Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Chr14

Parameters: 2 7 7 80 10 50 1000

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

Length: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31

Warning! 4503000 characters in sequence are not A, C, G, or T


File 752 of 770

Found at i:238469374 original size:40 final size:40

Alignment explanation

Indices: 238469308--238469474 Score: 160 Period size: 40 Copynumber: 4.2 Consensus size: 40 238469298 AAATTGAATG * * * 238469308 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * *** 238469347 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT * * 238469387 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT * * ** * 238469427 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT 238469467 ATATCCGG 1 ATATCCGG 238469475 TTATATTCCG Statistics Matches: 103, Mismatches: 20, Indels: 9 0.78 0.15 0.07 Matches are distributed among these distances: 39 16 0.16 40 85 0.83 41 2 0.02 ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT Found at i:238473419 original size:40 final size:40 Alignment explanation

Indices: 238473269--238473436 Score: 151 Period size: 40 Copynumber: 4.2 Consensus size: 40 238473259 CGGAATACAA * * * 238473269 CCGGATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGC 1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGC * ** * 238473309 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGC * * * * * 238473349 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC ** * * * 238473389 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC 238473429 CCGGATAT 1 CCGGATAT 238473437 CATTCAATTG Statistics Matches: 104, Mismatches: 21, Indels: 6 0.79 0.16 0.05 Matches are distributed among these distances: 39 1 0.01 40 102 0.98 41 1 0.01 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC Found at i:238481449 original size:40 final size:40 Alignment explanation

Indices: 238481299--238481466 Score: 151 Period size: 40 Copynumber: 4.2 Consensus size: 40 238481289 CGGAATACAA * * * 238481299 CCGGATATAACCA-CATGCACGAATGCCCTCGGGTCTTAGC 1 CCGGATATAATCACCA-GCACAAATGCCTTCGGGTCTTAGC * ** * 238481339 CCGGATAGAA-CGACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAATC-ACCAGCACAAATGCCTTCGGGTCTTAGC * * * * * 238481379 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC ** * * * 238481419 CCGGATATAATTTCCAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC 238481459 CCGGATAT 1 CCGGATAT 238481467 CATTCAATTG Statistics Matches: 104, Mismatches: 21, Indels: 6 0.79 0.16 0.05 Matches are distributed among these distances: 39 1 0.01 40 102 0.98 41 1 0.01 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25 Consensus pattern (40 bp): CCGGATATAATCACCAGCACAAATGCCTTCGGGTCTTAGC Found at i:238482726 original size:18 final size:18 Alignment explanation

Indices: 238482705--238482742 Score: 58 Period size: 18 Copynumber: 2.1 Consensus size: 18 238482695 ACTTTTCTTC * * 238482705 CTTTCTTTTTTTTTTTTT 1 CTTTCTTTGTTTTTGTTT 238482723 CTTTCTTTGTTTTTGTTT 1 CTTTCTTTGTTTTTGTTT 238482741 CT 1 CT 238482743 CTCATGTACG Statistics Matches: 18, Mismatches: 2, Indels: 0 0.90 0.10 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82 Consensus pattern (18 bp): CTTTCTTTGTTTTTGTTT Found at i:238486472 original size:13 final size:13 Alignment explanation

Indices: 238486450--238486482 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 238486440 AAAGGGTTGT 238486450 TTAT-TAAACTAA 1 TTATCTAAACTAA 238486462 TTATCTAAACTAA 1 TTATCTAAACTAA * 238486475 TTAACTAA 1 TTATCTAA 238486483 TTTAATTAAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 4 0.21 13 15 0.79 ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39 Consensus pattern (13 bp): TTATCTAAACTAA Found at i:238490386 original size:29 final size:27 Alignment explanation

Indices: 238490352--238490454 Score: 98 Period size: 29 Copynumber: 3.6 Consensus size: 27 238490342 TACTCAATCA * 238490352 CGCACACTTAGTGCCATGTGATTCAAGCC 1 CGCACACTTAGTGCCAT-T-ATTCAAGCT * * * 238490381 CGCACACATAGTGCCATATAGTCCAAACT 1 CGCACACTTAGTGCCAT-TA-TTCAAGCT * 238490410 CGCACACTTAGTGCCATACATTACAAGCT 1 CGCACACTTAGTGCCAT-TATT-CAAGCT * 238490439 CGCACACTCAGTGCCA 1 CGCACACTTAGTGCCA 238490455 ATCTCGTCAC Statistics Matches: 62, Mismatches: 10, Indels: 4 0.82 0.13 0.05 Matches are distributed among these distances: 28 2 0.03 29 60 0.97 ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21 Consensus pattern (27 bp): CGCACACTTAGTGCCATTATTCAAGCT Found at i:238520230 original size:29 final size:29 Alignment explanation

Indices: 238520197--238520298 Score: 186 Period size: 29 Copynumber: 3.5 Consensus size: 29 238520187 GTGACGAGAT * 238520197 TGGCACTAAGTGTGCATGCTGGAAAAATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA * 238520226 TGGCACTGAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 238520255 TGGCACTAAGTGTGCATGCTGGAAATATA 1 TGGCACTAAGTGTGCATGCTGGAAATATA 238520284 TGGCACTAAGTGTGC 1 TGGCACTAAGTGTGC 238520299 GAGCTCGAAG Statistics Matches: 70, Mismatches: 3, Indels: 0 0.96 0.04 0.00 Matches are distributed among these distances: 29 70 1.00 ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26 Consensus pattern (29 bp): TGGCACTAAGTGTGCATGCTGGAAATATA Found at i:238520314 original size:29 final size:29 Alignment explanation

Indices: 238520197--238520358 Score: 107 Period size: 29 Copynumber: 5.6 Consensus size: 29 238520187 GTGACGAGAT * ** 238520197 TGGCACTAAGTGTGC-ATGCTGGAAAAATA 1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA * * ** 238520226 TGGCACTGAGTGTGC-ATGCTGGAAATATA 1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA * ** 238520255 TGGCACTAAGTGTGC-ATGCTGGAAATATA 1 TGGCACTAAGTGTGCGA-GCTCGAAACGTA ** 238520284 TGGCACTAAGTGTGCGAGCTCGAAGGGTA 1 TGGCACTAAGTGTGCGAGCTCGAAACGTA ** * * * 238520313 TGGCACTGTGTGTGCGGGCT-TAAATCGCA 1 TGGCACTAAGTGTGCGAGCTCGAAA-CGTA 238520342 TGGCACTAAGTGTGCGA 1 TGGCACTAAGTGTGCGA 238520359 AATCGAGTAT Statistics Matches: 114, Mismatches: 17, Indels: 4 0.84 0.13 0.03 Matches are distributed among these distances: 28 2 0.02 29 111 0.97 30 1 0.01 ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25 Consensus pattern (29 bp): TGGCACTAAGTGTGCGAGCTCGAAACGTA Found at i:238520327 original size:58 final size:59 Alignment explanation

Indices: 238520193--238520319 Score: 179 Period size: 58 Copynumber: 2.2 Consensus size: 59 238520183 TACGGTGACG * * * 238520193 AGAT-TGGCACTAAGTGTGCATGCTGGAAAAATATGGCACTGAGTGTGC-ATGCTGGAA 1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA * 238520250 ATATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAA 1 AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA * * 238520308 GGGTATGGCACT 1 AGATATGGCACT 238520320 GTGTGTGCGG Statistics Matches: 61, Mismatches: 7, Indels: 3 0.86 0.10 0.04 Matches are distributed among these distances: 57 3 0.05 58 57 0.93 59 1 0.02 ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25 Consensus pattern (59 bp): AGATATGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAA Found at i:238528883 original size:40 final size:39 Alignment explanation

Indices: 238528772--238528922 Score: 142 Period size: 40 Copynumber: 3.8 Consensus size: 39 238528762 TTAATCACGT * * * 238528772 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA * * * 238528812 GCACGAATGCCTTCGGGCCTTAGCCCGGATATAGCCACTA 1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA * *** * 238528852 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA 1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTA * * 238528892 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT 1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAT 238528923 CATTCAATTT Statistics Matches: 93, Mismatches: 17, Indels: 3 0.82 0.15 0.03 Matches are distributed among these distances: 39 15 0.16 40 78 0.84 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26 Consensus pattern (39 bp): GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA Found at i:238528906 original size:80 final size:79 Alignment explanation

Indices: 238528772--238528922 Score: 198 Period size: 80 Copynumber: 1.9 Consensus size: 79 238528762 TTAATCACGT * 238528772 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC 238528837 CGGATATAGCCACTA 65 CGGATATAGCCACTA * * ** * * 238528852 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 238528915 CCGGATAT 64 CCGGATAT 238528923 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 5 0.84 0.09 0.07 Matches are distributed among these distances: 79 17 0.27 80 45 0.73 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:238536812 original size:40 final size:39 Alignment explanation

Indices: 238536767--238536932 Score: 172 Period size: 40 Copynumber: 4.2 Consensus size: 39 238536757 CGGAATATAA 238536767 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC 1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGG-CTTAGC * * * * 238536807 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC ** * * 238536846 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-CTTAGC ** * * * * 238536886 CCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGC 1 CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC 238536925 CCGGATAT 1 CCGGATAT 238536933 CATTCAATTT Statistics Matches: 105, Mismatches: 19, Indels: 5 0.81 0.15 0.04 Matches are distributed among these distances: 39 46 0.44 40 59 0.56 ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26 Consensus pattern (39 bp): CCGGATATAATCACTAGCACAAATGCCTTCGGGCTTAGC Found at i:238536889 original size:79 final size:79 Alignment explanation

Indices: 238536783--238536932 Score: 205 Period size: 79 Copynumber: 1.9 Consensus size: 79 238536773 ATAATCACGT * 238536783 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAAC-CAGCA-GAATTGCCTTCGGGCTTAGC 238536846 CCGGATATAGCCACTA 64 CCGGATATAGCCACTA * * ** * * 238536862 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCAGCATAATTGTCTTCGGGCTTAGCCC 1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC 238536927 GGATAT 66 GGATAT 238536933 CATTCAATTT Statistics Matches: 62, Mismatches: 7, Indels: 4 0.85 0.10 0.05 Matches are distributed among these distances: 78 3 0.05 79 59 0.95 ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26 Consensus pattern (79 bp): GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACCAGCAGAATTGCCTTCGGGCTTAGCCC GGATATAGCCACTA Found at i:238538338 original size:21 final size:21 Alignment explanation

Indices: 238538287--238538329 Score: 79 Period size: 21 Copynumber: 2.1 Consensus size: 21 238538277 AAAACATGTT 238538287 TCATGACATGTTTAGCCCATA 1 TCATGACATGTTTAGCCCATA 238538308 TCATGACATGTTT-GCCCATA 1 TCATGACATGTTTAGCCCATA 238538328 TC 1 TC 238538330 TTTGTCATGG Statistics Matches: 22, Mismatches: 0, Indels: 1 0.96 0.00 0.04 Matches are distributed among these distances: 20 9 0.41 21 13 0.59 ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35 Consensus pattern (21 bp): TCATGACATGTTTAGCCCATA Found at i:238540216 original size:21 final size:21 Alignment explanation

Indices: 238540191--238540230 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 238540181 AACGGGACTG * 238540191 CTGATGTGGGAAGTTAACTAA 1 CTGATGTGGCAAGTTAACTAA * 238540212 CTGATGTGGCCAGTTAACT 1 CTGATGTGGCAAGTTAACT 238540231 TGCCACGTTG Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30 Consensus pattern (21 bp): CTGATGTGGCAAGTTAACTAA Found at i:238541426 original size:2 final size:2 Alignment explanation

Indices: 238541419--238541448 Score: 60 Period size: 2 Copynumber: 15.0 Consensus size: 2 238541409 GCAAACAAAC 238541419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 238541449 GCATCATTTT Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 2 28 1.00 ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50 Consensus pattern (2 bp): AT Found at i:238541956 original size:33 final size:33 Alignment explanation

Indices: 238541919--238541996 Score: 88 Period size: 33 Copynumber: 2.4 Consensus size: 33 238541909 TGGCCCTGCC * * 238541919 ATGGTCTTACACTC-GTAATGTCATAACCCAGTT 1 ATGGTCTTACACTCAG-AATGCCATAACCCAGCT * * 238541952 ATGGTCTTATCA-TCAGGATGCCATAGCCCAGCT 1 ATGGTCTTA-CACTCAGAATGCCATAACCCAGCT 238541985 ATGGTCTTACAC 1 ATGGTCTTACAC 238541997 ATATACATAT Statistics Matches: 38, Mismatches: 4, Indels: 6 0.79 0.08 0.12 Matches are distributed among these distances: 32 2 0.05 33 33 0.87 34 3 0.08 ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31 Consensus pattern (33 bp): ATGGTCTTACACTCAGAATGCCATAACCCAGCT Found at i:238542251 original size:16 final size:16 Alignment explanation

Indices: 238542232--238542267 Score: 56 Period size: 16 Copynumber: 2.3 Consensus size: 16 238542222 AACCTAACCC * 238542232 AAAAAAAAA-ACAAAG 1 AAAAAAAAAGAAAAAG 238542247 AAAAAAAAAGAAAAAG 1 AAAAAAAAAGAAAAAG 238542263 AAAAA 1 AAAAA 238542268 CCTACCCCAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 9 0.47 16 10 0.53 ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00 Consensus pattern (16 bp): AAAAAAAAAGAAAAAG Found at i:238542282 original size:16 final size:15 Alignment explanation

Indices: 238542263--238542297 Score: 61 Period size: 15 Copynumber: 2.3 Consensus size: 15 238542253 AAAGAAAAAG * 238542263 AAAAACCTACCCCAA 1 AAAAACCTAACCCAA 238542278 AAAAACCTAACCCAA 1 AAAAACCTAACCCAA 238542293 AAAAA 1 AAAAA 238542298 AAAGAAGAAA Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 15 19 1.00 ACGTcount: A:0.63, C:0.31, G:0.00, T:0.06 Consensus pattern (15 bp): AAAAACCTAACCCAA Found at i:238542298 original size:16 final size:15 Alignment explanation

Indices: 238542263--238542298 Score: 54 Period size: 16 Copynumber: 2.3 Consensus size: 15 238542253 AAAGAAAAAG * 238542263 AAAAACCTACCCCAA 1 AAAAACCTACCCAAA 238542278 AAAAACCTAACCCAAA 1 AAAAACCT-ACCCAAA 238542294 AAAAA 1 AAAAA 238542299 AAGAAGAAAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 8 0.42 16 11 0.58 ACGTcount: A:0.64, C:0.31, G:0.00, T:0.06 Consensus pattern (15 bp): AAAAACCTACCCAAA Found at i:238544892 original size:12 final size:12 Alignment explanation

Indices: 238544872--238544907 Score: 54 Period size: 12 Copynumber: 3.0 Consensus size: 12 238544862 ATTCATTTAA 238544872 CATTCATGCATT 1 CATTCATGCATT * 238544884 CATTTATGCATT 1 CATTCATGCATT * 238544896 CATTCATTCATT 1 CATTCATGCATT 238544908 GCATATTCCA Statistics Matches: 21, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 12 21 1.00 ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47 Consensus pattern (12 bp): CATTCATGCATT Found at i:238547138 original size:62 final size:62 Alignment explanation

Indices: 238547062--238547186 Score: 250 Period size: 62 Copynumber: 2.0 Consensus size: 62 238547052 TTTGTAAGAG 238547062 CCTGCATTCGCTCTTTATCATTCAAATGAATATCAATGAAGATGCATTTCGTCATAATCTTT 1 CCTGCATTCGCTCTTTATCATTCAAATGAATATCAATGAAGATGCATTTCGTCATAATCTTT 238547124 CCTGCATTCGCTCTTTATCATTCAAATGAATATCAATGAAGATGCATTTCGTCATAATCTTT 1 CCTGCATTCGCTCTTTATCATTCAAATGAATATCAATGAAGATGCATTTCGTCATAATCTTT 238547186 C 1 C 238547187 ACATTATCAC Statistics Matches: 63, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 62 63 1.00 ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38 Consensus pattern (62 bp): CCTGCATTCGCTCTTTATCATTCAAATGAATATCAATGAAGATGCATTTCGTCATAATCTTT Found at i:238551968 original size:70 final size:69 Alignment explanation

Indices: 238551849--238552271 Score: 403 Period size: 71 Copynumber: 6.2 Consensus size: 69 238551839 GAGTTAAGCC * 238551849 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTG-TTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC 238551913 TGAGGTA 63 TGAGGTA * * ** * * 238551920 TTTTCAATTTTTGTGTTTTAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTG 1 TTTTCAATTTTTGT-TTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTG 238551985 AGGTA 65 AGGTA * * 238551990 TTTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTCAATTTTTGTTTT--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCT 238552055 GAGGTA 64 GAGGTA * * * ** * * * 238552061 TTTTTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA 1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 238552117 ---A 66 GGTA *** ** * 238552118 TTTTTGTTTTTCA----AAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 1 TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA 238552179 GGTA 66 GGTA * * * 238552183 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAA-TTTT-TGTTTTAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGC 238552248 TGAGGTA 63 TGAGGTA * 238552255 TTTTCAATTTCTGTTTT 1 TTTTCAATTTTTGTTTT 238552272 CAATTTACGT Statistics Matches: 285, Mismatches: 44, Indels: 47 0.76 0.12 0.12 Matches are distributed among these distances: 53 31 0.11 57 9 0.03 60 2 0.01 62 2 0.01 65 5 0.02 66 4 0.01 69 34 0.12 70 64 0.22 71 70 0.25 72 64 0.22 ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39 Consensus pattern (69 bp): TTTTCAATTTTTGTTTTAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGA GGTA Found at i:238552157 original size:122 final size:124 Alignment explanation

Indices: 238551991--238552237 Score: 392 Period size: 122 Copynumber: 2.0 Consensus size: 124 238551981 GTTGAGGTAT 238551991 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG 1 TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG * * 238552056 AGGTATTTT-TA-GTTTATGTTTTAAATT-GACTCATATTGCGAGAGGTGAGTTAAGCC 66 AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC * * 238552112 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCT 1 TTTTAATTTTTG-TTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCT * * * * 238552177 GAGGTATTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCC 65 GAGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC 238552237 T 1 T 238552238 CAGGTCACGC Statistics Matches: 114, Mismatches: 8, Indels: 4 0.90 0.06 0.03 Matches are distributed among these distances: 121 12 0.11 122 60 0.53 123 1 0.01 124 13 0.11 125 28 0.25 ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39 Consensus pattern (124 bp): TTTTAATTTTTGTTTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTG AGGTATTTTCAATGTTTATGTTTTAAATTCAACTCATATTGCGAGAGGTGAGTTAAGCC Found at i:238552202 original size:263 final size:257 Alignment explanation

Indices: 238551682--238552274 Score: 1042 Period size: 263 Copynumber: 2.3 Consensus size: 257 238551672 TTTCAAGGAA * 238551682 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTGTTGT 1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT 238551747 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT 66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT 238551812 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT 131 TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT 238551877 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT 196 CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT 238551939 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT 1 AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT * 238552004 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGT 66 TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTA---TT--T 238552069 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA 126 TTA-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAA 238552134 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT 190 TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGT 238552199 TTT 255 TTT * * * * * * 238552202 AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCT 1 AA--TCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT 238552267 GTTTTCAA 64 GTTTTCAA 238552275 TTTACGTTGT Statistics Matches: 320, Mismatches: 8, Indels: 8 0.95 0.02 0.02 Matches are distributed among these distances: 257 120 0.38 260 2 0.01 262 4 0.01 263 131 0.41 265 63 0.20 ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37 Consensus pattern (257 bp): AATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTTGT TTTCAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTTAGT TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAATCAACT CATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTGTGTTTT Found at i:238552233 original size:72 final size:71 Alignment explanation

Indices: 238552112--238552277 Score: 244 Period size: 72 Copynumber: 2.3 Consensus size: 71 238552102 GAGTTAAGCC ** * * 238552112 TTTT-AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGC 1 TTTTCAATTTTTGTTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 238552176 TGAGGTA 65 TGAGGTA * 238552183 TTTTCAATTTTTGTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGC 1 TTTTCAATTTTTGT-TTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC 238552248 TGAGGTA 65 TGAGGTA * * 238552255 TTTTCAATTTCTGTTTTCAATTT 1 TTTTCAATTTTTGTTTTTAATTT 238552278 ACGTTGTTCA Statistics Matches: 86, Mismatches: 7, Indels: 4 0.89 0.07 0.04 Matches are distributed among these distances: 71 12 0.14 72 70 0.81 73 4 0.05 ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42 Consensus pattern (71 bp): TTTTCAATTTTTGTTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCT GAGGTA Found at i:238552607 original size:74 final size:76 Alignment explanation

Indices: 238552501--238552645 Score: 224 Period size: 74 Copynumber: 1.9 Consensus size: 76 238552491 TTTTTGCCTT * 238552501 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG--GACACG-CTGAGGTAATTT 1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTC-GAGGTAATTT 238552563 CAATTTCTGTTG 65 CAATTTCTGTTG * * * 238552575 TCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTATTTTC 1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC 238552640 AATTTC 66 AATTTC 238552646 CATTTTTCAA Statistics Matches: 64, Mismatches: 4, Indels: 4 0.89 0.06 0.06 Matches are distributed among these distances: 74 42 0.66 76 21 0.33 77 1 0.02 ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28 Consensus pattern (76 bp): TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAATTTC AATTTCTGTTG Found at i:238552613 original size:164 final size:166 Alignment explanation

Indices: 238552342--238552815 Score: 719 Period size: 164 Copynumber: 2.9 Consensus size: 166 238552332 CTACTTTTTC 238552342 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * 238552407 GTTGTCAAAAAAATCAACTCGTATTGCGAGTGGCGAGTTGAGCCTCAGGTCACACG-AGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTAGAGGTAT * * 238552471 TTTCAATTTCCGTTTTTCAATTTTTGCCTTTC-AAA 131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA 238552506 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * * 238552571 GTTGTCAAAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGATCACACGTCGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTAGAGGTAT * 238552636 TTTCAATTTCCATTTTTCAATTTCTGCATTTCAAAAAAA 131 TTTCAATTTCCGTTTTTCAATTTCTGCATTTC---AAAA 238552675 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTAATTTCAATTTCT 1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT * * * * ** * * 238552739 GTTTTC--AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAG--ACACGTTGAGGTAT 66 GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTAGAGGTAT * 238552800 TTTCAATTTCTGTTTT 131 TTTCAATTTCCGTTTT 238552816 CAAAAAATCA Statistics Matches: 286, Mismatches: 19, Indels: 10 0.91 0.06 0.03 Matches are distributed among these distances: 164 144 0.50 165 36 0.13 166 34 0.12 168 32 0.11 169 40 0.14 ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32 Consensus pattern (166 bp): AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT GTTGTCAAAAAAATCAACTCGTATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGTAGAGGTAT TTTCAATTTCCGTTTTTCAATTTCTGCATTTCAAAA Found at i:238552822 original size:150 final size:152 Alignment explanation

Indices: 238552672--238553013 Score: 421 Period size: 144 Copynumber: 2.3 Consensus size: 152 238552662 CATTTCAAAA * 238552672 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-ACA-CGCTGAGGTAATTTCAAT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACAGCGCTGAGCTAATTTCAAT * * * * ** 238552735 TTCTGT-TTTC-AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCA-A-GACACGTTGAG 66 TTCTATCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGATCACACACTGAG 238552796 GTA-TTTTCAATTTCTGTTTTC 131 GTATTTTTCAATTTCTGTTTTC * * * * * 238552817 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACA-GCGCTGAGCTAATTTCAA ** * 238552881 TTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTG 65 TTTCTATCTTTC-AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGATCACACACTG * * 238552946 AGGTATTTTTTCAATTTATATTTTTC 129 AGGTA-TTTTTCAATTTCT-GTTTTC * * 238552972 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGG 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG 238553014 GTTACATGTC Statistics Matches: 163, Mismatches: 22, Indels: 13 0.82 0.11 0.07 Matches are distributed among these distances: 144 38 0.23 145 2 0.01 147 21 0.13 148 4 0.02 150 34 0.21 151 1 0.01 152 11 0.07 154 11 0.07 155 5 0.03 156 36 0.22 ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33 Consensus pattern (152 bp): AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCACAGCGCTGAGCTAATTTCAAT TTCTATCTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGATCACACACTGAG GTATTTTTCAATTTCTGTTTTC Found at i:238552913 original size:77 final size:74 Alignment explanation

Indices: 238552672--238553178 Score: 373 Period size: 77 Copynumber: 6.5 Consensus size: 74 238552662 CATTTCAAAA * * * 238552672 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACA-CGCTGAGGTAATTTCAATT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTCAGCGCTGAGGTATTTTCAATT * 238552736 TCTGTTTTC 66 TCTATTTTC * * ** ** * * 238552745 --AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACA-CGTTGAGGTATTTTCAAT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGTCAGCGCTGAGGTATTTTCAAT * 238552807 TTCTGTTTTC 65 TTCTATTTTC * * * 238552817 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATTTTCAA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCA-GCGCTGAGGTATTTTCAA 238552881 TTTCTATCTTTC 64 TTTCTAT-TTTC * * * 238552893 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGATCACACACTGAGGTATTTTTT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT--GGTCA-GCGCTGAGGTA--TTTT * 238552957 CAATTTATATTTTTC 61 CAATTTCTA-TTTTC * * * * 238552972 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACA-TG-TCGAGGTATTTTC 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGG-T-CAGCGCT-GAGGTATTTTC ** * 238553035 AAAATCTGTTTTTC 62 AATTTCT-ATTTTC * * 238553049 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGA 1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGG-TCA-GCGCTGA * * 238553114 GCTATTTTCAATTTCTGTTTTTTTTTC 53 GGTATTTTCAATTTC-----TATTTTC 238553141 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC 1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC 238553179 TTTTTAATTT Statistics Matches: 350, Mismatches: 46, Indels: 67 0.76 0.10 0.14 Matches are distributed among these distances: 71 33 0.09 72 31 0.09 73 33 0.09 75 21 0.06 76 7 0.02 77 58 0.17 78 4 0.01 79 57 0.16 80 4 0.01 81 7 0.02 82 29 0.08 86 2 0.01 87 3 0.01 88 51 0.15 89 1 0.00 91 2 0.01 92 6 0.02 93 1 0.00 ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35 Consensus pattern (74 bp): AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGTCAGCGCTGAGGTATTTTCAATT TCTATTTTC Found at i:238552995 original size:79 final size:75 Alignment explanation

Indices: 238552672--238553178 Score: 402 Period size: 79 Copynumber: 6.5 Consensus size: 75 238552662 CATTTCAAAA * * 238552672 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-G-GACACGCTGAGGTAATTTCAAT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACACGCTGAGGTATTTTCAAT 238552735 TTCTGTTTTC 66 TTCTGTTTTC * * ** * * 238552745 --AAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCA-AGACACGTTGAGGTATTTTCAAT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACACGCTGAGGTATTTTCAAT 238552807 TTCTGTTTTC 66 TTCTGTTTTC * * * * * * 238552817 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCT-TGGCTCATGCGCTGAGCTATTTTCA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACA--CGCTGAGGTATTTTCA * 238552880 ATTTCTATCTTTC 64 ATTTCTGT-TTTC * * 238552893 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACTGAGGTATTTTTTC 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-CACACGCTGAGGTA--TTTTC * * 238552958 AATTTATATTTTTC 63 AATTTCT-GTTTTC * * * ** * 238552972 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACACGCT-GAGGTATTTTCA ** 238553036 AAATCTGTTTTTC 64 ATTTCTG-TTTTC * * * * 238553049 AAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTCACGTGCTG 1 -AA----------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACAC--GCTG * 238553113 AGCTATTTTCAATTTCTGTTTTTTTTTC 53 AGGTATTTTCAATTTCTG-----TTTTC 238553141 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC 1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC 238553179 TTTTTAATTT Statistics Matches: 347, Mismatches: 52, Indels: 61 0.75 0.11 0.13 Matches are distributed among these distances: 71 34 0.10 72 30 0.09 73 33 0.10 75 21 0.06 76 4 0.01 77 57 0.16 78 4 0.01 79 64 0.18 80 2 0.01 81 5 0.01 82 29 0.08 86 3 0.01 88 52 0.15 89 1 0.00 91 2 0.01 92 6 0.02 ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35 Consensus pattern (75 bp): AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACACGCTGAGGTATTTTCAAT TTCTGTTTTC Found at i:238553032 original size:156 final size:146 Alignment explanation

Indices: 238552672--238553178 Score: 410 Period size: 156 Copynumber: 3.3 Consensus size: 146 238552662 CATTTCAAAA * * 238552672 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-ACACGCTGAGGTAATTTCAATT 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTACATGCTGAGGTATTTTCAATT * * * * ** 238552736 TCTGTTTTCAAAATTCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATT 66 TCTATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAACACACACTGAGGTATT * 238552801 TTCAATTTCTGTTTTC 131 TTCAATTTATGTTTTC * * * * 238552817 -AAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCT-CATGCGCTGAGCTATTTTCA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG-TACAT--GCTGAGGTATTTTCA ** * 238552880 ATTTCTATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCACACACT 63 ATTTCTAT-TTTC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-A-CACACACT * 238552945 GAGGTATTTTTTCAATTTATATTTTTC 123 GAGGTA--TTTTCAATTTAT-GTTTTC * * 238552972 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATG-TCGAGGTATTTTCA 1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-TACATGCT-GAGGTATTTTC- * * ** 238553036 AAATCTGTTTTTCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTG 62 -AA--------T----TTCTATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA * * * * * 238553101 GCTCACGTGCTGAGCTATTTTCAATTTCTGTTTTTTTTTC 114 ACACAC--ACTGAGGTATTTTCAATTTATG-----TTTTC 238553141 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC 1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC 238553179 TTTTTAATTT Statistics Matches: 287, Mismatches: 37, Indels: 51 0.77 0.10 0.14 Matches are distributed among these distances: 144 38 0.13 145 2 0.01 147 20 0.07 148 4 0.01 150 34 0.12 151 1 0.00 152 11 0.04 154 11 0.04 155 6 0.02 156 45 0.16 157 3 0.01 158 5 0.02 165 15 0.05 166 1 0.00 167 42 0.15 169 16 0.06 170 33 0.11 ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35 Consensus pattern (146 bp): AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTACATGCTGAGGTATTTTCAATT TCTATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAACACACACTGAGGTATT TTCAATTTATGTTTTC Found at i:238553049 original size:14 final size:13 Alignment explanation

Indices: 238553030--238553065 Score: 54 Period size: 14 Copynumber: 2.7 Consensus size: 13 238553020 TGTCGAGGTA 238553030 TTTTCAAAATCTG 1 TTTTCAAAATCTG * 238553043 TTTTTCAAATTCTG 1 -TTTTCAAAATCTG 238553057 TTTTCAAAA 1 TTTTCAAAA 238553066 ATCAACTCAT Statistics Matches: 20, Mismatches: 2, Indels: 1 0.87 0.09 0.04 Matches are distributed among these distances: 13 8 0.40 14 12 0.60 ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50 Consensus pattern (13 bp): TTTTCAAAATCTG Found at i:238553123 original size:88 final size:88 Alignment explanation

Indices: 238552974--238553135 Score: 227 Period size: 88 Copynumber: 1.8 Consensus size: 88 238552964 TATTTTTCAA * * * * 238552974 AAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAA 1 AAAAATCAACTCACATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTCAAAA 238553039 TCTGTTTTTCAAATTCTGTTTTC 66 TCTGTTTTTCAAATTCTGTTTTC * * * * 238553062 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTG-CTGAGCTATTTTCAAT 1 AAAAATCAACTCACATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTC-GAGCTATTTTCAAA * 238553126 TTCTGTTTTT 65 ATCTGTTTTT 238553136 TTTTCAAAAA Statistics Matches: 64, Mismatches: 9, Indels: 2 0.85 0.12 0.03 Matches are distributed among these distances: 87 1 0.02 88 63 0.98 ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36 Consensus pattern (88 bp): AAAAATCAACTCACATTGCGAGAAGTGAGTTGAGCCTCGGCTCACATGTCGAGCTATTTTCAAAA TCTGTTTTTCAAATTCTGTTTTC Found at i:238553196 original size:30 final size:30 Alignment explanation

Indices: 238553160--238553221 Score: 99 Period size: 30 Copynumber: 2.1 Consensus size: 30 238553150 CAACTCATAT 238553160 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC 1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC * 238553190 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC 1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC 238553220 TG 1 TG 238553222 TTTTTCAAAA Statistics Matches: 30, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 30 29 0.97 31 1 0.03 ACGTcount: A:0.19, C:0.10, G:0.29, T:0.42 Consensus pattern (30 bp): TGCGAGAGGTGAGTTGAGTCTTTTAATTTC Found at i:238553322 original size:254 final size:248 Alignment explanation

Indices: 238552811--238553389 Score: 762 Period size: 254 Copynumber: 2.3 Consensus size: 248 238552801 TTCAATTTCT * * * 238552811 GTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGACCCTTGGCTCATGCGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT * 238552876 TTCAATTTC----TATCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT 66 TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT * * 238552937 CACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGA 131 CACACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGA * ** * * * ** 238553002 GTTGAGCCTCGGGTTACATGTCGAGGTATTTTCAAAATCTGTTTTTCAAATTCT 195 GTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA * * 238553056 GTTTTC-AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT * * 238553120 TTCAATTTCTGTTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA 66 TTCAATTTCTGTTTTTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTCA * * * * * * * 238553185 -ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGC 128 GA--TC-AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGC * 238553247 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAA 186 GAGAGGTGAGTTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA 238553310 G-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT 1 GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT 238553374 TTCAATTTCTGTTTTT 66 TTCAATTTCTGTTTTT 238553390 AATGTCTGTT Statistics Matches: 291, Mismatches: 28, Indels: 21 0.86 0.08 0.06 Matches are distributed among these distances: 244 62 0.21 245 6 0.02 248 13 0.04 249 30 0.10 250 1 0.00 251 3 0.01 252 2 0.01 253 5 0.02 254 146 0.50 255 5 0.02 256 13 0.04 257 5 0.02 ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37 Consensus pattern (248 bp): GTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATT TTCAATTTCTGTTTTTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGAT CACACACTGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAG TTGAACCTCCAGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAATTAA Found at i:238554054 original size:11 final size:11 Alignment explanation

Indices: 238554037--238554070 Score: 50 Period size: 12 Copynumber: 2.9 Consensus size: 11 238554027 ACCTAACCCA 238554037 AAAAAAACAAAG 1 AAAAAAA-AAAG 238554049 AAAAAAAAAAG 1 AAAAAAAAAAG 238554060 AAAAAGAAAAA 1 AAAAA-AAAAA 238554071 CCTACCAAAA Statistics Matches: 21, Mismatches: 0, Indels: 2 0.91 0.00 0.09 Matches are distributed among these distances: 11 9 0.43 12 12 0.57 ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00 Consensus pattern (11 bp): AAAAAAAAAAG Found at i:238554056 original size:17 final size:17 Alignment explanation

Indices: 238554036--238554070 Score: 54 Period size: 17 Copynumber: 2.1 Consensus size: 17 238554026 AACCTAACCC * 238554036 AAAAAAA-ACAAAGAAA 1 AAAAAAAGAAAAAGAAA 238554052 AAAAAAAGAAAAAGAAA 1 AAAAAAAGAAAAAGAAA 238554069 AA 1 AA 238554071 CCTACCAAAA Statistics Matches: 17, Mismatches: 1, Indels: 1 0.89 0.05 0.05 Matches are distributed among these distances: 16 7 0.41 17 10 0.59 ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00 Consensus pattern (17 bp): AAAAAAAGAAAAAGAAA Found at i:238554082 original size:13 final size:15 Alignment explanation

Indices: 238554066--238554098 Score: 52 Period size: 15 Copynumber: 2.3 Consensus size: 15 238554056 AAAGAAAAAG 238554066 AAAAACCT-A-CCAA 1 AAAAACCTAACCCAA 238554079 AAAAACCTAACCCAA 1 AAAAACCTAACCCAA 238554094 AAAAA 1 AAAAA 238554099 AAAAGAAGAA Statistics Matches: 18, Mismatches: 0, Indels: 2 0.90 0.00 0.10 Matches are distributed among these distances: 13 8 0.44 14 1 0.06 15 9 0.50 ACGTcount: A:0.67, C:0.27, G:0.00, T:0.06 Consensus pattern (15 bp): AAAAACCTAACCCAA Found at i:238554682 original size:2 final size:2 Alignment explanation

Indices: 238554666--238554704 Score: 62 Period size: 2 Copynumber: 19.5 Consensus size: 2 238554656 TTCTTATTAT 238554666 TA TA TA CTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T 1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T 238554705 TTTAAATACC Statistics Matches: 35, Mismatches: 0, Indels: 4 0.90 0.00 0.10 Matches are distributed among these distances: 1 1 0.03 2 32 0.91 3 2 0.06 ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49 Consensus pattern (2 bp): TA Found at i:238564057 original size:19 final size:18 Alignment explanation

Indices: 238564020--238564063 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 238564010 ATACATACAG 238564020 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 238564037 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 238564056 TACTAATT 1 TAATAATT 238564064 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:238566462 original size:27 final size:27 Alignment explanation

Indices: 238566422--238566488 Score: 102 Period size: 27 Copynumber: 2.5 Consensus size: 27 238566412 TTTAAAACCC * 238566422 TAGGGGT-ATATCGGTAA-TTTGCTCTT 1 TAGGGGTAATTTCGGTAATTTTGCTC-T 238566448 TAGGGGTAATTTCGGTAATTTTGCTCT 1 TAGGGGTAATTTCGGTAATTTTGCTCT 238566475 TAGGGGTAATTTCG 1 TAGGGGTAATTTCG 238566489 TGATCTACGC Statistics Matches: 38, Mismatches: 1, Indels: 3 0.90 0.02 0.07 Matches are distributed among these distances: 26 7 0.18 27 24 0.63 28 7 0.18 ACGTcount: A:0.19, C:0.10, G:0.28, T:0.42 Consensus pattern (27 bp): TAGGGGTAATTTCGGTAATTTTGCTCT Found at i:238568310 original size:19 final size:18 Alignment explanation

Indices: 238568273--238568316 Score: 54 Period size: 19 Copynumber: 2.4 Consensus size: 18 238568263 ATACATACAG 238568273 TAAT-ATTTTTCTAATAA 1 TAATAATTTTTCTAATAA * 238568290 TAATAATTTTATCTCATAA 1 TAATAATTTT-TCTAATAA * 238568309 TACTAATT 1 TAATAATT 238568317 AAAATTTCAT Statistics Matches: 23, Mismatches: 2, Indels: 2 0.85 0.07 0.07 Matches are distributed among these distances: 17 4 0.17 18 5 0.22 19 14 0.61 ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50 Consensus pattern (18 bp): TAATAATTTTTCTAATAA Found at i:238569780 original size:13 final size:13 Alignment explanation

Indices: 238569757--238569789 Score: 50 Period size: 13 Copynumber: 2.6 Consensus size: 13 238569747 AAGGATTTGT 238569757 TTATC-AAAATAA 1 TTATCTAAAATAA 238569769 TTATCTAAAATAA 1 TTATCTAAAATAA * 238569782 TTAACTAA 1 TTATCTAA 238569790 TTTAATTAAA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 12 5 0.26 13 14 0.74 ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36 Consensus pattern (13 bp): TTATCTAAAATAA Found at i:238574940 original size:71 final size:71 Alignment explanation

Indices: 238574856--238575019 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 238574846 CGATTTGTCT 238574856 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238574921 CTTTCA 66 CTTTCA 238574927 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238574992 CTTTCA 66 CTTTCA 238574998 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 238575020 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:238575057 original size:71 final size:70 Alignment explanation

Indices: 238574856--238575053 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 238574846 CGATTTGTCT * * * * 238574856 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238574921 CTTTCA 65 CTTTCA * * * * 238574927 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238574992 CTTTCA 65 CTTTCA * * 238574998 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 238575054 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:238582021 original size:71 final size:71 Alignment explanation

Indices: 238581937--238582100 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 238581927 CGATTTGTCT 238581937 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238582002 CTTTCA 66 CTTTCA 238582008 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238582073 CTTTCA 66 CTTTCA 238582079 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 238582101 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:238582138 original size:71 final size:70 Alignment explanation

Indices: 238581937--238582134 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 238581927 CGATTTGTCT * * * * 238581937 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238582002 CTTTCA 65 CTTTCA * * * * 238582008 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238582073 CTTTCA 65 CTTTCA * * 238582079 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 238582135 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:238588965 original size:66 final size:68 Alignment explanation

Indices: 238588887--238589073 Score: 281 Period size: 71 Copynumber: 2.7 Consensus size: 68 238588877 TAGTACCACT * 238588887 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT 1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT 238588949 CACG 65 CACG 238588953 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA 1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA 238589018 ATCACG 63 ATCACG 238589024 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG 1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG 238589074 GATACATCTC Statistics Matches: 114, Mismatches: 1, Indels: 7 0.93 0.01 0.06 Matches are distributed among these distances: 66 13 0.11 67 6 0.05 68 1 0.01 69 1 0.01 71 93 0.82 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (68 bp): CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC ACG Found at i:238588998 original size:71 final size:71 Alignment explanation

Indices: 238588910--238589073 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 238588900 CGATTTGTCT 238588910 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238588975 CTTTCA 66 CTTTCA 238588981 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 238589046 CTTTCA 66 CTTTCA 238589052 CGTAGCTCTCTTGTCTACATGG 1 CGTAGCTCTCTTGTCTACATGG 238589074 GATACATCTC Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35 Consensus pattern (71 bp): CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT CTTTCA Found at i:238589111 original size:71 final size:70 Alignment explanation

Indices: 238588910--238589107 Score: 258 Period size: 71 Copynumber: 2.8 Consensus size: 70 238588900 CGATTTGTCT * * * * 238588910 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238588975 CTTTCA 65 CTTTCA * * * * 238588981 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT 1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT 238589046 CTTTCA 65 CTTTCA * * 238589052 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC 1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC 238589108 TACAGGGTGT Statistics Matches: 120, Mismatches: 6, Indels: 5 0.92 0.05 0.04 Matches are distributed among these distances: 68 22 0.18 69 1 0.01 70 1 0.01 71 96 0.80 ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34 Consensus pattern (70 bp): CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC TTTCA Found at i:238591971 original size:29 final size:28 Alignment explanation

Indices: 238591937--238592039 Score: 116 Period size: 29 Copynumber: 3.6 Consensus size: 28 238591927 TACTCAATCA * 238591937 CGCACACTTAGTGCCATATGATTCAAGCC 1 CGCACACTTAGTGCCATAT-ATTCAAGCT * * * 238591966 CGCACACATAGTGCCATATAGTCCAAACT 1 CGCACACTTAGTGCCATATA-TTCAAGCT * * 238591995 CGCACACTTAGTGCCGTACATTACAAGCT 1 CGCACACTTAGTGCCATATATT-CAAGCT * 238592024 CGCACACTCAGTGCCA 1 CGCACACTTAGTGCCA 238592040 ATCTCGTCAC Statistics Matches: 61, Mismatches: 11, Indels: 4 0.80 0.14 0.05 Matches are distributed among these distances: 28 2 0.03 29 59 0.97 ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21 Consensus pattern (28 bp): CGCACACTTAGTGCCATATATTCAAGCT Found at i:238599979 original size:29 final size:28 Alignment explanation

Indices: 238599945--238600047 Score: 116 Period size: 29 Copynumber: 3.6 Consensus size: 28 238599935 TACTCAATCA * 238599945 CGCACACTTAGTGCCATATGATTCAAGCC 1 CGCACACTTAGTGCCATAT-ATTCAAGCT * * * 238599974 CGCACACATAGTGCCATATAGTCCAAACT 1 CGCACACTTAGTGCCATATA-TTCAAGCT * * 238600003 CGCACACTTAGTGCCGTACATTACAAGCT 1 CGCACACTTAGTGCCATATATT-CAAGCT * 238600032 CGCACACTCAGTGCCA 1 CGCACACTTAGTGCCA 238600048 ATCTCGTCAC Statistics Matches: 61, Mismatches: 11, Indels: 4 0.80 0.14 0.05 Matches are distributed among these distances: 28 2 0.03 29 59 0.97 ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21 Consensus pattern (28 bp): CGCACACTTAGTGCCATATATTCAAGCT Found at i:238604475 original size:40 final size:40 Alignment explanation

Indices: 238604406--238604549 Score: 112 Period size: 40 Copynumber: 3.6 Consensus size: 40 238604396 CAATTGAATG * * * * * 238604406 ATATCCGGGCTAAG-TCCGAAGACATTTATGCTGGAAATT 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT * *** 238604445 ATATCCGGGTTAAGACCCGAAGGCAATTATGCTAGTGGCT 1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT * * * **** 238604485 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCGTT 1 ATATCCGGGCTAAGACCCGAAGGCAATT-ATGCTAGAAACT * 238604525 CTATCCGGGCTAAGACCCGAAGGCA 1 ATATCCGGGCTAAGACCCGAAGGCA 238604550 TTCGTGCACG Statistics Matches: 85, Mismatches: 17, Indels: 4 0.80 0.16 0.04 Matches are distributed among these distances: 39 16 0.19 40 69 0.81 ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22 Consensus pattern (40 bp): ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT Found at i:238604570 original size:40 final size:40 Alignment explanation

Indices: 238604443--238604572 Score: 165 Period size: 40 Copynumber: 3.2 Consensus size: 40 238604433 ATGCTGGAAA * * * 238604443 TTATATCCGGGTTAAGACCCGAAGGCAATT-ATGCTAGTGG 1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG * * * 238604483 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG * 238604523 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG 1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG 238604563 TTATATCCGG 1 TTATATCCGG 238604573 TTGTATTCCG Statistics Matches: 77, Mismatches: 11, Indels: 4 0.84 0.12 0.04 Matches are distributed among these distances: 39 4 0.05 40 73 0.95 ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24 Consensus pattern (40 bp): TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG Found at i:238606066 original size:47 final size:48 Alignment explanation

Indices: 238605969--238606117 Score: 219 Period size: 48 Copynumber: 3.1 Consensus size: 48 238605959 TTTATACGAA * * * * 238605969 ATCACATATTGATGCCAACGTCATATCCCAAATATGGTCTTACATAGG 1 ATCACATATTGATGCCAATGCCATATCCCAGACATGGTCTTACATAGG * * * 238606017 ATCACATATCGATGCCAATGCCATCT-CCAGACATGGTCTTACATGGG 1 ATCACATATTGATGCCAATGCCATATCCCAGACATGGTCTTACATAGG * 238606064 ATCACATATTGATGCCAATGCCATGTCCCAGACATGGTCTTACATAGG 1 ATCACATATTGATGCCAATGCCATATCCCAGACATGGTCTTACATAGG 238606112 ATCACA 1 ATCACA 238606118 ATGCATAGCC Statistics Matches: 90, Mismatches: 10, Indels: 2 0.88 0.10 0.02 Matches are distributed among these distances: 47 42 0.47 48 48 0.53 ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27 Consensus pattern (48 bp): ATCACATATTGATGCCAATGCCATATCCCAGACATGGTCTTACATAGG Found at i:238606138 original size:36 final size:37 Alignment explanation

Indices: 238606079--238606180 Score: 111 Period size: 37 Copynumber: 2.8 Consensus size: 37 238606069 ATATTGATGC * 238606079 CAATGCCAT-GTCCCAGAC-ATGGTCTTACATAGGATCA 1 CAATGCCATAG-CCCA-ACTATGGTCTTACATAGCATCA ** * 238606116 CAATG-CATAGCCCAACTATGGTCTTACATTTCATTA 1 CAATGCCATAGCCCAACTATGGTCTTACATAGCATCA * * 238606152 CGATGCCATAGCCCAGCTATGGTCTTACA 1 CAATGCCATAGCCCAACTATGGTCTTACA 238606181 CGTACTCAAA Statistics Matches: 56, Mismatches: 6, Indels: 6 0.82 0.09 0.09 Matches are distributed among these distances: 35 2 0.04 36 26 0.46 37 28 0.50 ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27 Consensus pattern (37 bp): CAATGCCATAGCCCAACTATGGTCTTACATAGCATCA Found at i:238610021 original size:40 final size:40 Alignment explanation

Indices: 238609966--238610189 Score: 281 Period size: 40 Copynumber: 5.5 Consensus size: 40 238609956 TATTCGGATG 238609966 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * 238610006 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTG-CA--AGTTACT * * * 238610049 ATA-CCTGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACT 1 ATATCC-GGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT ** * * 238610089 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * * * 238610129 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT * 238610169 ATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAG 238610190 ATACTTGGGT Statistics Matches: 161, Mismatches: 18, Indels: 11 0.85 0.09 0.06 Matches are distributed among these distances: 39 13 0.08 40 110 0.68 41 3 0.02 42 2 0.01 43 33 0.20 ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27 Consensus pattern (40 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT Found at i:238610111 original size:83 final size:80 Alignment explanation

Indices: 238609966--238610189 Score: 285 Period size: 83 Copynumber: 2.8 Consensus size: 80 238609956 TATTCGGATG * 238609966 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCA 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCA ** * 238610031 TTTGTG-TGAGTAGTTGCT 66 TTCATGCT-AGT-G--ACT * * 238610049 ATA-CCTGGGCTAAGTCTCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGC 1 ATATCC-GGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGC 238610113 ATTCATGCTAGTGACT 65 ATTCATGCTAGTGACT * * * 238610129 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCGAAG 1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG 238610190 ATACTTGGGT Statistics Matches: 127, Mismatches: 10, Indels: 12 0.85 0.07 0.08 Matches are distributed among these distances: 79 14 0.11 80 39 0.31 81 4 0.03 82 3 0.02 83 66 0.52 84 1 0.01 ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27 Consensus pattern (80 bp): ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCA TTCATGCTAGTGACT Found at i:238614136 original size:40 final size:39 Alignment explanation

Indices: 238614091--238614298 Score: 202 Period size: 40 Copynumber: 5.2 Consensus size: 39 238614081 CGGAATACAA * 238614091 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 238614131 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * * * 238614171 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC 1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC * *** * 238614211 CCGGATGTGGTCACTAGCAC-AATGGCCTTCGGGTCTTAAC 1 CCGGATATAACCACT-GCACAAAT-GCCTTCGGGTCTTAGC ** * * * 238614251 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC 1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC 238614291 CCGGATAT 1 CCGGATAT 238614299 CATTCAATTG Statistics Matches: 141, Mismatches: 24, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 39 4 0.03 40 134 0.95 41 3 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (39 bp): CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC Found at i:238614231 original size:80 final size:80 Alignment explanation

Indices: 238614091--238614297 Score: 238 Period size: 80 Copynumber: 2.6 Consensus size: 80 238614081 CGGAATACAA * * * 238614091 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAAT- 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCAC-AATG * 238614155 GCCTTCGGGTATTAGC 65 GCCTTCGGGTATTAAC * * ** 238614171 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTGGTC-ACTAGCACAATG 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-AGAACGACTAGCACAATG * 238614235 GCCTTCGGGTCTTAAC 65 GCCTTCGGGTATTAAC ** * ** * * 238614251 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA 1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA 238614298 TCATTCAATT Statistics Matches: 107, Mismatches: 18, Indels: 5 0.82 0.14 0.04 Matches are distributed among these distances: 79 3 0.03 80 102 0.95 81 2 0.02 ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25 Consensus pattern (80 bp): CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAATGG CCTTCGGGTATTAAC Found at i:238622217 original size:39 final size:40 Alignment explanation

Indices: 238622073--238622248 Score: 167 Period size: 40 Copynumber: 4.4 Consensus size: 40 238622063 TGCACGAATC * ** * 238622073 GGTCTTAGCCCGGATAGAACGACTTGCACAAATGCCTTCG 1 GGTCTTAGCCCGGATATAATAACTAGCACAAATGCCTTCG * * * * * 238622113 GGTATTAGCCCGGATTTAACAACTTGCACGAATGCCTTCG 1 GGTCTTAGCCCGGATATAATAACTAGCACAAATGCCTTCG * ** * 238622153 GGTCTTAGCCCGGATGTGGTCACTAGCAC-AATGGCCTTCG 1 GGTCTTAGCCCGGATATAATAACTAGCACAAAT-GCCTTCG * * * * 238622193 GGTCTTA-ACCGGATATAATTACTAGCATAAATGTCTTCG 1 GGTCTTAGCCCGGATATAATAACTAGCACAAATGCCTTCG * 238622232 GGACTTAGCCCGGATAT 1 GGTCTTAGCCCGGATAT 238622249 CATTCAATTG Statistics Matches: 112, Mismatches: 21, Indels: 6 0.81 0.15 0.04 Matches are distributed among these distances: 39 30 0.27 40 82 0.73 ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27 Consensus pattern (40 bp): GGTCTTAGCCCGGATATAATAACTAGCACAAATGCCTTCG Found at i:238624885 original size:7 final size:7 Alignment explanation

Indices: 238624873--238624911 Score: 51 Period size: 7 Copynumber: 5.6 Consensus size: 7 238624863 TATCTTGAAT 238624873 TTTAAAC 1 TTTAAAC * 238624880 TTTAAAT 1 TTTAAAC * 238624887 TTTGAAC 1 TTTAAAC * 238624894 TTTAAAT 1 TTTAAAC 238624901 TTTAAAC 1 TTTAAAC 238624908 TTTA 1 TTTA 238624912 TATCTTGGTT Statistics Matches: 26, Mismatches: 6, Indels: 0 0.81 0.19 0.00 Matches are distributed among these distances: 7 26 1.00 ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51 Consensus pattern (7 bp): TTTAAAC Found at i:238624887 original size:14 final size:14 Alignment explanation

Indices: 238624870--238624911 Score: 75 Period size: 14 Copynumber: 3.0 Consensus size: 14 238624860 TTTTATCTTG 238624870 AATTTTAAACTTTA 1 AATTTTAAACTTTA * 238624884 AATTTTGAACTTTA 1 AATTTTAAACTTTA 238624898 AATTTTAAACTTTA 1 AATTTTAAACTTTA 238624912 TATCTTGGTT Statistics Matches: 26, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 14 26 1.00 ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50 Consensus pattern (14 bp): AATTTTAAACTTTA Found at i:238624891 original size:21 final size:21 Alignment explanation

Indices: 238624867--238624906 Score: 62 Period size: 21 Copynumber: 1.9 Consensus size: 21 238624857 ATTTTTTATC * 238624867 TTGAATTTTAAACTTTAAATT 1 TTGAACTTTAAACTTTAAATT * 238624888 TTGAACTTTAAATTTTAAA 1 TTGAACTTTAAACTTTAAA 238624907 CTTTATATCT Statistics Matches: 17, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 21 17 1.00 ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50 Consensus pattern (21 bp): TTGAACTTTAAACTTTAAATT Found at i:238626561 original size:16 final size:15 Alignment explanation

Indices: 238626540--238626587 Score: 69 Period size: 16 Copynumber: 3.1 Consensus size: 15 238626530 GATGTGAATA 238626540 ATAAAATATATAAAAT 1 ATAAAATAT-TAAAAT 238626556 ATAAAATATTAAAAT 1 ATAAAATATTAAAAT * 238626571 ATCAAAATATTAGAAT 1 AT-AAAATATTAAAAT 238626587 A 1 A 238626588 GTAATAATTA Statistics Matches: 30, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 15 8 0.27 16 22 0.73 ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31 Consensus pattern (15 bp): ATAAAATATTAAAAT Found at i:238626570 original size:8 final size:8 Alignment explanation

Indices: 238626536--238626587 Score: 61 Period size: 8 Copynumber: 6.5 Consensus size: 8 238626526 CAATGATGTG * 238626536 AATAATAA 1 AATATTAA 238626544 AATATATAA 1 AATAT-TAA 238626553 AATA-TAA 1 AATATTAA 238626560 AATATTAA 1 AATATTAA * 238626568 AATATCAA 1 AATATTAA * 238626576 AATATTAG 1 AATATTAA 238626584 AATA 1 AATA 238626588 GTAATAATTA Statistics Matches: 38, Mismatches: 4, Indels: 4 0.83 0.09 0.09 Matches are distributed among these distances: 7 7 0.18 8 24 0.63 9 7 0.18 ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31 Consensus pattern (8 bp): AATATTAA Found at i:238626805 original size:22 final size:24 Alignment explanation

Indices: 238626742--238626806 Score: 80 Period size: 25 Copynumber: 2.8 Consensus size: 24 238626732 CGTGATAATA * 238626742 TTAAAAATATGTACATAATATAGTG 1 TTAAAAATATATACATAATATAG-G * 238626767 TTAAAAATACATACATAATATA-G 1 TTAAAAATATATACATAATATAGG * 238626790 TT-AAGATATATACATAA 1 TTAAAAATATATACATAA 238626807 GATAACATGT Statistics Matches: 36, Mismatches: 4, Indels: 3 0.84 0.09 0.07 Matches are distributed among these distances: 22 13 0.36 23 3 0.08 25 20 0.56 ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34 Consensus pattern (24 bp): TTAAAAATATATACATAATATAGG Found at i:238626860 original size:25 final size:25 Alignment explanation

Indices: 238626832--238626965 Score: 86 Period size: 25 Copynumber: 5.6 Consensus size: 25 238626822 AAAAATTTAT 238626832 ATATATAAATAATATAATATTAAAG 1 ATATATAAATAATATAATATTAAAG * * * * 238626857 ATATATAAATAAAATAGTATAAAAT 1 ATATATAAATAATATAATATTAAAG * * 238626882 ATATATATACGTAATATAGA-ATTTAA- 1 ATATATA-A-ATAATATA-ATATTAAAG ** * 238626908 A-ATATACCTAATAT-AT-TAAAAG 1 ATATATAAATAATATAATATTAAAG * 238626930 A-ATATATATAATATAATATT-AAG 1 ATATATAAATAATATAATATTAAAG * 238626953 AAATAT-AATAATA 1 ATATATAAATAATA 238626966 ACAAAAAAAG Statistics Matches: 84, Mismatches: 17, Indels: 18 0.71 0.14 0.15 Matches are distributed among these distances: 21 4 0.05 22 12 0.14 23 18 0.21 24 5 0.06 25 33 0.39 26 2 0.02 27 10 0.12 ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35 Consensus pattern (25 bp): ATATATAAATAATATAATATTAAAG Found at i:238627522 original size:30 final size:30 Alignment explanation

Indices: 238627444--238627577 Score: 155 Period size: 30 Copynumber: 4.5 Consensus size: 30 238627434 TAGGTACAAG * * 238627444 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT 1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT * ** * * 238627474 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT 1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT * 238627504 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT 1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT * 238627534 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT 1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT 238627564 TGGTGGTGGAAAAG 1 TGGTGGTGGAAAAG 238627578 CTAAGATTTA Statistics Matches: 91, Mismatches: 12, Indels: 2 0.87 0.11 0.02 Matches are distributed among these distances: 29 2 0.02 30 89 0.98 ACGTcount: A:0.22, C:0.04, G:0.47, T:0.27 Consensus pattern (30 bp): TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT Found at i:238628468 original size:15 final size:15 Alignment explanation

Indices: 238628435--238628482 Score: 53 Period size: 15 Copynumber: 3.3 Consensus size: 15 238628425 TTGATTTTTT * * 238628435 AAAAAGCAGAATTTG 1 AAAAAGCAAAAATTG * 238628450 -AAAAGCATAAATTG 1 AAAAAGCAAAAATTG * 238628464 AAAAAACAAAAATTG 1 AAAAAGCAAAAATTG 238628479 AAAA 1 AAAA 238628483 TACCTCAGCG Statistics Matches: 28, Mismatches: 4, Indels: 2 0.82 0.12 0.06 Matches are distributed among these distances: 14 12 0.43 15 16 0.57 ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17 Consensus pattern (15 bp): AAAAAGCAAAAATTG Found at i:238628482 original size:104 final size:103 Alignment explanation

Indices: 238628372--238628571 Score: 271 Period size: 104 Copynumber: 1.9 Consensus size: 103 238628362 AAAACAGATT 238628372 TTGAAAATACCTC-GACATGTGACCC-AGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTT 1 TTGAAAATACCTCAG-C--GTG-CCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTT * * * 238628434 TAAAAAGCAGAATTTGAAAAGCATAAATTGAAAAAACAAAAA 62 TAAAAAGCAGAAATTGAAAAGCAGAAATCGAAAAAACAAAAA * * 238628476 TTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA 1 TTGAAAATACCTCAGCGTGCCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTAA * * 238628541 AGAGCAGAAATTGGAAAGCAGAAATCGAAAA 65 AAAGCAGAAATTGAAAAGCAGAAATCGAAAA 238628572 TACCTCAGCG Statistics Matches: 85, Mismatches: 7, Indels: 8 0.85 0.07 0.08 Matches are distributed among these distances: 101 3 0.04 102 3 0.04 103 31 0.36 104 47 0.55 105 1 0.01 ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25 Consensus pattern (103 bp): TTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTAAA AAGCAGAAATTGAAAAGCAGAAATCGAAAAAACAAAAA Found at i:238628598 original size:89 final size:89 Alignment explanation

Indices: 238628446--238628674 Score: 395 Period size: 89 Copynumber: 2.6 Consensus size: 89 238628436 AAAAGCAGAA * * * 238628446 TTTGAAAAGCATAAATTGAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTC 1 TTTGAAGAGCAGAAATTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTC 238628511 ACCTCTCGCAATATGAGTTGATTTT 65 ACCTCTCGCAATATGAGTTGATTTT * * * 238628536 TTTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA 1 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA 238628601 CCTCTCGCAATATGAGTTGATTTT 66 CCTCTCGCAATATGAGTTGATTTT 238628625 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCC 1 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCC 238628675 TCAAAACAGA Statistics Matches: 130, Mismatches: 9, Indels: 1 0.93 0.06 0.01 Matches are distributed among these distances: 89 114 0.88 90 16 0.12 ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24 Consensus pattern (89 bp): TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA CCTCTCGCAATATGAGTTGATTTT Found at i:238628651 original size:14 final size:14 Alignment explanation

Indices: 238628634--238628660 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 238628624 TTTTGAAGAG 238628634 CAGAAATTGAAAAA 1 CAGAAATTGAAAAA 238628648 CAGAAATTGAAAA 1 CAGAAATTGAAAA 238628661 TACCTCAGCG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15 Consensus pattern (14 bp): CAGAAATTGAAAAA Found at i:238628686 original size:33 final size:33 Alignment explanation

Indices: 238628644--238628707 Score: 128 Period size: 33 Copynumber: 1.9 Consensus size: 33 238628634 CAGAAATTGA 238628644 AAAACAGAAATTGAAAATACCTCAGCGTGCCTC 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCTC 238628677 AAAACAGAAATTGAAAATACCTCAGCGTGCC 1 AAAACAGAAATTGAAAATACCTCAGCGTGCC 238628708 CTGAGGCTCA Statistics Matches: 31, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 33 31 1.00 ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17 Consensus pattern (33 bp): AAAACAGAAATTGAAAATACCTCAGCGTGCCTC Found at i:238628847 original size:210 final size:210 Alignment explanation

Indices: 238628466--238628880 Score: 751 Period size: 210 Copynumber: 2.0 Consensus size: 210 238628456 ATAAATTGAA 238628466 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG ** 238628531 ATTTTTTTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA 66 ATTTTTTTGAAGAGCAGAAATT-GAAAAAAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA 238628596 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA 130 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA 238628661 TACCTCAGCGTGCCTC 195 TACCTCAGCGTGCCTC * 238628677 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG * * * 238628742 ATTTTTTTTGAAGAGCAGAAATT-AAAAAATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCA 66 A-TTTTTTTGAAGAGCAGAAATTGAAAAAAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA 238628806 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA 130 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA 238628871 TACCTCAGCG 195 TACCTCAGCG 238628881 CGCCCTGAGG Statistics Matches: 197, Mismatches: 6, Indels: 3 0.96 0.03 0.01 Matches are distributed among these distances: 210 111 0.56 211 65 0.33 212 21 0.11 ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25 Consensus pattern (210 bp): AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG ATTTTTTTGAAGAGCAGAAATTGAAAAAAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAA CTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAAT ACCTCAGCGTGCCTC Found at i:238628861 original size:14 final size:14 Alignment explanation

Indices: 238628844--238628870 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 238628834 TTTTGAAGAG 238628844 CAGAAATTGAAAAA 1 CAGAAATTGAAAAA 238628858 CAGAAATTGAAAA 1 CAGAAATTGAAAA 238628871 TACCTCAGCG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15 Consensus pattern (14 bp): CAGAAATTGAAAAA Found at i:238628933 original size:87 final size:89 Alignment explanation

Indices: 238628677--238629094 Score: 731 Period size: 87 Copynumber: 4.8 Consensus size: 89 238628667 AGCGTGCCTC 238628677 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 238628742 ATTTTTTTTGAAGAGCAGAAATT-A 66 A-TTTTTTTGAAGAGCAGAAATTGA * * 238628766 AAAA-ATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 238628830 ATTTTTTTGAAGAGCAGAAATTGA 66 ATTTTTTTGAAGAGCAGAAATTGA * * 238628854 AAAACAGAAATTGAAAATACCTCAGCGCGCCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTG 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 238628919 A-TTTTTTGAA-AGCAGAAATTGA 66 ATTTTTTTGAAGAGCAGAAATTGA 238628941 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCG-AATATGAGTTG 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 238629005 ATTTTTTTGAAGAGCA-AAATTGA 66 ATTTTTTTGAAGAGCAGAAATTGA * * 238629028 AAAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG 238629093 AT 66 AT 238629095 CTTTGGAACA Statistics Matches: 314, Mismatches: 10, Indels: 11 0.94 0.03 0.03 Matches are distributed among these distances: 86 12 0.04 87 151 0.48 88 90 0.29 89 61 0.19 ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27 Consensus pattern (89 bp): AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG ATTTTTTTGAAGAGCAGAAATTGA Found at i:238628942 original size:13 final size:13 Alignment explanation

Indices: 238628924--238628957 Score: 50 Period size: 14 Copynumber: 2.5 Consensus size: 13 238628914 AGTTGATTTT * 238628924 TTGAAAGCAGAAA 1 TTGAAAACAGAAA 238628937 TTGAAAAACAGAAA 1 TTG-AAAACAGAAA 238628951 TTGAAAA 1 TTGAAAA 238628958 TACCTCAGCG Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 13 7 0.37 14 12 0.63 ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18 Consensus pattern (13 bp): TTGAAAACAGAAA Found at i:238628950 original size:14 final size:14 Alignment explanation

Indices: 238628931--238628957 Score: 54 Period size: 14 Copynumber: 1.9 Consensus size: 14 238628921 TTTTTGAAAG 238628931 CAGAAATTGAAAAA 1 CAGAAATTGAAAAA 238628945 CAGAAATTGAAAA 1 CAGAAATTGAAAA 238628958 TACCTCAGCG Statistics Matches: 13, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 13 1.00 ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15 Consensus pattern (14 bp): CAGAAATTGAAAAA Found at i:238639883 original size:25 final size:25 Alignment explanation

Indices: 238639849--238639900 Score: 86 Period size: 25 Copynumber: 2.1 Consensus size: 25 238639839 GGTTTCTTGG 238639849 TTTTTTTTTTGGGGGTTAGGTTTTT 1 TTTTTTTTTTGGGGGTTAGGTTTTT ** 238639874 TTTTTTTTTTTTGGGTTAGGTTTTT 1 TTTTTTTTTTGGGGGTTAGGTTTTT 238639899 TT 1 TT 238639901 GGGGGGGCTT Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 25 25 1.00 ACGTcount: A:0.04, C:0.00, G:0.23, T:0.73 Consensus pattern (25 bp): TTTTTTTTTTGGGGGTTAGGTTTTT Found at i:238641759 original size:32 final size:32 Alignment explanation

Indices: 238641743--238641806 Score: 103 Period size: 32 Copynumber: 2.0 Consensus size: 32 238641733 TGTCTGCATT * 238641743 TTAGCATTTTAATAGTTAATGAATGATGGGCA 1 TTAGCATTTTAATAGTTAATGAATGATCGGCA * 238641775 TTAGCATTTTAATAGTTAATGGATGAT-GGCA 1 TTAGCATTTTAATAGTTAATGAATGATCGGCA 238641806 T 1 T 238641807 GATAAGCATT Statistics Matches: 31, Mismatches: 1, Indels: 1 0.94 0.03 0.03 Matches are distributed among these distances: 31 5 0.16 32 26 0.84 ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39 Consensus pattern (32 bp): TTAGCATTTTAATAGTTAATGAATGATCGGCA Found at i:238644960 original size:12 final size:12 Alignment explanation

Indices: 238644943--238644973 Score: 62 Period size: 12 Copynumber: 2.6 Consensus size: 12 238644933 ACTCGGGGAA 238644943 GAGGCCGTGGTC 1 GAGGCCGTGGTC 238644955 GAGGCCGTGGTC 1 GAGGCCGTGGTC 238644967 GAGGCCG 1 GAGGCCG 238644974 AGGTAGTACT Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 19 1.00 ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13 Consensus pattern (12 bp): GAGGCCGTGGTC Found at i:238649832 original size:32 final size:32 Alignment explanation

Indices: 238649796--238649878 Score: 143 Period size: 32 Copynumber: 2.7 Consensus size: 32 238649786 TGTATGCATT * 238649796 TTAGCATTTTAATAGTTAATGGATGATGGGCA 1 TTAGCATTTTAATAGTTAATGAATGATGGGCA 238649828 TTAGCATTTTAATAGTTAATGAATGATGGGCA 1 TTAGCATTTTAATAGTTAATGAATGATGGGCA 238649860 TTAGCATTTT-ATAG-TAATG 1 TTAGCATTTTAATAGTTAATG 238649879 TTAGGGCATG Statistics Matches: 50, Mismatches: 1, Indels: 2 0.94 0.02 0.04 Matches are distributed among these distances: 30 5 0.10 31 4 0.08 32 41 0.82 ACGTcount: A:0.33, C:0.06, G:0.22, T:0.40 Consensus pattern (32 bp): TTAGCATTTTAATAGTTAATGAATGATGGGCA Found at i:238658739 original size:37 final size:37 Alignment explanation

Indices: 238658689--238658763 Score: 132 Period size: 37 Copynumber: 2.0 Consensus size: 37 238658679 AAATTCACAA * 238658689 AAGAAAAAGAAAGAAATAAGCTTGCTAGGGTTCAGCT 1 AAGAAAAAGAAAGAAATAAGCTTACTAGGGTTCAGCT * 238658726 AAGAAAAAGAAAGAAATAAGCTTACTAGGGTTCGGCT 1 AAGAAAAAGAAAGAAATAAGCTTACTAGGGTTCAGCT 238658763 A 1 A 238658764 CCTATTTTGG Statistics Matches: 36, Mismatches: 2, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 37 36 1.00 ACGTcount: A:0.47, C:0.11, G:0.24, T:0.19 Consensus pattern (37 bp): AAGAAAAAGAAAGAAATAAGCTTACTAGGGTTCAGCT Found at i:238659645 original size:43 final size:42 Alignment explanation

Indices: 238659549--238659656 Score: 137 Period size: 43 Copynumber: 2.5 Consensus size: 42 238659539 TTTGCTTTAC 238659549 GACCATGTCTGGGACATTGGCATCGTATCTGACTTCATGTAA 1 GACCATGTCTGGGACATTGGCATCGTATCTGACTTCATGTAA * * * * * 238659591 GACCCTATCTGGGACAGTGGCATCGATGTTTGA-TTACATGTAA 1 GACCATGTCTGGGACATTGGCATCG-TATCTGACTT-CATGTAA * 238659634 TACCATGTCTGGGACATTGGCAT 1 GACCATGTCTGGGACATTGGCAT 238659657 TATATATTTT Statistics Matches: 55, Mismatches: 9, Indels: 3 0.82 0.13 0.04 Matches are distributed among these distances: 42 24 0.44 43 31 0.56 ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31 Consensus pattern (42 bp): GACCATGTCTGGGACATTGGCATCGTATCTGACTTCATGTAA Found at i:238663957 original size:40 final size:40 Alignment explanation

Indices: 238663878--238663999 Score: 147 Period size: 40 Copynumber: 3.0 Consensus size: 40 238663868 CGGATGATAA * * ** * 238663878 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT * * * 238663918 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-TTATAT * 238663958 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT 1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT 238663998 CC 1 CC 238664000 TGCTAAATCC Statistics Matches: 68, Mismatches: 12, Indels: 4 0.81 0.14 0.05 Matches are distributed among these distances: 39 2 0.03 40 64 0.94 41 2 0.03 ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28 Consensus pattern (40 bp): CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGTTATAT Found at i:238664282 original size:22 final size:22 Alignment explanation

Indices: 238664242--238664283 Score: 59 Period size: 22 Copynumber: 1.9 Consensus size: 22 238664232 GAATGTGCAT * 238664242 ATATGAAGTTATTCATTTAGCC 1 ATATGAAGTTATACATTTAGCC 238664264 ATATGAATGTTATAC-TTTAG 1 ATATGAA-GTTATACATTTAG 238664284 TCAAAACTAA Statistics Matches: 18, Mismatches: 1, Indels: 2 0.86 0.05 0.10 Matches are distributed among these distances: 22 12 0.67 23 6 0.33 ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43 Consensus pattern (22 bp): ATATGAAGTTATACATTTAGCC Found at i:238672015 original size:42 final size:41 Alignment explanation

Indices: 238671935--238672084 Score: 162 Period size: 41 Copynumber: 3.6 Consensus size: 41 238671925 GAGCTTGGTC 238671935 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT 1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT * * 238671976 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT 1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT * * * * * * 238672018 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC 1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT * 238672059 TCGAAGGGCTTTTGAGCCGGTGCTAA 1 TCGAAGGGCTTTTGAGCCAGTGCTAA 238672085 GAGTCGGACT Statistics Matches: 90, Mismatches: 14, Indels: 12 0.78 0.12 0.10 Matches are distributed among these distances: 39 4 0.04 40 9 0.10 41 37 0.41 42 28 0.31 43 12 0.13 ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27 Consensus pattern (41 bp): TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT Found at i:238672067 original size:41 final size:40 Alignment explanation

Indices: 238671915--238672084 Score: 161 Period size: 41 Copynumber: 4.2 Consensus size: 40 238671905 GCTAATCGGG * 238671915 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT 1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT * * 238671956 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT 1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT * * 238671999 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT 1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT * * 238672039 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT 1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT 238672080 G-CTAA 1 GTCTAA 238672085 GAGTCGGACT Statistics Matches: 107, Mismatches: 10, Indels: 26 0.75 0.07 0.18 Matches are distributed among these distances: 39 7 0.07 40 14 0.13 41 50 0.47 42 23 0.21 43 9 0.08 44 1 0.01 45 3 0.03 ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28 Consensus pattern (40 bp): GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT Found at i:238676876 original size:66 final size:65 Alignment explanation

Indices: 238676795--238676928 Score: 259 Period size: 66 Copynumber: 2.0 Consensus size: 65 238676785 CATGTAGACA 238676795 AGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATG 1 AGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACA-CATG 238676860 T 65 T 238676861 AGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACATGT 1 AGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACATGT 238676926 AGA 1 AGA 238676929 CAAGAGAGCT Statistics Matches: 68, Mismatches: 0, Indels: 1 0.99 0.00 0.01 Matches are distributed among these distances: 65 8 0.12 66 60 0.88 ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21 Consensus pattern (65 bp): AGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACATGT Found at i:238684416 original size:41 final size:41 Alignment explanation

Indices: 238684371--238684488 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 238684361 TGAAAGATAA 238684371 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 238684412 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 238684442 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 238684483 ATGTAG 1 ATGTAG 238684489 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:238684427 original size:71 final size:71 Alignment explanation

Indices: 238684339--238684502 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 238684329 GAGATGTATC 238684339 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 238684404 AGGACA 66 AGGACA 238684410 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 238684475 AGGACA 66 AGGACA 238684481 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 238684503 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:238689017 original size:41 final size:41 Alignment explanation

Indices: 238688972--238689089 Score: 98 Period size: 41 Copynumber: 3.1 Consensus size: 41 238688962 TGAAAGATAA 238688972 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC * * * * * 238689013 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A 1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 238689043 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC 238689084 ATGTAG 1 ATGTAG 238689090 ACAAGAGAGC Statistics Matches: 54, Mismatches: 10, Indels: 26 0.60 0.11 0.29 Matches are distributed among these distances: 29 1 0.02 30 8 0.15 31 9 0.17 32 1 0.02 33 3 0.06 34 1 0.02 35 1 0.02 36 1 0.02 37 1 0.02 38 3 0.06 39 1 0.02 40 9 0.17 41 14 0.26 42 1 0.02 ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21 Consensus pattern (41 bp): ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC Found at i:238689028 original size:71 final size:71 Alignment explanation

Indices: 238688940--238689103 Score: 328 Period size: 71 Copynumber: 2.3 Consensus size: 71 238688930 GAGATGTATC 238688940 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 238689005 AGGACA 66 AGGACA 238689011 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA 238689076 AGGACA 66 AGGACA 238689082 CCATGTAGACAAGAGAGCTACG 1 CCATGTAGACAAGAGAGCTACG 238689104 AGACAAATCG Statistics Matches: 93, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 71 93 1.00 ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19 Consensus pattern (71 bp): CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA AGGACA Found at i:238692441 original size:8 final size:8 Alignment explanation

Indices: 238692407--238692458 Score: 52 Period size: 8 Copynumber: 6.5 Consensus size: 8 238692397 TAGTGATGTG * 238692407 AATAATAA 1 AATATTAA * 238692415 AGTATATAA 1 AATAT-TAA 238692424 AATA-TAA 1 AATATTAA 238692431 AATATTAA 1 AATATTAA * 238692439 AATATCAA 1 AATATTAA * 238692447 AATATTAG 1 AATATTAA 238692455 AATA 1 AATA 238692459 ATAATAATTA Statistics Matches: 36, Mismatches: 6, Indels: 4 0.78 0.13 0.09 Matches are distributed among these distances: 7 7 0.19 8 23 0.64 9 6 0.17 ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31 Consensus pattern (8 bp): AATATTAA Found at i:238692448 original size:16 final size:15 Alignment explanation

Indices: 238692411--238692458 Score: 60 Period size: 16 Copynumber: 3.1 Consensus size: 15 238692401 GATGTGAATA * 238692411 ATAAAGTATATAAAAT 1 ATAAAATAT-TAAAAT 238692427 ATAAAATATTAAAAT 1 ATAAAATATTAAAAT * 238692442 ATCAAAATATTAGAAT 1 AT-AAAATATTAAAAT 238692458 A 1 A 238692459 ATAATAATTA Statistics Matches: 29, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 15 8 0.28 16 21 0.72 ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31 Consensus pattern (15 bp): ATAAAATATTAAAAT Found at i:238692630 original size:20 final size:20 Alignment explanation

Indices: 238692573--238692679 Score: 63 Period size: 22 Copynumber: 5.0 Consensus size: 20 238692563 AATACTACAT 238692573 AAATATGTACAT-ATATAAA 1 AAATATGTACATAATATAAA ** * 238692592 AAATAAATACGTGATAATATTAA 1 AAATATGTAC---ATAATATAAA 238692615 AAATATGTACATAATATAGTGTAA 1 AAATATGTACATAATATA----AA ** 238692639 AAATACATACATAATATAATTA 1 AAATATGTACATAATATAA--A * * 238692661 AAATATATACATAAGATAA 1 AAATATGTACATAATATAA 238692680 CATGTAGAAA Statistics Matches: 68, Mismatches: 10, Indels: 17 0.72 0.11 0.18 Matches are distributed among these distances: 19 8 0.12 20 8 0.12 22 20 0.29 23 14 0.21 24 18 0.26 ACGTcount: A:0.57, C:0.06, G:0.07, T:0.31 Consensus pattern (20 bp): AAATATGTACATAATATAAA Found at i:238692670 original size:22 final size:23 Alignment explanation

Indices: 238692610--238692679 Score: 88 Period size: 24 Copynumber: 3.0 Consensus size: 23 238692600 ACGTGATAAT * 238692610 ATTAAAAATATGTACATAATATA 1 ATTAAAAATATATACATAATATA * * 238692633 GTGTAAAAATACATACATAATATA 1 AT-TAAAAATATATACATAATATA * 238692657 ATT-AAAATATATACATAAGATA 1 ATTAAAAATATATACATAATATA 238692679 A 1 A 238692680 CATGTAGAAA Statistics Matches: 40, Mismatches: 6, Indels: 3 0.82 0.12 0.06 Matches are distributed among these distances: 22 18 0.45 23 2 0.05 24 20 0.50 ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31 Consensus pattern (23 bp): ATTAAAAATATATACATAATATA Found at i:238692725 original size:25 final size:25 Alignment explanation

Indices: 238692695--238692814 Score: 90 Period size: 25 Copynumber: 5.0 Consensus size: 25 238692685 AGAAAAAAAA * 238692695 ATATATAAATAATATAGTATTAA-AG 1 ATATATACATAATATAGTA-TAATAG * * 238692720 ATATATACATAAAATAGTATAATAT 1 ATATATACATAATATAGTATAATAG * * * 238692745 ATATATACGTAATATAGAAT-TTAG 1 ATATATACATAATATAGTATAATAG * * 238692769 A-ATATACCTAATATA-T-TAAAAG 1 ATATATACATAATATAGTATAATAG * * 238692791 A-ATATATATATATATAATATAATA 1 ATATATACATA-ATATAGTATAATA 238692815 TTAAGAAATA Statistics Matches: 75, Mismatches: 15, Indels: 10 0.75 0.15 0.10 Matches are distributed among these distances: 21 1 0.01 22 10 0.13 23 18 0.24 24 7 0.09 25 39 0.52 ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37 Consensus pattern (25 bp): ATATATACATAATATAGTATAATAG Found at i:238693151 original size:16 final size:16 Alignment explanation

Indices: 238693113--238693151 Score: 51 Period size: 16 Copynumber: 2.4 Consensus size: 16 238693103 ATCTCCAAAA * 238693113 AAAAACTAGCCTCTCC 1 AAAAACTAGCCTCTAC * 238693129 AAAAACTAGCCTTTAC 1 AAAAACTAGCCTCTAC * 238693145 AATAACT 1 AAAAACT 238693152 CTTCTCCTTG Statistics Matches: 20, Mismatches: 3, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 16 20 1.00 ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23 Consensus pattern (16 bp): AAAAACTAGCCTCTAC Found at i:238693395 original size:29 final size:30 Alignment explanation

Indices: 238693317--238693401 Score: 145 Period size: 30 Copynumber: 2.9 Consensus size: 30 238693307 GTGGTGGTAG * * 238693317 AGTGTGGCTAGTGGAGTAGGTAGTGGAGCA 1 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA 238693347 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA 1 AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA 238693377 AGTGT-GCTAGTGGAGTTGGTGGTGG 1 AGTGTGGCTAGTGGAGTTGGTGGTGG 238693402 CAAAGGCTAG Statistics Matches: 53, Mismatches: 2, Indels: 1 0.95 0.04 0.02 Matches are distributed among these distances: 29 20 0.38 30 33 0.62 ACGTcount: A:0.18, C:0.06, G:0.49, T:0.27 Consensus pattern (30 bp): AGTGTGGCTAGTGGAGTTGGTGGTGGAGCA Found at i:238694456 original size:13 final size:14 Alignment explanation

Indices: 238694424--238694456 Score: 57 Period size: 14 Copynumber: 2.4 Consensus size: 14 238694414 GATTTTTTTG 238694424 GAAAAACAAAATTT 1 GAAAAACAAAATTT * 238694438 GAAAAACAGAATTT 1 GAAAAACAAAATTT 238694452 GAAAA 1 GAAAA 238694457 TACCTCAGCG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 14 18 1.00 ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18 Consensus pattern (14 bp): GAAAAACAAAATTT Found at i:238694495 original size:92 final size:89 Alignment explanation

Indices: 238694079--238694606 Score: 489 Period size: 91 Copynumber: 5.9 Consensus size: 89 238694069 CTAGACATTG * * * * * 238694079 AAAACATAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAGT 1 AAAACAGAAATTGAAAATACCTCAGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGT * 238694144 TGA-TTTTT--AAAACAAAATTTGT 65 TGATTTTTTGAAAAACAAAATTTGA ** * * * * 238694166 AAAACAGATTTTGAAAATATCTCGGTATGTGACCCGAGGCTCAACTCACCTCTCGTAATATGAGT 1 AAAACAGAAATTGAAAATACCTCAGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGT * * ** 238694231 TGA-TTTTTGCAAAGCATAAATTAAAA 65 TGATTTTTTGAAAAACA-AAATT-TGA ** * * 238694257 AAAACATCAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT 1 AAAACAGAAATTGAAAATACCTCAGCATGTGACC-GAGGCTCAACTCACCTCTCGCAATATGAGT * 238694322 TGATTTTTTGACAAACATAAA-TTGAAAA 65 TGATTTTTTGAAAAACA-AAATTTG---A * * * * * 238694350 AAAAAAGAAATTGAAAATACCTCAGCGTGT-TCTGAGGCTGAACTCACCTCTCGCAATATGAGTT 1 AAAACAGAAATTGAAAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTT 238694414 GATTTTTTTGGAAAAACAAAATTTGA 66 GA-TTTTTT-GAAAAACAAAATTTGA * * * * * * 238694440 AAAACAGAATTTGAAAATACCTCAGCGTGTGAGTCAAGGCTCAACTCACCACTCGCAATATGAGC 1 AAAACAGAAATTGAAAATACCTCAGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGT * * 238694505 TGATTTTTTTGAAACACAGAATATTGA 65 TGA-TTTTTTGAAAAACAAAAT-TTGA * * * * * * * 238694532 AGAACAGAAATGGAAAACACCTCAGCATCT---TGAGGTTCAACTCACCTCTCGCAATATGAGCT 1 AAAACAGAAATTGAAAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTT 238694594 GATTTTTTTGAAA 66 GA-TTTTTTGAAA 238694607 GATAGAAATT Statistics Matches: 369, Mismatches: 57, Indels: 29 0.81 0.13 0.06 Matches are distributed among these distances: 87 62 0.17 88 41 0.11 89 5 0.01 90 36 0.10 91 100 0.27 92 88 0.24 93 37 0.10 ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28 Consensus pattern (89 bp): AAAACAGAAATTGAAAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTT GATTTTTTGAAAAACAAAATTTGA Found at i:238694604 original size:88 final size:87 Alignment explanation

Indices: 238694115--238694621 Score: 406 Period size: 92 Copynumber: 5.7 Consensus size: 87 238694105 ACGTGAGCCA * * * ** 238694115 AGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTT-AAAACA-AAATTTGTAAAACAGATT 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAA-TTGAAAAACAGAAA * * 238694176 TTGAAAATATCTC-G-GTATGTGACCCG 65 TTGAAAATACCTCAGCGTCTGT-----G * * * * * ** 238694202 AGGCTCAACTCACCTCTCGTAATATGAGTTGA--TTTTTGCAAAGCATAAATTAAAAAAAACATC 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTG-AAAACAGAAATT--GAAAAACAGA * * 238694265 AATTGAAAATACCTCGGCGTGTGACCTG 63 AATTGAAAATACCTCAGCGTCTG---TG * * * 238694293 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAAACATAAATTGAAAAAAAAAAG 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGA-AAACAGAAATTG---AAAAACAG * * 238694357 AAATTGAAAATACCTCAGCGTGTTCTG 62 AAATTGAAAATACCTCAGCGT-CTGTG * * 238694384 AGGCTGAACTCACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACA-AAATTTGAAAAACAGA 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT-G-AAAACAGAAA-TTGAAAAACAGA * * * 238694448 ATTTGAAAATACCTCAGCGTGTGAGTCA 63 AATTGAAAATACCTCAGCGTCT--GT-G * * 238694476 AGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAGAATATTGAAGAACAGAA 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAA-ACAGAA-ATTGAAAAACAGAA * * * 238694541 ATGGAAAACACCTCAGCATCT-TG 64 ATTGAAAATACCTCAGCGTCTGTG * * 238694564 AGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGATAGAAATTGAAAA 1 AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAA-ACAGAAATTGAAAA 238694622 TACCTCAACG Statistics Matches: 353, Mismatches: 41, Indels: 52 0.79 0.09 0.12 Matches are distributed among these distances: 87 42 0.12 88 46 0.13 89 9 0.03 90 33 0.09 91 89 0.25 92 92 0.26 93 39 0.11 94 2 0.01 96 1 0.00 ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28 Consensus pattern (87 bp): AGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAACAGAAATTGAAAAACAGAAAT TGAAAATACCTCAGCGTCTGTG Found at i:238694656 original size:75 final size:74 Alignment explanation

Indices: 238694528--238695393 Score: 571 Period size: 75 Copynumber: 11.3 Consensus size: 74 238694518 ACACAGAATA * * ** * 238694528 TTGAAGAACAGAAATGGAAAACACCTC-A-GCATCTTGAGGTTCAACTCACCTCTCGCAATATGA 1 TTGAA-AACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA * 238694591 GCTGATTTTT 65 GTTGATTTTT * 238694601 TTGAAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 1 TTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 238694666 GTTGA--TTT 65 GTTGATTTTT * * * * 238694674 TTGACAAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGA 1 TTGA-AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA * 238694737 GCTGATTTTT 65 GTTGATTTTT 238694747 TTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 1 TTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 238694812 GTTGA--TTT 65 GTTGATTTTT * * * * * 238694820 TTGACAAACAAAAATT-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGA 1 TTGA-AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 238694884 GTTGATTTTT 65 GTTGATTTTT ** * * * * 238694894 TTGAAAAACAGAAATTGAAAATAGAAATGGAAAACACTCAGCGTCTTGAGGTTCAACTCAGCTCT 1 TTG-AAAACAGAAATTGAAAAT--ACCT------CA-AC-GTGTCTTGAGGCTCAACTCACCTCT * 238694959 CGCAATATGAGCTGATTTTT 55 CGCAATATGAGTTGATTTTT * * ** * ** ** * 238694979 TTGAAACACATAAATT-AAAAAAATTAAAAACAGAAT-TTGAAAGGACCTCAACGTGTGGCC-CG 1 TTGAAA-ACAGAAATTGAAAATACCT--CAAC-GTGTCTTG--AGG--CTCAAC---TCACCTCT * * * * * *** 238695041 AGGACTAACTCACCTCTCGCAATATGAG 55 CGCAAT-A-TGA-GT-T-G--AT-TTTT **** * ** 238695069 TTGATTATTTCGAAAAGCAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC 1 TTGA--AAACAGAAA--------TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC * 238695134 ACAATATGAGTTGATTTTT 56 GCAATATGAGTTGATTTTT * * * * * 238695153 TTGATAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT 1 TTG---AAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATAT 238695218 GAGTTGA--TTT 63 GAGTTGATTTTT * * * * * 238695228 TTGACAAA-AAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCACAATATGA 1 TTGA-AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA * 238695290 GCTGATTTTT 65 GTTGATTTTT * * 238695300 TTGAAAGACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCACTTCTCGCAATATGA 1 TTGAAA-ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA 238695365 GTTGATTTTT 65 GTTGATTTTT * * 238695375 TTG-AAACATAAATTAAAAA 1 TTGAAAACAGAAATTGAAAA 238695394 AACAAAAATT Statistics Matches: 622, Mismatches: 108, Indels: 126 0.73 0.13 0.15 Matches are distributed among these distances: 70 35 0.06 71 39 0.06 72 76 0.12 73 117 0.19 74 25 0.04 75 126 0.20 76 3 0.00 77 59 0.09 78 6 0.01 80 5 0.01 82 7 0.01 83 5 0.01 84 14 0.02 85 57 0.09 86 1 0.00 87 3 0.00 88 1 0.00 89 3 0.00 90 7 0.01 91 7 0.01 92 4 0.01 94 6 0.01 96 3 0.00 97 2 0.00 98 3 0.00 99 2 0.00 100 6 0.01 ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29 Consensus pattern (74 bp): TTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG TTGATTTTT Found at i:238694743 original size:146 final size:145 Alignment explanation

Indices: 238694550--238694916 Score: 644 Period size: 146 Copynumber: 2.5 Consensus size: 145 238694540 AATGGAAAAC * * 238694550 ACCTCAGCATCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGATAGAAA 1 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA 238694615 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA 66 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA 238694680 AACAAAAATTGAAATT 131 AACAAAAATT-AAATT 238694696 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA 1 ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA 238694761 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA 66 TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA 238694826 AACAAAAATTAAATT 131 AACAAAAATTAAATT * * * * * 238694841 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTTGAAAAACAGA 1 ACCTCAGC--GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGA 238694906 AATTGAAAATA 64 AATTGAAAATA 238694917 GAAATGGAAA Statistics Matches: 212, Mismatches: 7, Indels: 3 0.95 0.03 0.01 Matches are distributed among these distances: 145 13 0.06 146 138 0.65 147 61 0.29 ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30 Consensus pattern (145 bp): ACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAA TTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA AACAAAAATTAAATT Found at i:238695346 original size:553 final size:558 Alignment explanation

Indices: 238694265--238695561 Score: 1563 Period size: 553 Copynumber: 2.3 Consensus size: 558 238694255 AAAAAACATC * * 238694265 AATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT 1 AATTAAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT * * * * * * 238694329 TTGACAAACATAAATTGAAAAAAAAAAGAAATTGAAAATACCTCAGCGTGTTCTGAGGCTGAACT 64 TTGAAAAACAGAAATTG---AAAAAAAGAAATGGAAAACACCTCAGCGTGCTCTGAGGCTCAACT * * 238694394 CACCTCTCGCAATATGAGTTGATTTTTTTGGAAAAACAAAATTTGAAAAACAGAATTTGAAAATA 126 CACCTCTCGCAATATGAGCTGATTTTTTTGGAAAAACAAAATTTGAAAAACAGAATTTGAAAAGA * * * 238694459 CCTCAGCGTGTGAGTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTTTGAAACACAG 191 CCTCAACGTGTGAGCCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTATTT-----ACAG ** * * 238694524 AATATTGAAGAACAGAAATGGAAAACACCTCAGCATCTTGAGGTTCAACTCACCTCTCGCAATAT 251 AATA-T-AAG-ACAGAAATGGAAAACACCTCAGCATCCCGAGGCTCAACTCACCTCTCACAATAT * * 238694589 GAGCTGATTTTTTTGAAAGATAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCT 313 GAGCTGATTTTTTTGAAAAATAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCT 238694654 CTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAAC 378 CTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAAC * * 238694719 TCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTT 443 TCACCTCTCACAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAACATGTCTT 238694784 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AC-AAACAAA 508 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAACAAAACAAA * * 238694832 AATT-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGAGTTGATTTTTTT 1 AATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT * * * 238694896 GAAAAACAGAAATTG-AAAATAGAAATGGAAAACA-CTCAGCGT-CT-TGAGGTTCAACTCAGCT 66 GAAAAACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTGCTCTGAGGCTCAACTCACCT * * 238694957 CTCGCAATATGAGCTGATTTTTTT-GAAACACATAAATTAAAAAAATTAAAAACAGAATTTGAAA 131 CTCGCAATATGAGCTGATTTTTTTGGAAAAACA-AAATT-------TGAAAAACAGAATTTGAAA * * * * 238695021 GGACCTCAACGTGTG-GCCCGAGGACT-AACTCACCTCTCGCAATATGAGTTGA-TTATTT-C-G 188 AGACCTCAACGTGTGAG-CCAAGG-CTCAACTCACCACTCGCAATATGAGCTGATTTATTTACAG * * * 238695081 -A-A-AAG-CAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCACAATATG 251 AATATAAGACAGAAATGGAAAACACCTCAGC--ATCCCGAGGCTCAACTCACCTCTCACAATATG * * * * 238695142 AGTTGATTTTTTTGATAAAAATAGAATTTGAAAATATCTCAGCGTGTCCTGAGGCTCAACTCACC 314 AGCTGATTTTTTTG--AAAAATAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACC 238695207 TCTCGCAATATGAGTTGATTTTTGACAAA-AAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAA 377 TCTCGCAATATGAGTTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAA 238695271 CTCACCTCTCACAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAACATGTCT 442 CTCACCTCTCACAATATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAACATGTCT * 238695336 TGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTGAAACATAAATTAAAAAAACAAA 507 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTG-AAC----------AAAACAAA 238695400 AATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTGAAA 1 AATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT---- * * ** * * * * * 238695465 AGAAGAATTTGTAAGGCAAAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCT 62 ------TTTTGAAAAACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTGCTCTGAGGCT * 238695530 CAACTCACCTCTCGCAATATGAGTTGATTTTT 121 CAACTCACCTCTCGCAATATGAGCTGATTTTT 238695562 GAAAAAACAG Statistics Matches: 632, Mismatches: 53, Indels: 74 0.83 0.07 0.10 Matches are distributed among these distances: 550 20 0.03 552 43 0.07 553 131 0.21 554 73 0.12 555 7 0.01 556 1 0.00 557 10 0.02 558 43 0.07 559 1 0.00 560 8 0.01 561 16 0.03 564 41 0.06 565 77 0.12 566 17 0.03 567 4 0.01 568 11 0.02 569 54 0.09 579 14 0.02 580 16 0.03 581 8 0.01 582 1 0.00 583 36 0.06 ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28 Consensus pattern (558 bp): AATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT GAAAAACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTGCTCTGAGGCTCAACTCACCT CTCGCAATATGAGCTGATTTTTTTGGAAAAACAAAATTTGAAAAACAGAATTTGAAAAGACCTCA ACGTGTGAGCCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTATTTACAGAATATAAGAC AGAAATGGAAAACACCTCAGCATCCCGAGGCTCAACTCACCTCTCACAATATGAGCTGATTTTTT TGAAAAATAGAAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG TTGATTTTTGACAAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTCTCACAA TATGAGCTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCA CCTCTCGCAATATGAGTTGATTTTTTGAACAAAACAAA Found at i:238695402 original size:15 final size:15 Alignment explanation

Indices: 238695378--238695408 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 238695368 GATTTTTTTG * 238695378 AAACATAAATTAAAA 1 AAACAAAAATTAAAA 238695393 AAACAAAAATTAAAA 1 AAACAAAAATTAAAA 238695408 A 1 A 238695409 TACCTCAGCG Statistics Matches: 15, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16 Consensus pattern (15 bp): AAACAAAAATTAAAA Found at i:238695576 original size:74 final size:73 Alignment explanation

Indices: 238695487--238695727 Score: 367 Period size: 74 Copynumber: 3.3 Consensus size: 73 238695477 AAGGCAAAAA 238695487 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA 1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA 238695552 GTTGATTT 66 GTTGATTT * * * * 238695560 TTGAAAAAACAGAAATTAAAAATACCTCGGCGTGCCCCGAGGCTCAGCTCACCTCT-GCAATATG 1 TTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATG 238695624 AGTTGATTT 65 AGTTGATTT * * * * 238695633 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA 1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA 238695698 GTTGATTTT 66 GTTGA-TTT * * 238695707 TTGAAAAGCATAAATTGAAAA 1 TTGAAAAACAGAAATTGAAAA 238695728 AACGAAAATT Statistics Matches: 152, Mismatches: 13, Indels: 5 0.89 0.08 0.03 Matches are distributed among these distances: 72 44 0.29 73 37 0.24 74 71 0.47 ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27 Consensus pattern (73 bp): TTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGA GTTGATTT Found at i:238695827 original size:91 final size:89 Alignment explanation

Indices: 238695644--238695813 Score: 270 Period size: 91 Copynumber: 1.9 Consensus size: 89 238695634 TGAAAAGCAT * * 238695644 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT 1 AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTT * 238695709 GAAAAGCATAAATTGAAAAAACGA 66 GAAAAGCAGAAATTGAAAAAACGA 238695733 AAATTGAAAATACCTCAGCGTGTGACCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTT 1 AAATTGAAAATACCTCAGCGTGT--CCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGA-TTT 238695798 TTTG-AAAGACAGAAAT 63 TTTGAAAAG-CAGAAAT 238695814 AAAAACATCA Statistics Matches: 74, Mismatches: 3, Indels: 5 0.90 0.04 0.06 Matches are distributed among these distances: 89 22 0.30 91 39 0.53 92 13 0.18 ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28 Consensus pattern (89 bp): AAATTGAAAATACCTCAGCGTGTCCTGAGGCCCAACTCACCTCTCGCAATATGAGTTGATTTTTT GAAAAGCAGAAATTGAAAAAACGA Found at i:238702781 original size:16 final size:15 Alignment explanation

Indices: 238702754--238702789 Score: 54 Period size: 16 Copynumber: 2.3 Consensus size: 15 238702744 TAAAGTATAT 238702754 AAATATAAAATATTA 1 AAATATAAAATATTA 238702769 AAATATCAAAATATTA 1 AAATAT-AAAATATTA * 238702785 GAATA 1 AAATA 238702790 ATAATAATTA Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 15 6 0.32 16 13 0.68 ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31 Consensus pattern (15 bp): AAATATAAAATATTA Found at i:238703001 original size:22 final size:22 Alignment explanation

Indices: 238702904--238703010 Score: 78 Period size: 22 Copynumber: 4.9 Consensus size: 22 238702894 AATACTACAT * 238702904 AAATATGTACAT-ATATAA--A 1 AAATATATACATAATATAATTA * * * 238702923 AAATAAATACGTGATA-ATATTA 1 AAATATATACATAATATA-ATTA * * 238702945 AAATATGTACATAATATAGTGTAAA 1 AAATATATACATAATATAAT-T--A * 238702970 AAATACATACATAATATAATTA 1 AAATATATACATAATATAATTA * 238702992 AAATATATACATAAGATAA 1 AAATATATACATAATATAA 238703011 CATGTAGAAA Statistics Matches: 67, Mismatches: 13, Indels: 13 0.72 0.14 0.14 Matches are distributed among these distances: 19 10 0.15 20 4 0.06 22 32 0.48 23 2 0.03 24 1 0.01 25 18 0.27 ACGTcount: A:0.57, C:0.06, G:0.07, T:0.31 Consensus pattern (22 bp): AAATATATACATAATATAATTA Found at i:238703055 original size:29 final size:28 Alignment explanation

Indices: 238702955--238703064 Score: 97 Period size: 29 Copynumber: 4.0 Consensus size: 28 238702945 AAATATGTAC * * 238702955 ATAATATAGT-GTAAAA-A-ATACATAC 1 ATAATATAGTATTAAAATATATACATAA 238702980 ATAATATA--ATTAAAATATATACATAA 1 ATAATATAGTATTAAAATATATACATAA * ** * 238703006 GATAACAT-GTAGAAAAAATATATATATAA 1 -ATAATATAGTA-TTAAAATATATACATAA 238703035 ATAATATAGTATTAAAGATATATACATAA 1 ATAATATAGTATTAAA-ATATATACATAA 238703064 A 1 A 238703065 ATAGTATAAT Statistics Matches: 66, Mismatches: 10, Indels: 14 0.73 0.11 0.16 Matches are distributed among these distances: 24 5 0.08 25 9 0.14 26 7 0.11 27 6 0.09 28 10 0.15 29 29 0.44 ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31 Consensus pattern (28 bp): ATAATATAGTATTAAAATATATACATAA Found at i:238703063 original size:25 final size:24 Alignment explanation

Indices: 238703027--238703156 Score: 108 Period size: 23 Copynumber: 5.6 Consensus size: 24 238703017 GAAAAAATAT * 238703027 ATATATAAATAATATAGTATTAAAG 1 ATATATACATAATATAGTATT-AAG * * 238703052 ATATATACATAAAATAGTA-TAAT 1 ATATATACATAATATAGTATTAAG * * * 238703075 ATATATACGTAATATAGAATTTAG 1 ATATATACATAATATAGTATTAAG * * * 238703099 A-ATATACCTAATATATTA-AAAG 1 ATATATACATAATATAGTATTAAG * * 238703121 A-ATATATATAATATAATATTAAG 1 ATATATACATAATATAGTATTAAG * 238703144 AAATATA-ATAATA 1 ATATATACATAATA 238703157 ACAAAAAAAA Statistics Matches: 85, Mismatches: 17, Indels: 8 0.77 0.15 0.07 Matches are distributed among these distances: 22 17 0.20 23 42 0.49 24 9 0.11 25 17 0.20 ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35 Consensus pattern (24 bp): ATATATACATAATATAGTATTAAG Found at i:238704700 original size:2 final size:2 Alignment explanation

Indices: 238704695--238704729 Score: 54 Period size: 2 Copynumber: 18.0 Consensus size: 2 238704685 TTATGAGAGA * 238704695 AT AT AT AT AT AT AT AT AT AT AT AT AT GT A- AT AT AT 1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 238704730 GTTAAGTTAT Statistics Matches: 30, Mismatches: 2, Indels: 2 0.88 0.06 0.06 Matches are distributed among these distances: 1 1 0.03 2 29 0.97 ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49 Consensus pattern (2 bp): AT Found at i:238706852 original size:47 final size:47 Alignment explanation

Indices: 238706798--238707012 Score: 270 Period size: 47 Copynumber: 4.5 Consensus size: 47 238706788 TTAGGATTTT ** * * * 238706798 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * 238706845 ATGTGATGAATGTGAACCTGTATATATATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATG--CATATA--TGTGATAAGGCCGAATGGCCA * * * * 238706896 ATGGGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGG-CA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA * * 238706942 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA 1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA 238706989 ATGTGATGAATGTGAACATGCATA 1 ATGTGATGAATGTGAACATGCATA 238707013 GTTTCATGCA Statistics Matches: 150, Mismatches: 13, Indels: 10 0.87 0.08 0.06 Matches are distributed among these distances: 46 44 0.29 47 60 0.40 49 9 0.06 51 37 0.25 ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27 Consensus pattern (47 bp): ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA Found at i:238706968 original size:23 final size:23 Alignment explanation

Indices: 238706900--238706969 Score: 58 Period size: 23 Copynumber: 3.0 Consensus size: 23 238706890 TGGCCAATGG 238706900 GATGAATGTGAACATGCGTATGT 1 GATGAATGTGAACATGCGTATGT * * 238706923 G-TGATAAGGCTG-A-ATG-GCAATGT 1 GATG--AATG-TGAACATGCG-TATGT 238706946 GATGAATGTGAACATGCGTATGT 1 GATGAATGTGAACATGCGTATGT 238706969 G 1 G 238706970 TGATAAGGCC Statistics Matches: 35, Mismatches: 4, Indels: 16 0.64 0.07 0.29 Matches are distributed among these distances: 21 2 0.06 22 7 0.20 23 17 0.49 24 7 0.20 25 2 0.06 ACGTcount: A:0.30, C:0.09, G:0.33, T:0.29 Consensus pattern (23 bp): GATGAATGTGAACATGCGTATGT Found at i:238706997 original size:93 final size:96 Alignment explanation

Indices: 238706798--238707012 Score: 292 Period size: 93 Copynumber: 2.2 Consensus size: 96 238706788 TTAGGATTTT ** * 238706798 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC 1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC * 238706863 TGTATATATATGTGTGATAAGGCCGAATGGCCA 66 --TATACATATGTGTGATAAGGCCGAATGGCCA * * * * * 238706896 ATGGGATGAATGTGAACATGCGTATGTGTGATAAGGCTGAATGGC-AATGTGATGAATGTGAA-C 1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC * * 238706959 -ATGCGTATGTGTGATAAGGCCGAATGGCCA 66 TATACATATGTGTGATAAGGCCGAATGGCCA 238706989 ATGTGATGAATGTGAACATGCATA 1 ATGTGATGAATGTGAACATGCATA 238707013 GTTTCATGCA Statistics Matches: 104, Mismatches: 13, Indels: 5 0.85 0.11 0.04 Matches are distributed among these distances: 93 49 0.47 96 1 0.01 97 17 0.16 98 37 0.36 ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27 Consensus pattern (96 bp): ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACC TATACATATGTGTGATAAGGCCGAATGGCCA Found at i:238709688 original size:36 final size:37 Alignment explanation

Indices: 238709642--238709751 Score: 134 Period size: 36 Copynumber: 2.9 Consensus size: 37 238709632 TATCACGATT 238709642 TGCACAAATGCCTTCGGGTCTTAGCCCGGATA-A-AAC 1 TGCAC-AATGCCTTCGGGTCTTAGCCCGGATATACAAC * 238709678 TGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCAC 1 TGCAC-AATGCCTTCGGGTCTTAGCCCGGATATA-CAAC * * 238709717 TAGCACAATTGCCTTCGGGTCTTAACCCGGTTATA 1 T-GCACAA-TGCCTTCGGGTCTTAGCCCGGATATA 238709752 ATTTCCAGCA Statistics Matches: 65, Mismatches: 4, Indels: 6 0.87 0.05 0.08 Matches are distributed among these distances: 36 31 0.48 37 1 0.02 39 5 0.08 40 28 0.43 ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25 Consensus pattern (37 bp): TGCACAATGCCTTCGGGTCTTAGCCCGGATATACAAC Done.