Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: A05

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32

Warning! 3970000 characters in sequence are not A, C, G, or T


File 311 of 318

Found at i:98204243 original size:19 final size:20

Alignment explanation

Indices: 98204213--98204269 Score: 64 Period size: 19 Copynumber: 2.8 Consensus size: 20 98204203 AACTTTAAAT 98204213 TTATTCCTATATTTATTA-TA 1 TTATT-CTATATTTATTATTA 98204233 TTATTCTATATATATATTATTA 1 TTATTCTATAT-T-TATTATTA * 98204255 TTATTTTAT-TTTATT 1 TTATTCTATATTTATT 98204270 TTAATTTTAC Statistics Matches: 33, Mismatches: 1, Indels: 7 0.80 0.02 0.17 Matches are distributed among these distances: 19 10 0.30 20 7 0.21 21 6 0.18 22 10 0.30 ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65 Consensus pattern (20 bp): TTATTCTATATTTATTATTA Found at i:98204361 original size:19 final size:18 Alignment explanation

Indices: 98204309--98204373 Score: 60 Period size: 19 Copynumber: 3.5 Consensus size: 18 98204299 AGATTATTTT * 98204309 TATTATTTTTAATTATATA 1 TATTATTTTT-CTTATATA * * 98204328 TATTATTATTACTTATTATG 1 TATTATT-TTTCTTA-TATA * 98204348 TATTATTTTTCTTA-AAA 1 TATTATTTTTCTTATATA 98204365 TATTATTTT 1 TATTATTTT 98204374 ACATCTCTTT Statistics Matches: 38, Mismatches: 6, Indels: 6 0.76 0.12 0.12 Matches are distributed among these distances: 17 10 0.26 19 16 0.42 20 12 0.32 ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63 Consensus pattern (18 bp): TATTATTTTTCTTATATA Found at i:98204371 original size:3 final size:3 Alignment explanation

Indices: 98204225--98204354 Score: 64 Period size: 3 Copynumber: 43.7 Consensus size: 3 98204215 ATTCCTATAT * 98204225 TTA TTA -TA TTA TT- CTA TATA TATA TTA TTA TTA TT- TTA TT- TTA 1 TTA TTA TTA TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA ** * 98204268 TT- TTAA TT- TTA CTT- TTA -TA TTA TATA TTA -TA AGA TTA TTT TTA 1 TTA TT-A TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA * 98204311 TTA TTT TTAA TTA -TA TATA TTA TTA TTA CTTA TTA TGTA TTA TT 1 TTA TTA TT-A TTA TTA T-TA TTA TTA TTA -TTA TTA T-TA TTA TT 98204355 TTTCTTAAAA Statistics Matches: 100, Mismatches: 9, Indels: 36 0.69 0.06 0.25 Matches are distributed among these distances: 2 19 0.19 3 56 0.56 4 25 0.25 ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64 Consensus pattern (3 bp): TTA Found at i:98207580 original size:20 final size:20 Alignment explanation

Indices: 98207555--98207600 Score: 83 Period size: 20 Copynumber: 2.3 Consensus size: 20 98207545 AGTTTTTAGA * 98207555 TTTATTATGACAAATTAAAT 1 TTTATTATGACAAATTAAAC 98207575 TTTATTATGACAAATTAAAC 1 TTTATTATGACAAATTAAAC 98207595 TTTATT 1 TTTATT 98207601 TTATAACTTT Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 20 25 1.00 ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48 Consensus pattern (20 bp): TTTATTATGACAAATTAAAC Found at i:98209008 original size:21 final size:21 Alignment explanation

Indices: 98208984--98209024 Score: 57 Period size: 21 Copynumber: 2.0 Consensus size: 21 98208974 TTTAGGGATA 98208984 AAAAATAAATAATA-AATTTTT 1 AAAAATAAA-AATATAATTTTT * 98209005 AAAAATTAAAATATAATTTT 1 AAAAATAAAAATATAATTTT 98209025 ATTATTATAT Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39 Consensus pattern (21 bp): AAAAATAAAAATATAATTTTT Found at i:98209020 original size:22 final size:21 Alignment explanation

Indices: 98208982--98209024 Score: 52 Period size: 22 Copynumber: 2.0 Consensus size: 21 98208972 ATTTTAGGGA 98208982 TAAAAAATAAATAATAAATTTT 1 TAAAAAATAAATAAT-AATTTT * 98209004 TAAAAATTAAA-ATATAATTTT 1 TAAAAAATAAATA-ATAATTTT 98209025 ATTATTATAT Statistics Matches: 19, Mismatches: 1, Indels: 3 0.83 0.04 0.13 Matches are distributed among these distances: 21 7 0.37 22 12 0.63 ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40 Consensus pattern (21 bp): TAAAAAATAAATAATAATTTT Found at i:98211577 original size:29 final size:29 Alignment explanation

Indices: 98211535--98211593 Score: 109 Period size: 29 Copynumber: 2.0 Consensus size: 29 98211525 CCAAATTGTG * 98211535 TGACTTATCAAACCAAGTTTTCACATTAA 1 TGACTTATCAAACCAAGCTTTCACATTAA 98211564 TGACTTATCAAACCAAGCTTTCACATTAA 1 TGACTTATCAAACCAAGCTTTCACATTAA 98211593 T 1 T 98211594 ATGAGAATAT Statistics Matches: 29, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 29 29 1.00 ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34 Consensus pattern (29 bp): TGACTTATCAAACCAAGCTTTCACATTAA Found at i:98214040 original size:92 final size:92 Alignment explanation

Indices: 98213843--98214025 Score: 307 Period size: 92 Copynumber: 2.0 Consensus size: 92 98213833 TTTTAAACAT * * * * 98213843 AAAATTAG-AAAATGAGTAAAAACTCTTGTAAAAAATTTGATCTCTCCAAAATAAGTGAAAATTA 1 AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATTTGACCTCTCCAAAATAAGCGAAAAATA 98213907 TTCCTTCTCTATTCCAAAAATAAGTCA 66 TTCCTTCTCTATTCCAAAAATAAGTCA 98213934 AAAATTAGAAAAATAAGTAAAAACTCTTGT-AAAAATTATGACCTCTCCAAAATAAGCGAAAAAT 1 AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATT-TGACCTCTCCAAAATAAGCGAAAAAT 98213998 ATTCCTTCTCTATTCCAAAAATAAGTCA 65 ATTCCTTCTCTATTCCAAAAATAAGTCA 98214026 TGAGAATGGT Statistics Matches: 86, Mismatches: 4, Indels: 3 0.92 0.04 0.03 Matches are distributed among these distances: 91 15 0.17 92 71 0.83 ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29 Consensus pattern (92 bp): AAAATTAGAAAAATAAGTAAAAACTCTTGTAAAAAATTTGACCTCTCCAAAATAAGCGAAAAATA TTCCTTCTCTATTCCAAAAATAAGTCA Found at i:98217577 original size:33 final size:33 Alignment explanation

Indices: 98217535--98217598 Score: 119 Period size: 33 Copynumber: 1.9 Consensus size: 33 98217525 ATGTTATAAA * 98217535 CATGCATGCATTGATAGAGTGAATTTAAGAGAT 1 CATGCATGCATTGATAGACTGAATTTAAGAGAT 98217568 CATGCATGCATTGATAGACTGAATTTAAGAG 1 CATGCATGCATTGATAGACTGAATTTAAGAG 98217599 GGCGTAATAG Statistics Matches: 30, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 33 30 1.00 ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30 Consensus pattern (33 bp): CATGCATGCATTGATAGACTGAATTTAAGAGAT Found at i:98228710 original size:27 final size:28 Alignment explanation

Indices: 98228663--98228715 Score: 65 Period size: 27 Copynumber: 1.9 Consensus size: 28 98228653 AAAATAGGAG * * 98228663 AAATAATATATTTGGTAATAATAATATA 1 AAATAATATATATGGTAATAAAAATATA 98228691 AAATAATA-ATAT-GTACATAAAAATA 1 AAATAATATATATGGTA-ATAAAAATA 98228716 CATATATATA Statistics Matches: 22, Mismatches: 2, Indels: 3 0.81 0.07 0.11 Matches are distributed among these distances: 26 3 0.14 27 11 0.50 28 8 0.36 ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34 Consensus pattern (28 bp): AAATAATATATATGGTAATAAAAATATA Found at i:98229051 original size:39 final size:39 Alignment explanation

Indices: 98228965--98229051 Score: 104 Period size: 39 Copynumber: 2.2 Consensus size: 39 98228955 TTTAAAATAT * * * 98228965 ATATATGTATATATAATAGCATTTAAGAATATATACATA 1 ATATATATATATATAATAGCATTAAAAAATATATACATA * * * 98229004 AGAAATATATA-ACTAATGGCATTAAAAAATATATACATA 1 ATATATATATATA-TAATAGCATTAAAAAATATATACATA 98229043 ATATATATA 1 ATATATATA 98229052 AAATACCAAA Statistics Matches: 39, Mismatches: 8, Indels: 2 0.80 0.16 0.04 Matches are distributed among these distances: 38 1 0.03 39 38 0.97 ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34 Consensus pattern (39 bp): ATATATATATATATAATAGCATTAAAAAATATATACATA Found at i:98236141 original size:6 final size:6 Alignment explanation

Indices: 98236130--98236165 Score: 72 Period size: 6 Copynumber: 6.0 Consensus size: 6 98236120 TAGGTTTCCA 98236130 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG 1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG 98236166 GAAACTTGCA Statistics Matches: 30, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 30 1.00 ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17 Consensus pattern (6 bp): AAAATG Found at i:98236354 original size:23 final size:24 Alignment explanation

Indices: 98236314--98236358 Score: 74 Period size: 23 Copynumber: 1.9 Consensus size: 24 98236304 AATTTCTCGA 98236314 AATTTTATCGAGGGTAAAATTGTC 1 AATTTTATCGAGGGTAAAATTGTC * 98236338 AATTTTAT-TAGGGTAAAATTG 1 AATTTTATCGAGGGTAAAATTG 98236359 AGGTAAGAAA Statistics Matches: 20, Mismatches: 1, Indels: 1 0.91 0.05 0.05 Matches are distributed among these distances: 23 12 0.60 24 8 0.40 ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40 Consensus pattern (24 bp): AATTTTATCGAGGGTAAAATTGTC Found at i:98237764 original size:46 final size:46 Alignment explanation

Indices: 98237711--98237802 Score: 184 Period size: 46 Copynumber: 2.0 Consensus size: 46 98237701 TAACAAGTTT 98237711 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC 1 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC 98237757 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC 1 AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC 98237803 TAACAATTTC 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:0.35, C:0.22, G:0.04, T:0.39 Consensus pattern (46 bp): AACTTATTTTCCAATTTAGTCCTTATCATAAACTAAGCTTACTAAC Found at i:98238512 original size:103 final size:104 Alignment explanation

Indices: 98238328--98238527 Score: 296 Period size: 103 Copynumber: 1.9 Consensus size: 104 98238318 ACAATTTAGC * ** * 98238328 CCCTGAGCTTTAATTAATGATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTACA 1 CCCTGAGCTTAAATTAACAATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTAAA * 98238393 CTAACTCTATTCATCTTCCTATTTAATTCTTATGAGAGT 66 CTAACTCTATTAATCTTCCTATTTAATTCTTATGAGAGT * * 98238432 CCCTGAGCTTAAATTAACAATTTT-TCCTGTTAAATTACTT-ATCAATCTTTAATATATTTTTAA 1 CCCTGAGCTTAAATTAACAATTTTCT-CGGTTAAATTACTTAACCAATCTTTAATATATTTTTAA * * 98238495 ATTAACTCTATTAATCTTCCTATTTTATTCTTA 65 ACTAACTCTATTAATCTTCCTATTTAATTCTTA 98238528 CAAGCTCGAT Statistics Matches: 86, Mismatches: 9, Indels: 3 0.88 0.09 0.03 Matches are distributed among these distances: 103 52 0.60 104 34 0.40 ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47 Consensus pattern (104 bp): CCCTGAGCTTAAATTAACAATTTTCTCGGTTAAATTACTTAACCAATCTTTAATATATTTTTAAA CTAACTCTATTAATCTTCCTATTTAATTCTTATGAGAGT Found at i:98240624 original size:44 final size:44 Alignment explanation

Indices: 98240511--98240616 Score: 182 Period size: 41 Copynumber: 2.5 Consensus size: 44 98240501 TCATTTTGAC 98240511 TTTTCATATAATTATTCTATACACTGTTAATGAATCTTAAAAAG 1 TTTTCATATAATTATTCTATACACTGTTAATGAATCTTAAAAAG 98240555 -TTT--TATAATTATTCTATACACTGTTAATGAATCTTAAAAAG 1 TTTTCATATAATTATTCTATACACTGTTAATGAATCTTAAAAAG * 98240596 TTTTCATATAATTATTATATA 1 TTTTCATATAATTATTCTATA 98240617 TATTGTTAGC Statistics Matches: 58, Mismatches: 1, Indels: 6 0.89 0.02 0.09 Matches are distributed among these distances: 41 38 0.66 42 3 0.05 43 3 0.05 44 14 0.24 ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46 Consensus pattern (44 bp): TTTTCATATAATTATTCTATACACTGTTAATGAATCTTAAAAAG Found at i:98242003 original size:23 final size:25 Alignment explanation

Indices: 98241966--98242023 Score: 75 Period size: 25 Copynumber: 2.4 Consensus size: 25 98241956 AATAAATTCG 98241966 TATAAAAAATCTAGTTATATT-ATT 1 TATAAAAAATCTAGTTATATTAATT * * 98241990 TATAAAATAT-TAGTTATTTTAAATT 1 TATAAAAAATCTAGTTATATT-AATT 98242015 TATAAAAAA 1 TATAAAAAA 98242024 AAAACCACAT Statistics Matches: 29, Mismatches: 3, Indels: 3 0.83 0.09 0.09 Matches are distributed among these distances: 23 9 0.31 24 9 0.31 25 11 0.38 ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45 Consensus pattern (25 bp): TATAAAAAATCTAGTTATATTAATT Found at i:98243133 original size:29 final size:29 Alignment explanation

Indices: 98243047--98243134 Score: 86 Period size: 29 Copynumber: 3.0 Consensus size: 29 98243037 GATTAAATTA * * * * 98243047 AAATTAAAGTTTAAGTATACATTTGAACC 1 AAATTAAAGTTCATGTATACAATTGCACC * * * 98243076 ATAATTAGAGTTTCATGTGTATAATTGCACC 1 A-AATTAAAG-TTCATGTATACAATTGCACC * 98243107 AAATTAAAGTTCATGTATACAACTGCAC 1 AAATTAAAGTTCATGTATACAATTGCAC 98243135 ATTAAATCAA Statistics Matches: 46, Mismatches: 11, Indels: 4 0.75 0.18 0.07 Matches are distributed among these distances: 29 17 0.37 30 14 0.30 31 15 0.33 ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34 Consensus pattern (29 bp): AAATTAAAGTTCATGTATACAATTGCACC Found at i:98243782 original size:18 final size:18 Alignment explanation

Indices: 98243748--98243782 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 98243738 TGTGTGATAC * 98243748 TTATAATTATAATTTAAT 1 TTATAATTATAAGTTAAT * 98243766 TTATAATTATTAGTTAA 1 TTATAATTATAAGTTAA 98243783 AAATTTGAGG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54 Consensus pattern (18 bp): TTATAATTATAAGTTAAT Found at i:98244758 original size:11 final size:10 Alignment explanation

Indices: 98244723--98244758 Score: 54 Period size: 11 Copynumber: 3.4 Consensus size: 10 98244713 ATAATAAAAA 98244723 TAATATTAAT 1 TAATATTAAT 98244733 TAAATATTAAT 1 T-AATATTAAT 98244744 TAATATTATAT 1 TAATATTA-AT 98244755 TAAT 1 TAAT 98244759 GTGAAATTAA Statistics Matches: 24, Mismatches: 0, Indels: 3 0.89 0.00 0.11 Matches are distributed among these distances: 10 8 0.33 11 16 0.67 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (10 bp): TAATATTAAT Found at i:98248157 original size:84 final size:84 Alignment explanation

Indices: 98248027--98248180 Score: 254 Period size: 84 Copynumber: 1.8 Consensus size: 84 98248017 ATCACGACGG * 98248027 GTTGGTTTCAAAGAAAATTTTAAAATTTCATTATGCTTATTTTCACTATTTTCAAACCGATTTTC 1 GTTGGTTTCAAAGAAAATTTTAAAATTTCATTATGATTATTTTCACTATTTTCAAACCGATTTTC 98248092 CAACAAATTATCACAACTA 66 CAACAAATTATCACAACTA * * * * * 98248111 GTTGGTTTCAATGAAAATTTTAATATTTCTTTCTGATTATTTTCACTCTTTTCAAACCGATTTTC 1 GTTGGTTTCAAAGAAAATTTTAAAATTTCATTATGATTATTTTCACTATTTTCAAACCGATTTTC 98248176 CAACA 66 CAACA 98248181 TAGGCAACTT Statistics Matches: 64, Mismatches: 6, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 84 64 1.00 ACGTcount: A:0.32, C:0.17, G:0.08, T:0.44 Consensus pattern (84 bp): GTTGGTTTCAAAGAAAATTTTAAAATTTCATTATGATTATTTTCACTATTTTCAAACCGATTTTC CAACAAATTATCACAACTA Found at i:98251167 original size:21 final size:21 Alignment explanation

Indices: 98251141--98251181 Score: 64 Period size: 21 Copynumber: 2.0 Consensus size: 21 98251131 AGACGAGCAA * * 98251141 TACTCCACAGCAGGTGGAGTG 1 TACTCCAAAACAGGTGGAGTG 98251162 TACTCCAAAACAGGTGGAGT 1 TACTCCAAAACAGGTGGAGT 98251182 TTGAGCAGAT Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 21 18 1.00 ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20 Consensus pattern (21 bp): TACTCCAAAACAGGTGGAGTG Found at i:98264980 original size:21 final size:21 Alignment explanation

Indices: 98264938--98264980 Score: 52 Period size: 21 Copynumber: 2.0 Consensus size: 21 98264928 TTAGACCTTG * 98264938 TCCTGTGATTTTTGTTTTCTC 1 TCCTGTGATTTTTGTTTCCTC * 98264959 TCCTGTTGGTTTTTG-TTCCTC 1 TCCTG-TGATTTTTGTTTCCTC 98264980 T 1 T 98264981 TGCTACATAA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 11 0.58 22 8 0.42 ACGTcount: A:0.02, C:0.21, G:0.16, T:0.60 Consensus pattern (21 bp): TCCTGTGATTTTTGTTTCCTC Found at i:98275184 original size:17 final size:18 Alignment explanation

Indices: 98275162--98275195 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 98275152 CAGCACTTGT 98275162 AAAAGA-CCAATAAAAGA 1 AAAAGATCCAATAAAAGA * 98275179 AAAAGATCCTATAAAAG 1 AAAAGATCCAATAAAAG 98275196 TTCCAATATT Statistics Matches: 15, Mismatches: 1, Indels: 1 0.88 0.06 0.06 Matches are distributed among these distances: 17 6 0.40 18 9 0.60 ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12 Consensus pattern (18 bp): AAAAGATCCAATAAAAGA Found at i:98277327 original size:20 final size:20 Alignment explanation

Indices: 98277304--98277362 Score: 70 Period size: 20 Copynumber: 3.0 Consensus size: 20 98277294 AAAATATATA 98277304 AAAAT-ATTTTTATACTTTTT 1 AAAATAATTTTTATA-TTTTT 98277324 AAAATAATTTTTA-ATTTTT 1 AAAATAATTTTTATATTTTT * 98277343 AAAATGA-TTTTATAATTTTT 1 AAAATAATTTTTAT-ATTTTT 98277363 TTAAATTTTA Statistics Matches: 35, Mismatches: 1, Indels: 6 0.83 0.02 0.14 Matches are distributed among these distances: 18 5 0.14 19 11 0.31 20 12 0.34 21 7 0.20 ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58 Consensus pattern (20 bp): AAAATAATTTTTATATTTTT Found at i:98277353 original size:18 final size:19 Alignment explanation

Indices: 98277304--98277362 Score: 75 Period size: 19 Copynumber: 3.0 Consensus size: 19 98277294 AAAATATATA 98277304 AAAAT-ATTTTTATACTTTTT 1 AAAATAATTTTTA-A-TTTTT 98277324 AAAATAATTTTTAATTTTT 1 AAAATAATTTTTAATTTTT * 98277343 AAAATGATTTTATAATTTTT 1 AAAATAATTTT-TAATTTTT 98277363 TTAAATTTTA Statistics Matches: 36, Mismatches: 1, Indels: 4 0.88 0.02 0.10 Matches are distributed among these distances: 19 15 0.42 20 14 0.39 21 7 0.19 ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58 Consensus pattern (19 bp): AAAATAATTTTTAATTTTT Found at i:98277354 original size:30 final size:29 Alignment explanation

Indices: 98277320--98277376 Score: 78 Period size: 29 Copynumber: 1.9 Consensus size: 29 98277310 TTTTTATACT * 98277320 TTTTAAAATAATTTTTAATTTTTAAAATGA 1 TTTTAAAAT-ATTTTTAAATTTTAAAATGA * * 98277350 TTTTATAATTTTTTTAAATTTTAAAAT 1 TTTTAAAATATTTTTAAATTTTAAAAT 98277377 TTAATTAGTT Statistics Matches: 24, Mismatches: 3, Indels: 1 0.86 0.11 0.04 Matches are distributed among these distances: 29 16 0.67 30 8 0.33 ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58 Consensus pattern (29 bp): TTTTAAAATATTTTTAAATTTTAAAATGA Found at i:98280623 original size:3 final size:3 Alignment explanation

Indices: 98280615--98280650 Score: 72 Period size: 3 Copynumber: 12.0 Consensus size: 3 98280605 GGAACGGTAG 98280615 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 98280651 TTAACTTCCT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (3 bp): ATT Found at i:98287824 original size:26 final size:26 Alignment explanation

Indices: 98287781--98287878 Score: 117 Period size: 26 Copynumber: 3.8 Consensus size: 26 98287771 TGGTACAAAT * * 98287781 TGATAATAGG-TTAAGTAAATGTTCCA 1 TGATAAT-GGATTAGGTAAATGTTTCA * * 98287807 TGTTAATGGATTAGGTAAATATTTCA 1 TGATAATGGATTAGGTAAATGTTTCA * * 98287833 TGATAATGGGTTAAGTAAATGTTTCA 1 TGATAATGGATTAGGTAAATGTTTCA * 98287859 TGATAATGGTTTAGGTAAAT 1 TGATAATGGATTAGGTAAAT 98287879 ATTTTATAAT Statistics Matches: 61, Mismatches: 10, Indels: 2 0.84 0.14 0.03 Matches are distributed among these distances: 25 2 0.03 26 59 0.97 ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39 Consensus pattern (26 bp): TGATAATGGATTAGGTAAATGTTTCA Found at i:98287866 original size:52 final size:52 Alignment explanation

Indices: 98287781--98287882 Score: 168 Period size: 52 Copynumber: 2.0 Consensus size: 52 98287771 TGGTACAAAT * 98287781 TGATAATAGGTTAAGTAAATGTTCCATGTTAATGGATTAGGTAAATATTTCA 1 TGATAATAGGTTAAGTAAATGTTCCATGATAATGGATTAGGTAAATATTTCA * * * 98287833 TGATAATGGGTTAAGTAAATGTTTCATGATAATGGTTTAGGTAAATATTT 1 TGATAATAGGTTAAGTAAATGTTCCATGATAATGGATTAGGTAAATATTT 98287883 TATAATGGGC Statistics Matches: 46, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 52 46 1.00 ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40 Consensus pattern (52 bp): TGATAATAGGTTAAGTAAATGTTCCATGATAATGGATTAGGTAAATATTTCA Found at i:98288626 original size:17 final size:17 Alignment explanation

Indices: 98288604--98288638 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 98288594 AAGAGTGGTC 98288604 AGATTAGTCAAACAGTG 1 AGATTAGTCAAACAGTG 98288621 AGATTAGTCAAACAGTG 1 AGATTAGTCAAACAGTG 98288638 A 1 A 98288639 AACATGCGAA 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:0.43, C:0.11, G:0.23, T:0.23 Consensus pattern (17 bp): AGATTAGTCAAACAGTG Found at i:98303550 original size:16 final size:18 Alignment explanation

Indices: 98303523--98303555 Score: 52 Period size: 17 Copynumber: 1.9 Consensus size: 18 98303513 TAAAATTGGG 98303523 TTGAGAAAATT-ATTTAA 1 TTGAGAAAATTAATTTAA 98303540 TTGAG-AAATTAATTTA 1 TTGAGAAAATTAATTTA 98303556 GTTAATTTAA Statistics Matches: 15, Mismatches: 0, Indels: 2 0.88 0.00 0.12 Matches are distributed among these distances: 16 5 0.33 17 10 0.67 ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42 Consensus pattern (18 bp): TTGAGAAAATTAATTTAA Found at i:98311832 original size:21 final size:20 Alignment explanation

Indices: 98311772--98311837 Score: 64 Period size: 21 Copynumber: 3.2 Consensus size: 20 98311762 TACATTTTAC * 98311772 TATATA-TATATATTAT-TT 1 TATATATTATATATTTTGTT * 98311790 TATATATTATCTATCATATTGTT 1 TATATATTA--TAT-ATTTTGTT 98311813 TATATCATTATATATTTTGTT 1 TATAT-ATTATATATTTTGTT 98311834 TATA 1 TATA 98311838 ATTTTTATTA Statistics Matches: 39, Mismatches: 3, Indels: 9 0.76 0.06 0.18 Matches are distributed among these distances: 18 6 0.15 19 2 0.05 21 14 0.36 22 6 0.15 23 7 0.18 24 4 0.10 ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59 Consensus pattern (20 bp): TATATATTATATATTTTGTT Found at i:98319424 original size:14 final size:14 Alignment explanation

Indices: 98319405--98319433 Score: 58 Period size: 14 Copynumber: 2.1 Consensus size: 14 98319395 TGATATGGAG 98319405 TATAATTCTATTCA 1 TATAATTCTATTCA 98319419 TATAATTCTATTCA 1 TATAATTCTATTCA 98319433 T 1 T 98319434 CCAATCCTCT 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:0.34, C:0.14, G:0.00, T:0.52 Consensus pattern (14 bp): TATAATTCTATTCA Found at i:98320482 original size:42 final size:43 Alignment explanation

Indices: 98320425--98320507 Score: 105 Period size: 42 Copynumber: 2.0 Consensus size: 43 98320415 AAAAAATTAG * * * 98320425 TAAAAAATATCAATTTTAAATATATATTTTAAGA-ATATAAGC 1 TAAAAAATATCAATTTTAAACACACATTTTAAGATATATAAGC * * * 98320467 TAAAACATATTAATTTTATACACACATTTTAAGATATATAA 1 TAAAAAATATCAATTTTAAACACACATTTTAAGATATATAA 98320508 TTTAAGGAAT Statistics Matches: 34, Mismatches: 6, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 42 28 0.82 43 6 0.18 ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39 Consensus pattern (43 bp): TAAAAAATATCAATTTTAAACACACATTTTAAGATATATAAGC Found at i:98329737 original size:23 final size:21 Alignment explanation

Indices: 98329695--98329738 Score: 61 Period size: 23 Copynumber: 2.0 Consensus size: 21 98329685 GTTTTCTTAG 98329695 CAAAAACAACAAAAAAACTAA 1 CAAAAACAACAAAAAAACTAA * 98329716 CAAAAACTAATAAAGAAAACTAA 1 CAAAAAC-AACAAA-AAAACTAA 98329739 ATCTCCAATT Statistics Matches: 20, Mismatches: 1, Indels: 2 0.87 0.04 0.09 Matches are distributed among these distances: 21 7 0.35 22 5 0.25 23 8 0.40 ACGTcount: A:0.73, C:0.16, G:0.02, T:0.09 Consensus pattern (21 bp): CAAAAACAACAAAAAAACTAA Found at i:98333426 original size:18 final size:18 Alignment explanation

Indices: 98333402--98333446 Score: 65 Period size: 18 Copynumber: 2.5 Consensus size: 18 98333392 GCGATTACAC 98333402 GGATGATGAAGG-AGATGA 1 GGATGATGAAGGAAGA-GA * 98333420 TGATGATGAAGGAAGAGA 1 GGATGATGAAGGAAGAGA 98333438 GGATGATGA 1 GGATGATGA 98333447 TGAAAATGGG Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 18 21 0.88 19 3 0.12 ACGTcount: A:0.40, C:0.00, G:0.42, T:0.18 Consensus pattern (18 bp): GGATGATGAAGGAAGAGA Found at i:98346311 original size:2 final size:2 Alignment explanation

Indices: 98346304--98346340 Score: 74 Period size: 2 Copynumber: 18.5 Consensus size: 2 98346294 GTTAATAATT 98346304 AG AG AG 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 AG AG AG A 98346341 AGGATCTGGC Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 35 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:98359527 original size:9 final size:9 Alignment explanation

Indices: 98359495--98359606 Score: 66 Period size: 9 Copynumber: 12.3 Consensus size: 9 98359485 ATACACTGAT * 98359495 ATAATAGTG 1 ATAATAGTA * 98359504 ATAATAATA 1 ATAATAGTA * 98359513 A-CATAGTA 1 ATAATAGTA 98359521 ATAATAGTA 1 ATAATAGTA * * 98359530 TTGATAGTA 1 ATAATAGTA * * 98359539 ATAAAAATA 1 ATAATAGTA * 98359548 AT-ATATTAA 1 ATAATAGT-A 98359557 ATAATAGTA 1 ATAATAGTA * 98359566 ATAAAATAGTG 1 AT--AATAGTA * * 98359577 CTAATAGTC 1 ATAATAGTA * 98359586 ATAATAGTG 1 ATAATAGTA * 98359595 ATAATAATA 1 ATAATAGTA 98359604 ATA 1 ATA 98359607 GCATGATAAA Statistics Matches: 77, Mismatches: 21, Indels: 10 0.71 0.19 0.09 Matches are distributed among these distances: 8 9 0.12 9 57 0.74 10 4 0.05 11 7 0.09 ACGTcount: A:0.54, C:0.03, G:0.11, T:0.33 Consensus pattern (9 bp): ATAATAGTA Found at i:98359537 original size:35 final size:36 Alignment explanation

Indices: 98359498--98359565 Score: 93 Period size: 35 Copynumber: 1.9 Consensus size: 36 98359488 CACTGATATA * * 98359498 ATAGTGATAATAATAACATAGT-AATAATAGTATTG 1 ATAGTAATAAAAATAACATAGTAAATAATAGTATTG * * 98359533 ATAGTAATAAAAATAATATATTAAATAATAGTA 1 ATAGTAATAAAAATAACATAGTAAATAATAGTA 98359566 ATAAAATAGT Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 35 18 0.64 36 10 0.36 ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34 Consensus pattern (36 bp): ATAGTAATAAAAATAACATAGTAAATAATAGTATTG Found at i:98359752 original size:3 final size:3 Alignment explanation

Indices: 98359744--98359917 Score: 63 Period size: 3 Copynumber: 56.3 Consensus size: 3 98359734 AAACATAGAA * * * * * * * 98359744 AAT AAT AAT AAT CAT AAT -AC AAT AGT AAT AGT AAT CAC AAA AAT AAT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT * * * * * 98359791 GAT AAT AAT AAT AAT AAT ATT AA- AGT AA- AGT AAAT AAT AAT ACT 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT * * 98359835 -AT ATAT AAAT ATAT ATAT ACAT ATGT AAT AGA- AAT ACAC ACGAT -AT 1 AAT A-AT -AAT A-AT A-AT A-AT A-AT AAT A-AT AAT A-AT A--AT AAT * * 98359881 AAT AAT AAT AAT AAT AAT AAT AAT AAA AAC AAT AAT A 1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A 98359918 CATATATATA Statistics Matches: 125, Mismatches: 33, Indels: 26 0.68 0.18 0.14 Matches are distributed among these distances: 2 7 0.06 3 95 0.76 4 21 0.17 5 2 0.02 ACGTcount: A:0.60, C:0.06, G:0.05, T:0.30 Consensus pattern (3 bp): AAT Found at i:98360046 original size:30 final size:28 Alignment explanation

Indices: 98360012--98360081 Score: 72 Period size: 30 Copynumber: 2.4 Consensus size: 28 98360002 TGGAGAGGGT 98360012 ATATATAATATAATAATAAT-ATAAATAATA 1 ATATATAATA-AA-AATAATGAT-AATAATA * 98360042 ATATATACATGAGAAATAATGATAATAATA 1 ATATATA-AT-AAAAATAATGATAATAATA 98360072 ATATA-AATAA 1 ATATATAATAA 98360082 CAGTAAAAAT Statistics Matches: 35, Mismatches: 2, Indels: 9 0.76 0.04 0.20 Matches are distributed among these distances: 27 1 0.03 28 2 0.06 29 1 0.03 30 25 0.71 31 5 0.14 32 1 0.03 ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33 Consensus pattern (28 bp): ATATATAATAAAAATAATGATAATAATA Found at i:98360741 original size:14 final size:15 Alignment explanation

Indices: 98360722--98360750 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 98360712 TATTTATTTA 98360722 TTTGG-TTTATTAGG 1 TTTGGTTTTATTAGG 98360736 TTTGGTTTTATTAGG 1 TTTGGTTTTATTAGG 98360751 CCCCGGGCAA Statistics Matches: 14, Mismatches: 0, Indels: 1 0.93 0.00 0.07 Matches are distributed among these distances: 14 5 0.36 15 9 0.64 ACGTcount: A:0.14, C:0.00, G:0.28, T:0.59 Consensus pattern (15 bp): TTTGGTTTTATTAGG Found at i:98361297 original size:67 final size:68 Alignment explanation

Indices: 98361008--98361305 Score: 422 Period size: 68 Copynumber: 4.4 Consensus size: 68 98360998 TCTTCCGCTA * * * * 98361008 AAACTTCAAGAAGATCTACTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGGAGAAATCCA 1 AAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAGAGATCCA 98361073 CTG 66 CTG * * * * * 98361076 AAACTTCAAGGAGATCTGCCGTGGCTTTTAGTCGCTCCAACGCCATTTCAGGAAGAAGAGGTTCG 1 AAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAGAGATCCA 98361141 CTG 66 CTG * * * 98361144 AAACTTCAAGGAGATCTGCTGTGGCCTTTAACCGCTCCAATGCCATTTCAGGGAA-AAGAGATCC 1 AAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCA-GGAAGAAGAGATCC 98361208 ACTG 65 ACTG * 98361212 AAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCA-TTCAGGGAA-AAGAGATCC 1 AAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCA-GGAAGAAGAGATCC * 98361275 TCTG 65 ACTG * 98361279 AAACTTCAAGGAGATCTGTTGTGGCTT 1 AAACTTCAAGGAGATCTGCTGTGGCTT 98361306 CAAGAAGATA Statistics Matches: 207, Mismatches: 22, Indels: 3 0.89 0.09 0.01 Matches are distributed among these distances: 67 48 0.23 68 155 0.75 69 4 0.02 ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25 Consensus pattern (68 bp): AAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAGAGATCCA CTG Found at i:98361520 original size:44 final size:43 Alignment explanation

Indices: 98361472--98362057 Score: 244 Period size: 44 Copynumber: 13.5 Consensus size: 43 98361462 ATCTATTTCT * 98361472 CTACTGCTTAGAGGGTTAAGATCTTGTAAATCCAGCCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAATCCA-CCTGTTACC * * * ** * * * 98361516 CTACTACTTAGGGGTTTAAGGTCTATCGT-CTTCGATCTGTTTCC 1 CTACTGCTTAGGGGGTTAAGATCT-T-GTAAATCCACCTGTTACC * 98361560 CTACTACTTAGGGGGTTAAGATC-TGTAAATTCCACCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAA-TCCACCTGTTACC * * * ** * * * * 98361603 CTACTGCTTAAGGGTTTAAGGTC-CAT-CATCTTTGATCTGTTTCC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAATC---CACCTGTTACC ** 98361647 CTACTGCTTAGGGGGTTAAGATC-TGTAAATTTAACCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAA-TCCACCTGTTACC * * * *** ** * * 98361690 CTACTGCTTAGGGGTTTAAGGTCCATCG-CCTTTGATCTGTTTCC 1 CTACTGCTTAGGGGGTTAAGAT-C-TTGTAAATCCACCTGTTACC 98361734 CTACTGCTTAGGGGGTTAAGAT-TTGTAAATCCAACCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAATCC-ACCTGTTACC * * * * *** * ** * 98361777 CTACTGTTTAGGGGTTTAAGGTTCATCG-CCTTCGATTTGTTTCC 1 CTACTGCTTAGGGGGTTAA-GATC-TTGTAAATCCACCTGTTACC ** 98361821 CTACTGCTTAGGGGGTTAAGATC-TGTAAATTTAGCCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAATCCA-CCTGTTACC * * * * ** ** * ** * 98361864 CTACTACTTAAGGAGTTAAG-GCCCGTCACTTTCGATTTGTTTCC 1 CTACTGCTTAGGGGGTTAAGATCTTGT-A-AATCCACCTGTTACC * * * * 98361908 CTACTGCTTAGGGGGATAAGATC-TGGAAATTCAACCTATTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAA-TCCACCTGTTACC * * * *** * * * 98361951 CTACTGCTTAGGGGTTTAAGGTTCATCG-CCTTCGATCTGTTTCC 1 CTACTGCTTAGGGGGTTAA-GATC-TTGTAAATCCACCTGTTACC ** 98361995 CTACTGCTTAGGGGGTTAAGATC-TGTAAATTTAGCCTGTTACC 1 CTACTGCTTAGGGGGTTAAGATCTTGTAAATCCA-CCTGTTACC * * 98362038 CTACTACTTAGGGAGTTAAG 1 CTACTGCTTAGGGGGTTAAG 98362058 GCCCGTCGCT Statistics Matches: 386, Mismatches: 127, Indels: 59 0.67 0.22 0.10 Matches are distributed among these distances: 41 8 0.02 42 8 0.02 43 165 0.43 44 188 0.49 45 10 0.03 46 7 0.02 ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36 Consensus pattern (43 bp): CTACTGCTTAGGGGGTTAAGATCTTGTAAATCCACCTGTTACC Found at i:98361624 original size:87 final size:87 Alignment explanation

Indices: 98361423--98362105 Score: 885 Period size: 87 Copynumber: 7.9 Consensus size: 87 98361413 TTTCAGCCTA * * * * * * * 98361423 TTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCAATCTATTTCTCTACTGCTTAGAGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT 98361488 TAAGATCTTGTAAA-TCCAGCCTG 66 TAAGATC-TGTAAATTCCA-CCTG * * * * 98361511 TTACCCTACTACTTAGGGGTTTAAGGTCTATCGTCTTCGATCTGTTTCCCTACTACTTAGGGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT 98361576 TAAGATCTGTAAATTCCACCTG 66 TAAGATCTGTAAATTCCACCTG * ** * 98361598 TTACCCTACTGCTTAAGGGTTTAAGGTCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT ** 98361663 TAAGATCTGTAAATTTAACCTG 66 TAAGATCTGTAAATTCCACCTG * 98361685 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTTGATCTGTTTCCCTACTGCTTAGGGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT * 98361750 TAAGATTTGTAAA-TCCAACCTG 66 TAAGATCTGTAAATTCC-ACCTG * * * 98361772 TTACCCTACTGTTTAGGGGTTTAAGGTTCATCGCCTTCGATTTGTTTCCCTACTGCTTAGGGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT * 98361837 TAAGATCTGTAAATT-TAGCCTG 66 TAAGATCTGTAAATTCCA-CCTG * * * * * * * 98361859 TTACCCTACTACTTAAGGAG-TTAAGGCCCGTCACTTTCGATTTGTTTCCCTACTGCTTAGGGGG 1 TTACCCTACTGCTT-AGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGG * * * * 98361923 ATAAGATCTGGAAATTCAACCTA 65 TTAAGATCTGTAAATTCCACCTG * 98361946 TTACCCTACTGCTTAGGGGTTTAAGGTTCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT 1 TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT * 98362011 TAAGATCTGTAAATT-TAGCCTG 66 TAAGATCTGTAAATTCCA-CCTG * * * * 98362033 TTACCCTACTACTTAGGGAG-TTAAGGCCCGTCGCTTTCGATCTGTTTCCCTACTGCTTAGGGGG 1 TTACCCTACTGCTTAGGG-GTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGG * 98362097 TCAA-ATCTG 65 TTAAGATCTG 98362106 CTATCTTCAA Statistics Matches: 525, Mismatches: 61, Indels: 20 0.87 0.10 0.03 Matches are distributed among these distances: 86 12 0.02 87 441 0.84 88 72 0.14 ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36 Consensus pattern (87 bp): TTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGCTTAGGGGGT TAAGATCTGTAAATTCCACCTG Found at i:98361907 original size:261 final size:260 Alignment explanation

Indices: 98361414--98362105 Score: 989 Period size: 261 Copynumber: 2.6 Consensus size: 260 98361404 ATCTATAATT * * * * * * * 98361414 TTCAGCCTATTACCCTATTGCTTAGGGGTTTAAGGCCCATCACCTTCAATCTATTTCTCTACTGC 1 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC * 98361479 TTAGAGGGTTAAGATCTTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGGTCTATCG 66 TTAGGGGGTTAAGAT-TTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGGTC-ATCG * * * 98361544 TCTTCGATCTGTTTCCCTACTACTTAGGGGGTTAAGATCTGTAAATTCCACCTGTTACCCTACTG 129 CCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCCACCTGTTACCCTACTA * * * 98361609 CTTAAGGGTTTAAGGTCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTA 194 CTTAAGGGTTTAAGGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGGA 98361674 AA 259 AA * * * 98361676 TTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTTGATCTGTTTCCCTACTGC 1 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC * ** 98361741 TTAGGGGGTTAAGATTTGTAAATCCAACCTGTTACCCTACTGTTTAGGGGTTTAAGGTTCATCGC 66 TTAGGGGGTTAAGATTTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGG-TCATCGC * * 98361806 CTTCGATTTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATT-TAGCCTGTTACCCTACTA 130 CTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCCA-CCTGTTACCCTACTA * * 98361870 CTTAAGGAG-TTAAGGCCCGTCA-CTTTCGATTTGTTTCCCTACTGCTTAGGGGGATAAGATCTG 194 CTTAAGG-GTTTAAGGCCCATCATCTTT-GATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTG 98361933 GAAA 257 GAAA * 98361937 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTTCATCGCCTTCGATCTGTTTCCCTACTGC 1 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC * ** * * 98362002 TTAGGGGGTTAAGATCTGTAAATTTAGCCTGTTACCCTACTACTTAGGGAG-TTAAGGCCCGTCG 66 TTAGGGGGTTAAGATTTGTAAATCCAGCCTGTTACCCTACTACTTAGGG-GTTTAAGG-TCATCG * * 98362066 CTTTCGATCTGTTTCCCTACTGCTTAGGGGGTCAA-ATCTG 129 CCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTG 98362106 CTATCTTCAA Statistics Matches: 385, Mismatches: 40, Indels: 12 0.88 0.09 0.03 Matches are distributed among these distances: 260 10 0.03 261 302 0.78 262 73 0.19 ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36 Consensus pattern (260 bp): TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTCCCTACTGC TTAGGGGGTTAAGATTTGTAAATCCAGCCTGTTACCCTACTACTTAGGGGTTTAAGGTCATCGCC TTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCCACCTGTTACCCTACTACT TAAGGGTTTAAGGCCCATCATCTTTGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGGAAA Found at i:98362256 original size:44 final size:44 Alignment explanation

Indices: 98362098--98362897 Score: 396 Period size: 44 Copynumber: 18.2 Consensus size: 44 98362088 CTTAGGGGGT * * * * 98362098 CAAATCTGCTATCTTCAA-CTTGTTCCTTATAAACACAGGGATGT 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG ** * * * ** * 98362142 C--ATGCTGAAATCTTCAATCTGCTTCACTGTAAGTACAGTAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGGATGG * * * * 98362186 CAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGATGG 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG * * 98362230 CAAATCTGTTATTTTCAA-CTTGTTCCCTATAAGCATAGGGAT-G 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG * ** * * * * * 98362273 C-CATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGGATGG * * * * 98362318 CAGATATGTTATCTTCGATCTGTTCCCTATAAGCACAGGGATGC 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG * 98362362 CAAATCTGTTATTTTCAA-CTTGTTCCCTATAAGCACAGGGAT-G 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG * ** ** * * * * * 98362405 C-CATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAAGAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGGATGG * * * * * * * * 98362450 TAGATCTGCTATCTTCGATATGTTTCCTATAAACACAGGGATGC 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG * * 98362494 CAAATCTGTTATTTTCAA-CTTGTTCCCTATAAGCATAGGGAT-G 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG * ** * * * * * 98362537 C-CATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGGATGG * * * * * * * * 98362582 TAGATCTGTTACCTTCCATCTATTCCCTACAAGTACAGGGATGC 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG * * 98362626 CAAATCTGCTATTTTCAA-CTTGTTCCCTATAAGCACAGGGAT-G 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG * ** * * * * * 98362669 C-CATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGGATGG * * * * * * * * 98362714 CAGATCTGTTACCTTCCATCTATTCCCTACAAGTATAGGGATGC 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG * * 98362758 CAAATCTGCTATTTTCAA-CTTGTTCCCTATAAGCACAGGGAT-G 1 CAAATCTGTTATCTTCAATC-TGTTCCCTATAAGCACAGGGATGG * ** * * * * 98362801 C-CATGCTGAAATCTTCGATCTGCTTCACTGTAAGCAC-GGGAATGT 1 CAAAT-CTGTTATCTTCAATCTG-TTCCCTATAAGCACAGGG-ATGG * ** * * * 98362846 CAGATCTGTTATCTTTGATCTGTTCCCTATAAACATAGGGATGC 1 CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG 98362890 CAAATCTG 1 CAAATCTG 98362898 CAATCTTCGA Statistics Matches: 554, Mismatches: 165, Indels: 74 0.70 0.21 0.09 Matches are distributed among these distances: 42 12 0.02 43 80 0.14 44 365 0.66 45 85 0.15 46 12 0.02 ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32 Consensus pattern (44 bp): CAAATCTGTTATCTTCAATCTGTTCCCTATAAGCACAGGGATGG Found at i:98362914 original size:132 final size:132 Alignment explanation

Indices: 98362098--98362898 Score: 1251 Period size: 132 Copynumber: 6.1 Consensus size: 132 98362088 CTTAGGGGGT * * * * * 98362098 CAAATCTGCTATCTTCAACTTGTTCCTTATAAACACAGGGATGTCATGCTGAAATCTTCAATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * * 98362163 CTTCACTGTAAGTACAGTAATGTCAGATCTGCTATCTTCGATCTGTTCCCTATAAACACAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT * 98362228 GG 131 GC * * 98362230 CAAATCTGTTATTTTCAACTTGTTCCCTATAAGCATAGGGATGCCATGCTGAAATCTTCGATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * 98362295 CTTCACTGTAAGCACAGGAATGTCAGATATGTTATCTTCGATCTGTTCCCTATAAGCACAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT 98362360 GC 131 GC * * 98362362 CAAATCTGTTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTTGATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * * * * 98362427 CTTCACTGTAAGCACAAGAATGTTAGATCTGCTATCTTCGATATGTTTCCTATAAACACAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT 98362492 GC 131 GC * * 98362494 CAAATCTGTTATTTTCAACTTGTTCCCTATAAGCATAGGGATGCCATGCTGAAATCTTCGATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * * * * ** 98362559 CTTCACTGTAAGCACAGGAATGTTAGATCTGTTACCTTCCATCTATTCCCTACAAGTACAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT 98362624 GC 131 GC 98362626 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * * * ** * 98362691 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTACCTTCCATCTATTCCCTACAAGTATAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT 98362756 GC 131 GC 98362758 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG 1 CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG * * * 98362823 CTTCACTGTAAGCACGGGAATGTCAGATCTGTTATCTTTGATCTGTTCCCTATAAACATAGGGAT 66 CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT 98362888 GC 131 GC 98362890 CAAATCTGC 1 CAAATCTGC 98362899 AATCTTCGAT Statistics Matches: 623, Mismatches: 46, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 132 623 1.00 ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32 Consensus pattern (132 bp): CAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAATCTTCGATCTG CTTCACTGTAAGCACAGGAATGTCAGATCTGTTATCTTCGATCTGTTCCCTATAAACACAGGGAT GC Found at i:98363025 original size:88 final size:88 Alignment explanation

Indices: 98362923--98363132 Score: 357 Period size: 88 Copynumber: 2.4 Consensus size: 88 98362913 TCTCTGCCGC * * 98362923 TACAGAGACGCCAAATCATCTTGGATTTACTTCAACGTAAACACATGAAAGCCAAATCAGCTATG 1 TACAGAGATGCCAAATCATCTTGGATCTACTTCAACGTAAACACATGAAAGCCAAATCAGCTATG * 98362988 TCTTCGATCTGCTCCCCGCCTGG 66 TCTTCGATCTGCTCCCCGCCTGA * * * 98363011 TACAGAGATGCCAAATCATCTTGGATCTGCTTCAACGTAAACACGTGAAAGCTAAATCAGCTATG 1 TACAGAGATGCCAAATCATCTTGGATCTACTTCAACGTAAACACATGAAAGCCAAATCAGCTATG 98363076 TCTTCGATCTGCTCCCCGCCTGA 66 TCTTCGATCTGCTCCCCGCCTGA * 98363099 TACAGAGATGCCAAATCATCTTGGATCTGCTTCA 1 TACAGAGATGCCAAATCATCTTGGATCTACTTCA 98363133 GCAAAGGTCA Statistics Matches: 116, Mismatches: 6, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 88 116 1.00 ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26 Consensus pattern (88 bp): TACAGAGATGCCAAATCATCTTGGATCTACTTCAACGTAAACACATGAAAGCCAAATCAGCTATG TCTTCGATCTGCTCCCCGCCTGA Found at i:98363027 original size:396 final size:395 Alignment explanation

Indices: 98362220--98362982 Score: 1048 Period size: 396 Copynumber: 1.9 Consensus size: 395 98362210 CCCTATAAAC * * * 98362220 ACAGGGATGGCAAATCTGTTATTTTCAACTTGTTCCCTATAAGCATAGGGATGCCATGCTGAAAT 1 ACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAAT * * * * 98362285 CTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATATGTTATCTTCGATCTGTTCCCTATAA 66 CTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATATGTTACCTTCCATCTATTCCCTACAA * 98362350 GCACAGGGATGCCAAATCTGTTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA 131 GCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA * * * 98362415 ATCTTTGATCTGCTTCACTGTAAGCACAAGAATGTTAGATCTGCTATCTTCGATATGTTTCCTAT 196 ATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGATATGTTCCCTAT ** * * * * * ** 98362480 AAACACAGGGATGCCAAATCTGTTATTTTCAACTTGTTCCCTATAAGCATAGGGATGCCATGCTG 261 AAACACAGGGATGCCAAATCTGCAATCTTCAACTTGTTCCCTAGAAGCACAGAGACGCCATAAT- * * * ** * * * * 98362545 AAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTTAGATCTGTTACCTTCCATCTATTCCCT 325 AAATCTTCGATCTACTTCACTGTAAACACAGGAAAGCCAAATCAGTTACCTTCCATCTATCCCCG 98362610 ACAAGT 390 ACAAGT 98362616 ACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAAT 1 ACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAAT * 98362681 CTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGTTACCTTCCATCTATTCCCTACAA 66 CTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATATGTTACCTTCCATCTATTCCCTACAA * * 98362746 GTATAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA 131 GCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA ** * * * 98362811 ATCTTCGATCTGCTTCACTGTAAGCACGGGAATGTCAGATCTGTTATCTTTGATCTGTTCCCTAT 196 ATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGATATGTTCCCTAT * * * * ** 98362876 AAACATAGGGATGCCAAATCTGCAATCTTCGATTTGTTCTCT-GCCGCTACAGAGACGCCA-AAT 261 AAACACAGGGATGCCAAATCTGCAATCTTCAACTTGTTCCCTAGAAGC-ACAGAGACGCCATAAT * * * * 98362939 -CATCTTGGATTTACTTCAAC-GTAAACACATGAAAGCCAAATCAG 325 AAATCTTCGATCTACTTC-ACTGTAAACACAGGAAAGCCAAATCAG 98362983 CTATGTCTTC Statistics Matches: 320, Mismatches: 45, Indels: 7 0.86 0.12 0.02 Matches are distributed among these distances: 393 30 0.09 394 2 0.01 395 3 0.01 396 285 0.89 ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31 Consensus pattern (395 bp): ACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAAAT CTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATATGTTACCTTCCATCTATTCCCTACAA GCACAGGGATGCCAAATCTGCTATTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA ATCTTCGATCTGCTTCACTGTAAGCACAAGAATGTCAGATCTGCTATCTTCGATATGTTCCCTAT AAACACAGGGATGCCAAATCTGCAATCTTCAACTTGTTCCCTAGAAGCACAGAGACGCCATAATA AATCTTCGATCTACTTCACTGTAAACACAGGAAAGCCAAATCAGTTACCTTCCATCTATCCCCGA CAAGT Found at i:98363115 original size:47 final size:47 Alignment explanation

Indices: 98362973--98363116 Score: 126 Period size: 47 Copynumber: 3.2 Consensus size: 47 98362963 ACACATGAAA * 98362973 GCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGGTACAGAGAT 1 GCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACAGAGAT * ** * * * 98363020 GCCAAAT---C-A--TCTTGGATCTGCTTCAACG--T-AAACACGTGAAA 1 GCCAAATCAGCTATGTCTTCGATCTGC-TCCCCGCCTGATACA-GAG-AT * 98363061 GCTAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACAGAGAT 1 GCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACAGAGAT 98363108 GCCAAATCA 1 GCCAAATCA 98363117 TCTTGGATCT Statistics Matches: 70, Mismatches: 15, Indels: 24 0.64 0.14 0.22 Matches are distributed among these distances: 39 3 0.04 40 3 0.04 41 18 0.26 42 4 0.06 43 1 0.01 44 2 0.03 45 1 0.01 46 4 0.06 47 27 0.39 48 3 0.04 49 4 0.06 ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25 Consensus pattern (47 bp): GCCAAATCAGCTATGTCTTCGATCTGCTCCCCGCCTGATACAGAGAT Found at i:98364988 original size:8 final size:8 Alignment explanation

Indices: 98364977--98365047 Score: 56 Period size: 8 Copynumber: 8.8 Consensus size: 8 98364967 CTTTTTGGCA * 98364977 TTTTTTGT 1 TTTTTTAT 98364985 TTTTTTAT 1 TTTTTTAT * * 98364993 TGTTTTGT 1 TTTTTTAT * * 98365001 TTTCTTCT 1 TTTTTTAT 98365009 TTTTCTT-T 1 TTTT-TTAT 98365017 TTTGTGTT-T 1 TTT-T-TTAT 98365026 TTTTTTAT 1 TTTTTTAT 98365034 TTTTTTAT 1 TTTTTTAT 98365042 TTTTTT 1 TTTTTT 98365048 TAAATTTTGA Statistics Matches: 52, Mismatches: 8, Indels: 6 0.79 0.12 0.09 Matches are distributed among these distances: 7 2 0.04 8 41 0.79 9 9 0.17 ACGTcount: A:0.04, C:0.04, G:0.07, T:0.85 Consensus pattern (8 bp): TTTTTTAT Found at i:98364989 original size:9 final size:9 Alignment explanation

Indices: 98364977--98365048 Score: 56 Period size: 9 Copynumber: 7.7 Consensus size: 9 98364967 CTTTTTGGCA 98364977 TTTTTTGTTT 1 TTTTTTG-TT 98364987 TTTTATTGTT 1 TTTT-TTGTT * 98364997 TTGTTTTCTT 1 TT-TTTTGTT * * 98365007 CTTTTTCTT 1 TTTTTTGTT * 98365016 TTTTGTGTT 1 TTTTTTGTT 98365025 TTTTTT-TAT 1 TTTTTTGT-T * 98365034 TTTTTTATT 1 TTTTTTGTT 98365043 TTTTTT 1 TTTTTT 98365049 AAATTTTGAA Statistics Matches: 52, Mismatches: 6, Indels: 9 0.78 0.09 0.13 Matches are distributed among these distances: 8 1 0.02 9 32 0.62 10 14 0.27 11 5 0.10 ACGTcount: A:0.04, C:0.04, G:0.07, T:0.85 Consensus pattern (9 bp): TTTTTTGTT Found at i:98375221 original size:153 final size:153 Alignment explanation

Indices: 98375059--98375363 Score: 479 Period size: 153 Copynumber: 2.0 Consensus size: 153 98375049 TTAAAAGGTT * 98375059 AAAAGTTAATTTTAATC-CAATATTGACTAAAGAATACTCTCATATCTCATATTAACCTTATAAA 1 AAAAGTTAATTTTAATCTC-ATATTGACTAAAGAATACTCTCATATCTCACATTAACCTTATAAA * * 98375123 TAAGTGACAAATTCTTCACTATTTTCATTAAAAAGTTAACTTTTA-TCCCATATTGACTAGATAA 65 TAAGTGACAAATTCTTCACTATTTTCATTAAAAAGTTAA-TTTTACTCCCACATTAACTAGATAA * 98375187 TACTTTCATAGCTCGCTTTCATTAA 129 TACTTTCATAGCTCACTTTCATTAA * * * * * 98375212 AAAAGTTAATTTTAATCTCATATTGACTAGATAATGCTCTCGTATCTCACATTTACCTTATAAAT 1 AAAAGTTAATTTTAATCTCATATTGACTAAAGAATACTCTCATATCTCACATTAACCTTATAAAT * * 98375277 AAGTGACAATTTCTTCATTATTTTCATTAAAAAGTTAATTTTACTCCCACATTAACTAGATAATA 66 AAGTGACAAATTCTTCACTATTTTCATTAAAAAGTTAATTTTACTCCCACATTAACTAGATAATA 98375342 CTTTCATAGCTCACTTTCATTA 131 CTTTCATAGCTCACTTTCATTA 98375364 TTTTCATTAG Statistics Matches: 139, Mismatches: 11, Indels: 4 0.90 0.07 0.03 Matches are distributed among these distances: 152 5 0.04 153 133 0.96 154 1 0.01 ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40 Consensus pattern (153 bp): AAAAGTTAATTTTAATCTCATATTGACTAAAGAATACTCTCATATCTCACATTAACCTTATAAAT AAGTGACAAATTCTTCACTATTTTCATTAAAAAGTTAATTTTACTCCCACATTAACTAGATAATA CTTTCATAGCTCACTTTCATTAA Found at i:98375402 original size:67 final size:67 Alignment explanation

Indices: 98375290--98375417 Score: 193 Period size: 67 Copynumber: 1.9 Consensus size: 67 98375280 TGACAATTTC * * * 98375290 TTCATTATTTTCATTAAAAAGTTAATTTTACTCCCACATTAACTAGATAATACTTTCATAGCTCA 1 TTCATTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAATACTTCCATAGCTCA 98375355 CT 66 CT * * * * 98375357 TTCATTATTTTCATTAGAAAGTTAATTTTAATCCCATATTGACTAGAGAGTACTTCCATAG 1 TTCATTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAATACTTCCATAG 98375418 TTTGCTTCTT Statistics Matches: 54, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 67 54 1.00 ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41 Consensus pattern (67 bp): TTCATTATTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAGAATACTTCCATAGCTCA CT Found at i:98375466 original size:23 final size:22 Alignment explanation

Indices: 98375436--98375481 Score: 65 Period size: 22 Copynumber: 2.0 Consensus size: 22 98375426 TTCAATGTTT 98375436 CCTTAAAAAAAATAATTTTAACC 1 CCTT-AAAAAAATAATTTTAACC ** 98375459 CCTTAAAAAGTTAATTTTAACC 1 CCTTAAAAAAATAATTTTAACC 98375481 C 1 C 98375482 TCACTGGCTA Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 22 17 0.81 23 4 0.19 ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33 Consensus pattern (22 bp): CCTTAAAAAAATAATTTTAACC Found at i:98375775 original size:21 final size:22 Alignment explanation

Indices: 98375749--98375790 Score: 77 Period size: 22 Copynumber: 2.0 Consensus size: 22 98375739 ACTATTTTCA 98375749 TTAAAAA-TTAATTTTAATCCC 1 TTAAAAAGTTAATTTTAATCCC 98375770 TTAAAAAGTTAATTTTAATCC 1 TTAAAAAGTTAATTTTAATCC 98375791 TGTATTGACT Statistics Matches: 20, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 21 7 0.35 22 13 0.65 ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43 Consensus pattern (22 bp): TTAAAAAGTTAATTTTAATCCC Found at i:98375883 original size:93 final size:94 Alignment explanation

Indices: 98375770--98375986 Score: 249 Period size: 93 Copynumber: 2.3 Consensus size: 94 98375760 TTTTAATCCC * * * * 98375770 TTAAAAAGTTAATTTTAATCCTGTATTGACTAAAGAACACTCTCAT-GCTCACATTTACTCTA-T 1 TTAAAAATTTAATTTTAATCCCGCATTGACTAAAGAACACTCTCATAGCTCACATTGACT-TACT * * * * 98375833 CAATAAGTGTCAACTTCTTTACTATTTTCA 65 AAAAAAGTATCAACTTCTTCACTATTTTCA * * * * * 98375863 TTAAAAATTTAATTTCAATCCCGCATTGACTAGAGAACATTCTCATATCTCATATTGACTTACTA 1 TTAAAAATTTAATTTTAATCCCGCATTGACTAAAGAACACTCTCATAGCTCACATTGACTTACTA * * 98375928 AAAAAGTATTAATTTCTTCACTATTTTCA 66 AAAAAGTATCAACTTCTTCACTATTTTCA * * 98375957 TTAAAAATTTTAATTTTAATCTCACATTGA 1 TTAAAAA-TTTAATTTTAATCCCGCATTGA 98375987 ATTGGGAATA Statistics Matches: 103, Mismatches: 18, Indels: 4 0.82 0.14 0.03 Matches are distributed among these distances: 93 42 0.41 94 42 0.41 95 19 0.18 ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41 Consensus pattern (94 bp): TTAAAAATTTAATTTTAATCCCGCATTGACTAAAGAACACTCTCATAGCTCACATTGACTTACTA AAAAAGTATCAACTTCTTCACTATTTTCA Found at i:98376138 original size:21 final size:21 Alignment explanation

Indices: 98376096--98376138 Score: 52 Period size: 21 Copynumber: 2.0 Consensus size: 21 98376086 ACTATTTTTA * 98376096 TTAAAAATTAATTTTGATTCC 1 TTAAAAATTAATTTTGAATCC * 98376117 TTAAAAAGTTAGTTTT-AATCC 1 TTAAAAA-TTAATTTTGAATCC 98376138 T 1 T 98376139 ACATTTGTAA Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 12 0.63 22 7 0.37 ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47 Consensus pattern (21 bp): TTAAAAATTAATTTTGAATCC Found at i:98376395 original size:43 final size:44 Alignment explanation

Indices: 98376346--98376429 Score: 161 Period size: 44 Copynumber: 1.9 Consensus size: 44 98376336 CATAGCTCAC 98376346 TTCTTCACTATTTTTATT-AAAAAAGTTAATTTTAATCCCACAA 1 TTCTTCACTATTTTTATTAAAAAAAGTTAATTTTAATCCCACAA 98376389 TTCTTCACTATTTTTATTAAAAAAAGTTAATTTTAATCCCA 1 TTCTTCACTATTTTTATTAAAAAAAGTTAATTTTAATCCCA 98376430 TATTGACTAG Statistics Matches: 40, Mismatches: 0, Indels: 1 0.98 0.00 0.02 Matches are distributed among these distances: 43 18 0.45 44 22 0.55 ACGTcount: A:0.37, C:0.15, G:0.02, T:0.45 Consensus pattern (44 bp): TTCTTCACTATTTTTATTAAAAAAAGTTAATTTTAATCCCACAA Found at i:98384287 original size:36 final size:36 Alignment explanation

Indices: 98384240--98384310 Score: 142 Period size: 36 Copynumber: 2.0 Consensus size: 36 98384230 ATACGGATAC 98384240 TTGCTCAAACGAGCTTTACCACCAACACACATCTGA 1 TTGCTCAAACGAGCTTTACCACCAACACACATCTGA 98384276 TTGCTCAAACGAGCTTTACCACCAACACACATCTG 1 TTGCTCAAACGAGCTTTACCACCAACACACATCTG 98384311 GGCACTGAGT Statistics Matches: 35, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 36 35 1.00 ACGTcount: A:0.32, C:0.34, G:0.11, T:0.23 Consensus pattern (36 bp): TTGCTCAAACGAGCTTTACCACCAACACACATCTGA Found at i:98385948 original size:26 final size:27 Alignment explanation

Indices: 98385905--98385955 Score: 70 Period size: 26 Copynumber: 1.9 Consensus size: 27 98385895 TAATTAATAT 98385905 ACATTTAAATAATTATAATCAAAATCC 1 ACATTTAAATAATTATAATCAAAATCC * 98385932 ACATTATAAA-AA-TATAATTAAAAT 1 ACATT-TAAATAATTATAATCAAAAT 98385956 TTATTCCAAA Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 26 11 0.50 27 7 0.32 28 4 0.18 ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33 Consensus pattern (27 bp): ACATTTAAATAATTATAATCAAAATCC Found at i:98387311 original size:20 final size:20 Alignment explanation

Indices: 98387292--98387329 Score: 51 Period size: 20 Copynumber: 1.9 Consensus size: 20 98387282 TATATTAATA 98387292 AATTTAA-TATTATAAAAAT 1 AATTTAATTATTATAAAAAT * * 98387311 ACTTTAATTTTTATAAAAA 1 AATTTAATTATTATAAAAA 98387330 CCTAACCTCT Statistics Matches: 16, Mismatches: 2, Indels: 1 0.84 0.11 0.05 Matches are distributed among these distances: 19 6 0.38 20 10 0.62 ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45 Consensus pattern (20 bp): AATTTAATTATTATAAAAAT Found at i:98387607 original size:20 final size:19 Alignment explanation

Indices: 98387584--98387629 Score: 56 Period size: 21 Copynumber: 2.3 Consensus size: 19 98387574 TTAAAATGTA 98387584 AAATTATATTTTAAATTCTT 1 AAATTATATTTTAAATT-TT * * 98387604 AAATTTTTTTTTTAAATTTT 1 AAA-TTATATTTTAAATTTT 98387624 AAATTA 1 AAATTA 98387630 GTAAAAGTAA Statistics Matches: 22, Mismatches: 3, Indels: 3 0.79 0.11 0.11 Matches are distributed among these distances: 19 2 0.09 20 8 0.36 21 12 0.55 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (19 bp): AAATTATATTTTAAATTTT Found at i:98388134 original size:14 final size:16 Alignment explanation

Indices: 98388112--98388149 Score: 53 Period size: 14 Copynumber: 2.5 Consensus size: 16 98388102 TATGAATAAG 98388112 ATATAAAAT-ATTA-A 1 ATATAAAATCATTATA * 98388126 ATATTAAATCATTATA 1 ATATAAAATCATTATA 98388142 ATATAAAA 1 ATATAAAA 98388150 GTGACAAATT Statistics Matches: 20, Mismatches: 2, Indels: 2 0.83 0.08 0.08 Matches are distributed among these distances: 14 8 0.40 15 4 0.20 16 8 0.40 ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37 Consensus pattern (16 bp): ATATAAAATCATTATA Found at i:98388993 original size:3 final size:3 Alignment explanation

Indices: 98388985--98389013 Score: 58 Period size: 3 Copynumber: 9.7 Consensus size: 3 98388975 TTCTTAAAAC 98388985 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA 98389014 GCTTTAAAAA Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 26 1.00 ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66 Consensus pattern (3 bp): TAT Found at i:98390769 original size:5 final size:5 Alignment explanation

Indices: 98390759--98390786 Score: 56 Period size: 5 Copynumber: 5.6 Consensus size: 5 98390749 TTGTGTGTTC 98390759 TTTAT TTTAT TTTAT TTTAT TTTAT TTT 1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT 98390787 CACAAATTGG Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 5 23 1.00 ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82 Consensus pattern (5 bp): TTTAT Found at i:98395221 original size:5 final size:5 Alignment explanation

Indices: 98395207--98395243 Score: 67 Period size: 5 Copynumber: 7.6 Consensus size: 5 98395197 TTGTGTGTTC 98395207 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT 1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT 98395244 TCACAATATA Statistics Matches: 32, Mismatches: 0, Indels: 1 0.97 0.00 0.03 Matches are distributed among these distances: 4 4 0.12 5 28 0.88 ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81 Consensus pattern (5 bp): TTTAT Found at i:98397840 original size:27 final size:26 Alignment explanation

Indices: 98397780--98397841 Score: 63 Period size: 27 Copynumber: 2.3 Consensus size: 26 98397770 ATTTTATTTT 98397780 ATTTTATTAGGATAATTAATATTAAG 1 ATTTTATTAGGATAATTAATATTAAG * * * 98397806 ATAATTATTAGGATTATTCAA-ATTTAGG 1 AT-TTTATTAGGATAATT-AATA-TTAAG 98397834 ATTTTATT 1 ATTTTATT 98397842 TTAATTATCT Statistics Matches: 29, Mismatches: 4, Indels: 5 0.76 0.11 0.13 Matches are distributed among these distances: 26 2 0.07 27 19 0.66 28 8 0.28 ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48 Consensus pattern (26 bp): ATTTTATTAGGATAATTAATATTAAG Found at i:98404301 original size:7 final size:7 Alignment explanation

Indices: 98404291--98404361 Score: 67 Period size: 7 Copynumber: 10.0 Consensus size: 7 98404281 CTTTTTCTTT 98404291 TTATTTA 1 TTATTTA 98404298 TTATTTA 1 TTATTTA 98404305 TTATTT- 1 TTATTTA * * 98404311 TCCTTTCTTT 1 T--TAT-TTA 98404321 TTATTTA 1 TTATTTA 98404328 TTATTTA 1 TTATTTA 98404335 TTATTTA 1 TTATTTA 98404342 TTATTTTA 1 TTA-TTTA 98404350 TT-TTTA 1 TTATTTA 98404356 TT-TTTA 1 TTATTTA 98404362 GTTAAATATT Statistics Matches: 56, Mismatches: 3, Indels: 11 0.80 0.04 0.16 Matches are distributed among these distances: 6 11 0.20 7 32 0.57 8 10 0.18 9 2 0.04 10 1 0.02 ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75 Consensus pattern (7 bp): TTATTTA Found at i:98404318 original size:30 final size:30 Alignment explanation

Indices: 98404284--98404340 Score: 114 Period size: 30 Copynumber: 1.9 Consensus size: 30 98404274 TCTTTTTCTT 98404284 TTTCTTTTTATTTATTATTTATTATTTTCC 1 TTTCTTTTTATTTATTATTTATTATTTTCC 98404314 TTTCTTTTTATTTATTATTTATTATTT 1 TTTCTTTTTATTTATTATTTATTATTT 98404341 ATTATTTTAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 30 27 1.00 ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75 Consensus pattern (30 bp): TTTCTTTTTATTTATTATTTATTATTTTCC Found at i:98404338 original size:37 final size:36 Alignment explanation

Indices: 98404278--98404348 Score: 124 Period size: 37 Copynumber: 1.9 Consensus size: 36 98404268 AATCTTTCTT * 98404278 TTTCTTTTTCTTTTTATTTATTATTTATTATTTTCC 1 TTTCTTTTTATTTTTATTTATTATTTATTATTTTCC 98404314 TTTCTTTTTATTTATTATTTATTATTTATTATTTT 1 TTTCTTTTTATTT-TTATTTATTATTTATTATTTT 98404349 ATTTTTATTT Statistics Matches: 33, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 36 12 0.36 37 21 0.64 ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76 Consensus pattern (36 bp): TTTCTTTTTATTTTTATTTATTATTTATTATTTTCC Found at i:98405587 original size:9 final size:9 Alignment explanation

Indices: 98405575--98405608 Score: 52 Period size: 9 Copynumber: 3.8 Consensus size: 9 98405565 AATAAAATTT 98405575 AAAAAAATA 1 AAAAAAATA 98405584 AAAAAAATA 1 AAAAAAATA 98405593 AAAAAAA-A 1 AAAAAAATA 98405601 AAGAAAAA 1 AA-AAAAA 98405609 AATTACTAAT Statistics Matches: 24, Mismatches: 0, Indels: 2 0.92 0.00 0.08 Matches are distributed among these distances: 8 3 0.12 9 21 0.88 ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06 Consensus pattern (9 bp): AAAAAAATA Found at i:98405607 original size:17 final size:17 Alignment explanation

Indices: 98405574--98405607 Score: 52 Period size: 17 Copynumber: 2.0 Consensus size: 17 98405564 TAATAAAATT 98405574 TAAAAAAATAAAAAAAA 1 TAAAAAAATAAAAAAAA 98405591 TAAAAAAA-AAAAGAAAA 1 TAAAAAAATAAAA-AAAA 98405608 AAATTACTAA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 4 0.25 17 12 0.75 ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09 Consensus pattern (17 bp): TAAAAAAATAAAAAAAA Found at i:98406238 original size:27 final size:26 Alignment explanation

Indices: 98406178--98406239 Score: 63 Period size: 27 Copynumber: 2.3 Consensus size: 26 98406168 ATTTTATTTT 98406178 ATTTTATTAGGATAATTAATATTAAG 1 ATTTTATTAGGATAATTAATATTAAG * * * 98406204 ATAATTATTAGGATTATTCAA-ATTTAGG 1 AT-TTTATTAGGATAATT-AATA-TTAAG 98406232 ATTTTATT 1 ATTTTATT 98406240 TTAATTATCT Statistics Matches: 29, Mismatches: 4, Indels: 5 0.76 0.11 0.13 Matches are distributed among these distances: 26 2 0.07 27 19 0.66 28 8 0.28 ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48 Consensus pattern (26 bp): ATTTTATTAGGATAATTAATATTAAG Found at i:98406254 original size:10 final size:10 Alignment explanation

Indices: 98406235--98406266 Score: 57 Period size: 10 Copynumber: 3.3 Consensus size: 10 98406225 ATTTAGGATT 98406235 TTAT-TTTAA 1 TTATCTTTAA 98406244 TTATCTTTAA 1 TTATCTTTAA 98406254 TTATCTTTAA 1 TTATCTTTAA 98406264 TTA 1 TTA 98406267 AATGTATTTA Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 9 4 0.18 10 18 0.82 ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62 Consensus pattern (10 bp): TTATCTTTAA Found at i:98407368 original size:23 final size:21 Alignment explanation

Indices: 98407319--98407375 Score: 69 Period size: 23 Copynumber: 2.6 Consensus size: 21 98407309 AAGATATGAT * 98407319 ACTTGTGTGCATTTTATTGGC 1 ACTTGTGTGCATTTTATTAGC * 98407340 GCTTGTGTGCATTTATATTTAGC 1 ACTTGTGTGCATTT-TA-TTAGC * 98407363 ATTTGTGTGCATT 1 ACTTGTGTGCATT 98407376 CTTGAAGTGT Statistics Matches: 30, Mismatches: 4, Indels: 2 0.83 0.11 0.06 Matches are distributed among these distances: 21 13 0.43 22 2 0.07 23 15 0.50 ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49 Consensus pattern (21 bp): ACTTGTGTGCATTTTATTAGC Found at i:98413756 original size:6 final size:6 Alignment explanation

Indices: 98413738--98413770 Score: 57 Period size: 6 Copynumber: 5.3 Consensus size: 6 98413728 CGTCCAACCC 98413738 AAAATA GAAAATA AAAATA AAAATA AAAATA AA 1 AAAATA -AAAATA AAAATA AAAATA AAAATA AA 98413771 TAATTATAAA Statistics Matches: 26, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 6 20 0.77 7 6 0.23 ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15 Consensus pattern (6 bp): AAAATA Found at i:98422136 original size:41 final size:41 Alignment explanation

Indices: 98422087--98422170 Score: 159 Period size: 41 Copynumber: 2.0 Consensus size: 41 98422077 TAAGTCATTA 98422087 ATTAGCACTCAAGAAATCAAAATTTAAACTCCGTTATTGTC 1 ATTAGCACTCAAGAAATCAAAATTTAAACTCCGTTATTGTC * 98422128 ATTAGCACTCAAGAAATCAAAATTTAAATTCCGTTATTGTC 1 ATTAGCACTCAAGAAATCAAAATTTAAACTCCGTTATTGTC 98422169 AT 1 AT 98422171 ACTCTTTCCT Statistics Matches: 42, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 41 42 1.00 ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33 Consensus pattern (41 bp): ATTAGCACTCAAGAAATCAAAATTTAAACTCCGTTATTGTC Found at i:98422516 original size:18 final size:18 Alignment explanation

Indices: 98422493--98422533 Score: 82 Period size: 18 Copynumber: 2.3 Consensus size: 18 98422483 ATTTAGATTT 98422493 AATAGTTCAATTTTAAAA 1 AATAGTTCAATTTTAAAA 98422511 AATAGTTCAATTTTAAAA 1 AATAGTTCAATTTTAAAA 98422529 AATAG 1 AATAG 98422534 GTTTATGTAA Statistics Matches: 23, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37 Consensus pattern (18 bp): AATAGTTCAATTTTAAAA Found at i:98423352 original size:32 final size:30 Alignment explanation

Indices: 98423291--98423352 Score: 81 Period size: 30 Copynumber: 2.0 Consensus size: 30 98423281 ATTATTAAAA 98423291 TATTTTTATATATGTTATTATATTAATTAT 1 TATTTTTATATATGTTATTATATTAATTAT * 98423321 TATTTTTA-ATAATGTTACTTTTTATTAATTAT 1 TATTTTTATAT-ATGTTA--TTATATTAATTAT 98423353 ATGAAGTAAA Statistics Matches: 28, Mismatches: 1, Indels: 4 0.85 0.03 0.12 Matches are distributed among these distances: 29 2 0.07 30 14 0.50 32 12 0.43 ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63 Consensus pattern (30 bp): TATTTTTATATATGTTATTATATTAATTAT Found at i:98430834 original size:3 final size:3 Alignment explanation

Indices: 98430791--98430909 Score: 59 Period size: 3 Copynumber: 38.3 Consensus size: 3 98430781 TTTTTTAACC * * 98430791 TTA TTT TTA -TA TTA TATA TTA TAA TTA TT- TTA TTA TATA TTA TT- 1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA * * * 98430835 TATA TTA TTA TTA TCTA TTG TATA TTA TTT TTCA TAAA TTA TTA TT- 1 T-TA TTA TTA TTA T-TA TTA T-TA TTA TTA TT-A T-TA TTA TTA TTA * * 98430881 TTA -CA TTA TTA CTTA TATA TTG TTA TTA T 1 TTA TTA TTA TTA -TTA T-TA TTA TTA TTA T 98430910 GTTTTTACTT Statistics Matches: 88, Mismatches: 14, Indels: 28 0.68 0.11 0.22 Matches are distributed among these distances: 2 8 0.09 3 59 0.67 4 21 0.24 ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62 Consensus pattern (3 bp): TTA Found at i:98430926 original size:47 final size:46 Alignment explanation

Indices: 98430800--98430914 Score: 123 Period size: 47 Copynumber: 2.5 Consensus size: 46 98430790 CTTATTTTTA * * * 98430800 TATTATATATTATA-ATTA-TTTTAT-TATATATTA-TTTATATTAT 1 TATTATATATTGTATATTATTTTTATAAAT-TATTATTTTACATTAT * 98430843 TATTATCTATTGTATATTATTTTTCATAAATTATTATTTTACATTAT 1 TATTATATATTGTATATTATTTTT-ATAAATTATTATTTTACATTAT 98430890 TACTTATATATTGT-TATTATGTTTT 1 TA-TTATATATTGTATATTAT-TTTT 98430915 TACTTGTATT Statistics Matches: 60, Mismatches: 5, Indels: 9 0.81 0.07 0.12 Matches are distributed among these distances: 43 12 0.20 44 4 0.07 45 4 0.07 46 7 0.12 47 19 0.32 48 14 0.23 ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62 Consensus pattern (46 bp): TATTATATATTGTATATTATTTTTATAAATTATTATTTTACATTAT Found at i:98431369 original size:30 final size:29 Alignment explanation

Indices: 98431310--98431371 Score: 74 Period size: 29 Copynumber: 2.1 Consensus size: 29 98431300 CATTATATTT * 98431310 TATATTTTATATAATATTATTCTTATAAA 1 TATATTTTATATAATATTATTATTATAAA 98431339 TATATTTT-TATTATATATTA-TATTATTAAA 1 TATATTTTATA-TA-ATATTATTATTA-TAAA 98431369 TAT 1 TAT 98431372 CACATTTTTT Statistics Matches: 29, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 28 2 0.07 29 14 0.48 30 13 0.45 ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58 Consensus pattern (29 bp): TATATTTTATATAATATTATTATTATAAA Found at i:98435086 original size:13 final size:14 Alignment explanation

Indices: 98435068--98435096 Score: 51 Period size: 13 Copynumber: 2.1 Consensus size: 14 98435058 AAGATATTCT 98435068 TTTTCTAAAT-AAA 1 TTTTCTAAATGAAA 98435081 TTTTCTAAATGAAA 1 TTTTCTAAATGAAA 98435095 TT 1 TT 98435097 GAATCAGAAT Statistics Matches: 15, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 13 10 0.67 14 5 0.33 ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48 Consensus pattern (14 bp): TTTTCTAAATGAAA Found at i:98443946 original size:206 final size:205 Alignment explanation

Indices: 98443232--98443987 Score: 1208 Period size: 205 Copynumber: 3.7 Consensus size: 205 98443222 AGATGCTTGT * * * 98443232 ACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGTACTTACAAGGAAAAAAATCGAAGACATAGC 1 ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGG-AACAAATCGAAGACATAGC ** * * 98443297 TGATTTGGCTTTCACGTATTTACGTTGAAGCAAATCTAGGATGATTTGGCATCTCTGTATTGTTA 65 TGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCA * * * * 98443362 GAGAACAAATCGAAGTCTGGCATCTCCATTTCAACGTAGAACAGATACATAGCAGATCTCACCTT 130 GAGAACAAATCGAAGTCTGGAATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTCACCTT 98443427 CAGATGATCTC 195 CAGATGATCTC * 98443438 ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTTCTTACAAGGAACAAATCGAAGACATAGCT 1 ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT * 98443503 GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGTATCTCTGTATTGTCAG 66 GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG * * 98443568 AGAACAAATCGAAGTCTGGTATCTCCATTTCGACGGAGAGCAGATACATAACAGATCTCACCTTC 131 AGAACAAATCGAAGTCTGGAATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTCACCTTC 98443633 AGATGATCTC 196 AGATGATCTC * * * 98443643 ACTAAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGGAACAAATCGAAGCCATAGCT 1 ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT 98443708 GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG 66 GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG * * * * 98443773 AGAACAAATCGAAGTCTGGAATCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTT 131 AGAACAAATCGAAGTCTGGAATCTCCAT-TTCGACGGAGAGCAGATACATAGCAGATCTCACCTT * * 98443838 CAAATGAT-TAG 195 CAGATGATCT-C * * * * 98443849 AATGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCT 1 ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT * * 98443914 GATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG 66 GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG 98443979 AGAACAAAT 131 AGAACAAAT 98443988 TAAAGAAGCA Statistics Matches: 513, Mismatches: 35, Indels: 4 0.93 0.06 0.01 Matches are distributed among these distances: 205 302 0.59 206 211 0.41 ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29 Consensus pattern (205 bp): ACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT GATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG AGAACAAATCGAAGTCTGGAATCTCCATTTCGACGGAGAGCAGATACATAGCAGATCTCACCTTC AGATGATCTC Found at i:98443969 original size:411 final size:411 Alignment explanation

Indices: 98443236--98443987 Score: 1229 Period size: 411 Copynumber: 1.8 Consensus size: 411 98443226 GCTTGTACTG * 98443236 AAGCAGATCCAAGATGGTTTGGCATCCTTGTACTTACAAGGAAAAAAATCGAAGACATAGCTGAT 1 AAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAAAAAAATCGAAGACATAGCTGAT * * * 98443301 TTGGCTTTCACGTATTTACGTTGAAGCAAATCTAGGATGATTTGGCATCTCTGTATTGTTAGAGA 66 TTGGCTTTCACGTACTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA * * * * * 98443366 ACAAATCGAAGTCTGGCATCTCCATTTCAACGTAGAACAGATACATAGCAGATCTCACCTTCAGA 131 ACAAATCGAAGTCTGGAATCTCCATTTCAACGGAGAACAGACACATAGCAGATCTAACCTTCAAA * * 98443431 TGATCTCACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTTCTTACAAGGAACAAATCGAAGA 196 TGATCTCAATGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA * * 98443496 CATAGCTGATTTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGTATCTCTGTA 261 CATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTA 98443561 TTGTCAGAGAACAAATCGAAGTCTGGTATCTCCATTTCGACGGAGAGCAGATACATAACAGATCT 326 TTGTCAGAGAACAAATCGAAGTCTGGTATCTCCATTTCGACGGAGAGCAGATACATAACAGATCT 98443626 CACCTTCAGATGATCTCACTA 391 CACCTTCAGATGATCTCACTA ** * * 98443647 AAGCAGATCCAAGATGATTTGGCATCCTTGTGTTTACAAGG-AACAAATCGAAGCCATAGCTGAT 1 AAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAAAAAAATCGAAGACATAGCTGAT * 98443711 TTGGCTTTCACGTGCTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA 66 TTGGCTTTCACGTACTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA * * ** 98443776 ACAAATCGAAGTCTGGAATCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTCAA 131 ACAAATCGAAGTCTGGAATCTCCAT-TTCAACGGAGAACAGACACATAGCAGATCTAACCTTCAA * * * * 98443841 ATGAT-TAGAATGAAGTAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAA 195 ATGATCT-CAATGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA * 98443905 GACATAGCTGATTTGGTTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTG 259 GACATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTG 98443970 TATTGTCAGAGAACAAAT 324 TATTGTCAGAGAACAAAT 98443988 TAAAGAAGCA Statistics Matches: 312, Mismatches: 27, Indels: 4 0.91 0.08 0.01 Matches are distributed among these distances: 410 107 0.34 411 205 0.66 ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29 Consensus pattern (411 bp): AAGCAGATCCAAGATGATTTGGCATCCTTGTACTTACAAGGAAAAAAATCGAAGACATAGCTGAT TTGGCTTTCACGTACTTACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGA ACAAATCGAAGTCTGGAATCTCCATTTCAACGGAGAACAGACACATAGCAGATCTAACCTTCAAA TGATCTCAATGAAGCAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGA CATAGCTGATTTGGCTTTCACGTGCTTACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTA TTGTCAGAGAACAAATCGAAGTCTGGTATCTCCATTTCGACGGAGAGCAGATACATAACAGATCT CACCTTCAGATGATCTCACTA Found at i:98445628 original size:7 final size:7 Alignment explanation

Indices: 98445616--98445744 Score: 70 Period size: 7 Copynumber: 18.1 Consensus size: 7 98445606 ACCTTATTTT 98445616 TATATTA 1 TATATTA 98445623 TATATTA 1 TATATTA 98445630 TA-ATTA 1 TATATTA * 98445636 TTTTATTA 1 -TATATTA 98445644 TATATTA 1 TATATTA 98445651 TTTATATTA 1 --TATATTA 98445660 T-TATTA 1 TATATTA * * 98445666 TCTATTG 1 TATATTA * 98445673 TATATTG 1 TATATTA * 98445680 TATATTG 1 TATATTA * 98445687 TATATTG 1 TATATTA * 98445694 T-TTTTCA 1 TATATT-A * 98445701 TAAATTA 1 TATATTA * 98445708 TTATTATTT 1 -TA-TATTA * 98445717 TACATTA 1 TATATTA 98445724 T-TACTTA 1 TATA-TTA 98445731 TATATTA 1 TATATTA 98445738 T-TATTA 1 TATATTA 98445744 T 1 T 98445745 GTTTTTACTT Statistics Matches: 98, Mismatches: 13, Indels: 23 0.73 0.10 0.17 Matches are distributed among these distances: 6 20 0.20 7 56 0.57 8 12 0.12 9 10 0.10 ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60 Consensus pattern (7 bp): TATATTA Found at i:98445647 original size:16 final size:16 Alignment explanation

Indices: 98445618--98445666 Score: 68 Period size: 15 Copynumber: 3.2 Consensus size: 16 98445608 CTTATTTTTA 98445618 TATTATATATTATA-AT 1 TATT-TATATTATATAT 98445634 TATTT-TATTATATAT 1 TATTTATATTATATAT 98445649 TATTTATATTAT-TAT 1 TATTTATATTATATAT 98445664 TAT 1 TAT 98445667 CTATTGTATA Statistics Matches: 31, Mismatches: 0, Indels: 5 0.86 0.00 0.14 Matches are distributed among these distances: 14 7 0.23 15 14 0.45 16 10 0.32 ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63 Consensus pattern (16 bp): TATTTATATTATATAT Found at i:98445671 original size:19 final size:18 Alignment explanation

Indices: 98445609--98445678 Score: 72 Period size: 19 Copynumber: 3.8 Consensus size: 18 98445599 TTTTTTAACC 98445609 TTATT-TTTATATTATATA 1 TTATTATTTATATTAT-TA * * 98445627 TTA-TAATTATTTTATTA 1 TTATTATTTATATTATTA 98445644 TATATTATTTATATTATTA 1 T-TATTATTTATATTATTA 98445663 TTATCTATTGTATATT 1 TTAT-TATT-TATATT 98445679 GTATATTGTA Statistics Matches: 43, Mismatches: 4, Indels: 8 0.78 0.07 0.15 Matches are distributed among these distances: 17 4 0.09 18 16 0.37 19 17 0.40 20 6 0.14 ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64 Consensus pattern (18 bp): TTATTATTTATATTATTA Found at i:98446168 original size:17 final size:18 Alignment explanation

Indices: 98446148--98446203 Score: 64 Period size: 17 Copynumber: 3.2 Consensus size: 18 98446138 TTATATTTTA 98446148 TATTTTTATATAAT-TAT 1 TATTTTTATATAATATAT * 98446165 TATTCTTATA-AATATAT 1 TATTTTTATATAATATAT * 98446182 T-TTTATTATATATTATAT 1 TATTT-TTATATAATATAT 98446200 TATT 1 TATT 98446204 AAATATCACA Statistics Matches: 32, Mismatches: 3, Indels: 6 0.78 0.07 0.15 Matches are distributed among these distances: 16 5 0.16 17 18 0.56 18 7 0.22 19 2 0.06 ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62 Consensus pattern (18 bp): TATTTTTATATAATATAT Found at i:98446202 original size:15 final size:16 Alignment explanation

Indices: 98446137--98446209 Score: 60 Period size: 17 Copynumber: 4.6 Consensus size: 16 98446127 TTTCTAAACC * 98446137 ATTATATTTTA-TATT 1 ATTATATATTATTATT * 98446152 TTTATATAATTATTATT 1 ATTATAT-ATTATTATT * * * 98446169 CTTATAAATATATTTTT 1 ATTATATAT-TATTATT 98446186 ATTATATATTA-TATT 1 ATTATATATTATTATT * 98446201 ATTAAATAT 1 ATTATATAT 98446210 CACATTTTTT Statistics Matches: 46, Mismatches: 9, Indels: 6 0.75 0.15 0.10 Matches are distributed among these distances: 15 17 0.37 16 7 0.15 17 22 0.48 ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60 Consensus pattern (16 bp): ATTATATATTATTATT Found at i:98446207 original size:30 final size:31 Alignment explanation

Indices: 98446146--98446209 Score: 80 Period size: 31 Copynumber: 2.1 Consensus size: 31 98446136 CATTATATTT * 98446146 TATATTTTTATATAATTATTATTCTTATAAA 1 TATATTTTTATATAATTATTATTCATATAAA 98446177 TATATTTTTATTATATATTA-TATT-AT-TAAA 1 TATATTTTTA-TATA-ATTATTATTCATATAAA 98446207 TAT 1 TAT 98446210 CACATTTTTT Statistics Matches: 30, Mismatches: 1, Indels: 5 0.83 0.03 0.14 Matches are distributed among these distances: 30 7 0.23 31 11 0.37 32 8 0.27 33 4 0.13 ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59 Consensus pattern (31 bp): TATATTTTTATATAATTATTATTCATATAAA Found at i:98460056 original size:19 final size:19 Alignment explanation

Indices: 98460032--98460069 Score: 76 Period size: 19 Copynumber: 2.0 Consensus size: 19 98460022 AAGGAAAATC 98460032 ATTACAATTAATTAAATTA 1 ATTACAATTAATTAAATTA 98460051 ATTACAATTAATTAAATTA 1 ATTACAATTAATTAAATTA 98460070 TATGATCTTC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 19 1.00 ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42 Consensus pattern (19 bp): ATTACAATTAATTAAATTA Found at i:98467059 original size:22 final size:23 Alignment explanation

Indices: 98467008--98467059 Score: 54 Period size: 22 Copynumber: 2.3 Consensus size: 23 98466998 CTTTTATTTA * * 98467008 TATAAATAAAATAATAAATATGT 1 TATATATAAAATAATAAATATAT * * 98467031 AAT-TATACAATAA-AAATATAT 1 TATATATAAAATAATAAATATAT 98467052 TATATATA 1 TATATATA 98467060 TATGATTATG Statistics Matches: 23, Mismatches: 5, Indels: 3 0.74 0.16 0.10 Matches are distributed among these distances: 21 9 0.39 22 12 0.52 23 2 0.09 ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37 Consensus pattern (23 bp): TATATATAAAATAATAAATATAT Found at i:98467091 original size:97 final size:97 Alignment explanation

Indices: 98466984--98467179 Score: 302 Period size: 97 Copynumber: 2.0 Consensus size: 97 98466974 AATTCATCTA ** 98466984 TTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATATGTAATTATACAATAAAAATA 1 TTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATACATAATTATACAATAAAAATA * 98467049 TATTATATATATATGATTATGTTAAAAATATT 66 TATTATATATATATCATTATGTTAAAAATATT * * * 98467081 TTTAATTAATAACTCTTTTATTTATATAAATAAATTAATAATTACATAATTATATAATAAAAATA 1 TTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATACATAATTATACAATAAAAATA * * * * 98467146 TTTTTTATATTTATCATTATGTTAAATATATT 66 TATTATATATATATCATTATGTTAAAAATATT 98467178 TT 1 TT 98467180 ATTTTTAAAA Statistics Matches: 89, Mismatches: 10, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 97 89 1.00 ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48 Consensus pattern (97 bp): TTTAATTAATAACTCTTTTATTTATATAAATAAAATAATAAATACATAATTATACAATAAAAATA TATTATATATATATCATTATGTTAAAAATATT Found at i:98467509 original size:13 final size:15 Alignment explanation

Indices: 98467479--98467510 Score: 50 Period size: 13 Copynumber: 2.3 Consensus size: 15 98467469 TATTTTTTTA 98467479 TAATAGAAATATAAG 1 TAATAGAAATATAAG 98467494 TAATA-AAATA-AAG 1 TAATAGAAATATAAG 98467507 TAAT 1 TAAT 98467511 TACAACATTT Statistics Matches: 17, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 13 7 0.41 14 5 0.29 15 5 0.29 ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28 Consensus pattern (15 bp): TAATAGAAATATAAG Found at i:98468092 original size:3 final size:3 Alignment explanation

Indices: 98468084--98468119 Score: 72 Period size: 3 Copynumber: 12.0 Consensus size: 3 98468074 ACCATCTCTA 98468084 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT 98468120 TTGATTACAA Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 33 1.00 ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67 Consensus pattern (3 bp): ATT Found at i:98470379 original size:26 final size:26 Alignment explanation

Indices: 98470342--98470392 Score: 84 Period size: 26 Copynumber: 2.0 Consensus size: 26 98470332 TTGACGTGAT * 98470342 AAATGATATAGATGTGATATGTTGAC 1 AAATGATATAGATGTGACATGTTGAC * 98470368 AAATGATGTAGATGTGACATGTTGA 1 AAATGATATAGATGTGACATGTTGA 98470393 TATGTAATGT Statistics Matches: 23, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 26 23 1.00 ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33 Consensus pattern (26 bp): AAATGATATAGATGTGACATGTTGAC Found at i:98470555 original size:9 final size:9 Alignment explanation

Indices: 98470543--98470658 Score: 82 Period size: 9 Copynumber: 12.7 Consensus size: 9 98470533 TTAATTTTTT 98470543 TAAAAATTA 1 TAAAAATTA 98470552 TAAAAATTA 1 TAAAAATTA 98470561 TTAAAAATT- 1 -TAAAAATTA 98470570 TAAAAATGTTA 1 TAAAAA--TTA * 98470581 TAGAAATT- 1 TAAAAATTA * * 98470589 TGAATATT- 1 TAAAAATTA 98470597 TAAAAATTA 1 TAAAAATTA 98470606 TAAAAA-TA 1 TAAAAATTA 98470614 -AAAAATATA 1 TAAAAAT-TA * 98470623 TTAATAATT- 1 -TAAAAATTA 98470632 TATAAAATTA 1 TA-AAAATTA 98470642 TAACAAATTGA 1 TAA-AAATT-A 98470653 TAAAAA 1 TAAAAA 98470659 AGTGCCATGA Statistics Matches: 86, Mismatches: 8, Indels: 25 0.72 0.07 0.21 Matches are distributed among these distances: 7 5 0.06 8 21 0.24 9 25 0.29 10 21 0.24 11 14 0.16 ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35 Consensus pattern (9 bp): TAAAAATTA Found at i:98471137 original size:12 final size:12 Alignment explanation

Indices: 98471120--98471153 Score: 54 Period size: 11 Copynumber: 3.0 Consensus size: 12 98471110 CCGGCCCGCC 98471120 TATATTAATTTT 1 TATATTAATTTT 98471132 TATATT-ATTTT 1 TATATTAATTTT 98471143 TATA-TAATTTT 1 TATATTAATTTT 98471154 AAAATATATA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 10 1 0.05 11 14 0.67 12 6 0.29 ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68 Consensus pattern (12 bp): TATATTAATTTT Found at i:98471414 original size:11 final size:11 Alignment explanation

Indices: 98471376--98471415 Score: 53 Period size: 11 Copynumber: 3.6 Consensus size: 11 98471366 AATAACAACA 98471376 AAAATAGTAGC 1 AAAATAGTAGC * * * 98471387 AACATAATAGT 1 AAAATAGTAGC 98471398 AAAATAGTAGC 1 AAAATAGTAGC 98471409 AAAATAG 1 AAAATAG 98471416 GGAGAAAACA Statistics Matches: 23, Mismatches: 6, Indels: 0 0.79 0.21 0.00 Matches are distributed among these distances: 11 23 1.00 ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20 Consensus pattern (11 bp): AAAATAGTAGC Found at i:98474363 original size:18 final size:17 Alignment explanation

Indices: 98474320--98474366 Score: 51 Period size: 18 Copynumber: 2.6 Consensus size: 17 98474310 TTTTTTATAA 98474320 ATTTTTAT-AATTCTTT 1 ATTTTTATAAATTCTTT * 98474336 ATAATGTTATAAATTTCTTT 1 AT--TTTTATAAA-TTCTTT 98474356 ATTTTTATAAA 1 ATTTTTATAAA 98474367 CTTTTAATAT Statistics Matches: 25, Mismatches: 2, Indels: 6 0.76 0.06 0.18 Matches are distributed among these distances: 16 2 0.08 18 13 0.52 19 2 0.08 20 8 0.32 ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60 Consensus pattern (17 bp): ATTTTTATAAATTCTTT Found at i:98474958 original size:141 final size:141 Alignment explanation

Indices: 98474740--98475002 Score: 402 Period size: 141 Copynumber: 1.9 Consensus size: 141 98474730 TTGTTTTTTC ** ** * * 98474740 TTCTTCTTCCTTCTTCCTCTTGTCACTTTGCCTTTTTCTTTTATGGGTTCTTTCAGTATTTTTGG 1 TTCTTCTTCCTTCTTCCTCTTGTCACTTTGCCTTTTTCTTTTATAAGTTCTTTCAACATTTCTGA * * 98474805 ATTGCTTTGAAAAGAAATTTAAGAACATTTCTATG-TTTATTTTTTCTCTTATTCCTTTTTTTTT 66 ATTGCTTAGAAAAGAAATTTAAGAACATTTCTA-GATTCATTTTTTCTCTTATTCCTTTTTTTTT 98474869 TCGATAATTCAT 130 TCGATAATTCAT * 98474881 TTCTTCTTCCTTCTTCCTCTTGTCACTTTGCCTTTTTCTTTTCTAAGTTCTTTCAACATTTCTGA 1 TTCTTCTTCCTTCTTCCTCTTGTCACTTTGCCTTTTTCTTTTATAAGTTCTTTCAACATTTCTGA * * * 98474946 ATTGCTTAGAAAAGAAATTTAAGAACATTTTTAGATTCATTTTTTTTCTTCTTCCTT 66 ATTGCTTAGAAAAGAAATTTAAGAACATTTCTAGATTCATTTTTTCTCTTATTCCTT 98475003 CTTCCTCTCA Statistics Matches: 109, Mismatches: 12, Indels: 2 0.89 0.10 0.02 Matches are distributed among these distances: 140 1 0.01 141 108 0.99 ACGTcount: A:0.18, C:0.19, G:0.09, T:0.54 Consensus pattern (141 bp): TTCTTCTTCCTTCTTCCTCTTGTCACTTTGCCTTTTTCTTTTATAAGTTCTTTCAACATTTCTGA ATTGCTTAGAAAAGAAATTTAAGAACATTTCTAGATTCATTTTTTCTCTTATTCCTTTTTTTTTT CGATAATTCAT Found at i:98482400 original size:19 final size:19 Alignment explanation

Indices: 98482373--98482412 Score: 71 Period size: 19 Copynumber: 2.1 Consensus size: 19 98482363 ATAGGAGCAA * 98482373 CACTTGATGAACAATCTTT 1 CACTCGATGAACAATCTTT 98482392 CACTCGATGAACAATCTTT 1 CACTCGATGAACAATCTTT 98482411 CA 1 CA 98482413 TCCAAAATCT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33 Consensus pattern (19 bp): CACTCGATGAACAATCTTT Found at i:98493579 original size:5 final size:5 Alignment explanation

Indices: 98493553--98493610 Score: 62 Period size: 5 Copynumber: 10.8 Consensus size: 5 98493543 ATGTGTTAAA * * 98493553 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATTAT ATATT ATATT 1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATA-T-T ATATT ATATT 98493602 ATATT ATAT 1 ATATT ATAT 98493611 AAATAAGTAA Statistics Matches: 45, Mismatches: 4, Indels: 7 0.80 0.07 0.12 Matches are distributed among these distances: 5 32 0.71 6 9 0.20 7 4 0.09 ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55 Consensus pattern (5 bp): ATATT Found at i:98493589 original size:10 final size:9 Alignment explanation

Indices: 98493554--98493611 Score: 61 Period size: 8 Copynumber: 6.7 Consensus size: 9 98493544 TGTGTTAAAA 98493554 TATATATAT 1 TATATATAT * 98493563 TAAAT-TAT 1 TATATATAT 98493571 TAT-TATAT 1 TATATATAT 98493579 TATAGTATA- 1 TATA-TATAT 98493588 T-TATATAT 1 TATATATAT 98493596 TATATTATAT 1 TATA-TATAT 98493606 TATATA 1 TATATA 98493612 AATAAGTAAA Statistics Matches: 41, Mismatches: 2, Indels: 12 0.75 0.04 0.22 Matches are distributed among these distances: 7 5 0.12 8 14 0.34 9 9 0.22 10 13 0.32 ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55 Consensus pattern (9 bp): TATATATAT Found at i:98493596 original size:17 final size:17 Alignment explanation

Indices: 98493556--98493611 Score: 71 Period size: 17 Copynumber: 3.4 Consensus size: 17 98493546 TGTTAAAATA 98493556 TATATATTA-AAT-TAT 1 TATATATTATAATATAT * 98493571 TATTATATTATAGTATAT 1 TA-TATATTATAATATAT * 98493589 TATATATTATATTATAT 1 TATATATTATAATATAT 98493606 TATATA 1 TATATA 98493612 AATAAGTAAA Statistics Matches: 36, Mismatches: 2, Indels: 4 0.86 0.05 0.10 Matches are distributed among these distances: 15 2 0.06 16 7 0.19 17 22 0.61 18 5 0.14 ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55 Consensus pattern (17 bp): TATATATTATAATATAT Found at i:98494955 original size:18 final size:19 Alignment explanation

Indices: 98494932--98494970 Score: 62 Period size: 18 Copynumber: 2.1 Consensus size: 19 98494922 ATATATAGAT 98494932 ATATATATTGAATA-TTGA 1 ATATATATTGAATATTTGA * 98494950 ATATATATTGATTATTTGA 1 ATATATATTGAATATTTGA 98494969 AT 1 AT 98494971 TGAATTGAAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 18 13 0.68 19 6 0.32 ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49 Consensus pattern (19 bp): ATATATATTGAATATTTGA Found at i:98495256 original size:41 final size:41 Alignment explanation

Indices: 98495208--98495308 Score: 104 Period size: 38 Copynumber: 2.5 Consensus size: 41 98495198 TCGACCTCGA * 98495208 GTCGATGAGACACTGGGTGTCACTATA-TTT-CTTCGGATAG 1 GTCGATGAGACACTGGGTGTCACCA-ACTTTACTTCGGATAG * ** 98495248 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGATAG 1 -GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG * 98495287 GCCGATGAGACACTGGGTGTCA 1 GTCGATGAGACACTGGGTGTCA 98495309 AATATTGCTT Statistics Matches: 47, Mismatches: 8, Indels: 10 0.72 0.12 0.15 Matches are distributed among these distances: 37 1 0.02 38 16 0.34 39 14 0.30 40 4 0.09 41 12 0.26 ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29 Consensus pattern (41 bp): GTCGATGAGACACTGGGTGTCACCAACTTTACTTCGGATAG Found at i:98495488 original size:18 final size:19 Alignment explanation

Indices: 98495467--98495507 Score: 59 Period size: 19 Copynumber: 2.2 Consensus size: 19 98495457 AATGAAATGA 98495467 GAAATTGA-AT-TGAGAATT 1 GAAATTGAGATATGAG-ATT 98495485 GAAATTGAGATATGAGATT 1 GAAATTGAGATATGAGATT 98495504 GAAA 1 GAAA 98495508 ACATGAACCA Statistics Matches: 21, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 18 8 0.38 19 9 0.43 20 4 0.19 ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29 Consensus pattern (19 bp): GAAATTGAGATATGAGATT Found at i:98504319 original size:25 final size:25 Alignment explanation

Indices: 98504285--98504343 Score: 84 Period size: 25 Copynumber: 2.4 Consensus size: 25 98504275 TAAAATCAAT 98504285 TGAAA-GGTGCGTGATGGAAACAAC 1 TGAAACGGTGCGTGATGGAAACAAC * * * 98504309 TGAAACGGTGCGTGGTGGGAACAAT 1 TGAAACGGTGCGTGATGGAAACAAC 98504334 TGAAACGGTG 1 TGAAACGGTG 98504344 AGTTTTGAAT Statistics Matches: 31, Mismatches: 3, Indels: 1 0.89 0.09 0.03 Matches are distributed among these distances: 24 5 0.16 25 26 0.84 ACGTcount: A:0.32, C:0.12, G:0.37, T:0.19 Consensus pattern (25 bp): TGAAACGGTGCGTGATGGAAACAAC Found at i:98505566 original size:7 final size:7 Alignment explanation

Indices: 98505554--98505675 Score: 68 Period size: 7 Copynumber: 17.1 Consensus size: 7 98505544 ACTAATTAAT 98505554 CTAAACC 1 CTAAACC 98505561 CTAAACC 1 CTAAACC * 98505568 TCTTAACCC 1 -C-TAAACC * 98505577 CT-ATCC 1 CTAAACC ** 98505583 CATAAATA 1 C-TAAACC * 98505591 CTAAACT 1 CTAAACC 98505598 CTAAACC 1 CTAAACC * 98505605 CTTAACC 1 CTAAACC 98505612 CTAAACC 1 CTAAACC ** * 98505619 CTTGCATC 1 C-TAAACC * 98505627 TTAAACC 1 CTAAACC 98505634 CT-AACC 1 CTAAACC * 98505640 CTAACCC 1 CTAAACC 98505647 CTAAACC 1 CTAAACC * 98505654 CTAAATC 1 CTAAACC * * 98505661 ATAATCC 1 CTAAACC 98505668 CTAAACC 1 CTAAACC 98505675 C 1 C 98505676 GTAATTCATC Statistics Matches: 83, Mismatches: 26, Indels: 12 0.69 0.21 0.10 Matches are distributed among these distances: 6 10 0.12 7 61 0.73 8 7 0.08 9 5 0.06 ACGTcount: A:0.37, C:0.39, G:0.01, T:0.23 Consensus pattern (7 bp): CTAAACC Found at i:98505725 original size:7 final size:7 Alignment explanation

Indices: 98505713--98505810 Score: 61 Period size: 7 Copynumber: 13.4 Consensus size: 7 98505703 AGTTAACTCC * 98505713 TAAACCT 1 TAAACCA * 98505720 TAAACCC 1 TAAACCA 98505727 TAAACCA 1 TAAACCA * * * 98505734 TATATCT 1 TAAACCA 98505741 TAAACCA 1 TAAACCA 98505748 TAGTTAACTCA 1 TA---AAC-CA * 98505759 TAAACCT 1 TAAACCA * 98505766 TAAACCC 1 TAAACCA 98505773 TAAACCA 1 TAAACCA * * * 98505780 TATATCT 1 TAAACCA 98505787 TAAACCA 1 TAAACCA 98505794 TAAACCA 1 TAAACCA * 98505801 TAAACTA 1 TAAACCA 98505808 TAA 1 TAA 98505811 TAATAATTAA Statistics Matches: 69, Mismatches: 18, Indels: 8 0.73 0.19 0.08 Matches are distributed among these distances: 7 59 0.86 8 3 0.04 10 3 0.04 11 4 0.06 ACGTcount: A:0.47, C:0.26, G:0.01, T:0.27 Consensus pattern (7 bp): TAAACCA Found at i:98505744 original size:21 final size:21 Alignment explanation

Indices: 98505718--98505802 Score: 98 Period size: 21 Copynumber: 3.9 Consensus size: 21 98505708 ACTCCTAAAC * 98505718 CTTAAACCCTAAACCATATAT 1 CTTAAACCATAAACCATATAT * * 98505739 CTTAAACCATAGTTAACTCATAAAC 1 CTTAAACCATA---AAC-CATATAT * 98505764 CTTAAACCCTAAACCATATAT 1 CTTAAACCATAAACCATATAT 98505785 CTTAAACCATAAACCATA 1 CTTAAACCATAAACCATA 98505803 AACTATAATA Statistics Matches: 53, Mismatches: 7, Indels: 8 0.78 0.10 0.12 Matches are distributed among these distances: 21 32 0.60 22 3 0.06 24 3 0.06 25 15 0.28 ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27 Consensus pattern (21 bp): CTTAAACCATAAACCATATAT Found at i:98505755 original size:46 final size:46 Alignment explanation

Indices: 98505702--98505795 Score: 179 Period size: 46 Copynumber: 2.0 Consensus size: 46 98505692 CTTCAAATAC * 98505702 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA 1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA 98505748 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA 1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA 98505794 TA 1 TA 98505796 AACCATAAAC Statistics Matches: 47, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 46 47 1.00 ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29 Consensus pattern (46 bp): TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA Found at i:98507122 original size:34 final size:35 Alignment explanation

Indices: 98507078--98507144 Score: 100 Period size: 34 Copynumber: 1.9 Consensus size: 35 98507068 CAGTAAAATA * 98507078 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC 1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC * * 98507112 TTTTCTGTAAAATGATTTACTGGAAAATATTTT 1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT 98507145 CTGGTGTTTG Statistics Matches: 29, Mismatches: 3, Indels: 1 0.88 0.09 0.03 Matches are distributed among these distances: 34 17 0.59 35 12 0.41 ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45 Consensus pattern (35 bp): TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC Found at i:98516712 original size:86 final size:85 Alignment explanation

Indices: 98516563--98516822 Score: 386 Period size: 86 Copynumber: 3.1 Consensus size: 85 98516553 CCACTGCTGA * 98516563 TTTGCAGTTA-TAGCCACTTGTTGTCG-GTGCACAACATATTTGTAGATTAAACAAACTGCCACT 1 TTTGCAGTTACT-GCCACTTGTTGT-GAGTGCACAACATATTTGTAGATTAAACAAACTACCACT 98516626 TGGTTCGTGATTGAACCACATTG 64 TGGTTCGTGATTGAACCACA-TG * * * 98516649 TTTTCAGTTACTGCCACTTTTTGTGAGTGCACAACATATTTGCAGATTAAACAAACTACCACTTG 1 TTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTACCACTTG * 98516714 GTTCGTGA-T--ACCACATA 66 GTTCGTGATTGAACCACATG * 98516731 TTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTATAGATTAAACAAACTACCACTTG 1 TTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTACCACTTG * 98516796 GTTTGTGATTGAACCACACTG 66 GTTCGTGATTGAACCACA-TG 98516817 TTTGCA 1 TTTGCA 98516823 AATTAAACTG Statistics Matches: 157, Mismatches: 11, Indels: 12 0.87 0.06 0.07 Matches are distributed among these distances: 82 69 0.44 83 7 0.04 85 8 0.05 86 72 0.46 87 1 0.01 ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34 Consensus pattern (85 bp): TTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTACCACTTG GTTCGTGATTGAACCACATG Found at i:98518567 original size:21 final size:22 Alignment explanation

Indices: 98518528--98518593 Score: 64 Period size: 21 Copynumber: 3.0 Consensus size: 22 98518518 TTTCTTTTTA * 98518528 AATTAATTAATATAATAATAC-AT 1 AATTAATT-AT-TTATAATACTAT * * 98518551 GATTATATTATTT-TAATACTTT 1 AATTA-ATTATTTATAATACTAT 98518573 AATTAATTATTTATAATACTA 1 AATTAATTATTTATAATACTA 98518594 ATTTCGGTAT Statistics Matches: 35, Mismatches: 5, Indels: 7 0.74 0.11 0.15 Matches are distributed among these distances: 21 13 0.37 22 13 0.37 23 6 0.17 24 3 0.09 ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48 Consensus pattern (22 bp): AATTAATTATTTATAATACTAT Done.