75 bp): AGTTCATTGAAGTGCAATTTCTACTAAAAGTTTGTATTGATAGGATCATTGGCCACGAATTTAAG TATCCTTATT Found at i:592409 original size:21 final size:22 Alignment explanation

Indices: 592374--592415 Score: 59 Period size: 21 Copynumber: 2.0 Consensus size: 22 592364 CTGCTCTAGC * * 592374 TGTCCGATGCTTGGT-AAATAT 1 TGTCCGATCCATGGTGAAATAT 592395 TGTCCGATCCATGGTGAAATA 1 TGTCCGATCCATGGTGAAATA 592416 GTTCAACGCT Statistics Matches: 18, Mismatches: 2, Indels: 1 0.86 0.10 0.05 Matches are distributed among these distances: 21 13 0.72 22 5 0.28 ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33 Consensus pattern (22 bp): TGTCCGATCCATGGTGAAATAT Found at i:598056 original size:2 final size:2 Alignment explanation

Indices: 598051--598150 Score: 193 Period size: 2 Copynumber: 50.5 Consensus size: 2 598041 AGATTTAAAA 598051 TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 598092 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 598134 TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC T 598151 NNNNNNNNNN Statistics Matches: 97, Mismatches: 0, Indels: 2 0.98 0.00 0.02 Matches are distributed among these distances: 1 1 0.01 2 96 0.99 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:600027 original size:2 final size:2 Alignment explanation

Indices: 600020--600063 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 600010 NNNNNNNNNN 600020 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 600062 CT 1 CT 600064 GTGCTGAATT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:601489 original size:2 final size:2 Alignment explanation

Indices: 601482--601538 Score: 96 Period size: 2 Copynumber: 28.5 Consensus size: 2 601472 AGGATAACAG * * 601482 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA CA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 601524 GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA G 601539 TTTAAACACT Statistics Matches: 51, Mismatches: 4, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.04, G:0.47, T:0.00 Consensus pattern (2 bp): GA Found at i:604349 original size:79 final size:80 Alignment explanation

Indices: 604209--604358 Score: 248 Period size: 79 Copynumber: 1.9 Consensus size: 80 604199 TTTAGGAAAT * * * * 604209 ATATTGCCTTGTTTTTTGTTTTCAAAACACATATATAAGTTTTCGTTGTCTTCAGATTTGTCTTT 1 ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT 604274 ACTAAGGTAATTTCC 66 ACTAAGGTAATTTCC * 604289 ATATTGCCTTG-TTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTTTTCAAACTTGTCTTT 1 ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT 604353 ACTAAG 66 ACTAAG 604359 ATATTTTCTA Statistics Matches: 65, Mismatches: 5, Indels: 1 0.92 0.07 0.01 Matches are distributed among these distances: 79 54 0.83 80 11 0.17 ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47 Consensus pattern (80 bp): ATATTGCCTTGTTTTTTGTTTCCAAAACACATAAATAAGTTTTCGTTGTCTTCAAACTTGTCTTT ACTAAGGTAATTTCC Found at i:607705 original size:1 final size:1 Alignment explanation

Indices: 607701--607726 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 607691 CTAACCAAAN 607701 AAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAA 607727 GCAATGAAGT Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:611205 original size:174 final size:171 Alignment explanation

Indices: 610918--611253 Score: 573 Period size: 174 Copynumber: 1.9 Consensus size: 171 610908 AGTGATGAGA * * 610918 AATTAATCTTTAATATTTTCAACTGTTTTTCAAGTCACTGGTCATAGGGTCTCTCAGATAACTGT 1 AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGGTCAGAGGGTCTCTCAGATAACTGT * 610983 CCCTCTGAATACAAACGAGCTACTGAGATTCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC 66 CCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC * 611048 CCATCAACAATGTGTGACCTACAGAAGATGTTACCCCAAAG 131 CCATCAACAATGTGTGACCTACAAAAGATGTTACCCCAAAG * 611089 AATTAATCTTTCATATTTTCAACTGTTTTACAAGTCACTGGTCTTCAGAGGGTCTCTCAGATAAC 1 AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGG---TCAGAGGGTCTCTCAGATAAC * * 611154 TGTCCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGGCAAGAAGTGTTACATTGTGCG 63 TGTCCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCG * 611219 ACCCCATCAACAATGTGTGACCTACAAAAGGTGTT 128 ACCCCATCAACAATGTGTGACCTACAAAAGATGTT 611254 CCTCCAAGGT Statistics Matches: 154, Mismatches: 8, Indels: 3 0.93 0.05 0.02 Matches are distributed among these distances: 171 39 0.25 174 115 0.75 ACGTcount: A:0.30, C:0.21, G:0.19, T:0.29 Consensus pattern (171 bp): AATTAATCTTTAATATTTTCAACTGTTTTACAAGTCACTGGTCAGAGGGTCTCTCAGATAACTGT CCCTCTGAATACAAACGAGCTACTGAGATCCGATTGGCAGACAAGAAGTGTTAAATTGTGCGACC CCATCAACAATGTGTGACCTACAAAAGATGTTACCCCAAAG Found at i:615230 original size:34 final size:34 Alignment explanation

Indices: 615187--615373 Score: 123 Period size: 35 Copynumber: 5.5 Consensus size: 34 615177 ATCTACCCGC * * 615187 TGGTGTCAACCCGGGTCCCTGCAATTAAA-CCTGA 1 TGGTGTCAACCCGGGTCCATGC-ATTAAATCCGGA * * * 615221 TGGTGTCAACCCAGGTTCCATTCCTTAAATCCGGA 1 TGGTGTCAACCC-GGGTCCATGCATTAAATCCGGA * * * * 615256 TGGTGTCAACCCGGGAACCATTCCTTAAATCCCGA 1 TGGTGTCAACCCGGG-TCCATGCATTAAATCCGGA *** * * 615291 TGGTGTCAA-CCGGGGAAATACGCTTTAAATCCCGA 1 TGGTGTCAACCCGGGTCCAT--GCATTAAATCCGGA * * * 615326 TGGTGTCAACCCGGGAACCAT-TATT-AA-CCCGA 1 TGGTGTCAACCCGGG-TCCATGCATTAAATCCGGA * 615358 CGGTGTCAACCCGGGT 1 TGGTGTCAACCCGGGT 615374 TTCTTAAGTT Statistics Matches: 126, Mismatches: 20, Indels: 17 0.77 0.12 0.10 Matches are distributed among these distances: 32 19 0.15 33 4 0.03 34 26 0.21 35 70 0.56 36 5 0.04 37 2 0.02 ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24 Consensus pattern (34 bp): TGGTGTCAACCCGGGTCCATGCATTAAATCCGGA Found at i:615265 original size:35 final size:35 Alignment explanation

Indices: 615219--615369 Score: 159 Period size: 35 Copynumber: 4.4 Consensus size: 35 615209 AATTAAACCT ** * 615219 GATGGTGTCAACCCAGGTTCCATTCCTTAAATCCG 1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC * 615254 GATGGTGTCAACCCGGGAACCATTCCTTAAATCCC 1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC ** * 615289 GATGGTGTCAACCGGGGAA--ATACGCTTTAAATCCC 1 GATGGTGTCAACCCAGGAACCATTC-C-TTAAATCCC * * 615324 GATGGTGTCAACCCGGGAACCATT-ATT-AA-CCC 1 GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC * 615356 GACGGTGTCAACCC 1 GATGGTGTCAACCC 615370 GGGTTTCTTA Statistics Matches: 102, Mismatches: 10, Indels: 11 0.83 0.08 0.09 Matches are distributed among these distances: 32 16 0.16 33 5 0.05 34 3 0.03 35 76 0.75 37 2 0.02 ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23 Consensus pattern (35 bp): GATGGTGTCAACCCAGGAACCATTCCTTAAATCCC Found at i:616356 original size:18 final size:16 Alignment explanation

Indices: 616335--616372 Score: 58 Period size: 17 Copynumber: 2.2 Consensus size: 16 616325 ATTGTATTTA 616335 TTTTGTTTTTTGTTTATT 1 TTTTG-TTTTTGTTT-TT 616353 TTTTGTTTTTGTTTTT 1 TTTTGTTTTTGTTTTT 616369 TTTT 1 TTTT 616373 CTAATAATAA Statistics Matches: 20, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 16 6 0.30 17 9 0.45 18 5 0.25 ACGTcount: A:0.03, C:0.00, G:0.11, T:0.87 Consensus pattern (16 bp): TTTTGTTTTTGTTTTT Found at i:616361 original size:17 final size:16 Alignment explanation

Indices: 616331--616372 Score: 59 Period size: 16 Copynumber: 2.6 Consensus size: 16 616321 AAAAATTGTA * 616331 TTTATTTTGTTTTTTG 1 TTTATTTTTTTTTTTG 616347 TTTATTTTTTGTTTTTG 1 TTTATTTTTT-TTTTTG 616364 TTT-TTTTTT 1 TTTATTTTTT 616373 CTAATAATAA Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 16 15 0.62 17 9 0.38 ACGTcount: A:0.05, C:0.00, G:0.10, T:0.86 Consensus pattern (16 bp): TTTATTTTTTTTTTTG Found at i:617389 original size:141 final size:141 Alignment explanation

Indices: 617184--617517 Score: 461 Period size: 141 Copynumber: 2.4 Consensus size: 141 617174 AAACTAAATA * * 617184 GCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAGGACTAACAACTAGAGCTAG 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG * * * * 617249 TTGGAAAATAAAACTAGGTAAGCTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG 66 TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG 617314 TTAGTTAAAGG 131 TTAGTTAAAGG * * * * * 617325 GTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAGGGTTAACAACTTGTGCTAG 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG ** ** * * * * * 617390 TTCGATTATAATTCGAATTAAACTAAAGGTCTACCAACTATAGCTAGTTAAAAAATAAAACCAGG 66 TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG 617455 TTAGTTAAAGG 131 TTAGTTAAAGG * * * 617466 GCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAGGGCTAA 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAA 617518 AAACCGAAGC Statistics Matches: 167, Mismatches: 26, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 141 167 1.00 ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25 Consensus pattern (141 bp): GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACTAGAGCTAG TTCGAAAATAAAACGAAGTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGG TTAGTTAAAGG Found at i:617511 original size:47 final size:47 Alignment explanation

Indices: 617136--617610 Score: 286 Period size: 47 Copynumber: 10.1 Consensus size: 47 617126 GTAGCTACAA * * * * 617136 GGCTAACAACTAGAGCTAG-TCAGATTATAA-A-ACGAATTAAACTAAAT 1 GGCTAACAACTAAAGCTAGCT-AGA--ATAATATACTAATTAAGCTAAAG * * * 617183 AGCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAG 1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG * * * * * ** 617230 GACTAACAACTAGAGCTAGTTGGAA-AATAAAACTAGGTAAGCTAAAG 1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTAATTAAGCTAAAG * * * * * * * 617277 GGCTAACAACTAGAGCTAG-TAAAAAAATAAAACCAGGTT-AGTTAAAG 1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTA-ATTAAGCTAAAG * * * 617324 GGTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAG 1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG * *** * * * * 617371 GGTTAACAACTTGTGCTAGTTCGATTATAAT-T-CGAATTAAACTAAAG 1 GGCTAACAACTAAAGCTAGCTAGA--ATAATATACTAATTAAGCTAAAG * * * * * * * * * 617418 GTCTACCAACTATAGCTAGTTA-AAAAATAAAACCAGGTT-AGTTAAAG 1 GGCTAACAACTAAAGCTAGCTAGAATAAT-ATACTA-ATTAAGCTAAAG * * 617465 GGCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAG 1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG * ** * * * 617512 GGCTAAAAACCGAAGCTAGCTAGAATAATCTACTAATTAGGCTAGAG 1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG * * * * * * * 617559 AGCTAACAACTAAAACTAGCTAAAATAATCTACTAAATAAACTAAAA 1 GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG 617606 GGCTA 1 GGCTA 617611 CCAGCTAGAT Statistics Matches: 329, Mismatches: 83, Indels: 32 0.74 0.19 0.07 Matches are distributed among these distances: 44 4 0.01 45 4 0.01 46 11 0.03 47 288 0.88 48 17 0.05 49 5 0.02 ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24 Consensus pattern (47 bp): GGCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAAAG Found at i:617550 original size:141 final size:140 Alignment explanation

Indices: 617184--617570 Score: 431 Period size: 141 Copynumber: 2.7 Consensus size: 140 617174 AAACTAAATA * * * 617184 GCTAACAACTAAAGCTAGCTAGAATAATTTACTAATTAAGCTAGAGGACTAACAA-CTAGAGCTA 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGA-AGCTA * * ** * 617248 GTTGGAA-AATAAAACTAGGTAAGCTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA 65 GTTAGAATAAT--TACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA 617312 GGTTAGTTAAAGG 128 GGTTAGTTAAAGG * * * * * 617325 GTTAACAACTAAAGCTAGCTAGAATAATATACTAATTCAGCTAGAGGGTTAACAACTTG-TGCTA 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAAC-CGAAGCTA * * * * * * 617389 GTTCGATTATAATT-CGAATTAAACTAAAGGTCTACCAACTATAGCTAGTTAAAAAATAAAACCA 65 GTTAGA--ATAATTACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCA 617453 GGTTAGTTAAAGG 128 GGTTAGTTAAAGG * * * * 617466 GCTAACAACTAAAGCTAGCTAGAGTAATCTACTAATTAAGCTAAAGGGCTAAAAACCGAAGCTAG 1 GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGAAGCTAG * ** * * 617531 CTAGAATAATCTACTAATTAGGCTAGAGAGCTAACAACTA 66 TTAGAATAAT-TACTAATTAAACTAAAGGGCTAACAACTA 617571 AAACTAGCTA Statistics Matches: 202, Mismatches: 36, Indels: 16 0.80 0.14 0.06 Matches are distributed among these distances: 139 5 0.02 140 2 0.01 141 191 0.95 143 1 0.00 144 3 0.01 ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24 Consensus pattern (140 bp): GCTAACAACTAAAGCTAGCTAGAATAATATACTAATTAAGCTAGAGGGCTAACAACCGAAGCTAG TTAGAATAATTACTAATTAAACTAAAGGGCTAACAACTAGAGCTAGTAAAAAAATAAAACCAGGT TAGTTAAAGG Found at i:620121 original size:28 final size:28 Alignment explanation

Indices: 620089--620344 Score: 275 Period size: 28 Copynumber: 9.1 Consensus size: 28 620079 ATTAGCTAAT * ** 620089 TTATGTTCTGATCGTGAAGTAAACTGAC 1 TTATGTACTGATCGTTTAGTAAACTGAC ** * 620117 TTATGTACTGATCGTGAAGTCAACTGAC 1 TTATGTACTGATCGTTTAGTAAACTGAC * * 620145 TTATGTTCTAATCGTTTAGTAAACTGAC 1 TTATGTACTGATCGTTTAGTAAACTGAC * 620173 TT-TAGTACTGATCGTTTAGTAAACATTA- 1 TTAT-GTACTGATCGTTTAGTAAAC-TGAC * * * 620201 TAATGTACTGATCGTTAAGTAAATTGAC 1 TTATGTACTGATCGTTTAGTAAACTGAC * 620229 TTATGTACTGATCATTTAGTAAACT-AC 1 TTATGTACTGATCGTTTAGTAAACTGAC * 620256 GTTATGTACTGATCGTTCAGTAAACTGAC 1 -TTATGTACTGATCGTTTAGTAAACTGAC * * * * 620285 TAAGGTACTGATCGTTTAGTAAAATAAC 1 TTATGTACTGATCGTTTAGTAAACTGAC * * * 620313 TTTTATACTGATCGTTTAGAAAACTGAC 1 TTATGTACTGATCGTTTAGTAAACTGAC 620341 TTAT 1 TTAT 620345 AATTATACTT Statistics Matches: 189, Mismatches: 33, Indels: 12 0.81 0.14 0.05 Matches are distributed among these distances: 27 5 0.03 28 179 0.95 29 5 0.03 ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38 Consensus pattern (28 bp): TTATGTACTGATCGTTTAGTAAACTGAC Found at i:620178 original size:14 final size:16 Alignment explanation

Indices: 620155--620196 Score: 56 Period size: 14 Copynumber: 2.9 Consensus size: 16 620145 TTATGTTCTA 620155 ATCGTTTAGTAAACTG 1 ATCGTTTAGTAAACTG 620171 A-C-TTTAGT--ACTG 1 ATCGTTTAGTAAACTG 620183 ATCGTTTAGTAAAC 1 ATCGTTTAGTAAAC 620197 ATTATAATGT Statistics Matches: 22, Mismatches: 0, Indels: 8 0.73 0.00 0.27 Matches are distributed among these distances: 12 5 0.23 13 1 0.05 14 12 0.55 15 1 0.05 16 3 0.14 ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38 Consensus pattern (16 bp): ATCGTTTAGTAAACTG Found at i:620581 original size:25 final size:25 Alignment explanation

Indices: 620552--620599 Score: 60 Period size: 25 Copynumber: 1.9 Consensus size: 25 620542 GCTCATTTTG * * 620552 AATTAACTCCTGTGTTGCTCTTGAT 1 AATTAACTCCTGTGCTGCACTTGAT ** 620577 AATTAGGTCCTGTGCTGCACTTG 1 AATTAACTCCTGTGCTGCACTTG 620600 TTAAGAAGAT Statistics Matches: 19, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 25 19 1.00 ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40 Consensus pattern (25 bp): AATTAACTCCTGTGCTGCACTTGAT Found at i:620996 original size:2 final size:2 Alignment explanation

Indices: 620989--621053 Score: 75 Period size: 2 Copynumber: 34.5 Consensus size: 2 620979 AAACATTGAA * * 620989 AG AG AG AG AG AG AG A- AA AG -G AG AG AG AG AG AG AG A- AA AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG * 621028 -G AG AG AG AG AG AG AG AG AG AA AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG AG AG A 621054 AAGAAATTCT Statistics Matches: 55, Mismatches: 4, Indels: 8 0.82 0.06 0.12 Matches are distributed among these distances: 1 4 0.07 2 51 0.93 ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00 Consensus pattern (2 bp): AG Found at i:621014 original size:20 final size:20 Alignment explanation

Indices: 620989--621043 Score: 110 Period size: 20 Copynumber: 2.8 Consensus size: 20 620979 AAACATTGAA 620989 AGAGAGAGAGAGAGAAAAGG 1 AGAGAGAGAGAGAGAAAAGG 621009 AGAGAGAGAGAGAGAAAAGG 1 AGAGAGAGAGAGAGAAAAGG 621029 AGAGAGAGAGAGAGA 1 AGAGAGAGAGAGAGA 621044 GAGAAAGAGA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00 Consensus pattern (20 bp): AGAGAGAGAGAGAGAAAAGG Found at i:621058 original size:10 final size:10 Alignment explanation

Indices: 620986--621059 Score: 66 Period size: 10 Copynumber: 7.4 Consensus size: 10 620976 ATAAAACATT 620986 GAAAGAGAGA 1 GAAAGAGAGA 620996 G--AGAGAGA 1 GAAAGAGAGA 621004 -AAAG-GAGA 1 GAAAGAGAGA * 621012 GAGAGAGAGA 1 GAAAGAGAGA 621022 GAAAAGGAGAGA 1 G-AAA-GAGAGA 621034 GAGAGAGAGAGA 1 GA-A-AGAGAGA * 621046 GAAAGAGAAA 1 GAAAGAGAGA 621056 GAAA 1 GAAA 621060 TTCTTTCAGA Statistics Matches: 53, Mismatches: 3, Indels: 16 0.74 0.04 0.22 Matches are distributed among these distances: 8 11 0.21 9 5 0.09 10 16 0.30 11 4 0.08 12 16 0.30 13 1 0.02 ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00 Consensus pattern (10 bp): GAAAGAGAGA Found at i:629632 original size:3 final size:3 Alignment explanation

Indices: 629626--629651 Score: 52 Period size: 3 Copynumber: 8.7 Consensus size: 3 629616 CGGGGAAAAA 629626 AAT AAT AAT AAT AAT AAT AAT AAT AA 1 AAT AAT AAT AAT AAT AAT AAT AAT AA 629652 AAAGAAACAT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 23 1.00 ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31 Consensus pattern (3 bp): AAT Found at i:634241 original size:161 final size:161 Alignment explanation

Indices: 633976--634309 Score: 562 Period size: 161 Copynumber: 2.1 Consensus size: 161 633966 AACATCCACA * * * * 633976 AAGAAAATGAACGTAAACTTCAAATAACTGGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA 1 AAGAAAATGAGCGTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA 634041 AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC 66 AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC 634106 AAATTTCATTTCAATATGTTCATCATCTGCG 131 AAATTTCATTTCAATATGTTCATCATCTGCG * * 634137 AAGAAAATGAGCAG-AAACTGCAAACAACTAGAATTTTCCTACGTCCATGGGCCATAACTCTGTC 1 AAGAAAATGAGC-GTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTC * * * 634201 GAAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATTATAAACCTGTATAC 65 AAAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATAC * 634266 CAAATTTCATTTCAATATGTTCATCCTCTGCG 130 CAAATTTCATTTCAATATGTTCATCATCTGCG 634298 AAGAAAATGAGC 1 AAGAAAATGAGC 634310 NNNNNNNNNN Statistics Matches: 162, Mismatches: 10, Indels: 2 0.93 0.06 0.01 Matches are distributed among these distances: 161 161 0.99 162 1 0.01 ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29 Consensus pattern (161 bp): AAGAAAATGAGCGTAAACTGCAAACAACTAGAATTTTCCTAAGTCCAAGGGCCATAACTCTGTCA AAAATTGCTCTATCATACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACATGTATACC AAATTTCATTTCAATATGTTCATCATCTGCG Found at i:641490 original size:28 final size:28 Alignment explanation

Indices: 641456--643519 Score: 1998 Period size: 28 Copynumber: 73.8 Consensus size: 28 641446 ATTAGGACTT * 641456 TTTACAGTACTGTCATTGTGTCAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * ** 641484 TTTACAGTACTGGCACTGTGTCAAAACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 641512 -TTACCAGTACTGGCACTGTGTCAGGAC- 1 TTTA-CAGTACTGTCATTGTGTTAGGACA * 641539 TTTAACTA-TACTGTCATTGTGTTAGGGCA 1 TTT-AC-AGTACTGTCATTGTGTTAGGACA * * * 641568 TTTACAGTATTTTCATTGTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * * 641596 TTTACAGTATTGCCATCGTGTTCGGACT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 641624 TTTACTGTACTGTCATTGTGTCAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 641652 TTTACAGTACTGTCATTGTGTTATGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 641680 TTTACAGTACTGGCATTGTGTTAAGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 641708 TTTACAGTACTGTCATTGTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 641736 TTTACAGTATTTTCATTGTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * 641764 TTTACAGTATTGTCATCGTGTTCGGACT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 641792 TTTACTGTACTGTCATTGTGTCAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 641820 TTAACAGTACTGTCATTGTGTTATGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 641848 TTTACAGTACTGGCATTGTGTTAAGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 641876 TTTACAGTACTGTCATTATGTTAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA 641904 TTTACAGTACTGTCATT-T-TTGAAGGAC- 1 TTTACAGTACTGTCATTGTGTT--AGGACA * * * 641931 TTTACTGTACTGTCATTGTTTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * * * 641959 TTTAAAGTACTGCCGTTGTATTTGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * * * 641987 TTTACAGTAATATTATTGTGTAATGA-T 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 642014 TTTACTGTACTGTCATTGTGTCAGGAGA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 642042 TTAACAGTACTATCACTGTGTTAGGAC- 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 642069 TTTAACGGTACTGTCATTGTGTAAGGACT 1 TTT-ACAGTACTGTCATTGTGTTAGGACA * * * * 642098 TTTCCTGTACTGTCATTTTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA 642126 TTTACAGTACTGTCATTGTGTTAAGG-CA 1 TTTACAGTACTGTCATTGTGTT-AGGACA * 642154 TTTACAGTACTGTCATTGTGTTAAGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642182 TTTACAGTGCTGTCATTGTGTAAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 642210 TTTACAGTACTGTCATTATGTTAAGG-CA 1 TTTACAGTACTGTCATTGTGTT-AGGACA * * * 642238 TTTACAGAACTGTTATTGTGTTATGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 642266 TTTACAGTACTGTCATTATGTTAGGGCT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642294 TTTACTGTACTGTCATTGTGTCAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 642322 TTAACAGTGCTGTCATTGTGTTAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA ** * 642350 ACTGCAGTACTGTCATTGTGTTAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642378 TTTACAGTACTGTCGTTGTGGTAAGG-CA 1 TTTACAGTACTGTCATTGT-GTTAGGACA * * * * 642406 TTAATAGTACTGTTATTGTGTTAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * 642434 TTTACAATACTGTCATTGCGTCAGAACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * 642462 TTTAAAGTATTGTCATTGTGCTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * ** 642490 TTTACTGTACTGTCCTTGTGTTAGGGTA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642518 TTTACAGTACTGGCATTGTGTAAGGA-A 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642545 TTTTACTGTACTGTCATTGTGTCAGGAC- 1 -TTTACAGTACTGTCATTGTGTTAGGACA * * ** * * * 642573 TTTAACGGTTCTAACATTCTGTAAGGACT 1 TTT-ACAGTACTGTCATTGTGTTAGGACA * * * * * 642602 TTTAC-TTAAATGTCATTTTGTTAGGGCT 1 TTTACAGT-ACTGTCATTGTGTTAGGACA * * 642630 TTTACAGTTCTGTCATTGTGTTAAGG-CT 1 TTTACAGTACTGTCATTGTGTT-AGGACA * 642658 TTTACAGTACTGTCATTGTGGTAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 642686 TTTAACTA-TACTGTCATTGTGTTATGACA 1 TTT-AC-AGTACTGTCATTGTGTTAGGACA * 642715 TTTACAGTACTGTCATTGTGTAAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 642743 TTTACAGTACTGTCAATGTGTTATGG-CA 1 TTTACAGTACTGTCATTGTGTTA-GGACA * * * 642771 TTTACAGTACTATTATTGTGTTATGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642799 TTTACAGTGCTGTCATTGCGTTAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 642827 TTTACAGTACTGTCATTGTGTAAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA ** * 642855 TTTACAACACTGTCAATGTGTTAAGG-CA 1 TTTACAGTACTGTCATTGTGTT-AGGACA * * * 642883 TTTAAAGTACTGTTATTGTGTTATGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642911 TTTACAGTACTGTCATTGTGTTAGGGCT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 642939 TTTACTGTACTGTCATTGTGTCAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * * 642967 TTAACAGTGCTGTCATTGTGTCAAGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA ** * * * 642995 ACTGCAGTACTGTCATTGTGTAAGCACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 643023 TTTAAAGTATTGTCATTGTGTAAGGA-A 1 TTTACAGTACTGTCATTGTGTTAGGACA * 643050 TTTAACTGTACTGTCATTGTGTTAGGAC- 1 TTT-ACAGTACTGTCATTGTGTTAGGACA * * 643078 TTTAACAGTACTGGCATTGTGTAAGGA-A 1 TTT-ACAGTACTGTCATTGTGTTAGGACA ** * * 643106 TTTATTGTACTGTCATTGTGTAAGGACT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * ** 643134 TTTACTA-TAATGTCATTTTGTTAGGGTA 1 TTTAC-AGTACTGTCATTGTGTTAGGACA * 643162 TTTACAGTACTGTCATTGTGTTAGGACT 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * 643190 TTTACTGCACTGTCATTGTGTCAGGACC 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 643218 TTAACAGTACTGTCATTGTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * * 643246 ATTACAGTGCTGTCATTGTGTCAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 643274 TTTGA-AGTACTGTCATTTTGTTAGGACA 1 TTT-ACAGTACTGTCATTGTGTTAGGACA * * * 643302 TTTACAGTACTGTCAATGTGTTGGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 643330 TTAACAGTAGTGTCATTTTGTTAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 643358 TTTACAATACTGTCATTGTGTCAGGATA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 643386 TTTACAGTACTGTCATTGTGTCAGGACA 1 TTTACAGTACTGTCATTGTGTTAGGACA * * 643414 TTTACAGTACTGTTATTGTGTAAGGAC- 1 TTTACAGTACTGTCATTGTGTTAGGACA * * * 643441 TTTCACTGTACTGTCATTATGTCAGGACA 1 TTT-ACAGTACTGTCATTGTGTTAGGACA * * 643470 TTTACAGTACTGTCTTTGTGTTAGGGCA 1 TTTACAGTACTGTCATTGTGTTAGGACA * 643498 TTTACAGTACCGTCATTGTGTT 1 TTTACAGTACTGTCATTGTGTT 643520 GAATGTCAGG Statistics Matches: 1656, Mismatches: 335, Indels: 90 0.80 0.16 0.04 Matches are distributed among these distances: 26 2 0.00 27 97 0.06 28 1495 0.90 29 61 0.04 30 1 0.00 ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40 Consensus pattern (28 bp): TTTACAGTACTGTCATTGTGTTAGGACA Found at i:646197 original size:18 final size:19 Alignment explanation

Indices: 646162--646197 Score: 56 Period size: 19 Copynumber: 1.9 Consensus size: 19 646152 CCCCATGTGG 646162 GGCCAAATATGCAAAAAAA 1 GGCCAAATATGCAAAAAAA * 646181 GGCCAAATTTG-AAAAAA 1 GGCCAAATATGCAAAAAA 646198 TCTTCTTCTC Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 18 6 0.38 19 10 0.62 ACGTcount: A:0.56, C:0.14, G:0.17, T:0.14 Consensus pattern (19 bp): GGCCAAATATGCAAAAAAA Found at i:646436 original size:168 final size:167 Alignment explanation

Indices: 646250--646977 Score: 907 Period size: 168 Copynumber: 4.4 Consensus size: 167 646240 CATAGTCATA * 646250 ATGTCCATGAAA-CCCTCTACCACAATTGTGAAATTCATGCCCCCTGGGTCAGGGGTTCAGGCTC 1 ATGTCCAT-AAAGCCCTCTACCA-AATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTC * * * * 646314 TAGGGTAGGGCCAATATTGCCATAAAGTTAAAATGTATTAAATCTTAGAAAATCTACTTCTCTAC 64 TAGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTAC * 646379 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATA 129 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATG * * 646418 ATGTCCATAAAGCCCTCTACCTAAATCGTGAAATTCATGACCCCTGGGTCAAGGGTTCAGGCTCT 1 ATGTCCATAAAGCCCTCTACC-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT * 646483 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTTC 65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAG-AAAATCTTCTTCTCTAC 646548 TCCCATATATATTTGTTAAAAACTAAATGCA-AA--ATG 129 TCCCATATATATTTGTTAAAAACTAAATGCATAATTATG * * * * 646584 ATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCGTGACCCCTGGGTCAGGGGTTCAGGATCT 1 ATGTCCATAAAGCCCTCTAC-CAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT * 646649 AGGGTGGGGTCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT 65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT * * ** 646714 CCCATATACATTTGTTAAAAACTAAATGCCTGGTTATG 130 CCCATATATATTTGTTAAAAACTAAATGCATAATTATG * * * * * ** * 646752 ATGTCCATGAGGCCCTCTAACAAAATTGTGAAATTCTTAACCCCTTTGTTAGGGGTTCAGGCTCT 1 ATGTCCATAAAGCCCTCT-ACCAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCT * * * * * * 646817 AGGGTTGAGCCAATATGGCCTTATAG--AAAATGTTTTTAATCTTAAAAAATCTTCTTCTCTACT 65 AGGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT * * * ** ** * ** 646880 CCC-CACATGTGAGCAAAAAACTAAATACATGGTTATG 130 CCCATATATATTTGTTAAAAACTAAATGCATAATTATG * * * 646917 ATGTCCACT-AA-CTCCTCTACCTAAATTATGAAATTCATGGCCCCTGGGTCGGGGGTTCAGG 1 ATGTCCA-TAAAGC-CCTCTACC-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG 646978 ACATCGGGGG Statistics Matches: 494, Mismatches: 55, Indels: 25 0.86 0.10 0.04 Matches are distributed among these distances: 164 3 0.01 165 113 0.23 166 144 0.29 167 3 0.01 168 182 0.37 169 49 0.10 ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31 Consensus pattern (167 bp): ATGTCCATAAAGCCCTCTACCAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTA GGGTGGGGCCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACTC CCATATATATTTGTTAAAAACTAAATGCATAATTATG Found at i:647069 original size:333 final size:332 Alignment explanation

Indices: 646250--647066 Score: 866 Period size: 334 Copynumber: 2.5 Consensus size: 332 646240 CATAGTCATA * * * * * * 646250 ATGTCCATGAAACCCTCTACCACAATTGTGAAATTCATGCCCCCTGGGTCAGGGGTTCAGGCTCT 1 ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT * * * * * * * 646315 AGGGTAGGGCCAATATTGCCATAAAGTTAAAATGTATTAAATCTTAGAAAATCTACTTCTCTACT 66 AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT * * * * * 646380 CCCATATATATTTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTACCTAAATC 131 CCCA-ACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATC * * 646445 GTGAAATTCATGACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGT 195 GTGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAG- * * * ** ** 646510 TAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTTCTCCCATATATATTTGTTAAAAACTAAA 259 TAAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAA * 646575 TGCAAAATG 324 TACAAAATG * * 646584 ATGTCCATGAAGCCCTCTACTAAAATTGTGAAATTCGTGACCCCTGGGTCAGGGGTTCAGGATCT 1 ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT * * * 646649 AGGGTGGGGTCAATATGGCCATATAGTTAAAATGTATTAAATCTTAGAAAATCTTCTTCTCTACT 66 AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT * * * ** * * * * 646714 CCCATATACATTTGTTAAAAACTAAATGCCTGGTTATGATGTCCATGAGGCCCTCTAACAAAATT 131 CCCA-ACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATC * ** * * * * 646779 GTGAAATTCTTAACCCCTTTGTTAGGGGTTCAGGCTCTAGGGTTGAGCCAATATGGCCTTATAG- 195 GTGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAGT * * * 646843 AAAATGTTTTTAATCTTA-AAAAATCTTCTTCTCTACTCCC-CACATGTGAGCAAAAAACTAAAT 260 AAAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAAT ** 646906 ACATGGTTATG 325 ACA---AAATG * * 646917 ATGTCCACT-AA-CTCCTCTACCT-AAATTATGAAATTCATGGCCCCTGGGTCGGGGGTTCAGGA 1 ATGTCCA-TGAAGC-CCTCTA-CTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGA * * * 646979 -CATCGGG-GGAGGACAATATGGCAATATAGTGT-AAATGCA-TATAATGTTTA-AAAATTTTCT 63 TC-TAGGGTGG-GGACAATATGGCAATATAGT-TAAAATGCATTA-AAT-CTTAGAAAATCTTCT * * 647039 TCTCTATTCTC-ACACATCTGTATAAAAA 123 TCTCTACTCCCAACACATCTGT-TAAAAA 647067 ACTGACTAAT Statistics Matches: 414, Mismatches: 57, Indels: 26 0.83 0.11 0.05 Matches are distributed among these distances: 330 18 0.04 331 29 0.07 332 28 0.07 333 103 0.25 334 236 0.57 ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31 Consensus pattern (332 bp): ATGTCCATGAAGCCCTCTACTAAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGATCT AGGGTGGGGACAATATGGCAATATAGTTAAAATGCATTAAATCTTAGAAAATCTTCTTCTCTACT CCCAACACATCTGTTAAAAACTAAATGCATAATTATAATGTCCATAAAGCCCTCTAACAAAATCG TGAAATTCATAACCCCTGGGTCAAGGGTTCAGGCTCTAGGGTGGAGCCAATATGGCCATATAGTA AAATGTATTAAATCTTAGAAAAATCTTCTTCTCTACTCCCACACATATGAGCAAAAAACTAAATA CAAAATG Found at i:647766 original size:29 final size:29 Alignment explanation

Indices: 647724--647879 Score: 249 Period size: 29 Copynumber: 5.4 Consensus size: 29 647714 GCCAAAAAAC 647724 TATCGTGATACTGAGAAATATCTATACAT 1 TATCGTGATACTGAGAAATATCTATACAT * * 647753 TATCGTGATACTGAGATATATCTATACCT 1 TATCGTGATACTGAGAAATATCTATACAT * 647782 AATCGTGATACTGAGAAATATCTATACAT 1 TATCGTGATACTGAGAAATATCTATACAT * * 647811 TATCGTGATACGGACAAATATCTATACAT 1 TATCGTGATACTGAGAAATATCTATACAT * * 647840 TATCGTGATACGGACAAATATCTATACAT 1 TATCGTGATACTGAGAAATATCTATACAT 647869 TATCGTGATAC 1 TATCGTGATAC 647880 GGACAATCGT Statistics Matches: 119, Mismatches: 8, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 29 119 1.00 ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33 Consensus pattern (29 bp): TATCGTGATACTGAGAAATATCTATACAT Found at i:647918 original size:29 final size:29 Alignment explanation

Indices: 647885--648488 Score: 709 Period size: 29 Copynumber: 21.0 Consensus size: 29 647875 GATACGGACA * * 647885 ATCGTAATACTGACAAATATCTAAACATT 1 ATCGTGATACTGACAAATATCTATACATT * 647914 ATCGTGATACTGAAAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT * * 647943 ATCGTGATACTTACAAATATCTATACATC 1 ATCGTGATACTGACAAATATCTATACATT * * 647972 ATCGTGATACGGAC--A-ATCGTGATAC-TG 1 ATCGTGATACTGACAAATATC-T-ATACATT ** * * ** 647999 A-C-AAATATCT-ATACATCATCGTGATACGGACA 1 ATCGTGATA-CTGACAAAT-ATC-T-ATAC--ATT 648031 ATCGTGATACTGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT * * 648060 ATCGTAATACTGACAAATATCTAAACATT 1 ATCGTGATACTGACAAATATCTATACATT * * 648089 ATCGTGATACTGAAAAATATATATACATT 1 ATCGTGATACTGACAAATATCTATACATT * 648118 ATCGTGATACTGACAAATATCTATACATC 1 ATCGTGATACTGACAAATATCTATACATT * 648147 ATCGTGATACTGACAAATATCTATACATC 1 ATCGTGATACTGACAAATATCTATACATT * * * 648176 ATCGTGATACGGAC--A-ATC-GT-GA-T 1 ATCGTGATACTGACAAATATCTATACATT * * * 648199 A-CG-GACAAAT-ACAATGTATCTATACATT 1 ATCGTGA-TACTGACAA-ATATCTATACATT * 648227 ATCGTGATACGGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT 648256 ATCGTGATACTGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT * 648285 ATCGTGATACGGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT 648314 ATCGTGATACTGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT 648343 ATCGTGATACTGACAAATATCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT * 648372 ATCGTGATACTGACAAATAGCTATACATT 1 ATCGTGATACTGACAAATATCTATACATT * 648401 ATCGTGATACTGACAAATATCTATGCATT 1 ATCGTGATACTGACAAATATCTATACATT * * 648430 ATCGTCATACTGACAAATATCTATGCATT 1 ATCGTGATACTGACAAATATCTATACATT * * 648459 ATCGTCATACTGACAAATATCTATGCATT 1 ATCGTGATACTGACAAATATCTATACATT 648488 A 1 A 648489 ATAAAAATGA Statistics Matches: 500, Mismatches: 51, Indels: 48 0.83 0.09 0.08 Matches are distributed among these distances: 21 4 0.01 22 3 0.01 23 1 0.00 24 1 0.00 25 8 0.02 26 9 0.02 27 7 0.01 28 6 0.01 29 436 0.87 30 6 0.01 31 4 0.01 32 2 0.00 33 6 0.01 34 7 0.01 ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32 Consensus pattern (29 bp): ATCGTGATACTGACAAATATCTATACATT Found at i:647932 original size:73 final size:73 Alignment explanation

Indices: 647812--648098 Score: 359 Period size: 73 Copynumber: 3.9 Consensus size: 73 647802 TCTATACATT * * 647812 ATCGTGATACGGACAAATATCTATACATTATCGTGATACGGACAAATATCTATACATTATCGTGA 1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA 647877 TACGGACA 66 TACGGACA * * * 647885 ATCGTAATACTGACAAATATCTAAACATTATCGTGATACTGAAAAATATCTATACATTATCGTGA 1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA ** 647950 TACTTACA 66 TACGGACA * * * ** * 647958 A--AT-AT-CT-ATACATCATCGTGATACGGACAATCGTGATACTGACAAATATCTATACATCAT 1 ATCGTGATACTGACAAAT-ATC-T-ATAC--ATTATCGTGATACTGACAAATATCTATACATTAT 648018 CGTGATACGGACA 61 CGTGATACGGACA * * 648031 ATCGTGATACTGACAAATATCTATACATTATCGTAATACTGACAAATATCTAAACATTATCGTGA 1 ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA 648096 TAC 66 TAC 648099 TGAAAAATAT Statistics Matches: 179, Mismatches: 25, Indels: 20 0.80 0.11 0.09 Matches are distributed among these distances: 68 4 0.02 69 5 0.03 70 3 0.02 71 4 0.02 73 146 0.82 75 5 0.03 76 3 0.02 77 5 0.03 78 4 0.02 ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30 Consensus pattern (73 bp): ATCGTGATACTGACAAATATCTATACATTATCGTGATACTGACAAATATCTATACATTATCGTGA TACGGACA Found at i:647992 original size:15 final size:15 Alignment explanation

Indices: 647972--648046 Score: 61 Period size: 15 Copynumber: 5.1 Consensus size: 15 647962 TCTATACATC 647972 ATCGTGATACGGACA 1 ATCGTGATACGGACA * 647987 ATCGTGATACTGACAAA 1 ATCGTGATACGGAC--A 648004 TATC-T-ATAC--ATC- 1 -ATCGTGATACGGA-CA 648016 ATCGTGATACGGACA 1 ATCGTGATACGGACA * 648031 ATCGTGATACTGACA 1 ATCGTGATACGGACA 648046 A 1 A 648047 ATATCTATAC Statistics Matches: 49, Mismatches: 2, Indels: 18 0.71 0.03 0.26 Matches are distributed among these distances: 11 3 0.06 12 1 0.02 13 4 0.08 14 2 0.04 15 30 0.61 16 4 0.08 17 2 0.04 18 3 0.06 ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25 Consensus pattern (15 bp): ATCGTGATACGGACA Found at i:648006 original size:44 final size:44 Alignment explanation

Indices: 647943--648075 Score: 230 Period size: 44 Copynumber: 3.0 Consensus size: 44 647933 TCTATACATT * 647943 ATCGTGATACTTACAAATATCTATACATCATCGTGATACGGACA 1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA 647987 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA 1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA * * * 648031 ATCGTGATACTGACAAATATCTATACATTATCGTAATACTGACA 1 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA 648075 A 1 A 648076 ATATCTAAAC Statistics Matches: 85, Mismatches: 4, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 44 85 1.00 ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29 Consensus pattern (44 bp): ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACA Found at i:648107 original size:146 final size:146 Alignment explanation

Indices: 647841--648133 Score: 478 Period size: 146 Copynumber: 2.0 Consensus size: 146 647831 TCTATACATT * 647841 ATCGTGATACGGACAAATATCTATACATTATCGTGATACGGACAATCGTAATACTGACAAATATC 1 ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC * * * * * 647906 TAAACATTATCGTGATACTGAAAAATATCTATACATTATCGTGATACTTACAAATATCTATACAT 66 TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT 647971 CATCGTGATACGGACA 131 CATCGTGATACGGACA * * 647987 ATCGTGATACTGACAAATATCTATACATCATCGTGATACGGACAATCGTGATACTGACAAATATC 1 ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC * * 648052 TATACATTATCGTAATACTGACAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT 66 TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT * * 648117 TATCGTGATACTGACA 131 CATCGTGATACGGACA 648133 A 1 A 648134 ATATCTATAC Statistics Matches: 135, Mismatches: 12, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 146 135 1.00 ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30 Consensus pattern (146 bp): ATCGTGATACGGACAAATATCTATACATCATCGTGATACGGACAATCGTAATACTGACAAATATC TAAACATTATCGTAATACTGAAAAATATCTAAACATTATCGTGATACTGAAAAATATATATACAT CATCGTGATACGGACA Found at i:648196 original size:15 final size:15 Alignment explanation

Indices: 648176--648206 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 648166 TCTATACATC 648176 ATCGTGATACGGACA 1 ATCGTGATACGGACA 648191 ATCGTGATACGGACA 1 ATCGTGATACGGACA 648206 A 1 A 648207 ATACAATGTA Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19 Consensus pattern (15 bp): ATCGTGATACGGACA Found at i:655000 original size:2 final size:2 Alignment explanation

Indices: 654958--654982 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 654948 AAAATCCAAT 654958 TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA TA TA TA TA TA TA TA TA TA T 654983 CTCTCTATTT Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52 Consensus pattern (2 bp): TA Found at i:663362 original size:18 final size:18 Alignment explanation

Indices: 663339--663373 Score: 54 Period size: 18 Copynumber: 1.9 Consensus size: 18 663329 CCCCCACCCC 663339 CTCCAAAGAAA-CTGAAAT 1 CTCCAAA-AAAGCTGAAAT 663357 CTCCAAAAAAGCTGAAA 1 CTCCAAAAAAGCTGAAA 663374 ACAAACAAAA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 17 3 0.19 18 13 0.81 ACGTcount: A:0.51, C:0.23, G:0.11, T:0.14 Consensus pattern (18 bp): CTCCAAAAAAGCTGAAAT Found at i:672165 original size:17 final size:17 Alignment explanation

Indices: 672140--672178 Score: 69 Period size: 17 Copynumber: 2.3 Consensus size: 17 672130 GCTGATGAAA * 672140 TGATCCAAGGACTTCAC 1 TGATTCAAGGACTTCAC 672157 TGATTCAAGGACTTCAC 1 TGATTCAAGGACTTCAC 672174 TGATT 1 TGATT 672179 TGACAAACGT Statistics Matches: 21, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 17 21 1.00 ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31 Consensus pattern (17 bp): TGATTCAAGGACTTCAC Found at i:683323 original size:18 final size:18 Alignment explanation

Indices: 683300--683334 Score: 70 Period size: 18 Copynumber: 1.9 Consensus size: 18 683290 CCTTTCAGGC 683300 AGCATTTAGATACTTATT 1 AGCATTTAGATACTTATT 683318 AGCATTTAGATACTTAT 1 AGCATTTAGATACTTAT 683335 GTTAAATATT Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 17 1.00 ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43 Consensus pattern (18 bp): AGCATTTAGATACTTATT Found at i:683564 original size:14 final size:14 Alignment explanation

Indices: 683545--683573 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 683535 TGCAGTCAAC 683545 ATAAATATATATAT 1 ATAAATATATATAT 683559 ATAAATATATATAT 1 ATAAATATATATAT 683573 A 1 A 683574 ACTACTCAAG Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 15 1.00 ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41 Consensus pattern (14 bp): ATAAATATATATAT Found at i:685972 original size:18 final size:18 Alignment explanation

Indices: 685949--685986 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 685939 CCGATTGATA 685949 CAGATATTTAGAGTCCTT 1 CAGATATTTAGAGTCCTT * 685967 CAGATATTTCGAGTCCTT 1 CAGATATTTAGAGTCCTT 685985 CA 1 CA 685987 ATTTCTTTCT Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37 Consensus pattern (18 bp): CAGATATTTAGAGTCCTT Found at i:709086 original size:2 final size:2 Alignment explanation

Indices: 709079--709144 Score: 132 Period size: 2 Copynumber: 33.0 Consensus size: 2 709069 AGGAAACAAA 709079 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 709121 CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT 709145 GGGGGACACC Statistics Matches: 64, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 64 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:709518 original size:49 final size:48 Alignment explanation

Indices: 709446--709544 Score: 180 Period size: 49 Copynumber: 2.0 Consensus size: 48 709436 ACCAGGTACA * 709446 ATTTAAGCTCTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT 1 ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT 709494 NATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT 1 -ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT 709543 AT 1 AT 709545 ACATGTATAT Statistics Matches: 49, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 48 2 0.04 49 47 0.96 ACGTcount: A:0.26, C:0.28, G:0.12, T:0.32 Consensus pattern (48 bp): ATTTAAGCACTCCCGCCAGGATTCTACACACCATCTTTCAATGATTGT Found at i:714562 original size:2 final size:2 Alignment explanation

Indices: 714555--714619 Score: 130 Period size: 2 Copynumber: 32.5 Consensus size: 2 714545 GAGTGAAATT 714555 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG 714597 AG AG AG AG AG AG AG AG AG AG AG A 1 AG AG AG AG AG AG AG AG AG AG AG A 714620 ACGTTTCACA Statistics Matches: 63, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 63 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:718699 original size:140 final size:140 Alignment explanation

Indices: 718311--719081 Score: 802 Period size: 140 Copynumber: 5.5 Consensus size: 140 718301 TGCATGTAAA 718311 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA 1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA 718376 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG 66 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG 718441 TACATATATC 131 TACATATATC 718451 ATATAGTTAACTCGACAGTAAATGCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATA 1 ATATAGTTAACTCGACAGT---T-CATGTATCATATAGATAACTTGACAGTATTTCTTTCATATA * 718516 GTTAACTTGGCGGTATATGTGTTATAAAGGTAAATCGACAGTACATGTATCATACAGTAAACTCG 62 GTTAACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCG 718581 ATAGTACATATATC 127 ATAGTACATATATC * * 718595 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTAACAGTATTTCTTTCATATAGTAA 1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA * * * * * 718660 ACTTGGCGGCATATGTGTCATATAGTTTAATCGAGAGTACATGTATCATACAGTAAACTCGATAG 66 ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG 718725 TACATATATC 131 TACATATATC * * * * * ** * * 718735 ATATAGTTAAATCGACAGTACATGTATCATACAG-TAAACTCGATAGTACATATATCATATAGTT 1 ATATAGTTAACTCGACAGTTCATGTATCATATAGAT-AACTTGACAGTATTTCTTTCATATAGTT * * * * * * * * * 718799 AAATCGAG-AGTACATGTATCATACAA--TAAACTCGATAG-A-ATATATCATATTATAGTTAAA 65 AACTTG-GCGGTATATGTGTTATA-AAGTTAAA-TCGACAGTACATGTATC--A-TACAG-TAAA * * 718859 -TCGACAGTACATGTATC 123 CTCGATAGTACATATATC * * * * * * * * * ** * * * * * 718876 ATACAGTAAACTCGATAGTACATATATCATATAGTTAAATCGAGAGTACATGTATCATACAATAA 1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA * *** * * ** * * 718941 ACTCGATAGAATATATCATATTATAGTTAAATCGACAGTACATATATCATACAGTAAACTCGATA 66 ACTTGGCGGTATATGTGTTA-TAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATA 719006 GTACATATATC 130 GTACATATATC * * * * * * * * * 719017 ATATAGTTAAATCGACAATACATATATCATACAG-TAACTTGACGGTATATGTGTCATATAGTTA 1 ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA 719081 A 66 A 719082 ATTGACAGTA Statistics Matches: 538, Mismatches: 73, Indels: 40 0.83 0.11 0.06 Matches are distributed among these distances: 138 6 0.01 139 5 0.01 140 230 0.43 141 132 0.25 142 14 0.03 143 6 0.01 144 145 0.27 ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33 Consensus pattern (140 bp): ATATAGTTAACTCGACAGTTCATGTATCATATAGATAACTTGACAGTATTTCTTTCATATAGTTA ACTTGGCGGTATATGTGTTATAAAGTTAAATCGACAGTACATGTATCATACAGTAAACTCGATAG TACATATATC Found at i:719294 original size:142 final size:141 Alignment explanation

Indices: 718705--719379 Score: 478 Period size: 142 Copynumber: 4.8 Consensus size: 141 718695 AGTACATGTA * * * * * * * 718705 TCATACAG-TAAACTCGATAGTACATATATCATATAGTTAAATCGACAGTACATGTATCATACA- 1 TCATACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAG * * * * * 718768 GTAAACTCGATAGTACATATATCATATAGTTAAATCGAGAGTACATG--TATCATACAATAAACT 65 GT-AACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGT-AACT * * * 718831 CGATAGAATATATC-A 128 TG--ACAATATATCTG * * * * * * * 718846 T-ATTATAGTTAAA-TCGACAGTACATGTATCATACAG-TAAACTCGATAGTACATATATCATAT 1 TCA-TACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAA-TCGACAATACATATATAATAC * * * * * * * * * * * 718908 AGTTAAATCGAGAGTACATGTATCATACAATAAACTCGATAG-A-ATATATCATATTATAGTTAA 63 AGGTAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTAT-ATAATACAG-TAA * * * * * * 718971 ATCGACAGTACATATA 126 CTTGACAATATATCTG * * * * * 718987 TCATACAG-TAAACTCGATAGTACATATATCATATAGTTAAATCGACAATACATATATCATACA- 1 TCATACAGTTAAACT-GACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAG * * * * * * * * 719050 GTAACTTGACGGTATATGTGTCATATAGTTAAATTGACAGTACA--TATATCATACAGTAACTTG 65 GTAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGTAACTTG ** * 719113 ACGGTATATGTG 130 ACAATATATCTG * * * * * * * 719125 TCATATAGTTAAATTGACAGTATATGTGTTATAAAGTTAAGTCGACAACACATGTATAATACAGG 1 TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG * * 719190 TAACTCGATAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATATAGTTAACTTG 66 TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAG-TAACTTG * 719255 ACAATATATCTT 130 ACAATATATCTG * * * * * * * * 719267 TCATACAGTTAACCTGACGGTACATGTGTCATATAGTTAACTCGACAGTACATATATTATATAGT 1 TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG * 719332 TAACTCGACAGTACATATATTATATAGTTAACTCGACAGTACATGTAT 66 TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTAT 719380 CATACAGTTA Statistics Matches: 418, Mismatches: 97, Indels: 37 0.76 0.18 0.07 Matches are distributed among these distances: 138 58 0.14 139 49 0.12 140 46 0.11 141 131 0.31 142 133 0.32 143 1 0.00 ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32 Consensus pattern (141 bp): TCATACAGTTAAACTGACAGTACATGTGTCATAAAGTTAAATCGACAATACATATATAATACAGG TAACTCGACAGTACATATATCATATAGTTAACTCGACAGTACATGTATATAATACAGTAACTTGA CAATATATCTG Found at i:719395 original size:28 final size:28 Alignment explanation

Indices: 718249--719529 Score: 718 Period size: 28 Copynumber: 45.6 Consensus size: 28 718239 ATGAATGTAT * * * 718249 ATGTATCATATTGTTAACTTGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * ** * 718277 ATGTATCATAT-GGTAACTTGAGGGTGC 1 ATGTATCATATAGTTAAATCGACAGTAC ** * * 718304 ATGTAAAATATAGTTAACTCGACAGTTC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * 718332 ATGTATCATATAGATAACTTGACAGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * * * * 718360 TTCTTTCATATAGTTAACTTGGCGGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 718388 ATGTGTTATAAAGTTAAATCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 718416 ATGTATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * 718444 ATATATCATATAGTTAACTCGACAGTAAATGC 1 ATGTATCATATAGTTAAATCGACAGT--A--C * * * * 718476 ATGTATCATATAGATAACTTGACAGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * * * * 718504 TTCTTTCATATAGTTAACTTGGCGGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * 718532 ATGTGTTATAAAGGTAAATCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 718560 ATGTATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * * 718588 ATATATCATATAGTTAACTCGACAGTTC 1 ATGTATCATATAGTTAAATCGACAGTAC * * ** * 718616 ATGTATCATATAGATAACTTAACAGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * * * * 718644 TTCTTTCATATAG-TAAACTTGGCGGCAT 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * * 718672 ATGTGTCATATAGTTTAATCGAGAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 718700 ATGTATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * 718728 ATATATCATATAGTTAAATCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 718756 ATGTATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * 718784 ATATATCATATAGTTAAATCGAGAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 718812 ATGTATCATACA-ATAAACTCGATAG-A- 1 ATGTATCATATAGTTAAA-TCGACAGTAC * 718838 ATATATCATATTATAGTTAAATCGACAGTAC 1 ATGTATC--A-TATAGTTAAATCGACAGTAC * * 718869 ATGTATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * 718897 ATATATCATATAGTTAAATCGAGAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 718925 ATGTATCATACA-ATAAACTCGATAG-A- 1 ATGTATCATATAGTTAAA-TCGACAGTAC * 718951 ATATATCATATTATAGTTAAATCGACAGTAC 1 ATGTATC--A-TATAGTTAAATCGACAGTAC * * * 718982 ATATATCATACAG-TAAACTCGATAGTAC 1 ATGTATCATATAGTTAAA-TCGACAGTAC * * 719010 ATATATCATATAGTTAAATCGACAATAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * * 719038 ATATATCATACAG-TAACTTGACGGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * 719065 ATGTGTCATATAGTTAAATTGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * * 719093 ATATATCATACAG-TAACTTGACGGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 719120 ATGTGTCATATAGTTAAATTGACAGTAT 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * ** 719148 ATGTGTTATAAAGTTAAGTCGACAACAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * 719176 ATGTATAATACAGGTAACTCGATAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 719204 ATATATCATATAGTTAACTCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * * * 719232 ATGTATATAATATAGTTAACTTGACAATAT 1 ATG--TATCATATAGTTAAATCGACAGTAC * * * * * 719262 ATCTTTCATACAGTT-AACCTGACGGTAC 1 ATGTATCATATAGTTAAATC-GACAGTAC * * 719290 ATGTGTCATATAGTTAACTCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 719318 ATATATTATATAGTTAACTCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * * 719346 ATATATTATATAGTTAACTCGACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC * * 719374 ATGTATCATACAGTTAAATCGACATGT-G 1 ATGTATCATATAGTTAAATCGACA-GTAC * ** * 719402 ATACTAGAATATAGTTAAATCGCCAGTAC 1 AT-GTATCATATAGTTAAATCGACAGTAC * * * * * * 719431 ACG-ATCACACAGCTAACTCGATAAG-AC 1 ATGTATCATATAGTTAAATCGA-CAGTAC * * * 719458 ATATATCATACT-GTTAACCTCAACAGTAC 1 ATGTATCATA-TAGTTAA-ATCGACAGTAC ** * * 719487 ATGTAT--TCGAGTTAACTCAACAGTAC 1 ATGTATCATATAGTTAAATCGACAGTAC 719513 ATGTATCATATAGTTAA 1 ATGTATCATATAGTTAA 719530 CTCGGGAGTT Statistics Matches: 968, Mismatches: 235, Indels: 100 0.74 0.18 0.08 Matches are distributed among these distances: 26 29 0.03 27 118 0.12 28 671 0.69 29 78 0.08 30 35 0.04 31 13 0.01 32 24 0.02 ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33 Consensus pattern (28 bp): ATGTATCATATAGTTAAATCGACAGTAC Found at i:726767 original size:16 final size:16 Alignment explanation

Indices: 726748--726796 Score: 98 Period size: 16 Copynumber: 3.1 Consensus size: 16 726738 AACGAATGCT 726748 GGAGAAAACGTACCCA 1 GGAGAAAACGTACCCA 726764 GGAGAAAACGTACCCA 1 GGAGAAAACGTACCCA 726780 GGAGAAAACGTACCCA 1 GGAGAAAACGTACCCA 726796 G 1 G 726797 TTTATAGGGT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 16 33 1.00 ACGTcount: A:0.43, C:0.24, G:0.27, T:0.06 Consensus pattern (16 bp): GGAGAAAACGTACCCA Found at i:727214 original size:31 final size:31 Alignment explanation

Indices: 727176--727237 Score: 115 Period size: 31 Copynumber: 2.0 Consensus size: 31 727166 GATTTTCATA * 727176 GGGTACGTTTTCTCTTGGAGAAAACGTACCC 1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC 727207 GGGTACGTTTTCTCCTGGAGAAAACGTACCC 1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC 727238 TAGAGATTGG Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 31 30 1.00 ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27 Consensus pattern (31 bp): GGGTACGTTTTCTCCTGGAGAAAACGTACCC Found at i:727264 original size:16 final size:16 Alignment explanation

Indices: 727245--727294 Score: 91 Period size: 16 Copynumber: 3.1 Consensus size: 16 727235 CCCTAGAGAT 727245 TGGGTACGTTTTCTCC 1 TGGGTACGTTTTCTCC * 727261 TGGGTACGTTTTCTCT 1 TGGGTACGTTTTCTCC 727277 TGGGTACGTTTTCTCC 1 TGGGTACGTTTTCTCC 727293 TG 1 TG 727295 ATACCGAAAT Statistics Matches: 32, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 32 1.00 ACGTcount: A:0.06, C:0.22, G:0.26, T:0.46 Consensus pattern (16 bp): TGGGTACGTTTTCTCC Found at i:727620 original size:2 final size:2 Alignment explanation

Indices: 727615--727676 Score: 124 Period size: 2 Copynumber: 31.0 Consensus size: 2 727605 CATCTCTCGC 727615 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 727657 CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT 727677 GAAGTACACG Statistics Matches: 60, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 60 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:736651 original size:22 final size:21 Alignment explanation

Indices: 736468--736651 Score: 69 Period size: 22 Copynumber: 9.0 Consensus size: 21 736458 TTGCTGACAC 736468 ATCACTGAAATCTTAATGAG- 1 ATCACTGAAATCTTAATGAGA * * * ** * 736488 -TCAGTGAGATATTGCTGACA 1 ATCACTGAAATCTTAATGAGA 736508 CATCACTGAAATCTTAAT--GA 1 -ATCACTGAAATCTTAATGAGA * * ** ** * 736528 ATCAGTGAGATAATGCTGACA 1 ATCACTGAAATCTTAATGAGA 736549 CATCACTGAAATCTTAATGAG- 1 -ATCACTGAAATCTTAATGAGA * * * ** * 736570 -TCAGTGAGATATTGCTGACA 1 ATCACTGAAATCTTAATGAGA 736590 CATCACTGAAATCTTAAT--GA 1 -ATCACTGAAATCTTAATGAGA * * ** 736610 ATCAGTGAAATATTGCTGAGA 1 ATCACTGAAATCTTAATGAGA 736631 TATCACTGAAATCTTAATGAG 1 -ATCACTGAAATCTTAATGAG 736652 TCAGGGAGAT Statistics Matches: 106, Mismatches: 46, Indels: 22 0.61 0.26 0.13 Matches are distributed among these distances: 19 50 0.47 20 2 0.02 21 3 0.03 22 51 0.48 ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29 Consensus pattern (21 bp): ATCACTGAAATCTTAATGAGA Found at i:736929 original size:41 final size:41 Alignment explanation

Indices: 736458--736912 Score: 802 Period size: 41 Copynumber: 11.1 Consensus size: 41 736448 AATGATGAGT * 736458 TTGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 736499 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * * 736540 ATGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * 736581 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAAATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * * * * 736622 TTGCTGAGATATCACTGAAATCTTAATGAGTCAGGGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * 736663 TTGCTGACACATCACTGAAATCTTAATGCATCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * 736704 TTGCTGACACATCACTGAAATCTTAATGAACCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 736745 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * 736786 TTGCTGACACATCACTGAAATCTTAATGAACCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA * 736827 TTGCTGACACATCACTGAAATCTTAATGAGTCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 736868 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 1 TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA 736909 TTGC 1 TTGC 736913 CGAGATATCA Statistics Matches: 391, Mismatches: 23, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 41 391 1.00 ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29 Consensus pattern (41 bp): TTGCTGACACATCACTGAAATCTTAATGAATCAGTGAGATA Found at i:743094 original size:47 final size:47 Alignment explanation

Indices: 743025--743155 Score: 253 Period size: 47 Copynumber: 2.8 Consensus size: 47 743015 ACAACTATTG * 743025 TATACACAAGAAGTCTACTCTGAAATCTATTTCACTATACTGCAACA 1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA 743072 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA 1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA 743119 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTA 1 TATACACAAGAAGTCTACTCTGAAATCTATTTTACTA 743156 CTACCAGGAG Statistics Matches: 83, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 47 83 1.00 ACGTcount: A:0.38, C:0.21, G:0.08, T:0.32 Consensus pattern (47 bp): TATACACAAGAAGTCTACTCTGAAATCTATTTTACTATACTGCAACA Found at i:767386 original size:1 final size:1 Alignment explanation

Indices: 767380--767407 Score: 56 Period size: 1 Copynumber: 28.0 Consensus size: 1 767370 CCTCTCCCGA 767380 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT 767408 GGGGAGAGGC Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00 Consensus pattern (1 bp): T Found at i:769264 original size:2 final size:2 Alignment explanation

Indices: 769257--769302 Score: 92 Period size: 2 Copynumber: 23.0 Consensus size: 2 769247 TATCTTATAT 769257 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 769299 GA GA 1 GA GA 769303 TATTTTCAAA Statistics Matches: 44, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 44 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:776056 original size:17 final size:17 Alignment explanation

Indices: 776030--776067 Score: 51 Period size: 16 Copynumber: 2.2 Consensus size: 17 776020 TCTAAATATC * 776030 AAAATCTGAAACATTACA 1 AAAATCTGAAA-AATACA 776048 AAAAT-TGAAAAATACA 1 AAAATCTGAAAAATACA 776064 AAAA 1 AAAA 776068 AGGAGAAAAA Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 16 9 0.47 17 5 0.26 18 5 0.26 ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18 Consensus pattern (17 bp): AAAATCTGAAAAATACA Found at i:785624 original size:1 final size:1 Alignment explanation

Indices: 785618--785669 Score: 104 Period size: 1 Copynumber: 52.0 Consensus size: 1 785608 AGCTAAAGCT 785618 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 785670 GATCCAAGAA Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 51 1.00 ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00 Consensus pattern (1 bp): A Found at i:797827 original size:1 final size:1 Alignment explanation

Indices: 797821--797855 Score: 52 Period size: 1 Copynumber: 35.0 Consensus size: 1 797811 TACTTATTTA * * 797821 TTTTTTTTTTATTTATTTTTTTTTTTTTTTTTTTT 1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 797856 ACAAAAAATC Statistics Matches: 30, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 1 30 1.00 ACGTcount: A:0.06, C:0.00, G:0.00, T:0.94 Consensus pattern (1 bp): T Found at i:797834 original size:15 final size:15 Alignment explanation

Indices: 797814--797855 Score: 70 Period size: 15 Copynumber: 2.9 Consensus size: 15 797804 ATAATCTTAC 797814 TTATTTATTTTTTTT 1 TTATTTATTTTTTTT 797829 TTATTTATTTTTTTT 1 TTATTTATTTTTTTT 797844 TT-TTT-TTTTTTT 1 TTATTTATTTTTTT 797856 ACAAAAAATC Statistics Matches: 27, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 13 7 0.26 14 3 0.11 15 17 0.63 ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90 Consensus pattern (15 bp): TTATTTATTTTTTTT Found at i:798114 original size:2 final size:2 Alignment explanation

Indices: 798107--798131 Score: 50 Period size: 2 Copynumber: 12.5 Consensus size: 2 798097 ACGATCAGCC 798107 AT AT AT AT AT AT AT AT AT AT AT AT A 1 AT AT AT AT AT AT AT AT AT AT AT AT A 798132 NNNNNNNNNN Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 23 1.00 ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48 Consensus pattern (2 bp): AT Found at i:799216 original size:19 final size:19 Alignment explanation

Indices: 799138--799216 Score: 52 Period size: 19 Copynumber: 3.9 Consensus size: 19 799128 CGATAGGAAA 799138 ATAACTCTAGGAATATCTC 1 ATAACTCTAGGAATATCTC * * 799157 AAAACTCGATCTATGG-ATATTTC 1 ATAA--C--TCTA-GGAATATCTC * * * 799180 ATAACTTTCGGAAAATCTC 1 ATAACTCTAGGAATATCTC * 799199 ATAACTCTAGGGATATCT 1 ATAACTCTAGGAATATCT 799217 TAAGAGGCAG Statistics Matches: 43, Mismatches: 11, Indels: 12 0.65 0.17 0.18 Matches are distributed among these distances: 18 2 0.05 19 24 0.56 21 2 0.05 23 13 0.30 24 2 0.05 ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33 Consensus pattern (19 bp): ATAACTCTAGGAATATCTC Found at i:808463 original size:38 final size:38 Alignment explanation

Indices: 808420--808593 Score: 131 Period size: 38 Copynumber: 4.4 Consensus size: 38 808410 CAAAACACTA * * 808420 GAAAATCTCATAACTAAAGTGATATCTCGAATTGCTAG 1 GAAAATCTCATAACTAAAGTGATATCTCAAAATGCTAG * * 808458 GAAAATCTCATATTTCGAGCAAATAG-GATATCTCAAAACGCTAG 1 GAAAATCTCATA-----A-CTAA-AGTGATATCTCAAAATGCTAG ** 808502 GAAAATCTCATAACTCTA-TGGATATCTCAAAATGCTAG 1 GAAAATCTCATAACTAAAGT-GATATCTCAAAATGCTAG ** * 808540 GAAAATCTCATAACTCTAG-GAATATCTCATAACT-CTAG 1 GAAAATCTCATAACTAAAGTG-ATATCTCA-AAATGCTAG * * 808578 AAAAATCTAATAACTA 1 GAAAATCTCATAACTA 808594 TTTAAGAACA Statistics Matches: 112, Mismatches: 12, Indels: 24 0.76 0.08 0.16 Matches are distributed among these distances: 37 2 0.02 38 73 0.65 39 4 0.04 43 1 0.01 44 30 0.27 45 2 0.02 ACGTcount: A:0.42, C:0.18, G:0.13, T:0.28 Consensus pattern (38 bp): GAAAATCTCATAACTAAAGTGATATCTCAAAATGCTAG Found at i:808511 original size:19 final size:19 Alignment explanation

Indices: 808487--808592 Score: 117 Period size: 19 Copynumber: 5.6 Consensus size: 19 808477 CAAATAGGAT * * 808487 ATCTCAAAACGCTAGGAAA 1 ATCTCATAACTCTAGGAAA * 808506 ATCTCATAACTCTATGG-AT 1 ATCTCATAACTCTA-GGAAA * 808525 ATCTCA-AAATGCTAGGAAA 1 ATCTCATAACT-CTAGGAAA * 808544 ATCTCATAACTCTAGGAAT 1 ATCTCATAACTCTAGGAAA * 808563 ATCTCATAACTCTAGAAAA 1 ATCTCATAACTCTAGGAAA * 808582 ATCTAATAACT 1 ATCTCATAACT 808593 ATTTAAGAAC Statistics Matches: 73, Mismatches: 10, Indels: 8 0.80 0.11 0.09 Matches are distributed among these distances: 18 5 0.07 19 63 0.86 20 5 0.07 ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27 Consensus pattern (19 bp): ATCTCATAACTCTAGGAAA Found at i:808515 original size:82 final size:81 Alignment explanation

Indices: 808401--808551 Score: 223 Period size: 82 Copynumber: 1.9 Consensus size: 81 808391 TAAAACGCTA * * 808401 AGGATATCGCAAAACACTAGAAAATCTCATAACTAAA-GTGATATCTCGAATTGCTAGGAAAATC 1 AGGATATCGCAAAACACTAGAAAATCTCATAACTAAATG-GATATCTCAAAATGCTAGGAAAATC 808465 TCATATTTCGAGCAAAT 65 TCATATTTCGAGCAAAT * * ** 808482 AGGATATCTCAAAACGCTAGGAAAATCTCATAACTCTATGGATATCTCAAAATGCTAGGAAAATC 1 AGGATATCGCAAAACACTA-GAAAATCTCATAACTAAATGGATATCTCAAAATGCTAGGAAAATC 808547 TCATA 65 TCATA 808552 ACTCTAGGAA Statistics Matches: 62, Mismatches: 6, Indels: 3 0.87 0.08 0.04 Matches are distributed among these distances: 81 17 0.27 82 44 0.71 83 1 0.02 ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26 Consensus pattern (81 bp): AGGATATCGCAAAACACTAGAAAATCTCATAACTAAATGGATATCTCAAAATGCTAGGAAAATCT CATATTTCGAGCAAAT Found at i:808923 original size:48 final size:48 Alignment explanation

Indices: 808848--809257 Score: 525 Period size: 48 Copynumber: 8.2 Consensus size: 48 808838 AAATGGTTAG * * 808848 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGTGAA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA * 808896 TTTATACGTTGATTTGTACATTTGGGGACATGTTGATACCTTGGTGAA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA * * 808944 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGTGAGA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGA-A * 808993 -TTATACGTTGATTTGCACATTTGGGAACATGTTGATACCTTGGTGAA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA * * 809040 TTTATACGTTGATTTGCACATTTGTGGACATGTTGATACCTTGTTGAA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA * * 809088 TTTATACGTTGATTTGCACATTTAGGGACATGTTGATACCTTCAAAAATGGTGAG 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACC-T------TGGTGAA * * * 809143 TTTATACGTTGATTTGTACATTAGGGGACATGTTGATACCTTGGCGAGA 1 TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGA-A * * 809192 TTATACAAAATGTAGGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAG 1 TT-T-----A--TACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA 809248 TTTATACGTT 1 TTTATACGTT 809258 TATACCTAAA Statistics Matches: 321, Mismatches: 23, Indels: 36 0.84 0.06 0.09 Matches are distributed among these distances: 47 1 0.00 48 228 0.71 49 4 0.01 50 2 0.01 54 1 0.00 55 44 0.14 56 2 0.01 57 39 0.12 ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39 Consensus pattern (48 bp): TTTATACGTTGATTTGCACATTTGGGGACATGTTGATACCTTGGTGAA Found at i:809456 original size:2 final size:2 Alignment explanation

Indices: 809449--809492 Score: 88 Period size: 2 Copynumber: 22.0 Consensus size: 2 809439 CCTCAGCCCA 809449 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 809491 TC 1 TC 809493 ATTAATATTT Statistics Matches: 42, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 42 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:810778 original size:46 final size:46 Alignment explanation

Indices: 810725--811362 Score: 705 Period size: 46 Copynumber: 13.8 Consensus size: 46 810715 AAAAAAGTCC * * * ** 810725 TCCATAACGTGGACTTCTTTGGAAGTCTATATGACTTTATTGCACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * 810771 TCCATAACATGGAC-T-TTTGAGAAAGTCTATTTGATTACATTGCACG 1 TCCATAACATGGACTTCTTTG-G-GAGTCTATTTGACTACATTGCACG * * * * 810817 TCCTTAAAATGGACTTCTTTGGGAGTCTATTTGATTTCATTGCACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * 810863 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCATG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * * 810909 TCCATAACATGGACTT-TAGTGGAAGTCTATTTGACTAAATTGCACG 1 TCCATAACATGGACTTCT-TTGGGAGTCTATTTGACTACATTGCACG * ** 810955 TCCATAATAT-GTTTTCTTTGGGAGTCTATTTGACTACATTGCACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * * * 811000 TCCATAACATGGATTTCTTTGGGAGTTTATTTAACAACATTGCACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * ** * * 811046 TCTATAAAACAGACTTCTTTTGGAGTCTATTTGACTAAATTGCACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * * 811092 TCCATAACACGGACTT-TTGTGGAAGTCTATTTGACTACATTGCATG 1 TCCATAACATGGACTTCTT-TGGGAGTCTATTTGACTACATTGCACG * * * 811138 TCCATAAGATGGACTTCTTTGGGAGTCTATTTGACTACACTGTACG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * * * 811184 TCCATAACATGGATTTTTTTGGGAGTCTATTTGACTACATTGCATG 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG * 811230 TCCATAACATGGACTT-TTGTGGAAGTCTATTTGACTACATTGCACG 1 TCCATAACATGGACTTCTT-TGGGAGTCTATTTGACTACATTGCACG * * * * 811276 TCCATAAAATGGACTTCTTTAGTTAGGTAGTCTTTTTGACTACATTTCATG 1 TCCATAACATGGACTTCTTT-G---GG-AGTCTATTTGACTACATTGCACG * ** * * * 811327 TCCAAAAGGTGGACTTC-TTGGTAGTCTCTCTGACTA 1 TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTA 811363 TGTTGTGAGT Statistics Matches: 504, Mismatches: 72, Indels: 33 0.83 0.12 0.05 Matches are distributed among these distances: 44 4 0.01 45 56 0.11 46 395 0.78 47 7 0.01 48 4 0.01 49 1 0.00 50 3 0.01 51 34 0.07 ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37 Consensus pattern (46 bp): TCCATAACATGGACTTCTTTGGGAGTCTATTTGACTACATTGCACG Found at i:815358 original size:12 final size:12 Alignment explanation

Indices: 815343--815382 Score: 80 Period size: 12 Copynumber: 3.3 Consensus size: 12 815333 TCAATGAACT 815343 AGAATATGATAA 1 AGAATATGATAA 815355 AGAATATGATAA 1 AGAATATGATAA 815367 AGAATATGATAA 1 AGAATATGATAA 815379 AGAA 1 AGAA 815383 AACAGATGTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 28 1.00 ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23 Consensus pattern (12 bp): AGAATATGATAA Done.