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 6 of 5

Found at i:1631534 original size:28 final size:28

Alignment explanation

Indices: 1631055--1631531 Score: 465 Period size: 28 Copynumber: 17.0 Consensus size: 28 1631045 CGAAAGAGGA * * * 1631055 CAACTAACCTCATCGATTGTTAATTAGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * 1631083 CAACAAACTTTATCGATAGGTAATTGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631111 CATCTAACCTCATCGATACGTAATT-GT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631138 ACAACTAACCTCATCGCTTGGTAATTGGT 1 -CAACTAACCTCATCGATAGGTAATTGGT ** * * ** 1631167 CAACTAACCTCATAAAAAGGCAATAAGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * * ** 1631195 CCACTAACCTTATCTATAGGAAATAAGT 1 CAACTAACCTCATCGATAGGTAATTGGT 1631223 CAACTAACCTCATCGATAGGTAATTGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * * 1631251 TAGCTATA-CTCTTCGATATGTAATTGGT 1 CAACTA-ACCTCATCGATAGGTAATTGGT * * 1631279 CAACTAAACTCATCGATGGGTAATTGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631307 CAACTAACCTTATCGATAGGTAATAGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * 1631335 CAACTAACCTTATCGATAGGTAAGTAGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631363 CAACTAACCTCTTCGATAGGTAATTCGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631391 CTACTAACCTCATCGATAGATAATTGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * ** 1631419 CAACTAACCTTATCGAAAGGTAATAAGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * 1631447 CAACCAACCTCATCGATAGGTAGTTGGT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * 1631475 CTACTGACCTCATCGAAAGGTAATT-GT 1 CAACTAACCTCATCGATAGGTAATTGGT * * * 1631502 ACCACTAACCTCATCAAAAGGTAATTGGT 1 -CAACTAACCTCATCGATAGGTAATTGGT 1631531 C 1 C 1631532 CACGTTGAGG Statistics Matches: 364, Mismatches: 79, Indels: 12 0.80 0.17 0.03 Matches are distributed among these distances: 27 5 0.01 28 354 0.97 29 5 0.01 ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30 Consensus pattern (28 bp): CAACTAACCTCATCGATAGGTAATTGGT Found at i:1641060 original size:99 final size:100 Alignment explanation

Indices: 1640889--1641179 Score: 388 Period size: 104 Copynumber: 2.9 Consensus size: 100 1640879 GAAATCTAAC * * ** 1640889 AAAAAGCTTAGTGATTATA-TAATCTTGAAAAATAAAGTCGGTCATGTTTAGCTATCTTAGTGTT 1 AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT ********* 1640953 ATCTTTTTAGAGGGTTAATGTTTTT-TTTTTTTTT 66 ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAA * * * 1640987 TAAAAGTTTAGTGATAATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT 1 AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT 1641052 ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAAAAA 66 ATCTTTTTAGAGGGTTAATGTTTTT---AAAAAAAAAA 1641090 AAAGAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGT 1 AAA-AAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGT 1641155 TATCTTTTTAGAGGGTTAATGTTTT 65 TATCTTTTTAGAGGGTTAATGTTTT 1641180 GCTGTAAAGT Statistics Matches: 168, Mismatches: 19, Indels: 6 0.87 0.10 0.03 Matches are distributed among these distances: 98 16 0.10 99 66 0.39 103 2 0.01 104 84 0.50 ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40 Consensus pattern (100 bp): AAAAAGCTTAGTGATTATAGAAACCTTGAAAAATAAAGTCGGTCATGTTTAGAAATCTTAGTGTT ATCTTTTTAGAGGGTTAATGTTTTTAAAAAAAAAA Found at i:1643692 original size:10 final size:10 Alignment explanation

Indices: 1643677--1643705 Score: 58 Period size: 10 Copynumber: 2.9 Consensus size: 10 1643667 TCATTTGGGT 1643677 CCCTCTTTGC 1 CCCTCTTTGC 1643687 CCCTCTTTGC 1 CCCTCTTTGC 1643697 CCCTCTTTG 1 CCCTCTTTG 1643706 TTTGATGTCC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 10 19 1.00 ACGTcount: A:0.00, C:0.48, G:0.10, T:0.41 Consensus pattern (10 bp): CCCTCTTTGC Found at i:1655250 original size:26 final size:25 Alignment explanation

Indices: 1655221--1655275 Score: 67 Period size: 24 Copynumber: 2.2 Consensus size: 25 1655211 GTTTGTAATA 1655221 TTTTAATGATGTCCCGTGTACGCAGG- 1 TTTTAAT-A-GTCCCGTGTACGCAGGC ** 1655247 TTTTGGTAGTCCCGTGTACGCAGGC 1 TTTTAATAGTCCCGTGTACGCAGGC 1655272 TTTT 1 TTTT 1655276 GTAAATTGTT Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 24 16 0.62 25 5 0.19 26 5 0.19 ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38 Consensus pattern (25 bp): TTTTAATAGTCCCGTGTACGCAGGC Found at i:1656100 original size:11 final size:11 Alignment explanation

Indices: 1656078--1656108 Score: 53 Period size: 11 Copynumber: 2.7 Consensus size: 11 1656068 CTTAATGAAG 1656078 AAATTAATATAT 1 AAATT-ATATAT 1656090 AAATTATATAT 1 AAATTATATAT 1656101 AAATTATA 1 AAATTATA 1656109 CCCAGAATGT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 11 14 0.74 12 5 0.26 ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42 Consensus pattern (11 bp): AAATTATATAT Found at i:1664220 original size:2 final size:2 Alignment explanation

Indices: 1664213--1664259 Score: 94 Period size: 2 Copynumber: 23.5 Consensus size: 2 1664203 TTACTAGTCT 1664213 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 1664255 GA GA G 1 GA GA G 1664260 TCGCTTGGCT Statistics Matches: 45, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 45 1.00 ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00 Consensus pattern (2 bp): GA Found at i:1665323 original size:12 final size:13 Alignment explanation

Indices: 1665296--1665324 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 1665286 GGCAAATAGT 1665296 TTTTTAAAATTGA 1 TTTTTAAAATTGA 1665309 TTTTTAAAATT-A 1 TTTTTAAAATTGA 1665321 TTTT 1 TTTT 1665325 GTTAATTTTA Statistics Matches: 16, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 12 5 0.31 13 11 0.69 ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62 Consensus pattern (13 bp): TTTTTAAAATTGA Found at i:1667002 original size:2 final size:2 Alignment explanation

Indices: 1666997--1667048 Score: 104 Period size: 2 Copynumber: 26.0 Consensus size: 2 1666987 AGAGATTATG 1666997 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 1667039 GA GA GA GA GA 1 GA GA GA GA GA 1667049 TAAGACAAAT Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 50 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:1668446 original size:2 final size:2 Alignment explanation

Indices: 1668439--1668479 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 1668429 GAATGCACTG 1668439 TC 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 TC T 1668480 TATATTAAGT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:1673059 original size:14 final size:14 Alignment explanation

Indices: 1673040--1673067 Score: 56 Period size: 14 Copynumber: 2.0 Consensus size: 14 1673030 GGATGTCAGG 1673040 CCCCTTTTCCCAAC 1 CCCCTTTTCCCAAC 1673054 CCCCTTTTCCCAAC 1 CCCCTTTTCCCAAC 1673068 ATTAGATGTA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 14 1.00 ACGTcount: A:0.14, C:0.57, G:0.00, T:0.29 Consensus pattern (14 bp): CCCCTTTTCCCAAC Found at i:1675445 original size:4 final size:4 Alignment explanation

Indices: 1675436--1675517 Score: 53 Period size: 4 Copynumber: 20.0 Consensus size: 4 1675426 TGATTTGTAT * * * 1675436 ATTG ATTG ATTG ATTG ATTG AAAT- ATTG TTTG AATT- -TTG ATTG GTTG 1 ATTG ATTG ATTG ATTG ATTG -ATTG ATTG ATTG -ATTG ATTG ATTG ATTG * * 1675483 ATTTC ATTG ATTG ATTC ATCTTG ATTG ATTG ATTG 1 A-TTG ATTG ATTG ATTG A--TTG ATTG ATTG ATTG 1675518 TTTGGGTCAT Statistics Matches: 60, Mismatches: 10, Indels: 16 0.70 0.12 0.19 Matches are distributed among these distances: 2 2 0.03 3 2 0.03 4 46 0.77 5 7 0.12 6 3 0.05 ACGTcount: A:0.24, C:0.04, G:0.21, T:0.51 Consensus pattern (4 bp): ATTG Found at i:1682787 original size:2 final size:2 Alignment explanation

Indices: 1682780--1682810 Score: 55 Period size: 2 Copynumber: 16.0 Consensus size: 2 1682770 CAAAGATGTT 1682780 GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1682811 AAAGCCATGA Statistics Matches: 28, Mismatches: 0, Indels: 2 0.93 0.00 0.07 Matches are distributed among these distances: 1 1 0.04 2 27 0.96 ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00 Consensus pattern (2 bp): GA Found at i:1688175 original size:4 final size:4 Alignment explanation

Indices: 1688166--1688208 Score: 86 Period size: 4 Copynumber: 10.8 Consensus size: 4 1688156 CTTGCCCCTC 1688166 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT 1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT 1688209 CCAATGCACT Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 39 1.00 ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74 Consensus pattern (4 bp): TCTT Found at i:1689025 original size:4 final size:4 Alignment explanation

Indices: 1689016--1689054 Score: 78 Period size: 4 Copynumber: 9.8 Consensus size: 4 1689006 TTATCATCCC 1689016 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT 1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCT 1689055 CCATCGGCAA Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 35 1.00 ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74 Consensus pattern (4 bp): TCTT Found at i:1694346 original size:20 final size:20 Alignment explanation

Indices: 1694309--1694346 Score: 58 Period size: 20 Copynumber: 1.9 Consensus size: 20 1694299 TATGTTCACA * 1694309 TTTAACTTTTATTCAACAGG 1 TTTAACTTTCATTCAACAGG * 1694329 TTTAACTTTCATTGAACA 1 TTTAACTTTCATTCAACA 1694347 ATGATATTTT Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 20 16 1.00 ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45 Consensus pattern (20 bp): TTTAACTTTCATTCAACAGG Found at i:1706248 original size:21 final size:21 Alignment explanation

Indices: 1706222--1706286 Score: 71 Period size: 21 Copynumber: 3.1 Consensus size: 21 1706212 TTTTTCTATC 1706222 AAATATGTCAACATGCAAGAT 1 AAATATGTCAACATGCAAGAT * 1706243 AAATATG-CTGACATGCAAGAT 1 AAATATGTC-AACATGCAAGAT * * 1706264 -AGTAATGTCAACATGCAACAT 1 AAAT-ATGTCAACATGCAAGAT 1706285 AA 1 AA 1706287 CTACATTGAC Statistics Matches: 36, Mismatches: 4, Indels: 7 0.77 0.09 0.15 Matches are distributed among these distances: 20 3 0.08 21 31 0.86 22 2 0.06 ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23 Consensus pattern (21 bp): AAATATGTCAACATGCAAGAT Found at i:1706521 original size:42 final size:42 Alignment explanation

Indices: 1706421--1706523 Score: 161 Period size: 42 Copynumber: 2.5 Consensus size: 42 1706411 TGATGTATGA * 1706421 CATGTCGACATAAATAAGTTGCATGTAAACATAAATTAGTTG 1 CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG * * 1706463 CATGTCAACATAAATAAGTTGCATGTCAACATAAATAAGTTG 1 CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG * * 1706505 CATGTCGACTTCAATAAGT 1 CATGTCGACATAAATAAGT 1706524 AACATCCAGC Statistics Matches: 55, Mismatches: 6, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 42 55 1.00 ACGTcount: A:0.40, C:0.15, G:0.16, T:0.30 Consensus pattern (42 bp): CATGTCGACATAAATAAGTTGCATGTAAACATAAATAAGTTG Found at i:1706523 original size:21 final size:21 Alignment explanation

Indices: 1706421--1706510 Score: 153 Period size: 21 Copynumber: 4.3 Consensus size: 21 1706411 TGATGTATGA * 1706421 CATGTCGACATAAATAAGTTG 1 CATGTCAACATAAATAAGTTG * * 1706442 CATGTAAACATAAATTAGTTG 1 CATGTCAACATAAATAAGTTG 1706463 CATGTCAACATAAATAAGTTG 1 CATGTCAACATAAATAAGTTG 1706484 CATGTCAACATAAATAAGTTG 1 CATGTCAACATAAATAAGTTG 1706505 CATGTC 1 CATGTC 1706511 GACTTCAATA Statistics Matches: 64, Mismatches: 5, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 21 64 1.00 ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30 Consensus pattern (21 bp): CATGTCAACATAAATAAGTTG Found at i:1706634 original size:21 final size:21 Alignment explanation

Indices: 1706598--1706670 Score: 67 Period size: 21 Copynumber: 3.5 Consensus size: 21 1706588 ATTGTAATTT * ** 1706598 TCTTGCATGATAACATAGTTA 1 TCTTGCATGTTAACATAACTA * * 1706619 TGTTGCATGTTGACATAACTA 1 TCTTGCATGTTAACATAACTA * 1706640 TCTTGCATGTCAACAT-ACTTA 1 TCTTGCATGTTAACATAAC-TA * 1706661 TCTTACATGT 1 TCTTGCATGT 1706671 CGATATATTT Statistics Matches: 42, Mismatches: 9, Indels: 2 0.79 0.17 0.04 Matches are distributed among these distances: 20 2 0.05 21 40 0.95 ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40 Consensus pattern (21 bp): TCTTGCATGTTAACATAACTA Found at i:1708142 original size:21 final size:20 Alignment explanation

Indices: 1708116--1708173 Score: 62 Period size: 21 Copynumber: 2.8 Consensus size: 20 1708106 TTAGAGTATC 1708116 ATTCGTAAACTATAGTTAACG 1 ATTCGT-AACTATAGTTAACG * ** 1708137 ATTCGTTAACTATGGTTTGCG 1 ATTCG-TAACTATAGTTAACG * 1708158 GTTCGTAACTATAGTT 1 ATTCGTAACTATAGTT 1708174 CAAAATAAAT Statistics Matches: 31, Mismatches: 5, Indels: 3 0.79 0.13 0.08 Matches are distributed among these distances: 20 10 0.32 21 20 0.65 22 1 0.03 ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40 Consensus pattern (20 bp): ATTCGTAACTATAGTTAACG Found at i:1719223 original size:10 final size:11 Alignment explanation

Indices: 1719198--1719236 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 1719188 TTAAGTTCTC * 1719198 CTTAAAGATAG 1 CTTAAAGGTAG * 1719209 CTTAAATGT-G 1 CTTAAAGGTAG 1719219 CTTAAAGGTAG 1 CTTAAAGGTAG 1719230 CTTAAAG 1 CTTAAAG 1719237 ACGATCTTTA Statistics Matches: 24, Mismatches: 3, Indels: 2 0.83 0.10 0.07 Matches are distributed among these distances: 10 9 0.38 11 15 0.62 ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31 Consensus pattern (11 bp): CTTAAAGGTAG Found at i:1719287 original size:11 final size:11 Alignment explanation

Indices: 1719271--1719323 Score: 61 Period size: 11 Copynumber: 4.8 Consensus size: 11 1719261 TATATGTGTT * 1719271 GCTTAAAGGTA 1 GCTTAAAGATA 1719282 GCTTAAAGATA 1 GCTTAAAGATA * * 1719293 GCGTAAAGATG 1 GCTTAAAGATA ** 1719304 GCTTAAAGGCA 1 GCTTAAAGATA 1719315 GCTTAAAGA 1 GCTTAAAGA 1719324 CTATCTTTAA Statistics Matches: 34, Mismatches: 8, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 11 34 1.00 ACGTcount: A:0.40, C:0.11, G:0.26, T:0.23 Consensus pattern (11 bp): GCTTAAAGATA Found at i:1719344 original size:11 final size:11 Alignment explanation

Indices: 1719328--1719356 Score: 58 Period size: 11 Copynumber: 2.6 Consensus size: 11 1719318 TAAAGACTAT 1719328 CTTTAAGCCAC 1 CTTTAAGCCAC 1719339 CTTTAAGCCAC 1 CTTTAAGCCAC 1719350 CTTTAAG 1 CTTTAAG 1719357 GACAACTAAT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1719404 original size:11 final size:11 Alignment explanation

Indices: 1719388--1719452 Score: 112 Period size: 11 Copynumber: 5.9 Consensus size: 11 1719378 GTCCAAACTT 1719388 CTTTAAGCCAC 1 CTTTAAGCCAC * 1719399 CTTTAAGCTAC 1 CTTTAAGCCAC * 1719410 CTTTAAGCTAC 1 CTTTAAGCCAC 1719421 CTTTAAGCCAC 1 CTTTAAGCCAC 1719432 CTTTAAGCCAC 1 CTTTAAGCCAC 1719443 CTTTAAGCCA 1 CTTTAAGCCA 1719453 TTAATAAAAA Statistics Matches: 52, Mismatches: 2, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 11 52 1.00 ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31 Consensus pattern (11 bp): CTTTAAGCCAC Found at i:1719570 original size:14 final size:14 Alignment explanation

Indices: 1719551--1719588 Score: 67 Period size: 14 Copynumber: 2.7 Consensus size: 14 1719541 TTCTAGGAAG 1719551 AAAAAAAAACAAAA 1 AAAAAAAAACAAAA 1719565 AAAAAAAAACAAAA 1 AAAAAAAAACAAAA * 1719579 CAAAAAAAAC 1 AAAAAAAAAC 1719589 GCCCACGGCG Statistics Matches: 23, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 14 23 1.00 ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00 Consensus pattern (14 bp): AAAAAAAAACAAAA Found at i:1719578 original size:19 final size:18 Alignment explanation

Indices: 1719551--1719587 Score: 65 Period size: 19 Copynumber: 2.0 Consensus size: 18 1719541 TTCTAGGAAG 1719551 AAAAAAAAACAAAAAAAA 1 AAAAAAAAACAAAAAAAA 1719569 AAAAACAAAACAAAAAAAA 1 AAAAA-AAAACAAAAAAAA 1719588 CGCCCACGGC Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 18 5 0.28 19 13 0.72 ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00 Consensus pattern (18 bp): AAAAAAAAACAAAAAAAA Found at i:1721189 original size:112 final size:112 Alignment explanation

Indices: 1720992--1721205 Score: 401 Period size: 112 Copynumber: 1.9 Consensus size: 112 1720982 AACCCTGACG * * 1720992 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT * 1721057 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACC 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACC 1721104 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1 TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT 1721169 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATA 66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATA 1721206 CTTTATTAGT Statistics Matches: 99, Mismatches: 3, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 112 99 1.00 ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34 Consensus pattern (112 bp): TGCACCTGGGCACACGAAACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACC Found at i:1728567 original size:22 final size:22 Alignment explanation

Indices: 1728533--1728586 Score: 63 Period size: 22 Copynumber: 2.5 Consensus size: 22 1728523 CAAACGTTAC * * * 1728533 GCCAACGTCGAACTAATATTGG 1 GCCAACGTTGAACTAACATTAG * * 1728555 GTCAACGTTGAACTCACATTAG 1 GCCAACGTTGAACTAACATTAG 1728577 GCCAACGTTG 1 GCCAACGTTG 1728587 GACCAATGAA Statistics Matches: 26, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 22 26 1.00 ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24 Consensus pattern (22 bp): GCCAACGTTGAACTAACATTAG Found at i:1730083 original size:7 final size:7 Alignment explanation

Indices: 1730071--1730100 Score: 51 Period size: 7 Copynumber: 4.3 Consensus size: 7 1730061 AGAAAACTTC 1730071 ATTAATT 1 ATTAATT 1730078 ATTAATT 1 ATTAATT * 1730085 ATTAAGT 1 ATTAATT 1730092 ATTAATT 1 ATTAATT 1730099 AT 1 AT 1730101 ATAAACCTCG Statistics Matches: 21, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 7 21 1.00 ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53 Consensus pattern (7 bp): ATTAATT Done.