Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold419

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: 1725835
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29

Warning! 213561 characters in sequence are not A, C, G, or T


File 6 of 5

Found at i:1536167 original size:42 final size:42

Alignment explanation

Indices: 1536098--1536178 Score: 128 Period size: 42 Copynumber: 1.9 Consensus size: 42 1536088 TTTCTATTAA * * 1536098 TTATGTCGACATGCAAGATGAACATGTTGACATGCAAGATAG 1 TTATGTCAACATGCAACATGAACATGTTGACATGCAAGATAG 1536140 TTATGTCAACATGCAACAT-AACTATGTTGACATGCAAGA 1 TTATGTCAACATGCAACATGAAC-ATGTTGACATGCAAGA 1536179 AAACTGCAGT Statistics Matches: 36, Mismatches: 2, Indels: 2 0.90 0.05 0.05 Matches are distributed among these distances: 41 3 0.08 42 33 0.92 ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27 Consensus pattern (42 bp): TTATGTCAACATGCAACATGAACATGTTGACATGCAAGATAG Found at i:1536183 original size:21 final size:21 Alignment explanation

Indices: 1536099--1536183 Score: 91 Period size: 21 Copynumber: 4.0 Consensus size: 21 1536089 TTCTATTAAT 1536099 TATGTCGACATGCAAGATGAAC 1 TATGTCGACATGCAAGAT-AAC * ** 1536121 -ATGTTGACATGCAAGATAGT 1 TATGTCGACATGCAAGATAAC * * 1536141 TATGTCAACATGCAACATAAC 1 TATGTCGACATGCAAGATAAC * * 1536162 TATGTTGACATGCAAGAAAAC 1 TATGTCGACATGCAAGATAAC 1536183 T 1 T 1536184 GCAGTCAAAT Statistics Matches: 50, Mismatches: 12, Indels: 3 0.77 0.18 0.05 Matches are distributed among these distances: 20 1 0.02 21 49 0.98 ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26 Consensus pattern (21 bp): TATGTCGACATGCAAGATAAC Found at i:1536281 original size:21 final size:21 Alignment explanation

Indices: 1536257--1536359 Score: 127 Period size: 21 Copynumber: 4.9 Consensus size: 21 1536247 ATACACTTCC 1536257 TATTGATGTCAACATGCAACT 1 TATTGATGTCAACATGCAACT * * 1536278 TATTTATGTTAACATGCAACT 1 TATTGATGTCAACATGCAACT * * 1536299 TCTTGATGTCGACATGCAACT 1 TATTGATGTCAACATGCAACT * * 1536320 TATTTATGTCGACATGCAACT 1 TATTGATGTCAACATGCAACT * 1536341 TAGTT-ATGTTAACATGCAA 1 TA-TTGATGTCAACATGCAA 1536360 GATAAATATG Statistics Matches: 71, Mismatches: 10, Indels: 2 0.86 0.12 0.02 Matches are distributed among these distances: 21 69 0.97 22 2 0.03 ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37 Consensus pattern (21 bp): TATTGATGTCAACATGCAACT Found at i:1536340 original size:63 final size:63 Alignment explanation

Indices: 1536257--1536418 Score: 209 Period size: 63 Copynumber: 2.6 Consensus size: 63 1536247 ATACACTTCC * * * * *** * * 1536257 TATTGATGTCAACATGCAACTTATTTATGTTAACATGCAA-CTTCTTGATGTCGACATGCAACT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAAT-ATGTCGACATGAAACA * 1536320 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTTGACATGAAACA 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTCGACATGAAACA * 1536383 TATTTATGTCGACATGCAACTTAGTTATGTTGACAT 1 TATTTATGTCGACATGCAACTTAGTTATGTTAACAT 1536419 ACAGCTTATA Statistics Matches: 87, Mismatches: 11, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 63 85 0.98 64 2 0.02 ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36 Consensus pattern (63 bp): TATTTATGTCGACATGCAACTTAGTTATGTTAACATGCAAGATAAATATGTCGACATGAAACA Found at i:1536390 original size:21 final size:21 Alignment explanation

Indices: 1536268--1536427 Score: 167 Period size: 21 Copynumber: 7.6 Consensus size: 21 1536258 ATTGATGTCA * 1536268 ACATGCAACTTATTTATGTTA 1 ACATGCAACTTATTTATGTTG * * * 1536289 ACATGCAACTTCTTGATGTCG 1 ACATGCAACTTATTTATGTTG * 1536310 ACATGCAACTTATTTATGTCG 1 ACATGCAACTTATTTATGTTG * * 1536331 ACATGCAACTTAGTTATGTTA 1 ACATGCAACTTATTTATGTTG ** ** 1536352 ACATGCAAGATAAATATGTTG 1 ACATGCAACTTATTTATGTTG * * * 1536373 ACATGAAACATATTTATGTCG 1 ACATGCAACTTATTTATGTTG * 1536394 ACATGCAACTTAGTTATGTTG 1 ACATGCAACTTATTTATGTTG * * 1536415 ACATACAGCTTAT 1 ACATGCAACTTAT 1536428 AAGTTGCATG Statistics Matches: 113, Mismatches: 26, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 21 113 1.00 ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36 Consensus pattern (21 bp): ACATGCAACTTATTTATGTTG Found at i:1536478 original size:21 final size:21 Alignment explanation

Indices: 1536454--1536544 Score: 119 Period size: 21 Copynumber: 4.3 Consensus size: 21 1536444 TATTTATCTC * ** 1536454 GCATGTCAACATACGTAAGTT 1 GCATGTCGACATAAATAAGTT * 1536475 GCATGTTGACATAAATAAGTT 1 GCATGTCGACATAAATAAGTT * 1536496 GCATCTCGACATAAATAAGTT 1 GCATGTCGACATAAATAAGTT * * 1536517 GCATGTTGACATAAATAATTT 1 GCATGTCGACATAAATAAGTT 1536538 GCATGTC 1 GCATGTC 1536545 AGCATATTTA Statistics Matches: 60, Mismatches: 10, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 21 60 1.00 ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32 Consensus pattern (21 bp): GCATGTCGACATAAATAAGTT Found at i:1536550 original size:21 final size:22 Alignment explanation

Indices: 1536426--1536550 Score: 109 Period size: 21 Copynumber: 6.0 Consensus size: 22 1536416 CATACAGCTT * 1536426 ATAAGTTGCATGTCAG-CATAT 1 ATAAGTTGCATGTCAGACATAA * ** * * 1536447 TTATCTCGCATGTCA-ACATAC 1 ATAAGTTGCATGTCAGACATAA * * 1536468 GTAAGTTGCATGT-TGACATAA 1 ATAAGTTGCATGTCAGACATAA * 1536489 ATAAGTTGCATCTC-GACATAA 1 ATAAGTTGCATGTCAGACATAA * 1536510 ATAAGTTGCATGT-TGACATAA 1 ATAAGTTGCATGTCAGACATAA * 1536531 ATAATTTGCATGTCAG-CATA 1 ATAAGTTGCATGTCAGACATA 1536551 TTTATCTTGC Statistics Matches: 83, Mismatches: 16, Indels: 10 0.76 0.15 0.09 Matches are distributed among these distances: 21 82 0.99 22 1 0.01 ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33 Consensus pattern (22 bp): ATAAGTTGCATGTCAGACATAA Found at i:1536561 original size:42 final size:42 Alignment explanation

Indices: 1536473--1536567 Score: 120 Period size: 42 Copynumber: 2.3 Consensus size: 42 1536463 CATACGTAAG * 1536473 TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAG 1 TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAC * * ** * 1536515 TTGCATGTTGACATAAATAATTTGCATGTC-AGCATATTTATC 1 TTGCATGTTGACATAAATAAGTTGCATCTCGA-CATAAATAAC 1536557 TTGCATGTTGA 1 TTGCATGTTGA 1536568 TTTATGTCAA Statistics Matches: 46, Mismatches: 6, Indels: 2 0.85 0.11 0.04 Matches are distributed among these distances: 41 1 0.02 42 45 0.98 ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37 Consensus pattern (42 bp): TTGCATGTTGACATAAATAAGTTGCATCTCGACATAAATAAC Found at i:1561464 original size:19 final size:19 Alignment explanation

Indices: 1561437--1561473 Score: 65 Period size: 19 Copynumber: 1.9 Consensus size: 19 1561427 ATAGAATTGA * 1561437 CATTGCAGATAGCATTTGT 1 CATTACAGATAGCATTTGT 1561456 CATTACAGATAGCATTTG 1 CATTACAGATAGCATTTG 1561474 CATGTTCTTT Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35 Consensus pattern (19 bp): CATTACAGATAGCATTTGT Found at i:1562078 original size:13 final size:12 Alignment explanation

Indices: 1562060--1562106 Score: 53 Period size: 11 Copynumber: 4.0 Consensus size: 12 1562050 ACTAAACTCC 1562060 GGGTTTACTTTTT 1 GGGTTTAC-TTTT * 1562073 GGGTTTAC-TTG 1 GGGTTTACTTTT * 1562084 GGGTTTACTCTT 1 GGGTTTACTTTT 1562096 -GGTTTACTTTT 1 GGGTTTACTTTT 1562107 TGAAAATATG Statistics Matches: 29, Mismatches: 4, Indels: 4 0.78 0.11 0.11 Matches are distributed among these distances: 11 20 0.69 12 1 0.03 13 8 0.28 ACGTcount: A:0.09, C:0.11, G:0.26, T:0.55 Consensus pattern (12 bp): GGGTTTACTTTT Found at i:1565397 original size:2 final size:2 Alignment explanation

Indices: 1565390--1565434 Score: 90 Period size: 2 Copynumber: 22.5 Consensus size: 2 1565380 TTAACATATA 1565390 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 1565432 CT C 1 CT C 1565435 ATATATACAC Statistics Matches: 43, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 43 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1567827 original size:34 final size:34 Alignment explanation

Indices: 1567784--1568023 Score: 268 Period size: 34 Copynumber: 7.0 Consensus size: 34 1567774 ACTCTTTGAG * * * 1567784 GAAGTCTGGTTATACATATACTTGGAATTCTGTC 1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT ** * 1567818 GAAGTCTGGTTGCACATGTACTTGGGTTTCTGTT 1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT * ** * 1567852 GATGTCTGGTTATATGTGTACTTTGATTTCTGTT 1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT * * 1567886 GAAGTCTGGTTATAC-TGGTACTTGGACTTCAGTT 1 GAAGTCTGGTTATACAT-GTACTTGGATTTCTGTT * 1567920 GAAGTCTGGTTACACATGTACTTTGG-TTTCTGTT 1 GAAGTCTGGTTATACATGTAC-TTGGATTTCTGTT ** * 1567954 GAAGTCTGGTTATATGTGTACTTTGATTTCTGTT 1 GAAGTCTGGTTATACATGTACTTGGATTTCTGTT ** * 1567988 GAAGTCTGGTTATACATAAAGATTGGATTTCTGTT 1 GAAGTCTGGTTATACATGTA-CTTGGATTTCTGTT 1568023 G 1 G 1568024 TATTTTGTGA Statistics Matches: 170, Mismatches: 31, Indels: 9 0.81 0.15 0.04 Matches are distributed among these distances: 33 4 0.02 34 148 0.87 35 18 0.11 ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43 Consensus pattern (34 bp): GAAGTCTGGTTATACATGTACTTGGATTTCTGTT Found at i:1567911 original size:102 final size:102 Alignment explanation

Indices: 1567784--1568005 Score: 365 Period size: 102 Copynumber: 2.2 Consensus size: 102 1567774 ACTCTTTGAG * * 1567784 GAAGTCTGGTTATACATATACTTGGAATTCTGTCGAAGTCTGGTTGCACATGTACTTGGGTTTCT 1 GAAGTCTGGTTATACATATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTCT * 1567849 GTTGATGTCTGGTTATATGTGTACTTTGATTTCTGTT 66 GTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT * * * * 1567886 GAAGTCTGGTTATAC-TGGTACTTGGACTTCAGTTGAAGTCTGGTTACACATGTACTTTGGTTTC 1 GAAGTCTGGTTATACAT-ATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTC 1567950 TGTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT 65 TGTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT 1567988 GAAGTCTGGTTATACATA 1 GAAGTCTGGTTATACATA 1568006 AAGATTGGAT Statistics Matches: 110, Mismatches: 8, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 101 1 0.01 102 108 0.98 103 1 0.01 ACGTcount: A:0.20, C:0.13, G:0.24, T:0.43 Consensus pattern (102 bp): GAAGTCTGGTTATACATATACTTGGAATTCAGTCGAAGTCTGGTTACACATGTACTTGGGTTTCT GTTGAAGTCTGGTTATATGTGTACTTTGATTTCTGTT Found at i:1567963 original size:17 final size:17 Alignment explanation

Indices: 1567943--1567998 Score: 51 Period size: 17 Copynumber: 3.3 Consensus size: 17 1567933 ACATGTACTT 1567943 TGGTTTCTGTTGAAGTC 1 TGGTTTCTGTTGAAGTC * * * * 1567960 TGGTTATATG-TGTACTT 1 TGGTT-TCTGTTGAAGTC * 1567977 TGATTTCTGTTGAAGTC 1 TGGTTTCTGTTGAAGTC 1567994 TGGTT 1 TGGTT 1567999 ATACATAAAG Statistics Matches: 27, Mismatches: 10, Indels: 4 0.66 0.24 0.10 Matches are distributed among these distances: 16 3 0.11 17 21 0.78 18 3 0.11 ACGTcount: A:0.14, C:0.09, G:0.27, T:0.50 Consensus pattern (17 bp): TGGTTTCTGTTGAAGTC Found at i:1570562 original size:2 final size:2 Alignment explanation

Indices: 1570557--1570611 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1570547 GTAATATATG 1570557 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 1570599 CT CT CT CT CT CT C 1 CT CT CT CT CT CT C 1570612 GCAGCTCCTA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:1571826 original size:27 final size:28 Alignment explanation

Indices: 1571796--1571855 Score: 79 Period size: 27 Copynumber: 2.2 Consensus size: 28 1571786 TTATGCTCTT * 1571796 AATTTTCATCA-TTTGTTCCATGCAGTA 1 AATTTTCATCAGTTTGTTCCATGAAGTA * * 1571823 AA-TTTCTTCAGTTTGTTCCGTGAAGTA 1 AATTTTCATCAGTTTGTTCCATGAAGTA 1571850 AATTTT 1 AATTTT 1571856 ATTCAATGAT Statistics Matches: 28, Mismatches: 3, Indels: 3 0.82 0.09 0.09 Matches are distributed among these distances: 26 7 0.25 27 18 0.64 28 3 0.11 ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47 Consensus pattern (28 bp): AATTTTCATCAGTTTGTTCCATGAAGTA Found at i:1572038 original size:4 final size:4 Alignment explanation

Indices: 1572023--1572068 Score: 76 Period size: 4 Copynumber: 11.8 Consensus size: 4 1572013 ATCACCCGTT * 1572023 GTCC GT-C GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC 1572069 TGTAAACTTT Statistics Matches: 39, Mismatches: 2, Indels: 2 0.91 0.05 0.05 Matches are distributed among these distances: 3 3 0.08 4 36 0.92 ACGTcount: A:0.00, C:0.46, G:0.26, T:0.28 Consensus pattern (4 bp): GTCC Found at i:1572069 original size:12 final size:12 Alignment explanation

Indices: 1572018--1572071 Score: 76 Period size: 12 Copynumber: 4.7 Consensus size: 12 1572008 TTCTGATCAC 1572018 CCGT-TGTCCGT 1 CCGTCTGTCCGT * 1572029 -CGTCCGTCCGT 1 CCGTCTGTCCGT * 1572040 CCGTCCGTCCGT 1 CCGTCTGTCCGT 1572052 CCGTCTGTCCGT 1 CCGTCTGTCCGT 1572064 CCGTCTGT 1 CCGTCTGT 1572072 AAACTTTTCA Statistics Matches: 39, Mismatches: 2, Indels: 3 0.89 0.05 0.07 Matches are distributed among these distances: 10 3 0.08 11 6 0.15 12 30 0.77 ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31 Consensus pattern (12 bp): CCGTCTGTCCGT Found at i:1574570 original size:16 final size:17 Alignment explanation

Indices: 1574551--1574584 Score: 61 Period size: 17 Copynumber: 2.1 Consensus size: 17 1574541 CGTCACAATA 1574551 TACT-GGCGAGAAATGG 1 TACTCGGCGAGAAATGG 1574567 TACTCGGCGAGAAATGG 1 TACTCGGCGAGAAATGG 1574584 T 1 T 1574585 CGCACTCCAG Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 16 4 0.24 17 13 0.76 ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21 Consensus pattern (17 bp): TACTCGGCGAGAAATGG Found at i:1575489 original size:2 final size:2 Alignment explanation

Indices: 1575484--1575547 Score: 128 Period size: 2 Copynumber: 32.0 Consensus size: 2 1575474 TTAGTCTCTC 1575484 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 1575526 AG AG AG AG AG AG AG AG AG AG AG 1 AG AG AG AG AG AG AG AG AG AG AG 1575548 CAAATGTAGA Statistics Matches: 62, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 62 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1578607 original size:2 final size:2 Alignment explanation

Indices: 1578600--1578654 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1578590 GCAATTATAC 1578600 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 1578642 AG AG AG AG AG AG A 1 AG AG AG AG AG AG A 1578655 ATTCTTAAAA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1579812 original size:2 final size:2 Alignment explanation

Indices: 1579805--1579859 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1579795 GCAATTATAC 1579805 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 1579847 AG AG AG AG AG AG A 1 AG AG AG AG AG AG A 1579860 ATTCTTAAAA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1583356 original size:2 final size:2 Alignment explanation

Indices: 1583349--1583402 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1583339 ATGTAAGTGT 1583349 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 1583391 TC TC TC TC TC TC 1 TC TC TC TC TC TC 1583403 ATTTTCACCT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1583757 original size:2 final size:2 Alignment explanation

Indices: 1583750--1583807 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 1583740 TTTTCCTTAA 1583750 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 1583792 CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT 1583808 GGGGAACTTG Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:1586205 original size:2 final size:2 Alignment explanation

Indices: 1586198--1586253 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 1586188 CCTAGTAATA 1586198 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 1586240 TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC 1586254 CAAGAGTTAG Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:1588605 original size:19 final size:19 Alignment explanation

Indices: 1588573--1588615 Score: 50 Period size: 19 Copynumber: 2.3 Consensus size: 19 1588563 AGTTTTAACC * 1588573 AGTTTTAACCGGATATATT 1 AGTTTTAACCGGATATACT ** * 1588592 AGTTTTAATTGGATGTACT 1 AGTTTTAACCGGATATACT 1588611 AGTTT 1 AGTTT 1588616 ACAGTTATTT Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47 Consensus pattern (19 bp): AGTTTTAACCGGATATACT Found at i:1589029 original size:30 final size:30 Alignment explanation

Indices: 1588995--1589129 Score: 209 Period size: 30 Copynumber: 4.5 Consensus size: 30 1588985 AATACGTTGC * 1588995 CGGTCCAATAGATCACAGTCTATTGACCGG 1 CGGTCCAATAGATCACACTCTATTGACCGG 1589025 CGGTCCAATAGATCACACTCTATTGACCGG 1 CGGTCCAATAGATCACACTCTATTGACCGG 1589055 CGGTCCAATAGATCACACTCTATTGACCGG 1 CGGTCCAATAGATCACACTCTATTGACCGG * * * 1589085 CGGTCTAATAGATCGCAGTCTATTGACCGG 1 CGGTCCAATAGATCACACTCTATTGACCGG ** 1589115 CAAT-CAATAGATCAC 1 CGGTCCAATAGATCAC 1589130 TTTCAAACCT Statistics Matches: 97, Mismatches: 8, Indels: 1 0.92 0.08 0.01 Matches are distributed among these distances: 29 9 0.09 30 88 0.91 ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24 Consensus pattern (30 bp): CGGTCCAATAGATCACACTCTATTGACCGG Found at i:1593515 original size:21 final size:21 Alignment explanation

Indices: 1593458--1593517 Score: 93 Period size: 21 Copynumber: 2.9 Consensus size: 21 1593448 TGTAGCTATG * * 1593458 TTGCATGTTGACATAATTATC 1 TTGCATGTCGACATATTTATC * 1593479 TTGCATGTCAACATATTTATC 1 TTGCATGTCGACATATTTATC 1593500 TTGCATGTCGACATATTT 1 TTGCATGTCGACATATTT 1593518 GATAGAAAAA Statistics Matches: 35, Mismatches: 4, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 35 1.00 ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43 Consensus pattern (21 bp): TTGCATGTCGACATATTTATC Found at i:1595300 original size:19 final size:19 Alignment explanation

Indices: 1595276--1595313 Score: 67 Period size: 19 Copynumber: 2.0 Consensus size: 19 1595266 TCAAACGGTA * 1595276 TCAGGGTGAGTGTCGTCTG 1 TCAGGGTAAGTGTCGTCTG 1595295 TCAGGGTAAGTGTCGTCTG 1 TCAGGGTAAGTGTCGTCTG 1595314 CCATTAATAT Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 18 1.00 ACGTcount: A:0.13, C:0.16, G:0.39, T:0.32 Consensus pattern (19 bp): TCAGGGTAAGTGTCGTCTG Found at i:1595361 original size:14 final size:14 Alignment explanation

Indices: 1595342--1595370 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 1595332 CAACAAGAAC 1595342 GTCTATCTTTCCTA 1 GTCTATCTTTCCTA 1595356 GTCTATCTTTCCTA 1 GTCTATCTTTCCTA 1595370 G 1 G 1595371 AGTTATAATT 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:0.14, C:0.28, G:0.10, T:0.48 Consensus pattern (14 bp): GTCTATCTTTCCTA Found at i:1597712 original size:15 final size:15 Alignment explanation

Indices: 1597692--1597725 Score: 68 Period size: 15 Copynumber: 2.3 Consensus size: 15 1597682 ATAGATTTTG 1597692 ATATTTTATACCAAA 1 ATATTTTATACCAAA 1597707 ATATTTTATACCAAA 1 ATATTTTATACCAAA 1597722 ATAT 1 ATAT 1597726 AAACGAACGA Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41 Consensus pattern (15 bp): ATATTTTATACCAAA Found at i:1599022 original size:2 final size:2 Alignment explanation

Indices: 1599015--1599069 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 1599005 TTCAAGTGAG 1599015 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 1599057 GA GA GA GA GA GA G 1 GA GA GA GA GA GA G 1599070 CGCTAAATGT Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1600814 original size:17 final size:17 Alignment explanation

Indices: 1600788--1600826 Score: 51 Period size: 17 Copynumber: 2.3 Consensus size: 17 1600778 TTTATTACAC * 1600788 TTTTTTAAAACTGCAAA 1 TTTTTAAAAACTGCAAA * * 1600805 TTTTTAAAAATTTCAAA 1 TTTTTAAAAACTGCAAA 1600822 TTTTT 1 TTTTT 1600827 CATTGTTTAA Statistics Matches: 19, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 17 19 1.00 ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51 Consensus pattern (17 bp): TTTTTAAAAACTGCAAA Found at i:1635820 original size:2 final size:2 Alignment explanation

Indices: 1635813--1635851 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 1635803 AGACTGAAAA 1635813 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1635852 TTTAATGTCG Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1641313 original size:11 final size:11 Alignment explanation

Indices: 1641297--1641322 Score: 52 Period size: 11 Copynumber: 2.4 Consensus size: 11 1641287 GTATTGATCA 1641297 ACATCGTGTCT 1 ACATCGTGTCT 1641308 ACATCGTGTCT 1 ACATCGTGTCT 1641319 ACAT 1 ACAT 1641323 TGTACCCTTT Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 15 1.00 ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35 Consensus pattern (11 bp): ACATCGTGTCT Found at i:1646252 original size:2 final size:2 Alignment explanation

Indices: 1646247--1646323 Score: 122 Period size: 2 Copynumber: 38.5 Consensus size: 2 1646237 ATATATGGAA 1646247 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TA- AG 1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -AG AG 1646289 AG AG AG AG AG AG TA- 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 AG AG A 1646324 TGGTTAAGGA Statistics Matches: 71, Mismatches: 0, Indels: 8 0.90 0.00 0.10 Matches are distributed among these distances: 1 2 0.03 2 67 0.94 3 2 0.03 ACGTcount: A:0.51, C:0.00, G:0.47, T:0.03 Consensus pattern (2 bp): AG Found at i:1648076 original size:152 final size:152 Alignment explanation

Indices: 1647893--1648183 Score: 510 Period size: 152 Copynumber: 1.9 Consensus size: 152 1647883 AATAAATACG * * 1647893 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATATTTACCATCTTTGGTGTAGCTCTCAG 1 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG * * 1647958 GTCCATGATTGTAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT 66 GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT * 1648023 TAAATCAAATAAATACGAGTAA 131 AAAATCAAATAAATACGAGTAA * 1648045 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTGAG 1 ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG * * 1648110 GTCCATAATTGAAGACTGGATCTGGTGCTGTCAAAAAACATGTTTTAGTTAATAACATATCTTTT 66 GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT 1648175 AAAATCAAA 131 AAAATCAAA 1648184 ATTACAAAGC Statistics Matches: 131, Mismatches: 8, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 152 131 1.00 ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32 Consensus pattern (152 bp): ATGTCAATATGAAAAGTGTGATGAAACGAAAGCAAAATACTTACAATCTTTGGTGTAGCTCTCAG GTCCATAATTGAAGACTGGATCTGGTGCTATCAAAAAACATGTTTTAATTAATAACATATCTTTT AAAATCAAATAAATACGAGTAA Found at i:1654999 original size:7 final size:7 Alignment explanation

Indices: 1654975--1655041 Score: 80 Period size: 7 Copynumber: 9.6 Consensus size: 7 1654965 TTTAGATATT 1654975 GAATCTC 1 GAATCTC * * 1654982 CAATTTC 1 GAATCTC 1654989 GAATCTC 1 GAATCTC 1654996 GAATCTC 1 GAATCTC * * 1655003 GTATTTC 1 GAATCTC 1655010 GAATCTC 1 GAATCTC * * 1655017 GTATTTC 1 GAATCTC 1655024 GAATCTC 1 GAATCTC 1655031 GAATCTC 1 GAATCTC 1655038 GAAT 1 GAAT 1655042 GATCCTTCTC Statistics Matches: 48, Mismatches: 12, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 7 48 1.00 ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36 Consensus pattern (7 bp): GAATCTC Found at i:1655000 original size:21 final size:21 Alignment explanation

Indices: 1654975--1655041 Score: 89 Period size: 21 Copynumber: 3.2 Consensus size: 21 1654965 TTTAGATATT * 1654975 GAATCTCCAATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * 1654996 GAATCTCGTATTTCGAATCTC 1 GAATCTCGAATTTCGAATCTC * * * 1655017 GTATTTCGAATCTCGAATCTC 1 GAATCTCGAATTTCGAATCTC 1655038 GAAT 1 GAAT 1655042 GATCCTTCTC Statistics Matches: 39, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 21 39 1.00 ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36 Consensus pattern (21 bp): GAATCTCGAATTTCGAATCTC Found at i:1659730 original size:21 final size:21 Alignment explanation

Indices: 1659706--1659749 Score: 88 Period size: 21 Copynumber: 2.1 Consensus size: 21 1659696 TTGGTCTTTA 1659706 TTTAACTAGACTGTTGGAATC 1 TTTAACTAGACTGTTGGAATC 1659727 TTTAACTAGACTGTTGGAATC 1 TTTAACTAGACTGTTGGAATC 1659748 TT 1 TT 1659750 ATTGTTGTCG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 23 1.00 ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41 Consensus pattern (21 bp): TTTAACTAGACTGTTGGAATC Found at i:1660608 original size:2 final size:2 Alignment explanation

Indices: 1660601--1660653 Score: 106 Period size: 2 Copynumber: 26.5 Consensus size: 2 1660591 ACGATTTAAG 1660601 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 1660643 GA GA GA GA GA G 1 GA GA GA GA GA G 1660654 TATAAAATGT Statistics Matches: 51, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 51 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1663185 original size:2 final size:2 Alignment explanation

Indices: 1663178--1663213 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 1663168 AAGATGATAT 1663178 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 1663214 TTTACATGTA Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1663229 original size:4 final size:4 Alignment explanation

Indices: 1663222--1663319 Score: 178 Period size: 4 Copynumber: 24.5 Consensus size: 4 1663212 GATTTACATG 1663222 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA 1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA * * 1663270 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TCGA TCGA TAGA 1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA 1663318 TA 1 TA 1663320 TTTGTTAGTA Statistics Matches: 92, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 4 92 1.00 ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26 Consensus pattern (4 bp): TAGA Found at i:1665715 original size:2 final size:2 Alignment explanation

Indices: 1665708--1665742 Score: 52 Period size: 2 Copynumber: 17.5 Consensus size: 2 1665698 AGAAGCAAGG * * 1665708 GA GA GA GA GA GA GA GT GA AA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G 1665743 GGGGGGTTCT Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03 Consensus pattern (2 bp): GA Found at i:1668600 original size:2 final size:2 Alignment explanation

Indices: 1668593--1668644 Score: 95 Period size: 2 Copynumber: 26.0 Consensus size: 2 1668583 CTCTAGCTAC * 1668593 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1668635 GA GA GA GA GA 1 GA GA GA GA GA 1668645 ACCCAGAGTA Statistics Matches: 48, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:1672507 original size:2 final size:2 Alignment explanation

Indices: 1672500--1672566 Score: 134 Period size: 2 Copynumber: 33.5 Consensus size: 2 1672490 NNNNNNNNNG 1672500 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 1672542 TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC T 1672567 GCAAATAATG Statistics Matches: 65, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 65 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1677294 original size:57 final size:57 Alignment explanation

Indices: 1677117--1677294 Score: 216 Period size: 57 Copynumber: 3.1 Consensus size: 57 1677107 TGCAAAGACA * * * * 1677117 GATAGTGATAGTGTGCACAATGCACCAGAGCACCAAGCTGTGCTAACTGCATTGACT 1 GATAGTGATAGTGTCCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT * * * ** * 1677174 GATAGTAACAATGTGCCA-AATACATCAGATTACCAAGCTGTGCTAACTGCAATGAGT 1 GATAGTGATAGTGT-CCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT * * 1677231 GATAGTGATAGTGTCCACAATACATCAAAGCAACC-AGCTGTGCTAACTGCCTTGAGT 1 GATAGTGATAGTGTCCACAATACATCAGAGC-ACCAAGCTGTGCTAACTGCATTGAGT 1677288 GATAGTG 1 GATAGTG 1677295 TGCTCAATAC Statistics Matches: 100, Mismatches: 18, Indels: 6 0.81 0.15 0.05 Matches are distributed among these distances: 56 3 0.03 57 92 0.92 58 5 0.05 ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24 Consensus pattern (57 bp): GATAGTGATAGTGTCCACAATACATCAGAGCACCAAGCTGTGCTAACTGCATTGAGT Found at i:1686345 original size:2 final size:2 Alignment explanation

Indices: 1686338--1686402 Score: 130 Period size: 2 Copynumber: 32.5 Consensus size: 2 1686328 AGTATCAATT 1686338 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 1686380 TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC T 1686403 GTGTGCTACT 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:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1688103 original size:2 final size:2 Alignment explanation

Indices: 1688096--1688149 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 1688086 CATGTACAAC 1688096 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 1688138 AG AG AG AG AG AG 1 AG AG AG AG AG AG 1688150 CGATATTATT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): AG Found at i:1693195 original size:2 final size:2 Alignment explanation

Indices: 1693188--1693264 Score: 154 Period size: 2 Copynumber: 38.5 Consensus size: 2 1693178 NNNNNNNNNN 1693188 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1693230 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A 1693265 TGCATACATA Statistics Matches: 75, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 75 1.00 ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:1713203 original size:159 final size:160 Alignment explanation

Indices: 1712904--1713241 Score: 502 Period size: 160 Copynumber: 2.1 Consensus size: 160 1712894 AACATCCAGA * * 1712904 AAGAAAATGAGCGGAAACTGCACACAACTGGAATTTTCTAAGTCCAAAGGCCATAACTCTGTCAA 1 AAGAAAATGAGCGGAAACTGCAAACAACTGGAATTTTCTAAGTCCAAAGGCAATAACTCTGTCAA * * 1712969 AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATGATAAACCTGTATACTA 66 AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATACCA * 1713034 AATTTTATTTCAA-ATGTTCATCCTCTGCG 131 AATTTCATTTCAATATGTTCATCCTCTGCG * * 1713063 AAGAAAATGAGCGGAAACTGCAAATAACTGGAATTTTTCTACGTCC-AAGGACAATAACTCTGTC 1 AAGAAAATGAGCGGAAACTGCAAACAACTGGAA-TTTTCTAAGTCCAAAGG-CAATAACTCTGTC * * ** * * 1713127 GAAAATGGCTCGATCGTGCCCAATATTGAACTTGACCTAGATATTATCATAAT-AACCTGTATAC 64 AAAAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATAC * 1713191 CAAATTTCATTTCAATATGTTCATCCTCTGCT 129 CAAATTTCATTTCAATATGTTCATCCTCTGCG * 1713223 AAGAAAATGAACGGAAACT 1 AAGAAAATGAGCGGAAACT 1713242 TATGGTGGAC Statistics Matches: 161, Mismatches: 15, Indels: 5 0.89 0.08 0.03 Matches are distributed among these distances: 159 59 0.37 160 102 0.63 ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28 Consensus pattern (160 bp): AAGAAAATGAGCGGAAACTGCAAACAACTGGAATTTTCTAAGTCCAAAGGCAATAACTCTGTCAA AAATGGCTCGATCGTACCCAATATCAAACTTGACCTAGAAATAATCATAATAAACCTGTATACCA AATTTCATTTCAATATGTTCATCCTCTGCG Found at i:1713404 original size:49 final size:49 Alignment explanation

Indices: 1713327--1713994 Score: 698 Period size: 49 Copynumber: 13.6 Consensus size: 49 1713317 TAATTACAGG * * * * * * 1713327 TACATGTATTTACCACGTGCTGTATGATACAGGTGAAACACATACATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * 1713376 TACAGGTATTTACTATGTGTTGTATGATAGAGGTGAGATACATGCACGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * 1713425 TACATGTATTTACTATGTGTTGTATGATAGAGGTGAGATACATGCATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * * * * 1713474 TACAGGTATCTA-TAACATGCTGTATGATACAGGTGAAACACATACATAA 1 TACAGGTATTTACT-ACGTGTTGTATGATACAGGTGAGATACATGCATGA * * 1713523 TACAGGTATTTACTACGTGTTGTATGATACTGGTGAGATACATGCACGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * * * 1713572 TACAGTTATTTACTATGTGTTGTATGATACAGGTGAAACACATACATAA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * 1713621 TACAGGTATTTACTACGTGTTGTATGATACTGGTGAGATACATGCACGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * 1713670 TACAGTTATTTACTATGTGTTGTATGATACAAGTGAGACACATGCATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * * 1713719 TACAGGTATTTACCACCTGCTGTATGATTCAGGTGAGATACATGGATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * ** * 1713768 TACAGGTATTTACTACATGCTACTATGATACAGG-GCAATGACACAGTG--TGA 1 TACAGGTATTTACTACGTG-TTGTATGATACAGGTG--A-GATACA-TGCATGA * * ** * * * * 1713819 TACAGCTGTTTACTAAATGTTGTATGATATAGGTGAGAAATATGTATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * 1713868 TACAGGAATTTACAACATGTTGTATGATACAGATGAGATACATGCATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA * * * * * 1713917 TACAGGTAATAACTACGTGTTGTATGATACAGGTGCGTTATAT-CTATGA 1 TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGC-ATGA * 1713966 TACAGGTATTTACTATGTGTTGTATGATA 1 TACAGGTATTTACTACGTGTTGTATGATA 1713995 AAGGACAATG Statistics Matches: 510, Mismatches: 98, Indels: 22 0.81 0.16 0.03 Matches are distributed among these distances: 47 2 0.00 48 6 0.01 49 452 0.89 50 22 0.04 51 21 0.04 52 5 0.01 53 2 0.00 ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33 Consensus pattern (49 bp): TACAGGTATTTACTACGTGTTGTATGATACAGGTGAGATACATGCATGA Found at i:1724030 original size:55 final size:55 Alignment explanation

Indices: 1723964--1724255 Score: 318 Period size: 55 Copynumber: 5.5 Consensus size: 55 1723954 AACCCTAGAC * * 1723964 TAGAGTGGCCCGACTGACTAGCAACTGGCATGCTGTACCCTAAAATCTGACAGAT 1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT * * * * * 1724019 TAGAGTGGCCCGACTGACAAACTACTGGCGTGCTGTACCCTAGACTCTGACAGAC 1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT * 1724074 TAGAGTGACCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT 1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT * * * 1724129 TAGAGTGGCCCGACTGACTAACTACTGACAG-GCTGTAGCCT---A---GAC---- 1 TAGAGTGGCCCGACTGACTAGCTACTGGC-GTGCTGTACCCTAAAATCTGACAGAT * ** * * * * * * 1724174 TAGAGTGACTTGACTGAATAACTACTGACGTGCTGTAGCCTAGAATCTGACATAT 1 TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT 1724229 TAGAGTGGCCCGACTGACTAGCTACTG 1 TAGAGTGGCCCGACTGACTAGCTACTG 1724256 ACGTAGCATA Statistics Matches: 199, Mismatches: 26, Indels: 24 0.80 0.10 0.10 Matches are distributed among these distances: 44 1 0.01 45 35 0.18 48 1 0.01 49 3 0.02 51 3 0.02 52 1 0.01 55 154 0.77 56 1 0.01 ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23 Consensus pattern (55 bp): TAGAGTGGCCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGAT Found at i:1724243 original size:100 final size:100 Alignment explanation

Indices: 1724070--1724257 Score: 295 Period size: 100 Copynumber: 1.9 Consensus size: 100 1724060 AGACTCTGAC * * * 1724070 AGACTAGAGTGACCCGACTGACTAGCTACTGGCGTGCTGTACCCTAAAATCTGACAGATTAGAGT 1 AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT 1724135 GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT 66 GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT ** * * * 1724170 AGACTAGAGTGACTTGACTGAATAACTACTGACGTGCTGTAGCCTAGAATCTGACATATTAGAGT 1 AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT * 1724235 GGCCCGACTGACTAGCTACTGAC 66 GGCCCGACTGACTAACTACTGAC 1724258 GTAGCATATA Statistics Matches: 79, Mismatches: 9, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 100 79 1.00 ACGTcount: A:0.28, C:0.24, G:0.24, T:0.23 Consensus pattern (100 bp): AGACTAGAGTGACCCGACTGAATAACTACTGACGTGCTGTACCCTAAAATCTGACAGATTAGAGT GGCCCGACTGACTAACTACTGACAGGCTGTAGCCT Found at i:1725136 original size:30 final size:30 Alignment explanation

Indices: 1725100--1725181 Score: 155 Period size: 30 Copynumber: 2.7 Consensus size: 30 1725090 CCTAAACACA 1725100 TGATATCTGGTCCTACTACACATGATATCC 1 TGATATCTGGTCCTACTACACATGATATCC * 1725130 TGATATCTGGTCCAACTACACATGATATCC 1 TGATATCTGGTCCTACTACACATGATATCC 1725160 TGATATCTGGTCCTACTACACA 1 TGATATCTGGTCCTACTACACA 1725182 GGATCTTTTT Statistics Matches: 50, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 30 50 1.00 ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32 Consensus pattern (30 bp): TGATATCTGGTCCTACTACACATGATATCC Done.