Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold3

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: 1336734
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30

Warning! 151046 characters in sequence are not A, C, G, or T


File 5 of 4

Found at i:1234595 original size:21 final size:21

Alignment explanation

Indices: 1234554--1234597 Score: 63 Period size: 21 Copynumber: 2.1 Consensus size: 21 1234544 ATAGTTCGTA * 1234554 TAACGTGGGTGATCGTTCGTG 1 TAACGTGGGTGATCGTGCGTG 1234575 TAACGTGCGG-GATCGTGCGTG 1 TAACGTG-GGTGATCGTGCGTG 1234596 TA 1 TA 1234598 TCAGGAAAAT Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 21 19 0.90 22 2 0.10 ACGTcount: A:0.16, C:0.16, G:0.39, T:0.30 Consensus pattern (21 bp): TAACGTGGGTGATCGTGCGTG Found at i:1235620 original size:11 final size:11 Alignment explanation

Indices: 1235604--1235639 Score: 56 Period size: 11 Copynumber: 3.4 Consensus size: 11 1235594 GATCATGCGT 1235604 TATCGTTCGTG 1 TATCGTTCGTG * 1235615 TATCGTGCGTG 1 TATCGTTCGTG 1235626 -ATCGTTCGTG 1 TATCGTTCGTG 1235636 TATC 1 TATC 1235640 AGAATCGTGC Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 10 9 0.41 11 13 0.59 ACGTcount: A:0.11, C:0.19, G:0.28, T:0.42 Consensus pattern (11 bp): TATCGTTCGTG Found at i:1235629 original size:21 final size:21 Alignment explanation

Indices: 1235599--1235639 Score: 73 Period size: 21 Copynumber: 2.0 Consensus size: 21 1235589 TTAGTGATCA * 1235599 TGCGTTATCGTTCGTGTATCG 1 TGCGTGATCGTTCGTGTATCG 1235620 TGCGTGATCGTTCGTGTATC 1 TGCGTGATCGTTCGTGTATC 1235640 AGAATCGTGC Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 21 19 1.00 ACGTcount: A:0.10, C:0.20, G:0.29, T:0.41 Consensus pattern (21 bp): TGCGTGATCGTTCGTGTATCG Found at i:1237166 original size:161 final size:160 Alignment explanation

Indices: 1236556--1237548 Score: 1239 Period size: 160 Copynumber: 6.1 Consensus size: 160 1236546 GGTCCACCAA * * * 1236556 CAGTTTCCGTTCATTTTCTTTGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA 1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * * 1236621 TCATGATAAAATCTAGGTCAAGTGTGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG 66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG 1236686 CCCTTGGACATAGAAAATTTCCAGTTATTTG 131 CCCTTGGACATAGAAAA-TTCCAGTTATTTG ** * * 1236717 CAGTTTCAACTCATTTTCTTCGCAGGGGATGAACATATTGTAATGAAATTTGGTA-AAAGGTTTA 1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * 1236781 TCATGATGATATCTAGGTCAAGTTTGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG 66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG 1236846 CCCTTGGACATAGAAAATTTCCAGTTATTTG 131 CCCTTGGACATAGAAAA-TTCCAGTTATTTG ** * * 1236877 CAGTTTCAACTCATTTTCTTCGCAGGGGATGAACATATTGTAATGAAATTTGGTA-AAAGGTTTA 1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * * * 1236941 TCATGATGATATCTAGGTCAAGTTTGATATTGGGTATGATAGAGCAATTTTCAAACAGAGTTATG 66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTC-GACAGAGTTATG * 1237006 GCCCTTGGACTTAGGAAAATTCCAGTTATTTG 130 GCCCTTGGACATA-GAAAATTCCAGTTATTTG * 1237038 CAGTTTCCGCTCATTTTCTTTGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA 1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA * * * * * * 1237103 TCATGATAATATCTAGGTCAAGATCGATATTGGATACGATCAAGGAATTTTCGACAAAGTTATGG 66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG * 1237168 CCCTTGGACTTAGAAAAATTCCAGTTACATTGTATATG 131 CCCTTGGACATAG-AAAATTCCAGTT--A---T-T-TG * * * * 1237206 CAGTTTACGCTCATTTTCTTTGCAGAGGATGAACATATTG--ATGGAAATTTAGTATACAGGTTT 1 CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAAT-GAAATTTGGTATACAGGTTT * * 1237269 ATCATGTTAATATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATG 65 ATCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATG * * 1237334 GCTCTTGGACGTAGAAGAATTCCAG-T-TTTG 130 GCCCTTGGACATAGAA-AATTCCAGTTATTTG * * * * 1237364 CAGTTTCCGCTCATTTTCTTCGCAGAGGG-TGCACATATTGATATGAAATTTGGTATACAGCTTC 1 CAGTTTCCGCTCATTTTCTTCGCAG-GGGATGAACATATTGAAATGAAATTTGGTATACAGGTTT * * * * * 1237428 ATC-TAAATAATATCTAGGTCAAGTTTGAT-TTTGGTATGATGGAGCAATTTTTGTCAGAGTAGA 65 ATCAT-GATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAA--TTT-TC-GA-CAGA * * * ** 1237491 GTTATGTCCCTTGGACTTACAAAAATTCCAAATATTTG 124 GTTATGGCCCTTGGACATA-GAAAATTCCAGTTATTTG * * * 1237529 CAGTTTACGTTCAATTTCTT 1 CAGTTTCCGCTCATTTTCTT 1237549 TGTGGATGTT Statistics Matches: 744, Mismatches: 63, Indels: 46 0.87 0.07 0.05 Matches are distributed among these distances: 158 51 0.07 159 44 0.06 160 221 0.30 161 173 0.23 162 59 0.08 163 27 0.04 164 3 0.00 165 21 0.03 166 6 0.01 167 99 0.13 168 40 0.05 ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36 Consensus pattern (160 bp): CAGTTTCCGCTCATTTTCTTCGCAGGGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG CCCTTGGACATAGAAAATTCCAGTTATTTG Found at i:1239944 original size:33 final size:33 Alignment explanation

Indices: 1239906--1239994 Score: 169 Period size: 33 Copynumber: 2.7 Consensus size: 33 1239896 TCACAGGAAC 1239906 AGACTCCTCCAATATCCACAGAAGAACAGACAG 1 AGACTCCTCCAATATCCACAGAAGAACAGACAG * 1239939 AGACTCCTCCAATATCCACAGAGGAACAGACAG 1 AGACTCCTCCAATATCCACAGAAGAACAGACAG 1239972 AGACTCCTCCAATATCCACAGAA 1 AGACTCCTCCAATATCCACAGAA 1239995 AATGAAATCA Statistics Matches: 54, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 33 54 1.00 ACGTcount: A:0.40, C:0.31, G:0.15, T:0.13 Consensus pattern (33 bp): AGACTCCTCCAATATCCACAGAAGAACAGACAG Found at i:1240401 original size:6 final size:6 Alignment explanation

Indices: 1240390--1240453 Score: 53 Period size: 6 Copynumber: 11.0 Consensus size: 6 1240380 AGAAGAGAGG * ** * 1240390 GAGGAA GAGGAA GAAGACA GAGGAA GTTGAA GAGG-- G-GGAG GAGGAA 1 GAGGAA GAGGAA GAGGA-A GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA * 1240436 GAGGAA GAAGAA GAGGAA 1 GAGGAA GAGGAA GAGGAA 1240454 CTGCCAACCA Statistics Matches: 45, Mismatches: 9, Indels: 8 0.73 0.15 0.13 Matches are distributed among these distances: 3 2 0.04 4 1 0.02 5 1 0.02 6 36 0.80 7 5 0.11 ACGTcount: A:0.47, C:0.02, G:0.48, T:0.03 Consensus pattern (6 bp): GAGGAA Found at i:1242566 original size:2 final size:2 Alignment explanation

Indices: 1242559--1242618 Score: 90 Period size: 2 Copynumber: 31.5 Consensus size: 2 1242549 TTTAAAAGTT * 1242559 GA GA GA GA -A GA CA G- GA G- 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 1242598 GA GA GA GA GA GA GA GA GA GA G 1 GA GA GA GA GA GA GA GA GA GA G 1242619 CAAGCTTGCT Statistics Matches: 53, Mismatches: 2, Indels: 6 0.87 0.03 0.10 Matches are distributed among these distances: 1 3 0.06 2 50 0.94 ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1249324 original size:2 final size:2 Alignment explanation

Indices: 1249317--1249401 Score: 170 Period size: 2 Copynumber: 42.5 Consensus size: 2 1249307 ATGATTTAGC 1249317 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 1249359 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 1249401 A 1 A 1249402 TTTTTAAAAA Statistics Matches: 83, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 83 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:1251453 original size:8 final size:7 Alignment explanation

Indices: 1251428--1251557 Score: 63 Period size: 8 Copynumber: 17.7 Consensus size: 7 1251418 GCCTTTAGGT 1251428 CGAAGATG 1 CGAAG-TG 1251436 CGAGAGTG 1 CGA-AGTG 1251444 CGAAGTTG 1 CGAAG-TG 1251452 CGAAG-G 1 CGAAGTG 1251458 CGAAAGTG 1 CG-AAGTG * 1251466 CGATGGTG 1 CGA-AGTG * 1251474 CGACG-G 1 CGAAGTG * 1251480 CGAAGGAG 1 CGAA-GTG 1251488 CGAAAGTG 1 CG-AAGTG 1251496 CGAAGATG 1 CGAAG-TG * 1251504 CGACG-G 1 CGAAGTG * 1251510 CGAAGCG 1 CGAAGTG * 1251517 CGGAGATG 1 CGAAG-TG * 1251525 CGATG-G 1 CGAAGTG 1251531 CGAAAGTG 1 CG-AAGTG 1251539 CGAAGGTG 1 CGAA-GTG 1251547 CGAAG-G 1 CGAAGTG 1251553 CGAAG 1 CGAAG 1251558 GAGCGATATT Statistics Matches: 97, Mismatches: 11, Indels: 30 0.70 0.08 0.22 Matches are distributed among these distances: 6 21 0.22 7 21 0.22 8 51 0.53 9 4 0.04 ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10 Consensus pattern (7 bp): CGAAGTG Found at i:1251465 original size:22 final size:22 Alignment explanation

Indices: 1251435--1251556 Score: 82 Period size: 22 Copynumber: 5.2 Consensus size: 22 1251425 GGTCGAAGAT * * 1251435 GCGAGAGTGCGAAGTTGCGAAG 1 GCGAAAGTGCGAAGGTGCGAAG * * 1251457 GCGAAAGTGCGATGGTGCGACG 1 GCGAAAGTGCGAAGGTGCGAAG * * * 1251479 GCGAAGGAGCGAAAGTGCGAAG 1 GCGAAAGTGCGAAGGTGCGAAG * * * * 1251501 ATGCGACGGCGAAGCGCGGAGATGCGATG 1 --GCGA-----AAGTGCGAAGGTGCGAAG 1251530 GCGAAAGTGCGAAGGTGCGAAG 1 GCGAAAGTGCGAAGGTGCGAAG 1251552 GCGAA 1 GCGAA 1251557 GGAGCGATAT Statistics Matches: 74, Mismatches: 19, Indels: 14 0.69 0.18 0.13 Matches are distributed among these distances: 22 54 0.73 24 4 0.05 27 4 0.05 29 12 0.16 ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10 Consensus pattern (22 bp): GCGAAAGTGCGAAGGTGCGAAG Found at i:1251475 original size:30 final size:30 Alignment explanation

Indices: 1251457--1251514 Score: 80 Period size: 30 Copynumber: 1.9 Consensus size: 30 1251447 AGTTGCGAAG * 1251457 GCGAAAGTGCGATGGTGCGACGGCGAAGGA 1 GCGAAAGTGCGATGGTGCGAAGGCGAAGGA * * * 1251487 GCGAAAGTGCGAAGATGCGACGGCGAAG 1 GCGAAAGTGCGATGGTGCGAAGGCGAAG 1251515 CGCGGAGATG Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 30 26 1.00 ACGTcount: A:0.29, C:0.17, G:0.45, T:0.09 Consensus pattern (30 bp): GCGAAAGTGCGATGGTGCGAAGGCGAAGGA Found at i:1251524 original size:21 final size:21 Alignment explanation

Indices: 1251495--1251557 Score: 72 Period size: 21 Copynumber: 3.0 Consensus size: 21 1251485 GAGCGAAAGT * 1251495 GCGAAGATGCGACGGCGAAGC 1 GCGAAGATGCGAAGGCGAAGC * * * 1251516 GCGGAGATGCGATGGCGAAAGT 1 GCGAAGATGCGAAGGCG-AAGC * 1251538 GCGAAGGTGCGAAGGCGAAG 1 GCGAAGATGCGAAGGCGAAG 1251558 GAGCGATATT Statistics Matches: 35, Mismatches: 6, Indels: 2 0.81 0.14 0.05 Matches are distributed among these distances: 21 18 0.51 22 17 0.49 ACGTcount: A:0.29, C:0.17, G:0.46, T:0.08 Consensus pattern (21 bp): GCGAAGATGCGAAGGCGAAGC Found at i:1252569 original size:8 final size:8 Alignment explanation

Indices: 1252546--1252608 Score: 57 Period size: 8 Copynumber: 8.6 Consensus size: 8 1252536 GATAGTAGTA * 1252546 TCGCTTCT 1 TCGCATCT 1252554 TCGC--CT 1 TCGCATCT * 1252560 TCGCAACT 1 TCGCATCT 1252568 TCGC--CT 1 TCGCATCT 1252574 TCGCATCT 1 TCGCATCT 1252582 TCGCATCT 1 TCGCATCT * 1252590 TCGC--CG 1 TCGCATCT 1252596 TCGCATCT 1 TCGCATCT 1252604 TCGCA 1 TCGCA 1252609 CTTTCACTCC Statistics Matches: 47, Mismatches: 2, Indels: 12 0.77 0.03 0.20 Matches are distributed among these distances: 6 17 0.36 8 30 0.64 ACGTcount: A:0.10, C:0.41, G:0.16, T:0.33 Consensus pattern (8 bp): TCGCATCT Found at i:1252569 original size:14 final size:14 Alignment explanation

Indices: 1252552--1252585 Score: 59 Period size: 14 Copynumber: 2.4 Consensus size: 14 1252542 AGTATCGCTT 1252552 CTTCGCCTTCGCAA 1 CTTCGCCTTCGCAA * 1252566 CTTCGCCTTCGCAT 1 CTTCGCCTTCGCAA 1252580 CTTCGC 1 CTTCGC 1252586 ATCTTCGCCG Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.09, C:0.44, G:0.15, T:0.32 Consensus pattern (14 bp): CTTCGCCTTCGCAA Found at i:1252583 original size:22 final size:22 Alignment explanation

Indices: 1252558--1252608 Score: 84 Period size: 22 Copynumber: 2.3 Consensus size: 22 1252548 GCTTCTTCGC * 1252558 CTTCGCAACTTCGCCTTCGCAT 1 CTTCGCAACTTCGCCGTCGCAT * 1252580 CTTCGCATCTTCGCCGTCGCAT 1 CTTCGCAACTTCGCCGTCGCAT 1252602 CTTCGCA 1 CTTCGCA 1252609 CTTTCACTCC Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 22 27 1.00 ACGTcount: A:0.12, C:0.41, G:0.16, T:0.31 Consensus pattern (22 bp): CTTCGCAACTTCGCCGTCGCAT Found at i:1252606 original size:30 final size:30 Alignment explanation

Indices: 1252571--1252641 Score: 92 Period size: 30 Copynumber: 2.4 Consensus size: 30 1252561 CGCAACTTCG 1252571 CCTTCGCATCTTCGCA-T-CTTCGCCGTCGCA 1 CCTTCGCA-CTT-GCACTCCTTCGCCGTCGCA * * 1252601 TCTTCGCACTTTCACTCCTTCGCCGTCGCA 1 CCTTCGCACTTGCACTCCTTCGCCGTCGCA 1252631 CCTTCGCACTT 1 CCTTCGCACTT 1252642 TCGCCTTCGC Statistics Matches: 36, Mismatches: 3, Indels: 4 0.84 0.07 0.09 Matches are distributed among these distances: 28 2 0.06 29 4 0.11 30 30 0.83 ACGTcount: A:0.10, C:0.44, G:0.14, T:0.32 Consensus pattern (30 bp): CCTTCGCACTTGCACTCCTTCGCCGTCGCA Found at i:1252639 original size:8 final size:8 Alignment explanation

Indices: 1252557--1252671 Score: 59 Period size: 8 Copynumber: 15.4 Consensus size: 8 1252547 CGCTTCTTCG 1252557 CCTTCGCA 1 CCTTCGCA * 1252565 ACTTCG-- 1 CCTTCGCA 1252571 CCTTCGCA 1 CCTTCGCA * 1252579 TCTTCGCA 1 CCTTCGCA * 1252587 TCTTCG-- 1 CCTTCGCA * 1252593 CCGTCGCA 1 CCTTCGCA * 1252601 TCTTCGCA 1 CCTTCGCA * * * 1252609 CTTTCACT 1 CCTTCGCA 1252617 CCTTCG-- 1 CCTTCGCA * 1252623 CCGTCGCA 1 CCTTCGCA 1252631 CCTTCGCA 1 CCTTCGCA * 1252639 CTTTCG-- 1 CCTTCGCA 1252645 CCTTCGCA 1 CCTTCGCA * 1252653 ACTTCGCA 1 CCTTCGCA 1252661 -CTCTCGCA 1 CCT-TCGCA 1252669 CCT 1 CCT 1252672 CGACCTAAAG Statistics Matches: 79, Mismatches: 18, Indels: 19 0.68 0.16 0.16 Matches are distributed among these distances: 6 19 0.24 7 2 0.03 8 56 0.71 9 2 0.03 ACGTcount: A:0.11, C:0.44, G:0.14, T:0.30 Consensus pattern (8 bp): CCTTCGCA Found at i:1252644 original size:22 final size:22 Alignment explanation

Indices: 1252619--1252667 Score: 71 Period size: 22 Copynumber: 2.2 Consensus size: 22 1252609 CTTTCACTCC * 1252619 TTCGCCGTCGCACCTTCGCACT 1 TTCGCCGTCGCAACTTCGCACT * 1252641 TTCGCCTTCGCAACTTCGCACT 1 TTCGCCGTCGCAACTTCGCACT * 1252663 CTCGC 1 TTCGC 1252668 ACCTCGACCT Statistics Matches: 24, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 22 24 1.00 ACGTcount: A:0.10, C:0.45, G:0.16, T:0.29 Consensus pattern (22 bp): TTCGCCGTCGCAACTTCGCACT Found at i:1252661 original size:30 final size:28 Alignment explanation

Indices: 1252588--1252651 Score: 92 Period size: 30 Copynumber: 2.2 Consensus size: 28 1252578 ATCTTCGCAT * * 1252588 CTTCGCCGTCGCATCTTCGCACTTTCACTC 1 CTTCGCCGTCGCACCTTCGCACTTT--CGC 1252618 CTTCGCCGTCGCACCTTCGCACTTTCGC 1 CTTCGCCGTCGCACCTTCGCACTTTCGC 1252646 CTTCGC 1 CTTCGC 1252652 AACTTCGCAC Statistics Matches: 32, Mismatches: 2, Indels: 2 0.89 0.06 0.06 Matches are distributed among these distances: 28 8 0.25 30 24 0.75 ACGTcount: A:0.08, C:0.45, G:0.16, T:0.31 Consensus pattern (28 bp): CTTCGCCGTCGCACCTTCGCACTTTCGC Found at i:1252668 original size:30 final size:29 Alignment explanation

Indices: 1252588--1252669 Score: 89 Period size: 30 Copynumber: 2.8 Consensus size: 29 1252578 ATCTTCGCAT * 1252588 CTTCGCCGTCGCA-TCTTCGCACTTTCACTC 1 CTTCGCCGTCGCACTCTTCGCACTTT--CGC 1252618 CTTCGCCGTCGCAC-CTTCGCACTTTCGC 1 CTTCGCCGTCGCACTCTTCGCACTTTCGC * 1252646 CTTCGCAACTTCGCACTC-TCGCAC 1 CTTCGC--CGTCGCACTCTTCGCAC 1252670 CTCGACCTAA Statistics Matches: 46, Mismatches: 2, Indels: 8 0.82 0.04 0.14 Matches are distributed among these distances: 28 8 0.17 30 37 0.80 31 1 0.02 ACGTcount: A:0.11, C:0.45, G:0.15, T:0.29 Consensus pattern (29 bp): CTTCGCCGTCGCACTCTTCGCACTTTCGC Found at i:1261220 original size:2 final size:2 Alignment explanation

Indices: 1261213--1261254 Score: 84 Period size: 2 Copynumber: 21.0 Consensus size: 2 1261203 ACCTGCATAA 1261213 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 1261255 AAAATCAGCT 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): TC Found at i:1273613 original size:15 final size:15 Alignment explanation

Indices: 1273593--1273623 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 1273583 ACGCACTTCG 1273593 TGAAAAAAAAATCAA 1 TGAAAAAAAAATCAA * 1273608 TGAAAAAATAATCAA 1 TGAAAAAAAAATCAA 1273623 T 1 T 1273624 CAAACGACGT Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19 Consensus pattern (15 bp): TGAAAAAAAAATCAA Found at i:1294189 original size:16 final size:16 Alignment explanation

Indices: 1294168--1294227 Score: 84 Period size: 16 Copynumber: 3.8 Consensus size: 16 1294158 GACCCGCCTT * 1294168 GGCCGAGGAGTCCTGG 1 GGCCGAGGTGTCCTGG * 1294184 GGCCGAAGTGTCCTGG 1 GGCCGAGGTGTCCTGG * * 1294200 GGCCGAGGTGTCGTTG 1 GGCCGAGGTGTCCTGG 1294216 GGCCGAGGTGTC 1 GGCCGAGGTGTC 1294228 TGACATTCGT Statistics Matches: 39, Mismatches: 5, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 16 39 1.00 ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18 Consensus pattern (16 bp): GGCCGAGGTGTCCTGG Found at i:1299341 original size:203 final size:202 Alignment explanation

Indices: 1298992--1299396 Score: 801 Period size: 203 Copynumber: 2.0 Consensus size: 202 1298982 TGTACAATTG 1298992 TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC 1 TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC 1299057 TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC 66 TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC 1299122 TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT 131 TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT 1299187 CAGACGC 196 CAGACGC 1299194 NTCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTA 1 -TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTA 1299259 CTTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCAC 65 CTTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCAC 1299324 CTGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTT 130 CTGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTT 1299389 TCAGACGC 195 TCAGACGC 1299397 GAAGGTGTTG Statistics Matches: 202, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 203 202 1.00 ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32 Consensus pattern (202 bp): TCCAGGCATGACTGTTTTCATGGATGGTGGTATTGTGAGGTCCCCAATGACAAATTCATACGTAC TTCCCTGTGATTTGTGTGCCGTTATACCAAAGGCTGGAACAATAGGAAACATTGTTCTTTCCACC TGAACAGGAGATTTTGCTGTTAATAAGAAGTTCACTGTCACTGCCTTTATAGGAACACTTCCTTT CAGACGC Found at i:1304716 original size:69 final size:69 Alignment explanation

Indices: 1304642--1305136 Score: 578 Period size: 69 Copynumber: 7.2 Consensus size: 69 1304632 ACTTTTCCTT * ** 1304642 TTCTTATCTTTGTCATTATCTGAGGTGATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT 1304707 CCAA 66 CCAA * * * * * * * 1304711 TTCTTATTTTTGGCATTGTCTTAGGCCATTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT * ** 1304776 TCTT 66 CCAA * * 1304780 TTTTTATCTTTGTCATTGTC-GTAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGACAATCA 1 TTCTTATCTTTGTCATTGTCTG-AGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCA 1304844 TCCAA 65 TCCAA * * * * * * * * 1304849 TTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT * ** 1304914 TCTT 66 CCAA * * * 1304918 TTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCCCGAGAGTCAATCAT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT 1304983 CCAA 66 CCAA * * * * * * * * 1304987 TTCTTATTTTTGTCTTTGTCTGAGGCTACTTGAGCTGGTGTTCTTGAGTCACGAGAGTCACTCTT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT * ** 1305052 TCTT 66 CCAA * * * 1305056 TTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGGCACGAGAGTCAATCAT 1 TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT 1305121 CCAA 66 CCAA * 1305125 TTCTTATTTTTG 1 TTCTTATCTTTG 1305137 NNNNNNNNNN Statistics Matches: 346, Mismatches: 78, Indels: 4 0.81 0.18 0.01 Matches are distributed among these distances: 69 345 1.00 70 1 0.00 ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40 Consensus pattern (69 bp): TTCTTATCTTTGTCATTGTCTGAGGCCATTTGAGCAGGTGTTCTTGAGCCACGAGAGTCAATCAT CCAA Found at i:1304812 original size:138 final size:138 Alignment explanation

Indices: 1304630--1305136 Score: 865 Period size: 138 Copynumber: 3.7 Consensus size: 138 1304620 AGCTCTTGAA ** 1304630 TCACT-TTTCCTTTTCTTATCTTTGTCATTATCTGAGGTGATTTGAGCAGGTGTTCTTGAGCCAC 1 TCACTCTTT-CTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCAC * * * 1304694 GAGAGTCAATCATCCAATTCTTATTTTTGGCATTGTCTTAGGCCATTTGAGCTGGTGTTCTTGAG 65 GAGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG 1304759 TCACGAGAG 130 TCACGAGAG * * * 1304768 TCACTCTTTCTTTTTTTATCTTTGTCATTGTC-GTAGGCCATTTGAGCAGGTGTTCTTGAGCCAC 1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTG-AGGCAATTTGAGCAGGTGTTCTTGAGCCAC * 1304832 GAGAGACAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG 65 GAGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAG 1304897 TCACGAGAG 130 TCACGAGAG * 1304906 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCCCG 1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG * * 1304971 AGAGTCAATCATCCAATTCTTATTTTTGTCTTTGTCTGAGGCTACTTGAGCTGGTGTTCTTGAGT 66 AGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGT 1305036 CACGAGAG 131 CACGAGAG * 1305044 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGGCACG 1 TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG 1305109 AGAGTCAATCATCCAATTCTTATTTTTG 66 AGAGTCAATCATCCAATTCTTATTTTTG 1305137 NNNNNNNNNN Statistics Matches: 349, Mismatches: 17, Indels: 6 0.94 0.05 0.02 Matches are distributed among these distances: 137 1 0.00 138 344 0.99 139 4 0.01 ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41 Consensus pattern (138 bp): TCACTCTTTCTTTTCTTATCTTTGTCATTATCTGAGGCAATTTGAGCAGGTGTTCTTGAGCCACG AGAGTCAATCATCCAATTCTTATTTTTGGCTTTGTCTGAGGCCACTTGAGCTGGTGTTCTTGAGT CACGAGAG Found at i:1317374 original size:52 final size:52 Alignment explanation

Indices: 1317318--1317421 Score: 172 Period size: 52 Copynumber: 2.0 Consensus size: 52 1317308 CATACCTAAA * 1317318 TGATTACTGAATGAATTGACCCTAATTTGGGAAGCACCCAAATCCCACAGAC 1 TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC * * * 1317370 TGATTACTGATTGAATTGACCCTTATTGGGGAAGCGCCCAAATCCCACAGAC 1 TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC 1317422 CTGTTTTGAG Statistics Matches: 48, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 52 48 1.00 ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24 Consensus pattern (52 bp): TGATTACTGAATGAATTGACCCTAATTGGGGAAGCACCCAAATCCCACAGAC Found at i:1323196 original size:46 final size:46 Alignment explanation

Indices: 1323129--1323220 Score: 184 Period size: 46 Copynumber: 2.0 Consensus size: 46 1323119 TGATGACATT 1323129 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG 1 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG 1323175 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG 1 TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG 1323221 ACGTCAGCAT Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 46 46 1.00 ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35 Consensus pattern (46 bp): TCATCTCTGTTACTAAGCATGTGTAAAGATGCAATGTGTCTCACTG Found at i:1334785 original size:47 final size:47 Alignment explanation

Indices: 1334734--1335294 Score: 804 Period size: 47 Copynumber: 11.7 Consensus size: 47 1334724 GCAGTGTTCA * * * * 1334734 AAGTTTTCAAAATTGTATTCATTCAAGGTTCTGAATAGTTGTGCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC * * 1334781 AAGTTCTCAAAATTGTGTTCATTCAAAGTGCTCAATAGTTGTTCTCCAACTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTG-T-T----CTCC 1334834 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC * 1334881 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC 1334928 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC * 1334975 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC * 1335022 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC 1335069 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAAG-TGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAAT-AGTTGTTCTCC * * 1335116 AAGTTCTCAAAATTGTATTTATTCAAAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC * * * 1335163 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTTAATAATTGTGCTCC 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC * * * * 1335210 AAGTTTTCAAAATTGTGTTCATGCATTCAAAGTTCGCAATAGTTGTGCTCC 1 AAGTTCTCAAAA-T-TG-T-ATTCATTCAAAGTTCTCAATAGTTGTTCTCC * * 1335261 AAGTTTTCAAAATTGTGTTCATTCAAAGTTCTCA 1 AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCA 1335295 TAAATTGTAA Statistics Matches: 473, Mismatches: 25, Indels: 32 0.89 0.05 0.06 Matches are distributed among these distances: 46 3 0.01 47 376 0.79 48 5 0.01 49 4 0.01 50 2 0.00 51 40 0.08 52 1 0.00 53 40 0.08 54 2 0.00 ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39 Consensus pattern (47 bp): AAGTTCTCAAAATTGTATTCATTCAAAGTTCTCAATAGTTGTTCTCC Found at i:1335226 original size:21 final size:22 Alignment explanation

Indices: 1334859--1335226 Score: 185 Period size: 22 Copynumber: 15.8 Consensus size: 22 1334849 TATTCATTCA * * 1334859 AAGTTCTCAATAAGTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1334881 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * 1334906 AAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1334928 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * * 1334953 AAGTTCTCAATAAGTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1334975 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * 1335000 AAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1335022 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * 1335047 AAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1335069 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * * 1335094 AAGTTCTCAATAAGTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC ** * 1335116 AAGTTCTCAA-AATTGTATTTATTCA 1 AAGTTCTCAATAATTG----TGCTCC * 1335141 AAGTTCTCAATAATTGTTCTCC 1 AAGTTCTCAATAATTGTGCTCC * * 1335163 AAGTTCTCAA-AATTGTATTCATTCA 1 AAGTTCTCAATAATTG--TGC--TCC * 1335188 AAGTTCTTAATAATTGTGCTCC 1 AAGTTCTCAATAATTGTGCTCC * 1335210 AAGTTTTCAA-AATTGTG 1 AAGTTCTCAATAATTGTG 1335227 TTCATGCATT Statistics Matches: 284, Mismatches: 27, Indels: 71 0.74 0.07 0.19 Matches are distributed among these distances: 21 39 0.14 22 93 0.33 23 18 0.06 24 17 0.06 25 84 0.30 26 33 0.12 ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40 Consensus pattern (22 bp): AAGTTCTCAATAATTGTGCTCC Done.