Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.04

Sequence: scaffold121

Parameters: 2 7 7 80 10 50 500

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

Length: 1096690
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30

Warning! 96926 characters in sequence are not A, C, G, or T


File 2 of 3

Found at i:1356 original size:53 final size:53

Alignment explanation

Indices: 1293--1446 Score: 258 Period size: 51 Copynumber: 2.9 Consensus size: 53 1283 CTTTTTGCAT * 1293 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAAGAATTTTACAA 1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA * 1346 AATCCTTGTTGTCAAG--TTTTTGTATACAAGGTAGGTTCAATAATTTTACAA 1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA * * 1397 AATCCTTGTAGTCAAATTTTTTTGTATACAAGGTAGGTACAATAATTTTA 1 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTA 1447 ACATAACAAA Statistics Matches: 94, Mismatches: 5, Indels: 4 0.91 0.05 0.04 Matches are distributed among these distances: 51 47 0.50 53 47 0.50 ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41 Consensus pattern (53 bp): AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAATAATTTTACAA Found at i:1391 original size:51 final size:51 Alignment explanation

Indices: 1293--1446 Score: 236 Period size: 53 Copynumber: 2.9 Consensus size: 51 1283 CTTTTTGCAT * 1293 AATCCTTGTTGTCAAGTTTTTTTGTATACAAGGTAGGTACAAGAATTTTACAA 1 AATCCTTGTTGTCAAG--TTTTTGTATACAAGGTAGGTACAATAATTTTACAA * 1346 AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTTCAATAATTTTACAA 1 AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTACAATAATTTTACAA * * 1397 AATCCTTGTAGTCAAATTTTTTTGTATACAAGGTAGGTACAATAATTTTA 1 AATCCTTGTTGTC-AA-GTTTTTGTATACAAGGTAGGTACAATAATTTTA 1447 ACATAACAAA Statistics Matches: 94, Mismatches: 5, Indels: 4 0.91 0.05 0.04 Matches are distributed among these distances: 51 45 0.48 52 2 0.02 53 47 0.50 ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41 Consensus pattern (51 bp): AATCCTTGTTGTCAAGTTTTTGTATACAAGGTAGGTACAATAATTTTACAA Found at i:4878 original size:53 final size:54 Alignment explanation

Indices: 4820--4931 Score: 181 Period size: 54 Copynumber: 2.1 Consensus size: 54 4810 AATAAGCCTT * * * * 4820 TTTTACAAAATCCTTGTTGTCAA-GTTTTTTTGTATACGAGGTAGGTACAATAA 1 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA 4873 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA 1 TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA 4927 TTTTA 1 TTTTA 4932 ATGTGGCAAA Statistics Matches: 54, Mismatches: 4, Indels: 1 0.92 0.07 0.02 Matches are distributed among these distances: 53 22 0.41 54 32 0.59 ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41 Consensus pattern (54 bp): TTTTACAAAATCCTTATTGTCAAGGTGTTTTTGTATACAAGGTAGGAACAATAA Found at i:4983 original size:16 final size:16 Alignment explanation

Indices: 4959--4995 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 4949 GATAGATTTT 4959 AAAAATAAAAAATGTG 1 AAAAATAAAAAATGTG * * 4975 AAAAGTAAAAATTGTG 1 AAAAATAAAAAATGTG 4991 AAAAA 1 AAAAA 4996 AAATAATGCA Statistics Matches: 18, Mismatches: 3, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 16 18 1.00 ACGTcount: A:0.68, C:0.00, G:0.14, T:0.19 Consensus pattern (16 bp): AAAAATAAAAAATGTG Found at i:9029 original size:2 final size:2 Alignment explanation

Indices: 9022--9158 Score: 213 Period size: 2 Copynumber: 69.0 Consensus size: 2 9012 ATAAGATACA * 9022 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * * * * 9064 TC TT TC TC TC TC TT TC TC TC TC TC TT TC TC TC GC TC TC TT TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 9106 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 9147 TC TC TC TC TC TC 1 TC TC TC TC TC TC 9159 CTGTAACTTT Statistics Matches: 122, Mismatches: 12, Indels: 2 0.90 0.09 0.01 Matches are distributed among these distances: 1 1 0.01 2 121 0.99 ACGTcount: A:0.00, C:0.47, G:0.01, T:0.53 Consensus pattern (2 bp): TC Found at i:10086 original size:32 final size:32 Alignment explanation

Indices: 10045--10155 Score: 179 Period size: 32 Copynumber: 3.5 Consensus size: 32 10035 GTTTAGTGAT 10045 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC 1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC 10077 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC 1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC * * * 10109 GTACAATGCTGTTCAGTGCCCTGTAAAGTGGC 1 GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC 10141 GTACAGT-CTAGGTCA 1 GTACAGTGCT-GGTCA 10156 CTAGAACTAT Statistics Matches: 73, Mismatches: 5, Indels: 2 0.91 0.06 0.03 Matches are distributed among these distances: 31 2 0.03 32 71 0.97 ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26 Consensus pattern (32 bp): GTACAGTGCTGGTCAGTGCCCTGTACAGTGGC Found at i:10275 original size:21 final size:21 Alignment explanation

Indices: 10235--10285 Score: 61 Period size: 21 Copynumber: 2.5 Consensus size: 21 10225 GGGTCAGTGA * 10235 AATGTACAGTGAGATACAGAT 1 AATGTACAGTGAGATACAGAC * 10256 AATGTACAGT-AGATGTCAGAC 1 AATGTACAGTGAGAT-ACAGAC 10277 AATGT-CAGT 1 AATGTACAGT 10286 CAATTTTGGG Statistics Matches: 27, Mismatches: 2, Indels: 3 0.84 0.06 0.09 Matches are distributed among these distances: 20 8 0.30 21 19 0.70 ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25 Consensus pattern (21 bp): AATGTACAGTGAGATACAGAC Found at i:18365 original size:2 final size:2 Alignment explanation

Indices: 18358--18413 Score: 112 Period size: 2 Copynumber: 28.0 Consensus size: 2 18348 TATCTCCCCT 18358 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC 18400 AC AC AC AC AC AC AC 1 AC AC AC AC AC AC AC 18414 TTTAAGAATT Statistics Matches: 54, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 54 1.00 ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00 Consensus pattern (2 bp): AC Found at i:27207 original size:25 final size:25 Alignment explanation

Indices: 25487--27198 Score: 2309 Period size: 25 Copynumber: 68.5 Consensus size: 25 25477 CTCCGTGACT * ** 25487 AATGTCACAACACATGGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 25512 AATGTCACAACGTACAGTCAGCACC 1 AATGTCACAACATACAGTCTGCACC * 25537 ACTGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 25562 AATGTTACAACATACAGTCTACACC 1 AATGTCACAACATACAGTCTGCACC * 25587 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25612 AATGTCACAACATACAGTCTGAACC 1 AATGTCACAACATACAGTCTGCACC * * * 25637 AATGTTACAACATACAATCTGCAGC 1 AATGTCACAACATACAGTCTGCACC * 25662 AATGTCACAACATTCAGTCTGCA-C 1 AATGTCACAACATACAGTCTGCACC * * 25686 AATTTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 25711 AATTTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25736 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25761 AATGTCACAACATTCAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25786 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25811 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 25836 AATGTCACAACGTATAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 25861 AATGAT-ACAACATACAGTCTGCACT 1 AATG-TCACAACATACAGTCTGCACC ** * 25886 AATGTCACAACATTTAGTCTGCACA 1 AATGTCACAACATACAGTCTGCACC * 25911 AATGTCACAACATACAGTCTGCACT 1 AATGTCACAACATACAGTCTGCACC ** 25936 AATGTCACAACATACAGTCTGCATT 1 AATGTCACAACATACAGTCTGCACC ** * * * 25961 AATGTTTCAACAAACAGTTTACACC 1 AATGTCACAACATACAGTCTGCACC * 25986 AATATCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * ** 26011 AATGTTACAACATTTAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26036 AATGTTACAACATACCA-TCTGCACT 1 AATGTCACAACATA-CAGTCTGCACC * 26061 AATGTTACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26086 AATGTCACAACATACAGTCTGCATC 1 AATGTCACAACATACAGTCTGCACC * * * 26111 AATGTCCCAAAATACAATCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26136 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * ** 26161 AATGTCACAACGTATTGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26186 AATGTCACAACGTACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26211 AATGTCACAACATACCGTATGCACC 1 AATGTCACAACATACAGTCTGCACC * 26236 AATGTCACAACATACAGTCTGAACC 1 AATGTCACAACATACAGTCTGCACC * * 26261 AATGTTACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26286 AATGTCACAACGTACAGTCTTCACC 1 AATGTCACAACATACAGTCTGCACC * * 26311 AGTGTTACAACATACAGTCTGCA-C 1 AATGTCACAACATACAGTCTGCACC * * 26335 ATATCTCACAACATACAGTCTGCAACA 1 A-ATGTCACAACATACAGTCTGC-ACC ** * * 26362 AATGTCACAAGGTACCGTCTGCAAC 1 AATGTCACAACATACAGTCTGCACC * * ** * 26387 AATGTTACAATATTTAGACTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26412 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC ** 26437 AATGTCACAACATATTGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * * 26462 AATGTCACAACGTAAAATCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26487 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26512 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26537 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26562 AATGTCACAACGTACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26587 AATGTTACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * * 26612 AATGTCACAGCGTACAGACTGCACC 1 AATGTCACAACATACAGTCTGCACC 26637 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * * 26662 AATGTCACAACACACGGTTTGCACC 1 AATGTCACAACATACAGTCTGCACC * * * * 26687 AATATTATAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26712 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * * 26737 AATGAT-ACAACGTACAGTATGCACC 1 AATG-TCACAACATACAGTCTGCACC * 26762 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26787 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26812 AATGTCACAACATACCGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26837 AATGTCACAACGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * ** 26862 AATGTTACAACATTTAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26887 AATGTCACAATATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26912 AATGTCAAAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 26937 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 26962 AATGTCAAAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 26987 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 27012 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 27037 AATGACACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC ** 27062 AATGTCACAATGTACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC ** * 27087 AATGTCACAATGTGCAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC * 27112 AATGTCACAACATTCAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 27137 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 27162 AATGTCACAACATACAGTCTGCACC 1 AATGTCACAACATACAGTCTGCACC 27187 AATGTCACAACA 1 AATGTCACAACA 27199 CATGGTCTGT Statistics Matches: 1487, Mismatches: 190, Indels: 20 0.88 0.11 0.01 Matches are distributed among these distances: 24 27 0.02 25 1438 0.97 26 21 0.01 27 1 0.00 ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22 Consensus pattern (25 bp): AATGTCACAACATACAGTCTGCACC Found at i:28073 original size:20 final size:20 Alignment explanation

Indices: 28048--28086 Score: 53 Period size: 20 Copynumber: 1.9 Consensus size: 20 28038 AAATTATGAT 28048 AATATC-ATCATCATGAAACA 1 AATATCGATCATC-TGAAACA 28068 AATATCGGATCATCTGAAA 1 AATATC-GATCATCTGAAA 28087 TGATTGTCAT Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 20 6 0.35 21 5 0.29 22 6 0.35 ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26 Consensus pattern (20 bp): AATATCGATCATCTGAAACA Found at i:29245 original size:29 final size:29 Alignment explanation

Indices: 29193--29249 Score: 78 Period size: 29 Copynumber: 2.0 Consensus size: 29 29183 CAGTTCCGGC * * * 29193 GCACGTGGTTTTGAATAACCCTCAGGTGA 1 GCACATGGTTTTGAAGAACACTCAGGTGA * 29222 GCACATGGTTTTGAAGAATACTCAGGTG 1 GCACATGGTTTTGAAGAACACTCAGGTG 29250 CATGTATATT Statistics Matches: 24, Mismatches: 4, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 29 24 1.00 ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28 Consensus pattern (29 bp): GCACATGGTTTTGAAGAACACTCAGGTGA Found at i:46282 original size:2 final size:2 Alignment explanation

Indices: 46275--46322 Score: 96 Period size: 2 Copynumber: 24.0 Consensus size: 2 46265 TGTTTACTAT 46275 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 46317 GA GA GA 1 GA GA GA 46323 AGCTCAATGG Statistics Matches: 46, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 46 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:46755 original size:63 final size:63 Alignment explanation

Indices: 46632--46755 Score: 144 Period size: 63 Copynumber: 2.0 Consensus size: 63 46622 TTTCTGTCGA * * * * 46632 CATGCGACTTATCTATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATATTCATGTTGG 1 CATGCGACTTATCTATGTCAACATGCAGCTTAATTATGTCAACATGCAAGATAATAATGTTGG * * * * 46695 CATGCGACTTAAT-TATGTCGACATGC-GACTTATTTGTGTCAACATGCAAGTTAATAATGTT 1 CATGCGACTT-ATCTATGTCAACATGCAG-CTTAATTATGTCAACATGCAAGATAATAATGTT 46756 AACATGCAAG Statistics Matches: 51, Mismatches: 8, Indels: 4 0.81 0.13 0.06 Matches are distributed among these distances: 62 1 0.02 63 48 0.94 64 2 0.04 ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35 Consensus pattern (63 bp): CATGCGACTTATCTATGTCAACATGCAGCTTAATTATGTCAACATGCAAGATAATAATGTTGG Found at i:46847 original size:21 final size:21 Alignment explanation

Indices: 46645--46873 Score: 156 Period size: 21 Copynumber: 10.9 Consensus size: 21 46635 GCGACTTATC * 46645 TATGTCAACATGCAGGTTAAT 1 TATGTCAACATGCAAGTTAAT * * 46666 TATGTTAACATGCAAGAT-AT 1 TATGTCAACATGCAAGTTAAT *** * * 46686 TCATGTTGGCATGCGACTTAAT 1 T-ATGTCAACATGCAAGTTAAT * * * * 46708 TATGTCGACATGCGACTTATT 1 TATGTCAACATGCAAGTTAAT * 46729 TGTGTCAACATGCAAGTTAAT 1 TATGTCAACATGCAAGTTAAT * * * 46750 AATGTTAACATGCAAGAT-AT 1 TATGTCAACATGCAAGTTAAT *** * * 46770 TCATGTTGGCATGCGACTTAAT 1 T-ATGTCAACATGCAAGTTAAT * * * * 46792 TATGTCGACATGCGATTTATT 1 TATGTCAACATGCAAGTTAAT 46813 TATGTCAACATGCAAGTTAAT 1 TATGTCAACATGCAAGTTAAT * * * 46834 TATGTTAACATGCAAGATACT 1 TATGTCAACATGCAAGTTAAT * * 46855 TAAGTAAACATGCAAGTTA 1 TATGTCAACATGCAAGTTA 46874 TCCCGAATGT Statistics Matches: 164, Mismatches: 40, Indels: 8 0.77 0.19 0.04 Matches are distributed among these distances: 20 5 0.03 21 153 0.93 22 6 0.04 ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34 Consensus pattern (21 bp): TATGTCAACATGCAAGTTAAT Found at i:46865 original size:42 final size:41 Alignment explanation

Indices: 46645--46873 Score: 188 Period size: 42 Copynumber: 5.5 Consensus size: 41 46635 GCGACTTATC * 46645 TATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATAT 1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT *** * * ** * ** 46686 TCATGTTGGCATGCGACTTAATTATGTCGACATGCGACTTATT 1 T-ATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T * * 46729 TGTGTCAACATGCAAGTTAATAATGTTAACATGCAAGATAT 1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT *** * * ** * ** 46770 TCATGTTGGCATGCGACTTAATTATGTCGACATGCGATTTATT 1 T-ATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T 46813 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATACT 1 TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA-T * * 46855 TAAGTAAACATGCAAGTTA 1 TATGTCAACATGCAAGTTA 46874 TCCCGAATGT Statistics Matches: 136, Mismatches: 48, Indels: 7 0.71 0.25 0.04 Matches are distributed among these distances: 41 3 0.02 42 129 0.95 43 4 0.03 ACGTcount: A:0.33, C:0.14, G:0.18, T:0.34 Consensus pattern (41 bp): TATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATAT Found at i:46867 original size:84 final size:84 Alignment explanation

Indices: 46626--46852 Score: 409 Period size: 84 Copynumber: 2.7 Consensus size: 84 46616 AACATATTTC * * 46626 TGTCGACATGCGACTTATCTATGTCAACATGCAGGTTAATTATGTTAACATGCAAGATATTCATG 1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG 46691 TTGGCATGCGACTTAATTA 66 TTGGCATGCGACTTAATTA * * 46710 TGTCGACATGCGACTTATTTGTGTCAACATGCAAGTTAATAATGTTAACATGCAAGATATTCATG 1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG 46775 TTGGCATGCGACTTAATTA 66 TTGGCATGCGACTTAATTA * 46794 TGTCGACATGCGATTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA 1 TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATA 46853 CTTAAGTAAA Statistics Matches: 136, Mismatches: 7, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 84 136 1.00 ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35 Consensus pattern (84 bp): TGTCGACATGCGACTTATTTATGTCAACATGCAAGTTAATTATGTTAACATGCAAGATATTCATG TTGGCATGCGACTTAATTA Found at i:47226 original size:21 final size:21 Alignment explanation

Indices: 47200--47286 Score: 102 Period size: 21 Copynumber: 4.1 Consensus size: 21 47190 AAGATTTGAA * * 47200 CTTGCATGTTGACATAAGTCT 1 CTTGCATGTTGACATAATTAT *** 47221 CTTGCATAAGGACATAATTAT 1 CTTGCATGTTGACATAATTAT 47242 CTTGCATGTTGACATAATTAT 1 CTTGCATGTTGACATAATTAT * * 47263 CTTGGATGTAGACATAATTCAT 1 CTTGCATGTTGACATAATT-AT 47285 CT 1 CT 47287 AACATGTTAG Statistics Matches: 55, Mismatches: 10, Indels: 1 0.83 0.15 0.02 Matches are distributed among these distances: 21 51 0.93 22 4 0.07 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (21 bp): CTTGCATGTTGACATAATTAT Found at i:47277 original size:42 final size:43 Alignment explanation

Indices: 47200--47286 Score: 115 Period size: 42 Copynumber: 2.0 Consensus size: 43 47190 AAGATTTGAA * 47200 CTTGCATGTTGACATAAGTCTCTTGCATAAGGACATAATT-AT 1 CTTGCATGTTGACATAAGTATCTTGCATAAGGACATAATTCAT * * * 47242 CTTGCATGTTGACATAATTATCTTGGATGTA-GACATAATTCAT 1 CTTGCATGTTGACATAAGTATCTTGCAT-AAGGACATAATTCAT 47285 CT 1 CT 47287 AACATGTTAG Statistics Matches: 39, Mismatches: 4, Indels: 3 0.85 0.09 0.07 Matches are distributed among these distances: 42 34 0.87 43 5 0.13 ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38 Consensus pattern (43 bp): CTTGCATGTTGACATAAGTATCTTGCATAAGGACATAATTCAT Found at i:49306 original size:4 final size:4 Alignment explanation

Indices: 49297--49326 Score: 60 Period size: 4 Copynumber: 7.5 Consensus size: 4 49287 AGCAAAGATG 49297 ACTT ACTT ACTT ACTT ACTT ACTT ACTT AC 1 ACTT ACTT ACTT ACTT ACTT ACTT ACTT AC 49327 ATAACTAAGT Statistics Matches: 26, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 4 26 1.00 ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47 Consensus pattern (4 bp): ACTT Found at i:49353 original size:2 final size:2 Alignment explanation

Indices: 49340--49372 Score: 57 Period size: 2 Copynumber: 16.5 Consensus size: 2 49330 ACTAAGTTTG * 49340 CT CT CT CA CT CT CT CT CT CT CT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 49373 ATTGTACATT Statistics Matches: 29, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 29 1.00 ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45 Consensus pattern (2 bp): CT Found at i:50313 original size:19 final size:19 Alignment explanation

Indices: 50289--50327 Score: 78 Period size: 19 Copynumber: 2.1 Consensus size: 19 50279 TTCCTGGTAA 50289 TTTAAGATAATCTCCCTGT 1 TTTAAGATAATCTCCCTGT 50308 TTTAAGATAATCTCCCTGT 1 TTTAAGATAATCTCCCTGT 50327 T 1 T 50328 GTCCTGTTGT Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 19 20 1.00 ACGTcount: A:0.26, C:0.21, G:0.10, T:0.44 Consensus pattern (19 bp): TTTAAGATAATCTCCCTGT Found at i:61383 original size:24 final size:25 Alignment explanation

Indices: 61332--61394 Score: 74 Period size: 25 Copynumber: 2.6 Consensus size: 25 61322 TATGTGATGA * 61332 AGGGGGCTGGGCTATATAAAGTACC 1 AGGGGGCAGGGCTATATAAAGTACC * * * 61357 AGGGGGCAGAGCTATGTATAGTA-C 1 AGGGGGCAGGGCTATATAAAGTACC * 61381 AGGGGCCAGGGCTA 1 AGGGGGCAGGGCTA 61395 ACTACCTCAA Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 24 13 0.41 25 19 0.59 ACGTcount: A:0.27, C:0.16, G:0.40, T:0.17 Consensus pattern (25 bp): AGGGGGCAGGGCTATATAAAGTACC Found at i:64173 original size:2 final size:2 Alignment explanation

Indices: 64168--64225 Score: 116 Period size: 2 Copynumber: 29.0 Consensus size: 2 64158 TATACGTGTG 64168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 64210 TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC 64226 CTTTTTTCTC Statistics Matches: 56, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 56 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:65896 original size:26 final size:26 Alignment explanation

Indices: 65860--65937 Score: 104 Period size: 26 Copynumber: 3.0 Consensus size: 26 65850 TAATTCCCCA 65860 AAACTCTATTTCAATCTCTCCTTCAT 1 AAACTCTATTTCAATCTCTCCTTCAT * * 65886 AAACTCTATTTCAATCTAT-CTGTCAC 1 AAACTCTATTTCAATCTCTCCT-TCAT * * 65912 AAACTCTATTCCAATCTCTCCGTCAT 1 AAACTCTATTTCAATCTCTCCTTCAT 65938 CACATTGGCA Statistics Matches: 44, Mismatches: 6, Indels: 4 0.81 0.11 0.07 Matches are distributed among these distances: 25 2 0.05 26 41 0.93 27 1 0.02 ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38 Consensus pattern (26 bp): AAACTCTATTTCAATCTCTCCTTCAT Found at i:68956 original size:33 final size:33 Alignment explanation

Indices: 68895--69043 Score: 160 Period size: 33 Copynumber: 4.5 Consensus size: 33 68885 TGAATGATGG * * * 68895 TGTTCGACTCCACTAG-ATGTTCGTGAATGATTT 1 TGTTCTACTCCACTAGAAT-TACGAGAATGATTT * 68928 TTTTCTACTCCACTAGAATTACGAGAATGATTT 1 TGTTCTACTCCACTAGAATTACGAGAATGATTT * * * * 68961 TTTTCTACTCCGCTAGAAGTACGAGAATTATTT 1 TGTTCTACTCCACTAGAATTACGAGAATGATTT * * 68994 TGTTCTA-TACTACTAGAATTACGAGATTGATTT 1 TGTTCTACT-CCACTAGAATTACGAGAATGATTT 69027 TGTTCTA-TACCACTAGA 1 TGTTCTACT-CCACTAGA 69044 TGACCGGGAA Statistics Matches: 100, Mismatches: 14, Indels: 4 0.85 0.12 0.03 Matches are distributed among these distances: 32 1 0.01 33 97 0.97 34 2 0.02 ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40 Consensus pattern (33 bp): TGTTCTACTCCACTAGAATTACGAGAATGATTT Found at i:68977 original size:66 final size:66 Alignment explanation

Indices: 68895--69059 Score: 183 Period size: 66 Copynumber: 2.5 Consensus size: 66 68885 TGAATGATGG * * * * 68895 TGTTCGACTCCACTAGATGTTCGTGAATGATTTTTTTCTACT-CCACTAGAATTACGAGAATGAT 1 TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTA-TACCACTAGAATTACGAGAATGAT 68959 TT 65 TT * * * * * * 68961 TTTTCTACTCCGCTAGAAGTACGAGAATTATTTTGTTCTATACTACTAGAATTACGAGATTGATT 1 TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTATACCACTAGAATTACGAGAATGATT 69026 T 66 T * 69027 TGTTCTA-TACCACTAGATG-ACCGGGAATGATTT 1 TGTTCTACT-CCACTAGATGTA-CGAGAATGATTT 69060 GGCTTCAGAT Statistics Matches: 81, Mismatches: 15, Indels: 6 0.79 0.15 0.06 Matches are distributed among these distances: 65 3 0.04 66 78 0.96 ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39 Consensus pattern (66 bp): TGTTCTACTCCACTAGATGTACGAGAATGATTTTGTTCTATACCACTAGAATTACGAGAATGATT T Found at i:73116 original size:2 final size:2 Alignment explanation

Indices: 73109--73142 Score: 68 Period size: 2 Copynumber: 17.0 Consensus size: 2 73099 ATAAACCAAC 73109 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 73143 GTGGTGGAAT Statistics Matches: 32, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 32 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:73658 original size:14 final size:14 Alignment explanation

Indices: 73623--73669 Score: 67 Period size: 14 Copynumber: 3.3 Consensus size: 14 73613 GATGAGAGTG 73623 GGGGTGAAGGGGGT 1 GGGGTGAAGGGGGT * 73637 GGGGGTGAAGTGGGT 1 -GGGGTGAAGGGGGT * 73652 GGTGTGAAGGGGGT 1 GGGGTGAAGGGGGT 73666 GGGG 1 GGGG 73670 GTAAGGTGGG Statistics Matches: 28, Mismatches: 4, Indels: 1 0.85 0.12 0.03 Matches are distributed among these distances: 14 15 0.54 15 13 0.46 ACGTcount: A:0.13, C:0.00, G:0.70, T:0.17 Consensus pattern (14 bp): GGGGTGAAGGGGGT Found at i:73675 original size:14 final size:15 Alignment explanation

Indices: 73620--73680 Score: 81 Period size: 15 Copynumber: 4.1 Consensus size: 15 73610 AAAGATGAGA 73620 GTGGGGGTGAAGGGG 1 GTGGGGGTGAAGGGG * 73635 GTGGGGGTGAAGTGG 1 GTGGGGGTGAAGGGG * 73650 GT-GGTGTGAAGGGG 1 GTGGGGGTGAAGGGG 73664 GTGGGGGT-AAGGTGG 1 GTGGGGGTGAAGG-GG 73679 GT 1 GT 73681 AGACACAGGG Statistics Matches: 40, Mismatches: 4, Indels: 4 0.83 0.08 0.08 Matches are distributed among these distances: 14 16 0.40 15 24 0.60 ACGTcount: A:0.13, C:0.00, G:0.67, T:0.20 Consensus pattern (15 bp): GTGGGGGTGAAGGGG Found at i:74770 original size:2 final size:2 Alignment explanation

Indices: 74763--74817 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 74753 AATGCTTAAT 74763 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 74805 TC TC TC TC TC TC T 1 TC TC TC TC TC TC T 74818 GTGAGAGACT Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:78682 original size:2 final size:2 Alignment explanation

Indices: 78675--78729 Score: 110 Period size: 2 Copynumber: 27.5 Consensus size: 2 78665 TCATATAATA 78675 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 78717 TC TC TC TC TC TC T 1 TC TC TC TC TC TC T 78730 GAGACATCTA Statistics Matches: 53, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 53 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:80766 original size:1 final size:1 Alignment explanation

Indices: 80762--80789 Score: 56 Period size: 1 Copynumber: 28.0 Consensus size: 1 80752 ATACTCCACT 80762 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC 80790 TTACACACAT Statistics Matches: 27, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 27 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:81042 original size:106 final size:106 Alignment explanation

Indices: 80847--81048 Score: 334 Period size: 106 Copynumber: 1.9 Consensus size: 106 80837 TATATTTTGA * * * 80847 ATATTTTCCCATTCTTATGACAACAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAATTCAA 1 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA * * 80912 CAAATTCTCCATAAGATCTGCCTTAAACTTTNTAATATTCAT 66 CAAATTCACCATAAGAGCTGCCTTAAACTTT-TAATATTCAT * 80954 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCC-ATTAAGGAGGCTGGGAGGTAAA 1 ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA 81018 CAAATTCACCATAAGAGCTGCCTTAAACTTT 66 CAAATTCACCATAAGAGCTGCCTTAAACTTT 81049 GATATATGGT Statistics Matches: 89, Mismatches: 6, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 106 48 0.54 107 41 0.46 ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37 Consensus pattern (106 bp): ATATTTTCCCATTCTTATGACAAAAATAGTCTTTATTTTTCCTATTAAGGAGGCTGGGAAGTAAA CAAATTCACCATAAGAGCTGCCTTAAACTTTTAATATTCAT Found at i:82778 original size:2 final size:2 Alignment explanation

Indices: 82771--82830 Score: 99 Period size: 2 Copynumber: 31.5 Consensus size: 2 82761 AATTATTGGA 82771 TC TC TC TC -C TC TC -C TC TC -C TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 82810 TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC T 82831 TGCATCTTTA Statistics Matches: 55, Mismatches: 0, Indels: 6 0.90 0.00 0.10 Matches are distributed among these distances: 1 3 0.05 2 52 0.95 ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48 Consensus pattern (2 bp): TC Found at i:83187 original size:1 final size:1 Alignment explanation

Indices: 83181--83206 Score: 52 Period size: 1 Copynumber: 26.0 Consensus size: 1 83171 TTCATCAACT 83181 CCCCCCCCCCCCCCCCCCCCCCCCCC 1 CCCCCCCCCCCCCCCCCCCCCCCCCC 83207 TTTTCTCTTC Statistics Matches: 25, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 1 25 1.00 ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00 Consensus pattern (1 bp): C Found at i:84424 original size:58 final size:58 Alignment explanation

Indices: 84354--84514 Score: 259 Period size: 58 Copynumber: 2.8 Consensus size: 58 84344 TTGTCTTCAG 84354 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC 1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC * ** 84412 CAACAAATATGGGATTTCTTTAAGTGTTTTAGATTATGCAAGGGGGGTGGGGGTGGGC 1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC ** * * 84470 CAACAAATATGGGATTTCTTTGGGTGTGTAAGATTGTGCAAGGGG 1 CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGG 84515 AGGCAATAAA Statistics Matches: 95, Mismatches: 8, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 58 95 1.00 ACGTcount: A:0.27, C:0.09, G:0.35, T:0.30 Consensus pattern (58 bp): CAACAAATATGGGATTTCTTTAAGTGTTTAAGATTATGCAAGGGGGGTGGGGAAGGGC Found at i:86266 original size:14 final size:14 Alignment explanation

Indices: 86242--86275 Score: 59 Period size: 14 Copynumber: 2.4 Consensus size: 14 86232 TCTCCAAAAC 86242 TCTCTCGACTGTCAT 1 TCTC-CGACTGTCAT 86257 TCTCCGACTGTCAT 1 TCTCCGACTGTCAT 86271 TCTCC 1 TCTCC 86276 AAGGGGGGCT Statistics Matches: 19, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 14 15 0.79 15 4 0.21 ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38 Consensus pattern (14 bp): TCTCCGACTGTCAT Found at i:90591 original size:32 final size:32 Alignment explanation

Indices: 90550--90624 Score: 96 Period size: 32 Copynumber: 2.3 Consensus size: 32 90540 TAATACTTGA * 90550 TTAATACCAAAGAAAGGCAAAGATATCAATGT 1 TTAATACCAAAGAAAGGCAAAGACATCAATGT *** ** 90582 TTAATACCAAAGAGTTGTTAAGACATCAATGT 1 TTAATACCAAAGAAAGGCAAAGACATCAATGT 90614 TTAATACCAAA 1 TTAATACCAAA 90625 TGGGGATTTC Statistics Matches: 37, Mismatches: 6, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 32 37 1.00 ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27 Consensus pattern (32 bp): TTAATACCAAAGAAAGGCAAAGACATCAATGT Found at i:100730 original size:25 final size:25 Alignment explanation

Indices: 100701--100749 Score: 80 Period size: 25 Copynumber: 2.0 Consensus size: 25 100691 TTCCCCATCA * 100701 GCTGATCTAACATAAAGGGTATAAC 1 GCTGATCTAACACAAAGGGTATAAC * 100726 GCTGATCTAACACATAGGGTATAA 1 GCTGATCTAACACAAAGGGTATAA 100750 AATTAAGAAA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 25 22 1.00 ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24 Consensus pattern (25 bp): GCTGATCTAACACAAAGGGTATAAC Found at i:102761 original size:42 final size:42 Alignment explanation

Indices: 102682--102761 Score: 106 Period size: 42 Copynumber: 1.9 Consensus size: 42 102672 AAAATTACAC * * ** 102682 ATAAAATGCCGCAAAACCAAACACAGTTTTACAATATTTCAT 1 ATAAAATGCCACAAAACCAAACACAGATACACAATATTTCAT * * 102724 ATAAAATGCCACAAAACTAAACACAGATACACGATATT 1 ATAAAATGCCACAAAACCAAACACAGATACACAATATT 102762 ATTCATTAGC Statistics Matches: 32, Mismatches: 6, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 42 32 1.00 ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23 Consensus pattern (42 bp): ATAAAATGCCACAAAACCAAACACAGATACACAATATTTCAT Found at i:102948 original size:2 final size:2 Alignment explanation

Indices: 102941--102974 Score: 50 Period size: 2 Copynumber: 17.0 Consensus size: 2 102931 ACATTTTTCA * * 102941 TC TC TC TC TC TC TC TC TT TT TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 102975 CACACACACT Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56 Consensus pattern (2 bp): TC Found at i:107008 original size:2 final size:2 Alignment explanation

Indices: 107001--107036 Score: 72 Period size: 2 Copynumber: 18.0 Consensus size: 2 106991 TCAGGACAAT 107001 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 107037 ATATGTCTCC Statistics Matches: 34, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 34 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:107822 original size:2 final size:2 Alignment explanation

Indices: 107684--107806 Score: 145 Period size: 2 Copynumber: 65.5 Consensus size: 2 107674 TCTCTTTGAT * 107684 TC TC TC TC TC TC TC TC TC TC TC TC T- TC -C TC -C TC CC TC -C 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * * 107722 TC -C CC T- TC TC CC TC TC -C TC T- TC TC TT TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * 107760 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 107802 TC TC T 1 TC TC T 107807 GTGATCCAAT Statistics Matches: 104, Mismatches: 9, Indels: 16 0.81 0.07 0.12 Matches are distributed among these distances: 1 8 0.08 2 96 0.92 ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49 Consensus pattern (2 bp): TC Found at i:108617 original size:2 final size:2 Alignment explanation

Indices: 108610--108643 Score: 59 Period size: 2 Copynumber: 17.0 Consensus size: 2 108600 GTATGGTGCC * 108610 GA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 108644 ATATTCAAGA Statistics Matches: 30, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 2 30 1.00 ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00 Consensus pattern (2 bp): GA Found at i:112364 original size:2 final size:2 Alignment explanation

Indices: 112357--112463 Score: 125 Period size: 2 Copynumber: 56.0 Consensus size: 2 112347 ATGTCAACAA * 112357 TC TC TC TC TC -C TC TC TC TC TC TC -C TC AC TC TC TC TC TC -C 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * 112396 TC TC TC TC TC TC -C CC TC TC TC TC TC -C TC TT TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC * * * 112436 TC TT TC TC TC TT TC TT TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC 112464 CTTGAATACT Statistics Matches: 89, Mismatches: 11, Indels: 10 0.81 0.10 0.09 Matches are distributed among these distances: 1 5 0.06 2 84 0.94 ACGTcount: A:0.01, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:115116 original size:18 final size:18 Alignment explanation

Indices: 115093--115130 Score: 76 Period size: 18 Copynumber: 2.1 Consensus size: 18 115083 ACCTCAATGA 115093 ATGACAATGATCACATGT 1 ATGACAATGATCACATGT 115111 ATGACAATGATCACATGT 1 ATGACAATGATCACATGT 115129 AT 1 AT 115131 ACACACGCTA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29 Consensus pattern (18 bp): ATGACAATGATCACATGT Found at i:115818 original size:2 final size:2 Alignment explanation

Indices: 115811--115864 Score: 108 Period size: 2 Copynumber: 27.0 Consensus size: 2 115801 TTAACATACA 115811 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 115853 TC TC TC TC TC TC 1 TC TC TC TC TC TC 115865 AGTATAGAAT Statistics Matches: 52, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 52 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:146171 original size:69 final size:69 Alignment explanation

Indices: 146058--146289 Score: 428 Period size: 69 Copynumber: 3.4 Consensus size: 69 146048 NNNNNNNNNN 146058 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT 1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT 146123 TTAG 66 TTAG * 146127 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATATGAACAGATTCTTGGTTGACAGAAT 1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT 146192 TTAG 66 TTAG * 146196 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTTTTGGTTGACAGAAT 1 TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT 146261 TTAG 66 TTAG ** 146265 TATGACCCCTTACTCTTCAATGTTT 1 TACAACCCCTTACTCTTCAATGTTT 146290 TGCCTGTCAT Statistics Matches: 158, Mismatches: 5, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 69 158 1.00 ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37 Consensus pattern (69 bp): TACAACCCCTTACTCTTCAATGTTTGATTGATAAGGAATTTGAACAGATTCTTGGTTGACAGAAT TTAG Found at i:147773 original size:39 final size:36 Alignment explanation

Indices: 147730--147834 Score: 104 Period size: 43 Copynumber: 2.8 Consensus size: 36 147720 ATATTCTATT 147730 GACTGACTTACAAATATATGGAGGGACAGTTATTTCAAC 1 GACTGACTTACAAATATATGGAGGGACAGTTA-TTC--C ** ** 147769 GACTGACTTAATAACAAATATATGGAAAGATGGTTATTCC 1 GACTGAC-T--T-ACAAATATATGGAGGGACAGTTATTCC 147809 -ACTGACTTACAAATATATGGAGGGAC 1 GACTGACTTACAAATATATGGAGGGAC 147835 GGATATTCTA Statistics Matches: 55, Mismatches: 7, Indels: 12 0.74 0.09 0.16 Matches are distributed among these distances: 35 15 0.27 36 1 0.02 38 1 0.02 39 13 0.24 40 2 0.04 42 4 0.07 43 19 0.35 ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28 Consensus pattern (36 bp): GACTGACTTACAAATATATGGAGGGACAGTTATTCC Found at i:149409 original size:25 final size:25 Alignment explanation

Indices: 149340--149466 Score: 98 Period size: 25 Copynumber: 5.2 Consensus size: 25 149330 TCCTCTAATA * * 149340 ATCTATTTTAACAGGTACTCCACA- 1 ATCTATTTTAACAGGTACTCTAGAC * * * * 149364 ATTTGTTTT-ACATGTATTCTAGAC 1 ATCTATTTTAACAGGTACTCTAGAC * * 149388 ATCTATTTAAACAGGTACTCTAGAA 1 ATCTATTTTAACAGGTACTCTAGAC * * * 149413 ACCTATTTTGACAGGTATTCTAGAC 1 ATCTATTTTAACAGGTACTCTAGAC * * * 149438 ATAT-TTTTTACAGGTACCCTCAGAC 1 ATCTATTTTAACAGGTACTCT-AGAC 149463 ATCT 1 ATCT 149467 TTTGTTTACC Statistics Matches: 77, Mismatches: 23, Indels: 5 0.73 0.22 0.05 Matches are distributed among these distances: 23 10 0.13 24 26 0.34 25 41 0.53 ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38 Consensus pattern (25 bp): ATCTATTTTAACAGGTACTCTAGAC Found at i:153234 original size:2 final size:2 Alignment explanation

Indices: 153227--153265 Score: 78 Period size: 2 Copynumber: 19.5 Consensus size: 2 153217 AAAAATTAAT 153227 AG 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 AG A 153266 AGAAAAGAAA Statistics Matches: 37, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 37 1.00 ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00 Consensus pattern (2 bp): AG Found at i:159653 original size:28 final size:28 Alignment explanation

Indices: 159616--159737 Score: 156 Period size: 28 Copynumber: 4.3 Consensus size: 28 159606 TGATGTCCTT * 159616 TTCATGTAAAGTTTACACCTTATTTCCC 1 TTCATGTAAAGTTTACACCTTATTCCCC * * 159644 TTCATTTAAAGTTTACACCTTGTTCCCC 1 TTCATGTAAAGTTTACACCTTATTCCCC * * * 159672 TTCATTTATAGTTTACACCTTGTTCCCC 1 TTCATGTAAAGTTTACACCTTATTCCCC 159700 TTCATGTAAAGTTTACACCTTGATTTTCCCC 1 TTCATGTAAAGTTTACACCTT-A--TTCCCC 159731 -TCATGTA 1 TTCATGTA 159738 CGTTTTCCTC Statistics Matches: 84, Mismatches: 7, Indels: 4 0.88 0.07 0.04 Matches are distributed among these distances: 28 71 0.85 30 7 0.08 31 6 0.07 ACGTcount: A:0.22, C:0.26, G:0.08, T:0.43 Consensus pattern (28 bp): TTCATGTAAAGTTTACACCTTATTCCCC Found at i:164795 original size:21 final size:21 Alignment explanation

Indices: 164745--164795 Score: 52 Period size: 21 Copynumber: 2.4 Consensus size: 21 164735 GTGTTTTACT * * 164745 TTTTATCATAATTTGATGTAG 1 TTTTATCATAAATTGACGTAG 164766 -TTTAGTCATAAATTGACGT-G 1 TTTTA-TCATAAATTGACGTAG 164786 CTTTTATCAT 1 -TTTTATCAT 164796 TTTGTGGTGA Statistics Matches: 25, Mismatches: 2, Indels: 6 0.76 0.06 0.18 Matches are distributed among these distances: 20 5 0.20 21 16 0.64 22 4 0.16 ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49 Consensus pattern (21 bp): TTTTATCATAAATTGACGTAG Found at i:164937 original size:4 final size:4 Alignment explanation

Indices: 164928--164983 Score: 58 Period size: 4 Copynumber: 14.0 Consensus size: 4 164918 TACCCTTGTG * * * * * * 164928 TGTC TGTC TGTC CGTC CGTC CGTC CGTC TGTC TGTC TGTC CGTC CGTC 1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC 164976 TGTC TGTC 1 TGTC TGTC 164984 CGTCCGTAAC Statistics Matches: 48, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 48 1.00 ACGTcount: A:0.00, C:0.36, G:0.25, T:0.39 Consensus pattern (4 bp): TGTC Found at i:164958 original size:20 final size:20 Alignment explanation

Indices: 164933--164990 Score: 98 Period size: 20 Copynumber: 2.9 Consensus size: 20 164923 TTGTGTGTCT * 164933 GTCTGTCCGTCCGTCCGTCC 1 GTCTGTCTGTCCGTCCGTCC * 164953 GTCTGTCTGTCTGTCCGTCC 1 GTCTGTCTGTCCGTCCGTCC 164973 GTCTGTCTGTCCGTCCGT 1 GTCTGTCTGTCCGTCCGT 164991 AACAAAAATT Statistics Matches: 35, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 20 35 1.00 ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36 Consensus pattern (20 bp): GTCTGTCTGTCCGTCCGTCC Found at i:164988 original size:4 final size:4 Alignment explanation

Indices: 164937--164990 Score: 63 Period size: 4 Copynumber: 13.5 Consensus size: 4 164927 GTGTCTGTCT * * * * * 164937 GTCC GTCC GTCC GTCC GTCT GTCT GTCT GTCC GTCC GTCT GTCT GTCC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC 164985 GTCC GT 1 GTCC GT 164991 AACAAAAATT Statistics Matches: 46, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 4 46 1.00 ACGTcount: A:0.00, C:0.39, G:0.26, T:0.35 Consensus pattern (4 bp): GTCC Found at i:164988 original size:16 final size:16 Alignment explanation

Indices: 164928--164990 Score: 90 Period size: 16 Copynumber: 3.9 Consensus size: 16 164918 TACCCTTGTG * 164928 TGTCTGTCTGTCCGTC 1 TGTCTGTCCGTCCGTC * * * 164944 CGTCCGTCCGTCTGTC 1 TGTCTGTCCGTCCGTC 164960 TGTCTGTCCGTCCGTC 1 TGTCTGTCCGTCCGTC 164976 TGTCTGTCCGTCCGT 1 TGTCTGTCCGTCCGT 164991 AACAAAAATT Statistics Matches: 40, Mismatches: 7, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 16 40 1.00 ACGTcount: A:0.00, C:0.37, G:0.25, T:0.38 Consensus pattern (16 bp): TGTCTGTCCGTCCGTC Found at i:165388 original size:166 final size:167 Alignment explanation

Indices: 165014--165974 Score: 1468 Period size: 166 Copynumber: 5.8 Consensus size: 167 165004 GTCGCATTTA * * 165014 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATTCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT * ** 165079 TGTGGGATATATTTTTGTACCAATCGGACGTCAACTTATTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 165144 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 165181 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTA-AGGCATGCCATA * * 165245 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGATTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT * * * * 165310 TTT-GCCAAAATTTTAAAACAAATTTTCGTCAATGAAT 130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * 165347 TCTCAGCAACTGTTTATCTCAGATGCTTGAAATTTTTACACAGTATTTG-TATAGGCATGCCATA 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTA-AGGCATGCCATA * * 165411 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACAACTTTGCTTATTT 65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT 165476 TTTAACC-AAATTTTCAAACAAATTTTCGTCAAAGATT 130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * 165513 TCTCAGCAACTATTTATTGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT * * ** 165578 CGTGGGACATATTGTTGTACCAATCGGACGTCAACTTATTGTTAAATGACGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 165643 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT 131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * * 165680 TCTCAGCAGCTATTTATCGGAGATGCTTTAAATTTTAACACAGTATTTTTTAAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT * * 165745 CGTGGGATATATTTTTGTACCAATCGGACGTCATCTTCCTGTTAAATGA-GTACTTTG-TT-TAT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG-ACTTTGCTTATTT * * 165807 TTTAGCCAAAATTTTCAAACAAATTTTCCTCAAAGATT 130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT * * * 165845 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTAGGCATGCCATAT 1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT * * * * * * * 165910 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT 66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT 165975 GCATATTCAC Statistics Matches: 728, Mismatches: 58, Indels: 16 0.91 0.07 0.02 Matches are distributed among these distances: 165 146 0.20 166 316 0.43 167 266 0.37 ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39 Consensus pattern (167 bp): TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAAGGCATGCCATAT CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT Found at i:170126 original size:13 final size:13 Alignment explanation

Indices: 170108--170137 Score: 51 Period size: 13 Copynumber: 2.3 Consensus size: 13 170098 AAAAATGTTA * 170108 CTATCAAAAATTC 1 CTATCAAAAATCC 170121 CTATCAAAAATCC 1 CTATCAAAAATCC 170134 CTAT 1 CTAT 170138 GAACACCACC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 13 16 1.00 ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30 Consensus pattern (13 bp): CTATCAAAAATCC Found at i:172670 original size:11 final size:11 Alignment explanation

Indices: 172656--172685 Score: 51 Period size: 11 Copynumber: 2.7 Consensus size: 11 172646 TGTATGAAAA 172656 TTGCATGATAT 1 TTGCATGATAT 172667 TTGCATGATAT 1 TTGCATGATAT * 172678 TCGCATGA 1 TTGCATGA 172686 AACAACAGTG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 11 18 1.00 ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40 Consensus pattern (11 bp): TTGCATGATAT Found at i:177521 original size:2 final size:2 Alignment explanation

Indices: 177514--177627 Score: 119 Period size: 2 Copynumber: 59.0 Consensus size: 2 177504 CTCTATTCCC * * * 177514 CT CT CT CT AT -T CT CT CT CT CC CT CT CT CT CT CT AT -T CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT * * * 177554 CC CT CT CT CT CT CT CT CT CT AT -T CT CT CT CT CC CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT * * * 177595 CT AT -T CT CT CT CT CC CT CT CT CT TT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 177628 GTATTTTTGT Statistics Matches: 94, Mismatches: 14, Indels: 8 0.81 0.12 0.07 Matches are distributed among these distances: 1 4 0.04 2 90 0.96 ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49 Consensus pattern (2 bp): CT Found at i:177542 original size:25 final size:25 Alignment explanation

Indices: 177514--177617 Score: 167 Period size: 25 Copynumber: 4.2 Consensus size: 25 177504 CTCTATTCCC 177514 CTCTCTCTATTCTCTCTCTCCCTCT 1 CTCTCTCTATTCTCTCTCTCCCTCT * 177539 CTCTCTCTATTCTCTCCCTCTCTCTCT 1 CTCTCTCTATTCTCT--CTCTCCCTCT 177566 CTCTCTCTATTCTCTCTCT-CC-CT 1 CTCTCTCTATTCTCTCTCTCCCTCT 177589 CTCTCTCTATTCTCTCTCTCCCTCT 1 CTCTCTCTATTCTCTCTCTCCCTCT 177614 CTCT 1 CTCT 177618 TTCTCTCTCT Statistics Matches: 73, Mismatches: 2, Indels: 8 0.88 0.02 0.10 Matches are distributed among these distances: 23 21 0.29 24 3 0.04 25 25 0.34 27 24 0.33 ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48 Consensus pattern (25 bp): CTCTCTCTATTCTCTCTCTCCCTCT Found at i:182659 original size:10 final size:10 Alignment explanation

Indices: 182640--182817 Score: 80 Period size: 10 Copynumber: 17.7 Consensus size: 10 182630 AGTGCCATTT 182640 TTTACTGATA 1 TTTACTGATA 182650 GTTT-CTGATA 1 -TTTACTGATA 182660 TTTACTGATA 1 TTTACTGATA * 182670 TTGTACTGTTA 1 TT-TACTGATA * * * 182681 -GTGCTGAGA 1 TTTACTGATA * * 182690 ATTGCTGATA 1 TTTACTGATA 182700 TTTACTGATAA 1 TTTACTGAT-A ** 182711 TTTTACTG-CC 1 -TTTACTGATA * 182721 GTTACTGATA 1 TTTACTGATA * * * * 182731 ATTGCTGTTG 1 TTTACTGATA * 182741 GTT-CTGATA 1 TTTACTGATA 182750 TTTACTGATA 1 TTTACTGATA * 182760 TTTACTGATGCT 1 TTTACTGAT--A * 182772 TTTGCTG-TGA 1 TTTACTGAT-A ** 182782 GCT-CTGATA 1 TTTACTGATA * 182791 ATTACTGATA 1 TTTACTGATA 182801 TTTACTGATA 1 TTTACTGATA 182811 TTTACTG 1 TTTACTG 182818 TTGGTACTGA Statistics Matches: 125, Mismatches: 31, Indels: 23 0.70 0.17 0.13 Matches are distributed among these distances: 9 25 0.20 10 75 0.60 11 12 0.10 12 13 0.10 ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46 Consensus pattern (10 bp): TTTACTGATA Found at i:183664 original size:2 final size:2 Alignment explanation

Indices: 183657--183687 Score: 53 Period size: 2 Copynumber: 15.5 Consensus size: 2 183647 GCCCACCCTG * 183657 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT C 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C 183688 GCTCGCATAT Statistics Matches: 27, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 2 27 1.00 ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52 Consensus pattern (2 bp): CT Found at i:183882 original size:2 final size:2 Alignment explanation

Indices: 183875--183924 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 183865 ATGCTTTAAT 183875 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC 183917 TC TC TC TC 1 TC TC TC TC 183925 AGATAATCTA Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): TC Found at i:184043 original size:2 final size:2 Alignment explanation

Indices: 184036--184078 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 184026 GATTGAAAAC * 184036 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 184078 C 1 C 184079 ATTAATACTT Statistics Matches: 39, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47 Consensus pattern (2 bp): CT Found at i:184456 original size:134 final size:134 Alignment explanation

Indices: 184226--184478 Score: 400 Period size: 134 Copynumber: 1.9 Consensus size: 134 184216 GAAAAAAATA * * 184226 TTTTGTATGTCTGGGATTAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGACTATACACACGA 1 TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGAATATACACACGA * * 184291 CAGGGTGACCACGGCAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAG 66 CAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAGTCGCTGAAAAG 184356 ATTC 131 ATTC * * * 184360 TTTTGTATGTCTGGGATCAAGAAAACCCTCAGAACTAACAGACG-GCGCTCAGAATATATACACG 1 TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGA-GAGCACTCAGAATATACACACG ** * 184424 ACAGAGTGACCGTGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTTGCAG 65 ACAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAG 184479 CCTCAGAATA Statistics Matches: 108, Mismatches: 10, Indels: 2 0.90 0.08 0.02 Matches are distributed among these distances: 134 107 0.99 135 1 0.01 ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24 Consensus pattern (134 bp): TTTTGTATGTCTGGGATCAAGAAAAACCTCAGAACTAACAGAGAGCACTCAGAATATACACACGA CAGAGTGACCACGGCAAGGTGTGAAAATTGACCAACTGTGTATATGTCTGGCAGTCGCTGAAAAG ATTC Found at i:185140 original size:10 final size:10 Alignment explanation

Indices: 185125--185302 Score: 80 Period size: 10 Copynumber: 17.7 Consensus size: 10 185115 TCAGTACCAA * 185125 CAGTAAATCT 1 CAGTAAATAT 185135 CAGTAAATAT 1 CAGTAAATAT * 185145 CAGTAATTAT 1 CAGTAAATAT ** 185155 CAG-AGCTCA- 1 CAGTAAAT-AT * * 185164 CAGCAAAAGCAT 1 CAG-TAAA-TAT 185176 CAGTAAATAT 1 CAGTAAATAT 185186 CAGTAAATAT 1 CAGTAAATAT ** * 185196 CAG-AACCAA 1 CAGTAAATAT * * 185205 CAGCAATTAT 1 CAGTAAATAT * * 185215 CAGT-AACAG 1 CAGTAAATAT 185224 CAGTAAAATTAT 1 CAGT-AAA-TAT 185236 CAGTAAATAT 1 CAGTAAATAT * * * 185246 CAGCAATTCT 1 CAGTAAATAT * ** 185256 CAGCACTTA- 1 CAGTAAATAT 185265 CAGTACAATAT 1 CAGTA-AATAT 185276 CAGTAAATAT 1 CAGTAAATAT 185286 CAG-AAACTAT 1 CAGTAAA-TAT 185296 CAGTAAA 1 CAGTAAA 185303 AAATGGCACT Statistics Matches: 126, Mismatches: 29, Indels: 25 0.70 0.16 0.14 Matches are distributed among these distances: 9 24 0.19 10 76 0.60 11 18 0.14 12 8 0.06 ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24 Consensus pattern (10 bp): CAGTAAATAT Found at i:185150 original size:20 final size:20 Alignment explanation

Indices: 185088--185157 Score: 72 Period size: 20 Copynumber: 3.5 Consensus size: 20 185078 TCCCCTGCCT * 185088 GTAATTCTCAGTAATTATCA 1 GTAATTCTCAGTAAATATCA * * 185108 GCAATTCTCAGTACCA-A-CA 1 GTAATTCTCAGTA-AATATCA * 185127 GTAAATCTCAGTAAATATCA 1 GTAATTCTCAGTAAATATCA * 185147 GTAATTATCAG 1 GTAATTCTCAG 185158 AGCTCACAGC Statistics Matches: 39, Mismatches: 8, Indels: 6 0.74 0.15 0.11 Matches are distributed among these distances: 18 1 0.03 19 14 0.36 20 24 0.62 ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31 Consensus pattern (20 bp): GTAATTCTCAGTAAATATCA Found at i:185208 original size:41 final size:40 Alignment explanation

Indices: 185094--185210 Score: 130 Period size: 41 Copynumber: 2.9 Consensus size: 40 185084 GCCTGTAATT * * * * * * 185094 CTCAGTAATTATCAGCAATTCTCAGTACCAACAG-TAAAT 1 CTCAGTAAATATCAGTAATTATCAGAACCAACAGCAAAAG * 185133 CTCAGTAAATATCAGTAATTATCAGAGCTC-ACAGCAAAAG 1 CTCAGTAAATATCAGTAATTATCAGAAC-CAACAGCAAAAG * 185173 CATCAGTAAATATCAGTAAATATCAGAACCAACAGCAA 1 C-TCAGTAAATATCAGTAATTATCAGAACCAACAGCAA 185211 TTATCAGTAA Statistics Matches: 65, Mismatches: 9, Indels: 6 0.81 0.11 0.08 Matches are distributed among these distances: 39 27 0.42 40 6 0.09 41 32 0.49 ACGTcount: A:0.44, C:0.21, G:0.12, T:0.23 Consensus pattern (40 bp): CTCAGTAAATATCAGTAATTATCAGAACCAACAGCAAAAG Found at i:188548 original size:62 final size:63 Alignment explanation

Indices: 188431--188684 Score: 203 Period size: 62 Copynumber: 4.1 Consensus size: 63 188421 ATCGCCCGAG * * * ** * * * 188431 TTTTAATAAAACAAATGTAACATGTTCTTCCTCTGTAAGAGCTGAATCAGCAAGTCCCCTGAT 1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT * * 188494 TTTTAAGAAAACAAATGCATCATGCACTT-CTCGGTCAGGGCTGAATCAGCAAGTCGCCAGAT 1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT * * * * ** ** * * * * * 188556 TTTTAA-CAAACCAATGCAACATGCACTTCCCCTTTCAAAGCTTAATCAGCCATTCACCTGGT 1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT * * * * * * 188618 TTTTAAGAAAACAAAT--TTCATGCACTTCCTCGGTAAGGACTGTATCAGTAAGTCGCCC-GAA 1 TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTC-CCCTGAT 188679 TTTTAA 1 TTTTAA 188685 AAAGGGTCCG Statistics Matches: 145, Mismatches: 43, Indels: 8 0.74 0.22 0.04 Matches are distributed among these distances: 61 50 0.34 62 64 0.44 63 31 0.21 ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29 Consensus pattern (63 bp): TTTTAAGAAAACAAATGCATCATGCACTTCCTCGGTCAGGGCTGAATCAGCAAGTCCCCTGAT Found at i:189372 original size:10 final size:9 Alignment explanation

Indices: 189346--189371 Score: 52 Period size: 9 Copynumber: 2.9 Consensus size: 9 189336 TCCCGTAATT 189346 AAAAAAAAG 1 AAAAAAAAG 189355 AAAAAAAAG 1 AAAAAAAAG 189364 AAAAAAAA 1 AAAAAAAA 189372 ATTCATACAC Statistics Matches: 17, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 17 1.00 ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00 Consensus pattern (9 bp): AAAAAAAAG Found at i:193098 original size:2 final size:2 Alignment explanation

Indices: 193091--193131 Score: 82 Period size: 2 Copynumber: 20.5 Consensus size: 2 193081 TTATTCCCCG 193091 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T 193132 TACAGTTTGA Statistics Matches: 39, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 39 1.00 ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51 Consensus pattern (2 bp): TC Found at i:193842 original size:3 final size:3 Alignment explanation

Indices: 193836--193909 Score: 148 Period size: 3 Copynumber: 24.7 Consensus size: 3 193826 TATTAATGTA 193836 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT 193884 TCT TCT TCT TCT TCT TCT TCT TCT TC 1 TCT TCT TCT TCT TCT TCT TCT TCT TC 193910 AGAATACTGA Statistics Matches: 71, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 3 71 1.00 ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66 Consensus pattern (3 bp): TCT Found at i:196639 original size:21 final size:21 Alignment explanation

Indices: 196605--196684 Score: 90 Period size: 21 Copynumber: 3.8 Consensus size: 21 196595 AATTTAATGC * * * 196605 TATGCTATGGTATGCGATTT- 1 TATGATATGCTATGAGATTTG 196625 TAATGATATGCTATGAGATTTG 1 T-ATGATATGCTATGAGATTTG * 196647 TATGCTATGCTATGAGATTTG 1 TATGATATGCTATGAGATTTG * * 196668 TATGCTTTGCTATGAGA 1 TATGATATGCTATGAGA 196685 GATTGAAATG Statistics Matches: 53, Mismatches: 5, Indels: 3 0.87 0.08 0.05 Matches are distributed among these distances: 20 1 0.02 21 51 0.96 22 1 0.02 ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42 Consensus pattern (21 bp): TATGATATGCTATGAGATTTG Found at i:196666 original size:42 final size:42 Alignment explanation

Indices: 196605--196684 Score: 108 Period size: 42 Copynumber: 1.9 Consensus size: 42 196595 AATTTAATGC * * 196605 TATGCTATGGTATGCGATTT-TAATGATATGCTATGAGATTTG 1 TATGCTATGCTATGAGATTTGT-ATGATATGCTATGAGATTTG * * 196647 TATGCTATGCTATGAGATTTGTATGCTTTGCTATGAGA 1 TATGCTATGCTATGAGATTTGTATGATATGCTATGAGA 196685 GATTGAAATG Statistics Matches: 33, Mismatches: 4, Indels: 2 0.85 0.10 0.05 Matches are distributed among these distances: 42 32 0.97 43 1 0.03 ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42 Consensus pattern (42 bp): TATGCTATGCTATGAGATTTGTATGATATGCTATGAGATTTG Found at i:196907 original size:10 final size:10 Alignment explanation

Indices: 196889--196922 Score: 50 Period size: 10 Copynumber: 3.4 Consensus size: 10 196879 TATAATGTTG * 196889 TATGCTATGC 1 TATGGTATGC 196899 TATGGTATGC 1 TATGGTATGC * 196909 TATGGTATGA 1 TATGGTATGC 196919 TATG 1 TATG 196923 ACGAATGAGA Statistics Matches: 22, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 10 22 1.00 ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41 Consensus pattern (10 bp): TATGGTATGC Found at i:196908 original size:15 final size:15 Alignment explanation

Indices: 196888--196922 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 196878 ATATAATGTT 196888 GTATGCTATGCTATG 1 GTATGCTATGCTATG * 196903 GTATGCTATGGTATG 1 GTATGCTATGCTATG * 196918 ATATG 1 GTATG 196923 ACGAATGAGA Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.23, C:0.09, G:0.29, T:0.40 Consensus pattern (15 bp): GTATGCTATGCTATG Found at i:196973 original size:21 final size:21 Alignment explanation

Indices: 196935--197022 Score: 126 Period size: 21 Copynumber: 4.2 Consensus size: 21 196925 GAATGAGATT 196935 CTATGAGATTGT--ATGCTATG 1 CTATGAGATT-TCAATGCTATG * * 196955 GTATGAGATTCCAATGCTATG 1 CTATGAGATTTCAATGCTATG * 196976 CTATGAGATTTCTATGCTATG 1 CTATGAGATTTCAATGCTATG 196997 CTATGAGATTTCAATGCTATG 1 CTATGAGATTTCAATGCTATG 197018 CTATG 1 CTATG 197023 CTATGGTGTA Statistics Matches: 60, Mismatches: 6, Indels: 3 0.87 0.09 0.04 Matches are distributed among these distances: 20 9 0.15 21 51 0.85 ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39 Consensus pattern (21 bp): CTATGAGATTTCAATGCTATG Found at i:196992 original size:42 final size:41 Alignment explanation

Indices: 196935--197022 Score: 140 Period size: 42 Copynumber: 2.1 Consensus size: 41 196925 GAATGAGATT * * 196935 CTATGAGATTGTATGCTATGGTATGAGATTCCAATGCTATG 1 CTATGAGATTCTATGCTATGCTATGAGATTCCAATGCTATG * 196976 CTATGAGATTTCTATGCTATGCTATGAGATTTCAATGCTATG 1 CTATGAGA-TTCTATGCTATGCTATGAGATTCCAATGCTATG 197018 CTATG 1 CTATG 197023 CTATGGTGTA Statistics Matches: 43, Mismatches: 3, Indels: 1 0.91 0.06 0.02 Matches are distributed among these distances: 41 8 0.19 42 35 0.81 ACGTcount: A:0.26, C:0.14, G:0.22, T:0.39 Consensus pattern (41 bp): CTATGAGATTCTATGCTATGCTATGAGATTCCAATGCTATG Found at i:200509 original size:21 final size:21 Alignment explanation

Indices: 200485--200578 Score: 64 Period size: 21 Copynumber: 4.5 Consensus size: 21 200475 AACAAATAAA 200485 GACGAATTAGATATTTGTTCG 1 GACGAATTAGATATTTGTTCG * **** * 200506 GACGAATTTTGA-ACAAATTAG 1 GACGAA-TTAGATATTTGTTCG ** 200527 GACGAATTAGATATTTGTTTA 1 GACGAATTAGATATTTGTTCG * ** 200548 GACGAATAACTTATTTGTTCG 1 GACGAATTAGATATTTGTTCG * 200569 GACGTATTAG 1 GACGAATTAG 200579 CCTTTAGTTC Statistics Matches: 50, Mismatches: 21, Indels: 4 0.67 0.28 0.05 Matches are distributed among these distances: 20 4 0.08 21 42 0.84 22 4 0.08 ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36 Consensus pattern (21 bp): GACGAATTAGATATTTGTTCG Found at i:200514 original size:42 final size:42 Alignment explanation

Indices: 200451--200554 Score: 145 Period size: 42 Copynumber: 2.5 Consensus size: 42 200441 CGGGCGAGTA * ** 200451 AGATATTTTTTCGGATAAATTTTGAACAAATAAAGACGAATT 1 AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT * * 200493 AGATATTTGTTCGGACGAATTTTGAACAAATTAGGACGAATT 1 AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT ** 200535 AGATATTTGTTTAGACGAAT 1 AGATATTTGTTCGGACGAAT 200555 AACTTATTTG Statistics Matches: 55, Mismatches: 7, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 42 55 1.00 ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36 Consensus pattern (42 bp): AGATATTTGTTCGGACGAATTTTGAACAAATAAAGACGAATT Found at i:200612 original size:2 final size:2 Alignment explanation

Indices: 200605--200654 Score: 100 Period size: 2 Copynumber: 25.0 Consensus size: 2 200595 GTAAAAGAAC 200605 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA 200647 GA GA GA GA 1 GA GA GA GA 200655 NNNNNNNNNN Statistics Matches: 48, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 48 1.00 ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00 Consensus pattern (2 bp): GA Found at i:205046 original size:17 final size:17 Alignment explanation

Indices: 205024--205056 Score: 57 Period size: 17 Copynumber: 1.9 Consensus size: 17 205014 AATATGAGCA 205024 TTAATATATATTTTGCT 1 TTAATATATATTTTGCT * 205041 TTAATATTTATTTTGC 1 TTAATATATATTTTGC 205057 CGTGGCTTAG Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61 Consensus pattern (17 bp): TTAATATATATTTTGCT Found at i:207970 original size:22 final size:23 Alignment explanation

Indices: 207918--207963 Score: 67 Period size: 23 Copynumber: 2.0 Consensus size: 23 207908 CGTAGACGTA * * 207918 GAAGTTACGAATGACGTAAGATT 1 GAAGTTACGAATGACGTAAAATG 207941 GAAGTTACGAAT-ACGTAAAATG 1 GAAGTTACGAATGACGTAAAATG 207963 G 1 G 207964 TATTTACTAG Statistics Matches: 21, Mismatches: 2, Indels: 1 0.88 0.08 0.04 Matches are distributed among these distances: 22 9 0.43 23 12 0.57 ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24 Consensus pattern (23 bp): GAAGTTACGAATGACGTAAAATG Found at i:212839 original size:8 final size:8 Alignment explanation

Indices: 212826--212854 Score: 58 Period size: 8 Copynumber: 3.6 Consensus size: 8 212816 TGGTTTCACC 212826 CTGTCCGT 1 CTGTCCGT 212834 CTGTCCGT 1 CTGTCCGT 212842 CTGTCCGT 1 CTGTCCGT 212850 CTGTC 1 CTGTC 212855 TGTAGACGCA Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 8 21 1.00 ACGTcount: A:0.00, C:0.38, G:0.24, T:0.38 Consensus pattern (8 bp): CTGTCCGT Found at i:252805 original size:32 final size:33 Alignment explanation

Indices: 252730--252806 Score: 120 Period size: 33 Copynumber: 2.4 Consensus size: 33 252720 GATTTTGGTC 252730 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG * * 252763 TCAATATTCAATGTTGAAAAATGACCCCC-GGG 1 TCAATTTTCAACGTTGAAAAATGACCCCCTGGG * 252795 TCCATTTTCAAC 1 TCAATTTTCAAC 252807 CCGGGTCAAT Statistics Matches: 39, Mismatches: 5, Indels: 1 0.87 0.11 0.02 Matches are distributed among these distances: 32 12 0.31 33 27 0.69 ACGTcount: A:0.31, C:0.25, G:0.16, T:0.29 Consensus pattern (33 bp): TCAATTTTCAACGTTGAAAAATGACCCCCTGGG Found at i:256832 original size:169 final size:164 Alignment explanation

Indices: 256345--256922 Score: 445 Period size: 169 Copynumber: 3.5 Consensus size: 164 256335 AATGAATCAT * * * * * * 256345 CTGGCTGATTAGTTTCTAAGAAGTAGAT-TCTTTTAAAGATGTACTCTATATATTCCTATGTAAA 1 CTGGCTGATTAGTTTCTTAGACG-A-ATAT-TTTTAAAGGTTTACTCAATATATTCCTATGAAAA ** * * * * * * * * * * 256409 ACTTCCAACCCCCCATTGTTGCCACAAAATTCCCCCGGAGGTCATAATTTTTACAAC-TTGGAAT 63 AAGT-CGACCCCCCAATGTGGCCCCACAATACCCCCGGA-GTCATGATTTTCACGACAGT-GAAT * ** 256473 CTACACTACCCTACAATGCTTCCACACAAATTTCAGCTTTC 125 CTACACTACCTTAGGATGCTTCCACACAAA-TTCAGCTTTC * 256514 CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCTTATGAAAAAAG 1 CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAAG * * ** ** 256579 TCGACCCTCTAATGTGGCCCCACCCTACCCCCGGAGGTCATGATTTTCACGACTTTGAATCTACA 66 TCGACCCCCCAATGTGGCCCCACAATACCCCCGGA-GTCATGATTTTCACGACAGTGAATCTACA * 256644 CTACCTGAGGATGCTTCCACACAAATGTCAGCTTTC 130 CTACCTTAGGATGCTTCCACACAAAT-TCAGCTTTC * ** * * * 256680 CTGGTTTTTTTAGTTTCTTAGA-GGATGATTTTTAAAGTTTTACTCAATATATTCCTATGTTAAA 1 CTGG-CTGATTAGTTTCTTAGACGAAT-ATTTTTAAAGGTTTACTCAATATATTCCTATG-AAAA *** * * 256744 CTTTAAC-ACCCCCCCATTGTGGCCCCA-AATACCCCAATGGA-TCATGATTTTCAC-ATCAGTG 63 AAGT--CGA-CCCCCCAATGTGGCCCCACAATACCCC--CGGAGTCATGATTTTCACGA-CAGTG * 256805 AATCTACACTATCTTAGGATGCTTCCACACAAATTCCAGCTTTC 122 AATCTACACTACCTTAGGATGCTTCCACACAAATT-CAGCTTTC * * * ** * ** * * 256849 CTGGCCGACTAGATTT-TGAGATTAAGATTTTTAAAGAATTACTCAATATATTCCTTTG-TAAAA 1 CTGGCTGATTAG-TTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAA * 256912 TTCGACCCCCC 65 GTCGACCCCCC 256923 CCCCCCCCTA Statistics Matches: 332, Mismatches: 61, Indels: 37 0.77 0.14 0.09 Matches are distributed among these distances: 164 7 0.02 165 2 0.01 166 89 0.27 167 79 0.24 168 44 0.13 169 92 0.28 170 16 0.05 171 3 0.01 ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34 Consensus pattern (164 bp): CTGGCTGATTAGTTTCTTAGACGAATATTTTTAAAGGTTTACTCAATATATTCCTATGAAAAAAG TCGACCCCCCAATGTGGCCCCACAATACCCCCGGAGTCATGATTTTCACGACAGTGAATCTACAC TACCTTAGGATGCTTCCACACAAATTCAGCTTTC Found at i:257018 original size:11 final size:11 Alignment explanation

Indices: 257002--257026 Score: 50 Period size: 11 Copynumber: 2.3 Consensus size: 11 256992 GCGGGGGTCA 257002 TGATTTTTACC 1 TGATTTTTACC 257013 TGATTTTTACC 1 TGATTTTTACC 257024 TGA 1 TGA 257027 GGATGCTTCC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 11 14 1.00 ACGTcount: A:0.20, C:0.16, G:0.12, T:0.52 Consensus pattern (11 bp): TGATTTTTACC Found at i:281606 original size:178 final size:179 Alignment explanation

Indices: 281281--281643 Score: 435 Period size: 178 Copynumber: 2.0 Consensus size: 179 281271 GAGAAATGGA * * ** * 281281 GTACCC-ATATGCAATATTTTGTCAAAAAATTATTAAGTTTTAAAGCTAGTATTTCTTCATTGAT 1 GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTATTTCTTCATTAAT * * * * * 281345 AATCAGAAATCAAAATCCTAGCAATTTGCACACCTCTGATTTATGTACAATTGATCTGCAAAAAA 66 AACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAAA * 281410 AGAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG 131 ACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG * * * 281459 GTACCCTATATGTAATATTTTGCCAAAAAATGA-TAAGTTCAAAAGCTGGTATATTTTTCATTAA 1 GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTAT-TTCTTCATTAA * * * ** * * 281523 TTACCAG-AATTAAAATTCTAGCTCTGTACACACTTCTCATATATGTACAATTGATCTGCAAAAG 65 TAACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAA * * * * * ** 281587 AACTACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACCATAAGG 130 AACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG * 281637 ATACCCT 1 GTACCCT 281644 CTTGGCAGCC Statistics Matches: 154, Mismatches: 29, Indels: 4 0.82 0.16 0.02 Matches are distributed among these distances: 178 117 0.76 179 37 0.24 ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32 Consensus pattern (179 bp): GTACCCTATATGCAATATTTTGCCAAAAAATGATTAAGTTCAAAAGCTAGTATTTCTTCATTAAT AACCAGAAATCAAAATCCTAGCAATGTACACACCTCTCATATATGTACAATTGATCTGCAAAAAA ACAACGTCCTACCTTGAAAACTGTAGGAGAACTTATCCGTAAAATAAGG Found at i:285852 original size:200 final size:200 Alignment explanation

Indices: 285509--285903 Score: 790 Period size: 200 Copynumber: 2.0 Consensus size: 200 285499 AGGTATCTGA 285509 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA 1 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA 285574 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC 66 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC 285639 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA 131 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA 285704 CCCCC 196 CCCCC 285709 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA 1 CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA 285774 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC 66 CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC 285839 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA 131 AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA 285904 NCTCCCCCCC Statistics Matches: 195, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 200 195 1.00 ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35 Consensus pattern (200 bp): CAGCTATTTGTTATCACTATTGCAACACATTTGGAAAGAAAGAAGTTGTATATCATTTTTGCAAA CTACTTTCAAATGCAAGAAACACTTTACCTAATGAACAATTTAAAATACACAATTACGGTTTTAC AGACATTCATGTCAATTATTTATACAAGTGTTAACACCTTGTTAATTGCTTGAACTTCTATTCAA CCCCC Found at i:286557 original size:97 final size:97 Alignment explanation

Indices: 286391--286580 Score: 371 Period size: 97 Copynumber: 2.0 Consensus size: 97 286381 TGATATAAAT * 286391 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACTATATTTTGGCTTTGAGAAGTATCTTGA 1 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA 286456 TATTTTACCTGTAAAACTAAGAAAAAAATTCA 66 TATTTTACCTGTAAAACTAAGAAAAAAATTCA 286488 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA 1 TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA 286553 TATTTTACCTGTAAAACTAAGAAAAAAA 66 TATTTTACCTGTAAAACTAAGAAAAAAA 286581 ACTCAAGACC Statistics Matches: 92, Mismatches: 1, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 97 92 1.00 ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36 Consensus pattern (97 bp): TGTTCTTCCAGAGGTCAAGTGTATAAAATTTTAAAACAATATTTTGGCTTTGAGAAGTATCTTGA TATTTTACCTGTAAAACTAAGAAAAAAATTCA Found at i:287656 original size:53 final size:54 Alignment explanation

Indices: 287570--287686 Score: 157 Period size: 53 Copynumber: 2.2 Consensus size: 54 287560 TGCTAATACT * * * * 287570 TTATTTCAA-AAGTGGTTGTAATGAAATGTATACCCAACCACTATTGGAATAAA 1 TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA * * * 287623 TTATTTCAATAAAT-GTTATAATGCAATGCATACCCAAGCACTATTGAAATAAT 1 TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA 287676 TTATTTCAATA 1 TTATTTCAATA 287687 GTGGTTGAAT Statistics Matches: 56, Mismatches: 7, Indels: 2 0.86 0.11 0.03 Matches are distributed among these distances: 53 53 0.95 54 3 0.05 ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35 Consensus pattern (54 bp): TTATTTCAATAAATGGTTATAATGAAATGCATACCCAACCACTATTGAAATAAA Found at i:327706 original size:14 final size:15 Alignment explanation

Indices: 327687--327723 Score: 58 Period size: 14 Copynumber: 2.5 Consensus size: 15 327677 TTGCTTTTGA 327687 GTTTTTTTTTG-TTT 1 GTTTTTTTTTGTTTT * 327701 GTTTTTGTTTGTTTT 1 GTTTTTTTTTGTTTT 327716 GTTTTTTT 1 GTTTTTTT 327724 ATAATTTATT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 14 10 0.50 15 10 0.50 ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84 Consensus pattern (15 bp): GTTTTTTTTTGTTTT Found at i:331699 original size:2 final size:2 Alignment explanation

Indices: 331694--331735 Score: 77 Period size: 2 Copynumber: 21.5 Consensus size: 2 331684 CCCCCCCCCC 331694 CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT 1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT 331735 C 1 C 331736 ATTGAATACA Statistics Matches: 39, Mismatches: 0, Indels: 2 0.95 0.00 0.05 Matches are distributed among these distances: 1 1 0.03 2 38 0.97 ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50 Consensus pattern (2 bp): CT Found at i:343823 original size:27 final size:27 Alignment explanation

Indices: 343793--343869 Score: 71 Period size: 27 Copynumber: 3.1 Consensus size: 27 343783 CAAAATCACA 343793 AAAGTTTTACATAATAAAGGTCAGAGG 1 AAAGTTTTACATAATAAAGGTCAGAGG ** * 343820 AAAGAATTAC---A-AAA--TCACA-- 1 AAAGTTTTACATAATAAAGGTCAGAGG 343839 AAAGTTTTACATAATAAAGGTCAGAGG 1 AAAGTTTTACATAATAAAGGTCAGAGG 343866 AAAG 1 AAAG 343870 AATGACAAAA Statistics Matches: 36, Mismatches: 6, Indels: 16 0.62 0.10 0.28 Matches are distributed among these distances: 19 8 0.22 21 4 0.11 22 1 0.03 23 6 0.17 24 1 0.03 25 4 0.11 27 12 0.33 ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22 Consensus pattern (27 bp): AAAGTTTTACATAATAAAGGTCAGAGG Found at i:344006 original size:46 final size:46 Alignment explanation

Indices: 343779--343998 Score: 377 Period size: 46 Copynumber: 4.8 Consensus size: 46 343769 CAAGTATAAC 343779 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA 1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA 343825 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA 1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA * * * 343871 ATGACAAAATCGCAAAAGTTTTAAATAATAAAGGTCAGAGGAAAGA 1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA * ** 343917 ATGACAAAATTGCAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA 1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA * 343963 TTTACAAAATCACAAAAGTTTTACATAATAAAGGTC 1 ATTACAAAATCACAAAAGTTTTACATAATAAAGGTC 343999 TGGGGAAATT Statistics Matches: 165, Mismatches: 9, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 46 165 1.00 ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23 Consensus pattern (46 bp): ATTACAAAATCACAAAAGTTTTACATAATAAAGGTCAGAGGAAAGA Found at i:345252 original size:25 final size:25 Alignment explanation

Indices: 345220--345282 Score: 126 Period size: 25 Copynumber: 2.5 Consensus size: 25 345210 GAGGGCTATA 345220 ATATCAATGTACCCGTCCAAACACT 1 ATATCAATGTACCCGTCCAAACACT 345245 ATATCAATGTACCCGTCCAAACACT 1 ATATCAATGTACCCGTCCAAACACT 345270 ATATCAATGTACC 1 ATATCAATGTACC 345283 TGCCCAGATA Statistics Matches: 38, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 25 38 1.00 ACGTcount: A:0.37, C:0.30, G:0.08, T:0.25 Consensus pattern (25 bp): ATATCAATGTACCCGTCCAAACACT Found at i:345287 original size:89 final size:91 Alignment explanation

Indices: 345146--345327 Score: 280 Period size: 89 Copynumber: 2.0 Consensus size: 91 345136 AATGTACTTA * * 345146 TCCAAACACTATATCAATGTACCCGTCCAAATACTATGTCAATGTGACTGCCCAGATA-A-TTGT 1 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGACTGCCCAGATATACTTGT * 345209 AGAGGGCTATAATATCAATGTACCCG 66 AGAGGGCTATAATATCAATATACCCG 345235 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGT-ACCTGCCCAGATACTGTAC 1 TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGA-CTGCCCAGATA---TAC 345299 TTGTAGAGGGCTATAATATCAATATACCC 62 TTGTAGAGGGCTATAATATCAATATACCC 345328 ACCCAACTAC Statistics Matches: 84, Mismatches: 3, Indels: 7 0.89 0.03 0.07 Matches are distributed among these distances: 88 1 0.01 89 54 0.64 93 1 0.01 94 28 0.33 ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27 Consensus pattern (91 bp): TCCAAACACTATATCAATGTACCCGTCCAAACACTATATCAATGTGACTGCCCAGATATACTTGT AGAGGGCTATAATATCAATATACCCG Found at i:345543 original size:194 final size:195 Alignment explanation

Indices: 345296--346854 Score: 639 Period size: 194 Copynumber: 7.8 Consensus size: 195 345286 CCAGATACTG * 345296 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAACTACTTGTAGAGGGCTATAATATCAAT 1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT * * * 345361 TTAACTAACCAAATACTTGTATAGAGCTATAATATCAATGTACCCACCCAAATACCTGTAGAGGG 66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG * * * * * 345426 CTATGATATCATTGTAACTGTCCTAATACTTGTGGAGAGTT-ATAAT-TCAATTTAACTGTCCTA 131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGA-TTAATAATATCAATGTAACTGTCCAA 345489 A 195 A * * * * 345490 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT 1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT ** * * ** ** * 345555 GTAACTGTCCAAATACTTGTAGAGGGTTATAATAACAATGTATTCGTCCAAATACTTGTAGAGGG 66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG * 345620 TTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA 131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA * * **** * * * * * 345685 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATATCACT 1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT * ** * * * * * * *** * 345749 TTAACTGTCCTAATACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAATACTTGTAGAGGG 66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG * * * * * * * * ** * 345814 TTAAAATATCTATGTAACTGT-CTAAATAC-TGT-GACATCATTAGATTTCGTGGTGGCTCAATT 131 CTATAATATCAATGTAACTGTCCT-AATACTTATGGAGATTAATA-ATATC--AAT-G-T-AACT * ** 345876 TTCGTGGAA 189 GTC--CAAA * * * ** * * * * ** * 345885 TTCGTGGGTACATGTACCTCTCATCCATGAAT-TA-ACATCTTCCATTAATAAAT-T--AGGGTT 1 TAC-T-TGTAGA-G-GGCTATAAT--ATCAATATACCCA-C--CCA--AATACTTGTAGAGGGCT ** *** ** * 345945 ATAA-AGTC-A--T-A-TATTCTTTTGA-AGGTATA-AG--ATAATACACGAAAT-TACTTCC-C 55 ATAATA-TCAATGTAACTAACCAAAT-ACTTGTAGAGAGCTATAATA-AC--AATGTAC--CCAC * * ** * * * * * * * * * * 345998 CGC-TA-ACTTGTA-A--AATTTAAGCAATCCACGAAGATTGGCCCCCACTTATTTTAATGTTTC 113 C-CAAATACCTGTAGAGGGCTATAA--TATCAATGTA-ACT-G-TCCTA-ATA-CTT-ATG---- * * * * ** 346058 CACATTATTTGTGCAATGTACAATGTAACTGTCGTAA 165 GAGATTA---AT--AATAT-CAATGTAACTGTCCAAA * * ** * * 346095 TACTTGTAGAGGGCTATAATATCAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATATCAT 1 TACTTGTAGAGGGCTATAATATCAATATACCC-ACCCAAATACTTGTAGAGGGCTATAATATCAA ** * * * ** * * 346160 TG-AGACTGTCCAAATACTTGTAGATG-GATATAATATCAATGTAACTGCCCAGATACTTGTAGA 65 TGTA-ACTAACCAAATACTTGTAGA-GAGCTATAATAACAATGTACCCACCCAAATACCTGTAGA * * * * * * ** * * 346223 GGACTATAATTTCCATGTACCCGTCCAAATACTATATCAATGTACCCGTCCAAACACTATATCAA 128 GGGCTATAATATCAATGTAACTGTCCTAATACT-TATGGA-G-A----T--TAATA--ATATCAA * * 346288 TGTACCTGCCCAGATA 182 TGTAACTGTCCA-A-A * * * 346304 CTGTACTTGTAGAGGGTTATAATATCAATATACCCACCGAACTACTTGTAGAGGGCTATAATATC 1 ---TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATC * * * * 346369 AATTTAACTAACCAAATACTTGTATATAGCTATAATATCAATGTACCCACCCAAATACCTGTAGA 63 AATGTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGA * * * * 346434 GGGCTATGATATCATTGTAACTGTCCTAATACTTGTGGAGAGTT-ATAAT-TCAATTTAACTGTC 128 GGGCTATAATATCAATGTAACTGTCCTAATACTTATGGAGA-TTAATAATATCAATGTAACTGTC * 346497 CTAA 192 CAAA * * * * 346501 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT 1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT ** * * ** ** * 346566 GTAACTGTCCAAATACTTGTAGAGGGTTATAATAACAATGTATTCGTCCAAATACTTGTAGAGGG 66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG * 346631 TTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA 131 CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA * * **** * * * * * 346696 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATATCACT 1 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT * ** * * * * * * *** * 346760 TTAACTGTCCTAATACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAATACTTGTAGAGGG 66 GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG * * * 346825 TTAAAATATCTATGTAACTGT-CTAAATACT 131 CTATAATATCAATGTAACTGTCCT-AATACT 346855 GTGACATCAT Statistics Matches: 1018, Mismatches: 249, Indels: 196 0.70 0.17 0.13 Matches are distributed among these distances: 192 7 0.01 193 14 0.01 194 488 0.48 195 113 0.11 196 1 0.00 197 2 0.00 198 9 0.01 199 18 0.02 200 14 0.01 201 13 0.01 202 24 0.02 203 8 0.01 204 15 0.01 205 18 0.02 206 19 0.02 207 24 0.02 208 13 0.01 209 15 0.01 210 23 0.02 211 111 0.11 212 49 0.05 213 7 0.01 214 6 0.01 215 2 0.00 216 3 0.00 217 2 0.00 ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33 Consensus pattern (195 bp): TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAATACTTGTAGAGGGCTATAATATCAAT GTAACTAACCAAATACTTGTAGAGAGCTATAATAACAATGTACCCACCCAAATACCTGTAGAGGG CTATAATATCAATGTAACTGTCCTAATACTTATGGAGATTAATAATATCAATGTAACTGTCCAAA Found at i:345716 original size:39 final size:39 Alignment explanation

Indices: 345296--345843 Score: 564 Period size: 39 Copynumber: 14.1 Consensus size: 39 345286 CCAGATACTG * * * *** * 345296 TACTTGTAGAGGGCTATAATATCAATATACCCACCCAAC 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * ** 345335 TACTTGTAGAGGGCTATAATATCAATTTAACTAACCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * * *** 345374 TACTTGTATAGAGCTATAATATCAATGTACCCACCCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * * * 345413 TACCTGTAGAGGGCTATGATATCATTGTAACTGTCCTAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * * 345452 TACTTGTGGAGAGTTATAAT-TCAATTTAACTGTCCTAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * *** 345490 TACTTGAAGAGAGTTATAATATCAATGTACCCACCCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * 345529 TACTTGTAGAGGGCTATAATATCAATGTAACTGTCCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * 345568 TACTTGTAGAGGGTTATAATAACAATGT-ATTCGTCCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACT-GTCCAAA * 345607 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCTAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * 345646 TACTTATGGA-GATTAATAATATCAATGTAACTGTCCAAA 1 TACTTGTAGAGGGTT-ATAATATCAATGTAACTGTCCAAA * * * * 345685 TACTTGTAGAGGGCTATAATATCAATTTAACTGTTCAAG 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * * * * 345724 TACTTGTCGAGAG-AATAATATCACTTTAACTGTCCTAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * 345762 TACTTGTAGAGGGTTATAATATCAGTGTAACTGTCCAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA * * * 345801 TACTTGTAGAGGGTTAAAATATCTATGTAACTGTCTAAA 1 TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA 345840 TACT 1 TACT 345844 GTGACATCAT Statistics Matches: 426, Mismatches: 77, Indels: 12 0.83 0.15 0.02 Matches are distributed among these distances: 38 70 0.16 39 352 0.83 40 4 0.01 ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33 Consensus pattern (39 bp): TACTTGTAGAGGGTTATAATATCAATGTAACTGTCCAAA Found at i:346142 original size:40 final size:39 Alignment explanation

Indices: 346078--346854 Score: 540 Period size: 39 Copynumber: 19.5 Consensus size: 39 346068 GTGCAATGTA * ** 346078 CAATGTAACTGTCGTAATACTTGTAGAGGGCTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * 346117 CAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATAT 1 CAATGTAACCGTC-CAAATACTTGTAGAGGGCTATAATAT * * * * 346157 CATTG-AGACTGTCCAAATACTTGTAGATGGATATAATAT 1 CAATGTA-ACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * * 346196 CAATGTAACTGCCCAGATACTTGTAGAGGACTATAATTT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * ** * * 346235 CCATGTACCCGTCCAAATACTATATCAATGTACCCGTCCAAACACTATAT 1 CAATGTAACCGTCCAAATACT-TGT--A-G-A---GGGC-TATA--ATAT * * 346285 CAATGT-ACCTGCCCAGATACTGTACTTGTAGAGGGTTATAATAT 1 CAATGTAACC-GTCCA-A-A---TACTTGTAGAGGGCTATAATAT * ** * 346329 CAATAT-ACCCACCGAACTACTTGTAGAGGGCTATAATAT 1 CAATGTAACCGTCC-AAATACTTGTAGAGGGCTATAATAT * *** * ** 346368 CAATTTAACTAACCAAATACTTGTATATAGCTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * ** * * 346407 CAATGTACCCACCCAAATACCTGTAGAGGGCTATGATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * * * 346446 CATTGTAACTGTCCTAATACTTGTGGAGAGTTATAAT-T 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * * * 346484 CAATTTAACTGTCCTAATACTTGAAGAGAGTTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * ** 346523 CAATGTACCCACCCAAATACTTGTAGAGGGCTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * 346562 CAATGTAACTGTCCAAATACTTGTAGAGGGTTATAATAA 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT ** * 346601 CAATGTATTCGTCCAAATACTTGTAGAGGGTTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * ** 346640 CAATGTAACTGTCCTAATACTTATGGA-GATTAATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCT-ATAATAT * 346679 CAATGTAACTGTCCAAATACTTGTAGAGGGCTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * * * * 346718 CAATTTAACTGTTCAAGTACTTGTCGAGAG-AATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * * 346756 CACTTTAACTGTCCTAATACTTGTAGAGGGTTATAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * * 346795 CAGTGTAACTGTCCAAATACTTGTAGAGGGTTAAAATAT 1 CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT * * * 346834 CTATGTAACTGTCTAAATACT 1 CAATGTAACCGTCCAAATACT 346855 GTGACATCAT Statistics Matches: 586, Mismatches: 126, Indels: 52 0.77 0.16 0.07 Matches are distributed among these distances: 38 68 0.12 39 426 0.73 40 41 0.07 42 1 0.00 43 4 0.01 44 14 0.02 46 2 0.00 47 3 0.01 48 2 0.00 49 2 0.00 50 13 0.02 51 2 0.00 52 2 0.00 54 2 0.00 55 4 0.01 ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32 Consensus pattern (39 bp): CAATGTAACCGTCCAAATACTTGTAGAGGGCTATAATAT Found at i:346267 original size:25 final size:25 Alignment explanation

Indices: 346237--346293 Score: 105 Period size: 25 Copynumber: 2.3 Consensus size: 25 346227 TATAATTTCC * 346237 ATGTACCCGTCCAAATACTATATCA 1 ATGTACCCGTCCAAACACTATATCA 346262 ATGTACCCGTCCAAACACTATATCA 1 ATGTACCCGTCCAAACACTATATCA 346287 ATGTACC 1 ATGTACC 346294 TGCCCAGATA Statistics Matches: 31, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 25 31 1.00 ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26 Consensus pattern (25 bp): ATGTACCCGTCCAAACACTATATCA Found at i:347147 original size:40 final size:40 Alignment explanation

Indices: 347101--347207 Score: 128 Period size: 40 Copynumber: 2.7 Consensus size: 40 347091 CTGTCGTAAT * 347101 ACTTGTAGAGGGCTATAATATCAATGTA-CCCGTCAAAAAA 1 ACTTGTAGAGGGCTATAATATCAATGTAGACCGTC-AAAAA * * * * 347141 ACTTGTAGAGGGCTATAATATCATTG-AGACTGTCCAAAT 1 ACTTGTAGAGGGCTATAATATCAATGTAGACCGTCAAAAA * * 347180 ACTTGTAGATGGATATAATATCAATGTA 1 ACTTGTAGAGGGCTATAATATCAATGTA 347208 ACTGCCCAGA Statistics Matches: 57, Mismatches: 8, Indels: 4 0.83 0.12 0.06 Matches are distributed among these distances: 39 27 0.47 40 30 0.53 ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30 Consensus pattern (40 bp): ACTTGTAGAGGGCTATAATATCAATGTAGACCGTCAAAAA Found at i:347197 original size:39 final size:38 Alignment explanation

Indices: 347083--347237 Score: 132 Period size: 39 Copynumber: 3.9 Consensus size: 38 347073 GTGCAATGTA * ** * 347083 CAATGTAACTGTCGTAATACTTGTAGAGGGCTATAATAT 1 CAATGTAACTGCCCAAATACTTGTAGA-GGATATAATAT * * ** * * 347122 CAATGTACCCGTCAAAAAAACTTGTAGAGGGCTATAATAT 1 CAATGTAACTG-CCCAAATACTTGTAGA-GGATATAATAT * * 347162 CATTG-AGACTGTCCAAATACTTGTAGATGGATATAATAT 1 CAATGTA-ACTGCCCAAATACTTGTAGA-GGATATAATAT * 347201 CAATGTAACTGCCCAGATACTTGTAGAGGACTATAAT 1 CAATGTAACTGCCCAAATACTTGTAGAGGA-TATAAT 347238 TTCNNNNNNN Statistics Matches: 93, Mismatches: 19, Indels: 8 0.77 0.16 0.07 Matches are distributed among these distances: 38 3 0.03 39 60 0.65 40 30 0.32 ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30 Consensus pattern (38 bp): CAATGTAACTGCCCAAATACTTGTAGAGGATATAATAT Found at i:354865 original size:24 final size:24 Alignment explanation

Indices: 354817--354878 Score: 72 Period size: 24 Copynumber: 2.6 Consensus size: 24 354807 TCTGTTCATC * 354817 CTCATCACCTCAGTCATCCTCGTT 1 CTCATCGCCTCAGTCATCCTCGTT * * * 354841 CTCATCGCCTCATTCATCGTTGTT 1 CTCATCGCCTCAGTCATCCTCGTT * 354865 CTAATCG-CTCAGTC 1 CTCATCGCCTCAGTC 354879 GTCTTCATCA Statistics Matches: 32, Mismatches: 6, Indels: 1 0.82 0.15 0.03 Matches are distributed among these distances: 23 6 0.19 24 26 0.81 ACGTcount: A:0.16, C:0.37, G:0.11, T:0.35 Consensus pattern (24 bp): CTCATCGCCTCAGTCATCCTCGTT Found at i:366379 original size:8 final size:8 Alignment explanation

Indices: 366366--366417 Score: 50 Period size: 8 Copynumber: 6.5 Consensus size: 8 366356 AGGAATCACC 366366 CTGTCCGT 1 CTGTCCGT 366374 CTGTCCGT 1 CTGTCCGT * * 366382 CCGTCTGT 1 CTGTCCGT * * 366390 CCGTCAGT 1 CTGTCCGT 366398 CTGTCCGT 1 CTGTCCGT * * 366406 CCGTCTGT 1 CTGTCCGT 366414 CTGT 1 CTGT 366418 GCAATCGTGT Statistics Matches: 36, Mismatches: 8, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 8 36 1.00 ACGTcount: A:0.02, C:0.37, G:0.25, T:0.37 Consensus pattern (8 bp): CTGTCCGT Found at i:366385 original size:12 final size:12 Alignment explanation

Indices: 366368--366414 Score: 85 Period size: 12 Copynumber: 3.9 Consensus size: 12 366358 GAATCACCCT 366368 GTCCGTCTGTCC 1 GTCCGTCTGTCC 366380 GTCCGTCTGTCC 1 GTCCGTCTGTCC * 366392 GTCAGTCTGTCC 1 GTCCGTCTGTCC 366404 GTCCGTCTGTC 1 GTCCGTCTGTC 366415 TGTGCAATCG Statistics Matches: 33, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 33 1.00 ACGTcount: A:0.02, C:0.38, G:0.26, T:0.34 Consensus pattern (12 bp): GTCCGTCTGTCC Found at i:366417 original size:4 final size:4 Alignment explanation

Indices: 366368--366410 Score: 50 Period size: 4 Copynumber: 10.8 Consensus size: 4 366358 GAATCACCCT * * * * 366368 GTCC GTCT GTCC GTCC GTCT GTCC GTCA GTCT GTCC GTCC GTC 1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC 366411 TGTCTGTGCA Statistics Matches: 32, Mismatches: 7, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 4 32 1.00 ACGTcount: A:0.02, C:0.40, G:0.26, T:0.33 Consensus pattern (4 bp): GTCC Found at i:366686 original size:146 final size:145 Alignment explanation

Indices: 366422--367369 Score: 1304 Period size: 146 Copynumber: 6.5 Consensus size: 145 366412 GTCTGTGCAA * * 366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * 366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 366552 AGAAAAATACAAAAAT 131 AGAAAAATAC-AAAAT * * 366568 TCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 366633 TTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 366698 AGAAAAAATACAAAAT 131 AG-AAAAATACAAAAT * * * * 366714 TCGTGTCCGGCCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTACTTCATACAACGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 366779 TTATCACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 366844 AGAAAAAATACAAAAAT 131 AG-AAAAATAC-AAAAT * * 366861 TCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * * 366926 TTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC * 366991 AGAAAAAGTGCAAAAT 131 AGAAAAA-TACAAAAT ** * * * * 367007 TTTTGTCCGGCCCATATCTTT-TGTATGGAGAAACATTGGAAGTTCATAATTCACACAAATATTG 1 TCGTGTCCGGTCCATATCTTTCT-TATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG * * * * * * * 367071 CTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTAAGGTCAAGG-GAGTTG 65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCA-CTG 367135 G--GAAAAATAGTGCAAAAT 129 GCAGAAAAATA---CAAAAT * * * * 367153 TCGTGTCCGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTCTAACTTAACACAAATATT 1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT * * * 367216 GCTTAGGACCAAAGGGTGTGTCATGACCTTG-CCCAAGGTCATTTGGGCAAGGTCAAGGTCACTG 64 GCTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTG * 367280 GCAGAAAAAGTGCAAAAT 129 GCAGAAAAA-TACAAAAT * ** * 367298 TCGTGTCTGGT-CATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT 1 TCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT 367361 -CTTATGACC 64 GCTTATGACC 367370 AACAGTTTTA Statistics Matches: 720, Mismatches: 67, Indels: 32 0.88 0.08 0.04 Matches are distributed among these distances: 143 1 0.00 144 14 0.02 145 99 0.14 146 461 0.64 147 144 0.20 148 1 0.00 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29 Consensus pattern (145 bp): TCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC AGAAAAATACAAAAT Found at i:366980 original size:293 final size:293 Alignment explanation

Indices: 366422--367369 Score: 1371 Period size: 293 Copynumber: 3.2 Consensus size: 293 366412 GTCTGTGCAA ** * 366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC 1 TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC * 366552 AG-AAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTA 131 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA 366616 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA 196 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA * * 366681 AGGTCAAGGTCACTGGCAGAAAAAATACAAAAT 261 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT * * * 366714 TCGTGTCCGGCCCATATCTTTCTTATTGAGAAACATTGGAAGTTCTTACTTCATACAACGATTGC 1 TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * 366779 TTATCACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGC 66 TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC * 366844 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTA 131 AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA * * 366909 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCA 196 CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA 366974 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT 261 AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT ** * * * 367007 TTTTGTCCGGCCCATATCTTT-TGTATGGAGAAACATTGGAAGTTCATAATTCACACAAATATTG 1 TCGTGTCCGGCCCATATCTTTCT-TATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTG * * * * * * 367071 CTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTAAGGTCAAGG-GAGTTG 65 CTTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCA-CTG * * * 367135 G--GAAAAATAGTGC-AAAATTCGTGTCCGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATG 129 GCAGAAAAA-A-TACAAAAATTCGTGTCCGGTCCA-TATCTTTCGTATGGAGAAACATTGGAA-G * * * * * * 367195 TTCTAACTTAACACAAATATTGCTTAGGACCAAAGGGTGTGTCATGACCTTG-CCCAAGGTCATT 190 TTCTTACTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATT * 367259 TGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT 255 CGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT * * ** * 367298 TCGTGTCTGG-TCATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT 1 TCGTGTCCGGCCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATT 367361 -CTTATGACC 64 GCTTATGACC 367370 AACAGTTTTA Statistics Matches: 596, Mismatches: 50, Indels: 22 0.89 0.07 0.03 Matches are distributed among these distances: 290 14 0.02 291 106 0.18 292 211 0.35 293 265 0.44 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29 Consensus pattern (293 bp): TCGTGTCCGGCCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC TTATGACCTAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC AGAAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGGAGAAACATTGGAAGTTCTTA CTTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCA AGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT Found at i:367240 original size:439 final size:435 Alignment explanation

Indices: 366422--367369 Score: 1334 Period size: 439 Copynumber: 2.2 Consensus size: 435 366412 GTCTGTGCAA * 366422 TCGTGTCCGGTACATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCATACAAAGATTGC 1 TCGTGTCCGGT-CATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * * * * 366487 TTATGACCTAAGGGTGTGTCATGACCTTGGCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGC 65 TTATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC * * * 366552 AGAAAAATACAAAAATTCGTGTCCGGTCCATATCTTTCGTATGAAGAAACATTGGAAGTTCTTAC 130 AGAAAAATACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATAA * * 366617 TTCACACAAAGATTGCTTATGACCTAAGGGTGTGTCATGATCTTGACCCAAGGTCATTCGGGCAA 195 TTCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCAA * 366682 GGTCAAGGTCACTGGCAGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATTGAGAAA 260 GGTCAAGGTCACTGG-AGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATGGAGAAA * * * * * * 366747 CATTGGAAGTTCTTACTTCATACAACGATTGCTTATCACCTAAGGGTGTGTCATGACCTTGACCC 324 CATTGGAAGTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTTG-CCC 366812 AAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAAT 388 AAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATAC-AAAAT * * 366861 TCGTGTCCGGTCCATATTTTTCGTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC 1 TCGTGTCCGGT-CATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGC * 366926 TTATGACCTAAGGGTGTATCATGATCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC 65 TTATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGC * ** * * 366991 AGAAAAAGTGC-AAAATTTTTGTCCGGCCCATATCTTTTGTATGGAGAAACATTGGAAGTTCATA 130 AGAAAAA-TACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATA * * * * * 367055 ATTCACACAAATATTGCTTATGACCTTAGGATGTGTCATGACCTTGATCCAAGGTCATTTGGGTA 194 ATTCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCA * * * * 367120 AGGTCAAGG-GAGTTGG-GAAAAATAGTGCAAAATTCGTGTCCGG-TCATTATCTTTCTTATGGA 259 AGGTCAAGGTCA-CTGGAGAAAAA-A-TACAAAATTCGTGTCCGGCCCA-TATCTTTCTTATGGA * * * 367182 GAAGCATT-GAATGTTCTAACTTAACACAAATATTGCTTAGGACCAAAGGGTGTGTCATGACCTT 320 GAAACATTGGAA-GTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTT * * * 367246 GCCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAAAAGTGCAAAAT 384 GCCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAT * ** * 367298 TCGTGTCTGGTCATTATCTTTCTTATGGAGAGGCATT-GAATGTTCTTACTTCACACAAATATT- 1 TCGTGTCCGGTCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATTG 367361 CTTATGACC 64 CTTATGACC 367370 AACAGTTTTA Statistics Matches: 454, Mismatches: 47, Indels: 19 0.87 0.09 0.04 Matches are distributed among these distances: 436 14 0.03 437 61 0.13 438 50 0.11 439 327 0.72 440 2 0.00 ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29 Consensus pattern (435 bp): TCGTGTCCGGTCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACACAAAGATTGCT TATGACCTAAGGGTGTATCATGACCTTGACCCAAGGTCACTCGGGCAAGGTCAAGGTCACTGGCA GAAAAATACAAAAATTCGTGTCCGGCCCATATCTTTCGTATGAAGAAACATTGGAAGTTCATAAT TCACACAAAGATTGCTTATGACCTAAGGATGTGTCATGACCTTGACCCAAGGTCATTCGGGCAAG GTCAAGGTCACTGGAGAAAAAATACAAAATTCGTGTCCGGCCCATATCTTTCTTATGGAGAAACA TTGGAAGTTCTAACTTAACACAAAGATTGCTTAGCACCAAAGGGTGTGTCATGACCTTGCCCAAG GTCATTCGGGCAAGGTCAAGGTCACTGGCAGAAAAAATACAAAAT Found at i:375786 original size:166 final size:162 Alignment explanation

Indices: 375187--376246 Score: 1042 Period size: 166 Copynumber: 6.6 Consensus size: 162 375177 AAACTTTGCC * * * * * ** 375187 AGAATATTTTTAAAGATTTTCTGTATATATTCCTATGTAAACATTTAAACCGCCATCATGGCCCC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAA-A-TTGATCCCCCATTGTGGCCCC * * * * ** * * * * * * * 375252 GCCCAACCACTAGAGACTGTGATTT-TACAAACTTGCATTTACACTACCCGAGGATGCCTCTAC- 64 ACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT ** * * * 375315 ACAAGTTTAAGCTTTTCTGGCC-AATAGTCTTTAAAA 128 TTAA-TTTGAGCTTTTCTGGCCTAATAGT-TTTTAGA * * 375351 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTACAAATTCATCCCCCATTGTGGCCTCA 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTA-AAATTGATCCCCCATTGTGGCCCCA * * * * * * * ** 375416 CCCTACCCCTGGG-CTATTATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCA 65 CCCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTTT * * 375480 AATTTGGGCTTTCCTGGCCTAATAG-TTTT-G- 130 AATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA * * * 375510 AGAAGATTTTTAAAGATTTTCTCTATATA----TA---AAAATTTATCTCCCATTGTGGCCCCGC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCAC * * * * ** 375568 CCTACCCCCAAGGACCATGATTTGAACAAATTTGAATCTACATTATCTGAGGATAG-TTACACGC 66 CCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGAT-GCTTCCACTT * * * * 375632 CAATTTGAGCTTTTTTGGCCAAATAGTTTTTAAA 129 TAATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA ** * * 375666 AGAATTTTTTTTATAGATTTTCTCTATATATTCCTGTATG-AAAA-TGTATCCCCCTATTGTAGC 1 AGAA-GATTTTTAAAGATTTTCTCTATATATTCC--TATGTAAAATTG-ATCCCCC-ATTGTGGC * * 375729 CCCTCCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCC 61 CCCACCCTACCC-CAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCC * * 375794 ATTTTATTTTGA-CTTTTCCTGGCCTAATAGTTTTTGAGA 125 ACTTTAATTTGAGCTTTT-CTGGCCTAATAGTTTTT-AGA * ** * 375833 AGAAGATTTTTAAAGATTTTCTCTATATGTTCCTATGTAAAAATCCATTCCCCCCTTGTGGCCCC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGT-AAAATTGA-TCCCCCATTGTGGCCCC * * * 375898 ACCATACCACCAGGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACT 64 ACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT 375963 TTAATTTGAGCTTTTCTGGCCTAATAGTTTTT-G- 128 TTAATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA 375996 AGAAG-------AAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCC 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCC-ATTGTGGCCCC * * 376054 ACCCTACCCCCGGGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCA-T 64 ACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACT * 376118 ATTAATTTGAGCTTTTCTGGCCTGATAGTTTTTGAGA 128 -TTAATTTGAGCTTTTCTGGCCTAATAGTTTTT-AGA * 376155 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCACTTGTGGCCCT 1 AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCCA-TTGTGGCCCC * * 376220 TCCCTACCCCGGGGACCATGATTTGAA 64 ACCCTACCCCAGGGACCATGATTTGAA 376247 TCTACACTAC Statistics Matches: 750, Mismatches: 100, Indels: 91 0.80 0.11 0.10 Matches are distributed among these distances: 151 26 0.03 152 7 0.01 153 59 0.08 154 5 0.01 155 13 0.02 156 127 0.17 157 24 0.03 158 1 0.00 159 34 0.05 161 10 0.01 162 45 0.06 163 35 0.05 164 44 0.06 165 42 0.06 166 260 0.35 167 18 0.02 ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35 Consensus pattern (162 bp): AGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCAC CCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCACTTTA ATTTGAGCTTTTCTGGCCTAATAGTTTTTAGA Found at i:375842 original size:156 final size:153 Alignment explanation

Indices: 375680--376164 Score: 600 Period size: 156 Copynumber: 3.0 Consensus size: 153 375670 TTTTTTTTAT * * 375680 AGATTTTCTCTATATATTCCTGTATGAAAATGTATCCCCCTATTGTAGCCCCTCCCTACCCACAG 1 AGATTTTCTCTATATATTCCT-TATGAAAAT-TATCCCCC-ATTGTGGCCCCACCCTACCCACAG * 375745 GGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTATTTTGA-CTT 63 GGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTT 375809 TTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAA 128 TT-CTGGCCTAATAGTTTTT--G-AGAAG-------A * * * * 375846 AGATTTTCTCTATATGTTCC-TATGTAAAAATCCATTCCCCCCTTGTGGCCCCACCATA-CCACC 1 AGATTTTCTCTATATATTCCTTATG--AAAAT-TA-TCCCCCATTGTGGCCCCACCCTACCCA-C * * 375909 AGGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACTTTAATTTGAGC 61 AGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGC 375974 TTTTCTGGCCTAATAGTTTTTGAGAAGA 126 TTTTCTGGCCTAATAGTTTTTGAGAAGA * * 376002 AGATTTTCTCTATATATTCC-TATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCCG 1 AGATTTTCTCTATATATTCCTTATG-AAAA-TT-ATCCCCC-ATTGTGGCCCCACCCTACCCACA * * * 376066 GGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTAATTTGAGCT 62 GGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCT * 376131 TTTCTGGCCTGATAGTTTTTGAGAAGA 127 TTTCTGGCCTAATAGTTTTTGAGAAGA 376158 AGATTTT 1 AGATTTT 376165 TAAAGATTTT Statistics Matches: 287, Mismatches: 23, Indels: 28 0.85 0.07 0.08 Matches are distributed among these distances: 155 10 0.03 156 135 0.47 157 2 0.01 163 5 0.02 164 5 0.02 165 3 0.01 166 116 0.40 167 11 0.04 ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35 Consensus pattern (153 bp): AGATTTTCTCTATATATTCCTTATGAAAATTATCCCCCATTGTGGCCCCACCCTACCCACAGGGA CCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTC TGGCCTAATAGTTTTTGAGAAGA Found at i:376089 original size:322 final size:315 Alignment explanation

Indices: 375363--376319 Score: 998 Period size: 322 Copynumber: 3.0 Consensus size: 315 375353 AAGATTTTTA * * * 375363 AAGATTTTCTCTATATATTCCTATGTACAAATTCATCCCCCATTGTGGCCTCACCCTA-CCCCTG 1 AAGATTTTCTCTATATATTCCTATGTA-AAATTGATCCCCCATTGTGGCCCCACCCTACCCCCAG * * * * * * * * * 375427 GG-CTATTATTTAAACAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCA-AATTTGGGC- 65 GGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCA-T-ATTATTTTGACT 375489 TTTCCTGGCCTAATAG-TTTT--G-AGAAGATTTTTAAAGATTTTCTCTATA-----TA--TAAA 128 TTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATTTCCTATGTAAA * * * * * 375543 AATTTATCTCCCATTGTGGCCCCGCCCTACCCCCAAGGACCATGATTTGAACAAATTTGAATCTA 193 AATTCATCCCCCCTTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAA-TTGAATCTA * * * * * * 375608 CATTATCTGAGGATAG-TTACACGCCAATTTGAGCTTTTTTGGCCAAATAGTTTTTAAAAGAATT 256 CACTACCTGAGGAT-GCTTCCAC-ACAATTTGAGCTTTTCTGGCCAAATAGTTTTT--GAGAA-- * 375672 TTTTTT 315 -----G * * 375678 ATAGATTTTCTCTATATATTCCTGTATG-AAAA-TGTATCCCCCTATTGTAGCCCCTCCCTACCC 1 A-AGATTTTCTCTATATATTCC--TATGTAAAATTG-ATCCCCC-ATTGTGGCCCCACCCTACCC * * * 375741 ACAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTATTTTGA 61 CCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGA 375806 CTTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATGTTCCTATGT 126 CTTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATAT-TTCCTATGT * * * 375871 AAAAATCCATTCCCCCCTTGTGGCCCCACCATACCACCAGGGACTATGATTTGAACAAACTTGAA 190 AAAAATTCA-TCCCCCCTTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAA-TTGAA ** * 375936 TCTACACTACCTGAGGATGCTTCCACTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAG 252 TCTACACTACCTGAGGATGCTTCCAC-ACAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG * 376001 AAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCCCCAATTGTGGCCCCACCCTACCCCCG 1 AAGATTTTCTCTATATATTCCTATGTAAAA-TTGATCCCCC-ATTGTGGCCCCACCCTACCCCCA * * 376066 GGGACCATGCTTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTAATTTGAGCT 64 GGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGA-CT * 376131 TTT-CTGGCCTGATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAA 128 TTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATAT-TTCCTATGTAA * * ** * 376195 AACTTGATCCCCCACTTGTGGCCCTTCCCTACCCCGGGGACCATGA--T-------TTGAATCTA 192 AAATTCATCCCCC-CTTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAATTGAATCTA * * * * 376251 CACTACCTGAGGATGCCTCCACACAAGTTTAAGCTTTTCAGGCCGAATAGTTTTTGAGAAG 256 CACTACCTGAGGATGCTTCCACACAA-TTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG 376312 AAGATTTT 1 AAGATTTT 376320 TGAAAAATAC Statistics Matches: 551, Mismatches: 61, Indels: 64 0.82 0.09 0.09 Matches are distributed among these distances: 310 2 0.00 311 69 0.13 315 2 0.00 316 30 0.05 317 15 0.03 318 17 0.03 319 57 0.10 320 8 0.01 321 21 0.04 322 184 0.33 323 35 0.06 329 2 0.00 330 4 0.01 331 11 0.02 332 94 0.17 ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35 Consensus pattern (315 bp): AAGATTTTCTCTATATATTCCTATGTAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCAGG GACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATGCTTCCATATTATTTTGACTTTT CCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATTTCCTATGTAAAAAT TCATCCCCCCTTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAATTGAATCTACACTA CCTGAGGATGCTTCCACACAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAGAAG Found at i:382367 original size:14 final size:15 Alignment explanation

Indices: 382348--382379 Score: 57 Period size: 15 Copynumber: 2.2 Consensus size: 15 382338 TGCACATTGA 382348 TTTCTT-AATTTTTT 1 TTTCTTAAATTTTTT 382362 TTTCTTAAATTTTTT 1 TTTCTTAAATTTTTT 382377 TTT 1 TTT 382380 AATAAAAATA Statistics Matches: 17, Mismatches: 0, Indels: 1 0.94 0.00 0.06 Matches are distributed among these distances: 14 6 0.35 15 11 0.65 ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78 Consensus pattern (15 bp): TTTCTTAAATTTTTT Found at i:387277 original size:16 final size:16 Alignment explanation

Indices: 387236--387277 Score: 66 Period size: 16 Copynumber: 2.6 Consensus size: 16 387226 GAATATGTTG * * 387236 TCTATAAAATATGTAA 1 TCTATAAAAAAGGTAA 387252 TCTATAAAAAAGGTAA 1 TCTATAAAAAAGGTAA 387268 TCTATAAAAA 1 TCTATAAAAA 387278 TAATTCACAC Statistics Matches: 24, Mismatches: 2, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 16 24 1.00 ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31 Consensus pattern (16 bp): TCTATAAAAAAGGTAA Found at i:391727 original size:25 final size:25 Alignment explanation

Indices: 391698--391748 Score: 93 Period size: 25 Copynumber: 2.0 Consensus size: 25 391688 TTGATGAAAT * 391698 ATAATCAATGGTTAAATTAGACCAA 1 ATAATCAATGGTTAAATTAGAACAA 391723 ATAATCAATGGTTAAATTAGAACAA 1 ATAATCAATGGTTAAATTAGAACAA 391748 A 1 A 391749 CTAAGAAGAA Statistics Matches: 25, Mismatches: 1, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27 Consensus pattern (25 bp): ATAATCAATGGTTAAATTAGAACAA Found at i:401991 original size:15 final size:15 Alignment explanation

Indices: 401948--402003 Score: 60 Period size: 15 Copynumber: 3.7 Consensus size: 15 401938 TGCACAATGT * 401948 ACTAAACTAAACTGG 1 ACTAAACTAAACTGA * * 401963 ACTGAATCT-GACTGA 1 ACT-AAACTAAACTGA 401978 ACTAAACTAAACTGA 1 ACTAAACTAAACTGA * 401993 ACTGAACTAAA 1 ACTAAACTAAA 402004 TCACTTTTTT Statistics Matches: 33, Mismatches: 6, Indels: 4 0.77 0.14 0.09 Matches are distributed among these distances: 14 4 0.12 15 25 0.76 16 4 0.12 ACGTcount: A:0.46, C:0.20, G:0.12, T:0.21 Consensus pattern (15 bp): ACTAAACTAAACTGA Found at i:403276 original size:21 final size:21 Alignment explanation

Indices: 403137--403324 Score: 100 Period size: 21 Copynumber: 9.0 Consensus size: 21 403127 TATTTATGTT * * 403137 AAAGTTTCGCGTTTATTCACA 1 AAAGTTTCGCGTTTATTCGCG * ** * * 403158 AAACTAACGCGTTTATTTGCA 1 AAAGTTTCGCGTTTATTCGCG ** * 403179 AAAGTTTCTTGTTTATTCGCT 1 AAAGTTTCGCGTTTATTCGCG * * 403200 AAAGTTACGCG-TTATATCACG 1 AAAGTTTCGCGTTTAT-TCGCG * * 403221 AACGTTT-GCGTTTATTTGCG 1 AAAGTTTCGCGTTTATTCGCG *** * 403241 AAAGAAAACCGCGTTTATTTGCG 1 AAAG--TTTCGCGTTTATTCGCG * 403264 AAAGTTTCGCG-TTATATCGCT 1 AAAGTTTCGCGTTTAT-TCGCG * 403285 AAAGTTTTC-CATTTATTCGCG 1 AAAG-TTTCGCGTTTATTCGCG * 403306 AAA--TTCGCGTTTAGTCGCG 1 AAAGTTTCGCGTTTATTCGCG 403325 GAATTTTTTT Statistics Matches: 124, Mismatches: 34, Indels: 20 0.70 0.19 0.11 Matches are distributed among these distances: 18 3 0.02 19 10 0.08 20 17 0.14 21 69 0.56 22 8 0.06 23 17 0.14 ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37 Consensus pattern (21 bp): AAAGTTTCGCGTTTATTCGCG Done.