Tandem Repeats Finder Program written by: Gary Benson Department of Biomathematical Sciences Mount Sinai School of Medicine Version 4.00 Sequence: NFA 2003-09-04 Parameters: 2 7 7 80 10 50 500 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 500 Length: 6021225 ACGTcount: A:0.15, C:0.35, G:0.35, T:0.15 File 2 of 7 Found at i:574 original size:18 final size:18 Alignment explanation
Indices: 505--572 Score: 120 Period size: 18 Copynumber: 3.8 Consensus size: 18 495 CCCCCCGGCC 505 GCCGAATACACGCCCGCT 1 GCCGAATACACGCCCGCT 523 GCCGAATACACGCCCGCT 1 GCCGAATACACGCCCGCT 541 GCCGAATACACGCCCGCT 1 GCCGAATACACGCCCGCT * 559 GCCGAGTACA-GCCC 1 GCCGAATACACGCCC 573 CGAACCGGAG Statistics Matches: 49, Mismatches: 1, Indels: 1 0.96 0.02 0.02 Matches are distributed among these distances: 17 4 0.08 18 45 0.92 ACGTcount: A:0.22, C:0.44, G:0.24, T:0.10 Consensus pattern (18 bp): GCCGAATACACGCCCGCT Found at i:2077 original size:22 final size:22 Alignment explanation
Indices: 2045--2087 Score: 77 Period size: 22 Copynumber: 2.0 Consensus size: 22 2035 TTTTGTGCCT * 2045 TGTGGATTCCTCGAGGAATCCC 1 TGTGGAGTCCTCGAGGAATCCC 2067 TGTGGAGTCCTCGAGGAATCC 1 TGTGGAGTCCTCGAGGAATCC 2088 ACCGGTTTGT Statistics Matches: 20, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 22 20 1.00 ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26 Consensus pattern (22 bp): TGTGGAGTCCTCGAGGAATCCC Found at i:12624 original size:24 final size:24 Alignment explanation
Indices: 12582--12658 Score: 118 Period size: 24 Copynumber: 3.2 Consensus size: 24 12572 CGGCCAGCAG * * * 12582 CAGGGCGGCCAGGCGCAGGGCCAA 1 CAGGGCGGTCAGCCACAGGGCCAA 12606 CAGGGCGGTCAGCCACAGGGCCAA 1 CAGGGCGGTCAGCCACAGGGCCAA * 12630 CAGGGTGGTCAGCCACAGGGCCAA 1 CAGGGCGGTCAGCCACAGGGCCAA 12654 CAGGG 1 CAGGG 12659 TGGCCAGGCG Statistics Matches: 49, Mismatches: 4, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 24 49 1.00 ACGTcount: A:0.23, C:0.31, G:0.42, T:0.04 Consensus pattern (24 bp): CAGGGCGGTCAGCCACAGGGCCAA Found at i:12659 original size:24 final size:24 Alignment explanation
Indices: 12597--12661 Score: 121 Period size: 24 Copynumber: 2.7 Consensus size: 24 12587 CGGCCAGGCG * 12597 CAGGGCCAACAGGGCGGTCAGCCA 1 CAGGGCCAACAGGGTGGTCAGCCA 12621 CAGGGCCAACAGGGTGGTCAGCCA 1 CAGGGCCAACAGGGTGGTCAGCCA 12645 CAGGGCCAACAGGGTGG 1 CAGGGCCAACAGGGTGG 12662 CCAGGCGCAG Statistics Matches: 40, Mismatches: 1, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 24 40 1.00 ACGTcount: A:0.25, C:0.29, G:0.40, T:0.06 Consensus pattern (24 bp): CAGGGCCAACAGGGTGGTCAGCCA Found at i:33999 original size:21 final size:21 Alignment explanation
Indices: 33974--34019 Score: 67 Period size: 21 Copynumber: 2.2 Consensus size: 21 33964 CGACGAGGTG 33974 AAGGCCCGCCC-CGCGGCGAAC 1 AAGG-CCGCCCGCGCGGCGAAC * 33995 AAGGCTGCCCGCGCGGCGAAC 1 AAGGCCGCCCGCGCGGCGAAC 34016 AAGG 1 AAGG 34020 GCCAGGGCGC Statistics Matches: 23, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 20 5 0.22 21 18 0.78 ACGTcount: A:0.22, C:0.39, G:0.37, T:0.02 Consensus pattern (21 bp): AAGGCCGCCCGCGCGGCGAAC Found at i:34004 original size:24 final size:21 Alignment explanation
Indices: 33981--34019 Score: 71 Period size: 21 Copynumber: 1.9 Consensus size: 21 33971 GTGAAGGCCC 33981 GCCC-CGCGGCGAACAAGGCT 1 GCCCGCGCGGCGAACAAGGCT 34001 GCCCGCGCGGCGAACAAGG 1 GCCCGCGCGGCGAACAAGG 34020 GCCAGGGCGC Statistics Matches: 18, Mismatches: 0, Indels: 1 0.95 0.00 0.05 Matches are distributed among these distances: 20 4 0.22 21 14 0.78 ACGTcount: A:0.21, C:0.38, G:0.38, T:0.03 Consensus pattern (21 bp): GCCCGCGCGGCGAACAAGGCT Found at i:39933 original size:18 final size:18 Alignment explanation
Indices: 39912--39953 Score: 57 Period size: 18 Copynumber: 2.3 Consensus size: 18 39902 CGGCGGCGGG 39912 GGTGGCACCGGCGGTTCC 1 GGTGGCACCGGCGGTTCC ** * 39930 GGTGGGTCCGGGGGTTCC 1 GGTGGCACCGGCGGTTCC 39948 GGTGGC 1 GGTGGC 39954 GGTGGTGGCG Statistics Matches: 20, Mismatches: 4, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 18 20 1.00 ACGTcount: A:0.02, C:0.26, G:0.52, T:0.19 Consensus pattern (18 bp): GGTGGCACCGGCGGTTCC Found at i:63164 original size:18 final size:18 Alignment explanation
Indices: 63137--63182 Score: 56 Period size: 18 Copynumber: 2.6 Consensus size: 18 63127 GGTCGGCCGG * ** 63137 GCCGTCGTGGTCGGTTCC 1 GCCGTGGTGGTCGGCGCC * 63155 GGCGTGGTGGTCGGCGCC 1 GCCGTGGTGGTCGGCGCC 63173 GCCGTGGTGG 1 GCCGTGGTGG 63183 GTTCCGGCGT Statistics Matches: 23, Mismatches: 5, Indels: 0 0.82 0.18 0.00 Matches are distributed among these distances: 18 23 1.00 ACGTcount: A:0.00, C:0.28, G:0.50, T:0.22 Consensus pattern (18 bp): GCCGTGGTGGTCGGCGCC Found at i:63167 original size:36 final size:35 Alignment explanation
Indices: 63127--63240 Score: 119 Period size: 36 Copynumber: 3.3 Consensus size: 35 63117 GCTGCGTCCG * 63127 GGTCGGCCGGGCCGTCGTGGTCGGTTCCGGCGTGGT 1 GGTCGG-CGGGCCGTCGTGGTCGGTTCCGGCGTCGT * * 63163 GGTCGGC--GCCGCCGTGGTGGGTTCCGGCGTCGT 1 GGTCGGCGGGCCGTCGTGGTCGGTTCCGGCGTCGT * 63196 CGTCGGCGGTTG-CGTCGTGGTCGGTTCCGGC-TCGCT 1 GGTCGGCGG--GCCGTCGTGGTCGGTTCCGGCGTCG-T * 63232 GGTCTGCGG 1 GGTCGGCGG 63241 CGGAGGCGGC Statistics Matches: 65, Mismatches: 8, Indels: 10 0.78 0.10 0.12 Matches are distributed among these distances: 33 29 0.45 35 4 0.06 36 31 0.48 37 1 0.02 ACGTcount: A:0.00, C:0.29, G:0.47, T:0.24 Consensus pattern (35 bp): GGTCGGCGGGCCGTCGTGGTCGGTTCCGGCGTCGT Found at i:63186 original size:33 final size:33 Alignment explanation
Indices: 63137--63226 Score: 99 Period size: 33 Copynumber: 2.6 Consensus size: 33 63127 GGTCGGCCGG * * * 63137 GCCGTCGTGGTCGGTTCCGGCGTGGTGGTCGGC 1 GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC * 63170 GCCGCCGTGGTGGGTTCCGGCGTCGTCGTCGGC 1 GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC * * 63203 GGTTGCGTCGTGGTCGGTTCCGGC 1 -G--CCGCCGTGGTCGGTTCCGGC 63227 TCGCTGGTCT Statistics Matches: 47, Mismatches: 7, Indels: 3 0.82 0.12 0.05 Matches are distributed among these distances: 33 29 0.62 34 1 0.02 36 17 0.36 ACGTcount: A:0.00, C:0.29, G:0.47, T:0.24 Consensus pattern (33 bp): GCCGCCGTGGTCGGTTCCGGCGTCGTCGTCGGC Found at i:68181 original size:14 final size:13 Alignment explanation
Indices: 68162--68195 Score: 50 Period size: 14 Copynumber: 2.5 Consensus size: 13 68152 TTGGCCGGTG * 68162 GCGGCGGCTCGGCC 1 GCGGCGGCCCGG-C 68176 GCGGCGGCCCGGC 1 GCGGCGGCCCGGC 68189 GCGGCGG 1 GCGGCGG 68196 GGTGGCCCGC Statistics Matches: 19, Mismatches: 1, Indels: 1 0.90 0.05 0.05 Matches are distributed among these distances: 13 8 0.42 14 11 0.58 ACGTcount: A:0.00, C:0.41, G:0.56, T:0.03 Consensus pattern (13 bp): GCGGCGGCCCGGC Found at i:70015 original size:18 final size:20 Alignment explanation
Indices: 69975--70018 Score: 56 Period size: 21 Copynumber: 2.2 Consensus size: 20 69965 GGGCGCCGAA 69975 TAGCCGGGCTGCTGCTGACCG 1 TAGCCGGGCTGCTGCTGA-CG * 69996 TAGCCGGGCTGTTGC-G-CG 1 TAGCCGGGCTGCTGCTGACG 70014 TAGCC 1 TAGCC 70019 CTGGCCGTAG Statistics Matches: 22, Mismatches: 1, Indels: 3 0.85 0.04 0.12 Matches are distributed among these distances: 18 7 0.32 20 1 0.05 21 14 0.64 ACGTcount: A:0.09, C:0.32, G:0.39, T:0.20 Consensus pattern (20 bp): TAGCCGGGCTGCTGCTGACG Found at i:70152 original size:15 final size:15 Alignment explanation
Indices: 70109--70235 Score: 76 Period size: 15 Copynumber: 8.3 Consensus size: 15 70099 CCTGCCTGCC 70109 GCCCTGCTGGCCGTA 1 GCCCTGCTGGCCGTA * * * 70124 ACCCGGTTGGCCGTA 1 GCCCTGCTGGCCGTA * 70139 GCCCTGCTGACCGTA 1 GCCCTGCTGGCCGTA ** * 70154 GCCGGGCTCGG-CATA 1 GCCCTGCT-GGCCGTA * ** 70169 GCCCTGGTCACCGTA 1 GCCCTGCTGGCCGTA 70184 GCCGGGCTGCTGGCCGTA 1 GCC---CTGCTGGCCGTA * * * 70202 ACCCGGCTGGTCGTA 1 GCCCTGCTGGCCGTA ** 70217 GCCGGGCTGGCCGTA 1 GCCCTGCTGGCCGTA 70232 GCCC 1 GCCC 70236 GCACCCTGCT Statistics Matches: 80, Mismatches: 27, Indels: 10 0.68 0.23 0.09 Matches are distributed among these distances: 15 68 0.85 16 1 0.01 18 11 0.14 ACGTcount: A:0.10, C:0.37, G:0.35, T:0.17 Consensus pattern (15 bp): GCCCTGCTGGCCGTA Found at i:70247 original size:36 final size:35 Alignment explanation
Indices: 70202--70271 Score: 95 Period size: 36 Copynumber: 2.0 Consensus size: 35 70192 GCTGGCCGTA * * * 70202 ACCCGGCTGGTCGTAGCCGGGCTGGCCGTAGCCCGC 1 ACCCGGCTGGCCGTACCCGGGCTCGCCGTA-CCCGC * 70238 ACCCTGCTGGCCGTACCCGGGCTCGCCGTACCCG 1 ACCCGGCTGGCCGTACCCGGGCTCGCCGTACCCG 70272 GGCTGCCCGT Statistics Matches: 30, Mismatches: 4, Indels: 1 0.86 0.11 0.03 Matches are distributed among these distances: 35 4 0.13 36 26 0.87 ACGTcount: A:0.09, C:0.43, G:0.34, T:0.14 Consensus pattern (35 bp): ACCCGGCTGGCCGTACCCGGGCTCGCCGTACCCGC Found at i:70267 original size:15 final size:15 Alignment explanation
Indices: 70247--70275 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 70237 CACCCTGCTG 70247 GCCGTACCCGGGCTC 1 GCCGTACCCGGGCTC 70262 GCCGTACCCGGGCT 1 GCCGTACCCGGGCT 70276 GCCCGTAACC Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.07, C:0.45, G:0.34, T:0.14 Consensus pattern (15 bp): GCCGTACCCGGGCTC Found at i:70281 original size:15 final size:15 Alignment explanation
Indices: 70243--70282 Score: 55 Period size: 15 Copynumber: 2.7 Consensus size: 15 70233 CCCGCACCCT * 70243 GCTGGCCGTACCCGG 1 GCTGCCCGTACCCGG 70258 GCT-CGCCGTACCCGG 1 GCTGC-CCGTACCCGG 70273 GCTGCCCGTA 1 GCTGCCCGTA 70283 ACCCTGATCG Statistics Matches: 22, Mismatches: 1, Indels: 4 0.81 0.04 0.15 Matches are distributed among these distances: 15 21 0.95 16 1 0.05 ACGTcount: A:0.07, C:0.42, G:0.35, T:0.15 Consensus pattern (15 bp): GCTGCCCGTACCCGG Found at i:70387 original size:15 final size:15 Alignment explanation
Indices: 70315--70394 Score: 54 Period size: 15 Copynumber: 5.1 Consensus size: 15 70305 TGGCCGCCCT * 70315 GCTGGTCGTAGCCGG 1 GCTGGCCGTAGCCGG * * 70330 GCTCGCCGTACCCCGG 1 GCTGGCCGTA-GCCGG * * 70346 CCT-GCCGTAGCCGCCCT 1 GCTGGCCGTAGCCG---G * 70363 GCTGGTCGTAGCCGG 1 GCTGGCCGTAGCCGG * 70378 GCTGGCCGTACCCGG 1 GCTGGCCGTAGCCGG 70393 GC 1 GC 70395 GCGCCCTGCT Statistics Matches: 49, Mismatches: 11, Indels: 10 0.70 0.16 0.14 Matches are distributed among these distances: 14 3 0.06 15 29 0.59 16 6 0.12 17 2 0.04 18 9 0.18 ACGTcount: A:0.06, C:0.40, G:0.38, T:0.16 Consensus pattern (15 bp): GCTGGCCGTAGCCGG Found at i:71503 original size:17 final size:17 Alignment explanation
Indices: 71481--71513 Score: 66 Period size: 17 Copynumber: 1.9 Consensus size: 17 71471 GCTTCTCGCT 71481 TGTGGCTGCCTCGGTGG 1 TGTGGCTGCCTCGGTGG 71498 TGTGGCTGCCTCGGTG 1 TGTGGCTGCCTCGGTG 71514 TCGGGGCCGC Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 16 1.00 ACGTcount: A:0.00, C:0.24, G:0.45, T:0.30 Consensus pattern (17 bp): TGTGGCTGCCTCGGTGG Found at i:73220 original size:18 final size:18 Alignment explanation
Indices: 73199--73233 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 73189 GCGATCTCGG * * 73199 CGCTGGCCGCGGTGCTGA 1 CGCTGCCCGCGCTGCTGA 73217 CGCTGCCCGCGCTGCTG 1 CGCTGCCCGCGCTGCTG 73234 GCCGTGCTCG Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.03, C:0.40, G:0.40, T:0.17 Consensus pattern (18 bp): CGCTGCCCGCGCTGCTGA Found at i:77151 original size:78 final size:78 Alignment explanation
Indices: 77018--77280 Score: 492 Period size: 78 Copynumber: 3.4 Consensus size: 78 77008 GGCTGCTGCG * * 77018 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCACCACGCAGGCCGCCCCGCTC 1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC 77083 AGGCGAGATGTGA 66 AGGCGAGATGTGA 77096 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC 1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC 77161 AGGCGAGATGTGA 66 AGGCGAGATGTGA 77174 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC 1 CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC 77239 AGGCGAGATGTGA 66 AGGCGAGATGTGA 77252 CACC-CTCTGAGCGGGTCAGCGGCCGGAGG 1 CACCGC-CTGAGCGGGTCAGCGGCCGGAGG 77281 TGCCGCCTTC Statistics Matches: 182, Mismatches: 2, Indels: 2 0.98 0.01 0.01 Matches are distributed among these distances: 77 1 0.01 78 181 0.99 ACGTcount: A:0.16, C:0.34, G:0.40, T:0.10 Consensus pattern (78 bp): CACCGCCTGAGCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTGACCACGTAGGCCGCCCCGCTC AGGCGAGATGTGA Found at i:77872 original size:15 final size:15 Alignment explanation
Indices: 77852--77884 Score: 66 Period size: 15 Copynumber: 2.2 Consensus size: 15 77842 CGAGCCGGGT 77852 GCCCGCGCCGACGCG 1 GCCCGCGCCGACGCG 77867 GCCCGCGCCGACGCG 1 GCCCGCGCCGACGCG 77882 GCC 1 GCC 77885 GCTGTCGAGC Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 18 1.00 ACGTcount: A:0.06, C:0.55, G:0.39, T:0.00 Consensus pattern (15 bp): GCCCGCGCCGACGCG Found at i:81614 original size:16 final size:16 Alignment explanation
Indices: 81593--81626 Score: 59 Period size: 16 Copynumber: 2.1 Consensus size: 16 81583 CGGAGTTCCG * 81593 TCTCGCAGCGGGAAGA 1 TCTCGCAGCAGGAAGA 81609 TCTCGCAGCAGGAAGA 1 TCTCGCAGCAGGAAGA 81625 TC 1 TC 81627 CGGTGGCCGC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 16 17 1.00 ACGTcount: A:0.26, C:0.26, G:0.32, T:0.15 Consensus pattern (16 bp): TCTCGCAGCAGGAAGA Found at i:93133 original size:27 final size:27 Alignment explanation
Indices: 93095--93176 Score: 119 Period size: 27 Copynumber: 3.0 Consensus size: 27 93085 CTCGGACCGG 93095 ACGGCGGCTGATCGCCCGGCGCGCCGT 1 ACGGCGGCTGATCGCCCGGCGCGCCGT * 93122 ACGGCGGCTGATCGCCGGGCGCGCCGT 1 ACGGCGGCTGATCGCCCGGCGCGCCGT * ** * 93149 ACGGCGGTTGGCCACCCGGCGCGCCGT 1 ACGGCGGCTGATCGCCCGGCGCGCCGT 93176 A 1 A 93177 GGACTGGCCG Statistics Matches: 49, Mismatches: 6, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 49 1.00 ACGTcount: A:0.09, C:0.39, G:0.41, T:0.11 Consensus pattern (27 bp): ACGGCGGCTGATCGCCCGGCGCGCCGT Found at i:93701 original size:27 final size:27 Alignment explanation
Indices: 93624--93695 Score: 90 Period size: 27 Copynumber: 2.7 Consensus size: 27 93614 GGGTCAGTGA * * 93624 CCGTACGGCGGCTGTCCGCCGTGCCCG 1 CCGTACGGCGGTTGTCCGCCGGGCCCG * * * * 93651 CCATAGGGCGGTTGGCCGCCGGGCGCG 1 CCGTACGGCGGTTGTCCGCCGGGCCCG 93678 CCGTACGGCGGTTGTCCG 1 CCGTACGGCGGTTGTCCG 93696 TAGGGCTGTT Statistics Matches: 36, Mismatches: 9, Indels: 0 0.80 0.20 0.00 Matches are distributed among these distances: 27 36 1.00 ACGTcount: A:0.06, C:0.38, G:0.42, T:0.15 Consensus pattern (27 bp): CCGTACGGCGGTTGTCCGCCGGGCCCG Found at i:93706 original size:15 final size:15 Alignment explanation
Indices: 93677--93721 Score: 54 Period size: 15 Copynumber: 3.0 Consensus size: 15 93667 CGCCGGGCGC 93677 GCCGTACGGCGGTTG 1 GCCGTACGGCGGTTG * * * 93692 TCCGTAGGGCTGTTG 1 GCCGTACGGCGGTTG * 93707 GCCGTACAGCGGTTG 1 GCCGTACGGCGGTTG 93722 CTCGCCGGTC Statistics Matches: 23, Mismatches: 7, Indels: 0 0.77 0.23 0.00 Matches are distributed among these distances: 15 23 1.00 ACGTcount: A:0.09, C:0.24, G:0.42, T:0.24 Consensus pattern (15 bp): GCCGTACGGCGGTTG Found at i:93751 original size:15 final size:15 Alignment explanation
Indices: 93731--93771 Score: 57 Period size: 15 Copynumber: 2.7 Consensus size: 15 93721 GCTCGCCGGT * 93731 CTGCCCGTATG-GCGC 1 CTGCCCGTACGCG-GC 93746 CTGCCCGTACGCGGC 1 CTGCCCGTACGCGGC 93761 CTGCCCGTACG 1 CTGCCCGTACG 93772 GGAGTTGGCC Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 15 23 0.96 16 1 0.04 ACGTcount: A:0.07, C:0.44, G:0.32, T:0.17 Consensus pattern (15 bp): CTGCCCGTACGCGGC Found at i:94003 original size:22 final size:22 Alignment explanation
Indices: 93960--94003 Score: 54 Period size: 22 Copynumber: 2.0 Consensus size: 22 93950 CCGCTTGGCC * * 93960 AGGTGTTCGATCGCCTGCGCGT 1 AGGTGTCCGATCGCCAGCGCGT 93982 AGGTGTCCGA-CGCCAGCAGCGT 1 AGGTGTCCGATCGCCAGC-GCGT 94004 GTCCGGGCTC Statistics Matches: 19, Mismatches: 2, Indels: 2 0.83 0.09 0.09 Matches are distributed among these distances: 21 6 0.32 22 13 0.68 ACGTcount: A:0.14, C:0.30, G:0.36, T:0.20 Consensus pattern (22 bp): AGGTGTCCGATCGCCAGCGCGT Found at i:96694 original size:30 final size:27 Alignment explanation
Indices: 96639--96695 Score: 69 Period size: 27 Copynumber: 2.0 Consensus size: 27 96629 CGCGGTAGGT * * 96639 CACCGCCGCCTTGCCGCTGGGCGCGAA 1 CACCACCGCCTTGCCGCCGGGCGCGAA 96666 CACCACCGCCTTGTCGCGCCGGGTCGCGAA 1 CACCACCGCCTTG-C-CGCCGGG-CGCGAA 96696 GTAGCCCAGC Statistics Matches: 25, Mismatches: 2, Indels: 3 0.83 0.07 0.10 Matches are distributed among these distances: 27 12 0.48 28 1 0.04 29 6 0.24 30 6 0.24 ACGTcount: A:0.12, C:0.44, G:0.32, T:0.12 Consensus pattern (27 bp): CACCACCGCCTTGCCGCCGGGCGCGAA Found at i:109890 original size:17 final size:18 Alignment explanation
Indices: 109857--109891 Score: 54 Period size: 17 Copynumber: 2.0 Consensus size: 18 109847 CGAGACCATC * 109857 CGCATGGACGGCGCGCTG 1 CGCATGGACGCCGCGCTG 109875 CGCATGG-CGCCGCGCTG 1 CGCATGGACGCCGCGCTG 109892 ATCTCTCGTC Statistics Matches: 16, Mismatches: 1, Indels: 1 0.89 0.06 0.06 Matches are distributed among these distances: 17 9 0.56 18 7 0.44 ACGTcount: A:0.09, C:0.37, G:0.43, T:0.11 Consensus pattern (18 bp): CGCATGGACGCCGCGCTG Found at i:111540 original size:16 final size:17 Alignment explanation
Indices: 111486--111553 Score: 111 Period size: 17 Copynumber: 4.0 Consensus size: 17 111476 CGGGGCGGCC 111486 GTTGCCCGTTTTCGTGG 1 GTTGCCCGTTTTCGTGG * 111503 GTTGCCCGTTTCCGTGG 1 GTTGCCCGTTTTCGTGG 111520 GTTGCCCGTTTTCGT-G 1 GTTGCCCGTTTTCGTGG 111536 GTTGCCCGTTTTCCGTGG 1 GTTGCCCGTTTT-CGTGG 111554 ATTCAGAGAA Statistics Matches: 47, Mismatches: 2, Indels: 3 0.90 0.04 0.06 Matches are distributed among these distances: 16 13 0.28 17 33 0.70 18 1 0.02 ACGTcount: A:0.00, C:0.26, G:0.34, T:0.40 Consensus pattern (17 bp): GTTGCCCGTTTTCGTGG Found at i:115014 original size:15 final size:15 Alignment explanation
Indices: 114994--115024 Score: 62 Period size: 15 Copynumber: 2.1 Consensus size: 15 114984 GACGACGCCG 114994 GGGTGACCGAGGATC 1 GGGTGACCGAGGATC 115009 GGGTGACCGAGGATC 1 GGGTGACCGAGGATC 115024 G 1 G 115025 ACAGATCGCG Statistics Matches: 16, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.19, C:0.19, G:0.48, T:0.13 Consensus pattern (15 bp): GGGTGACCGAGGATC Found at i:115651 original size:15 final size:15 Alignment explanation
Indices: 115631--115660 Score: 51 Period size: 15 Copynumber: 2.0 Consensus size: 15 115621 CGGCGGCGCG 115631 GCCACCACCGTCGGC 1 GCCACCACCGTCGGC * 115646 GCCACCGCCGTCGGC 1 GCCACCACCGTCGGC 115661 CCCTCGGTGA Statistics Matches: 14, Mismatches: 1, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.10, C:0.53, G:0.30, T:0.07 Consensus pattern (15 bp): GCCACCACCGTCGGC Found at i:119257 original size:39 final size:39 Alignment explanation
Indices: 119214--119295 Score: 94 Period size: 39 Copynumber: 2.1 Consensus size: 39 119204 CGCTTGCGGC * 119214 GCGGGCGCGG-CGGCCGCGGCGCCGGGTCGCGCCTGCGCG 1 GCGGG-GCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG * * * * * 119253 GCGGGGCGGCCGGCGGTGGTGGCGGGGCGTGCCTGCGCG 1 GCGGGGCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG 119292 GCGG 1 GCGG 119296 CCGGTGCGCG Statistics Matches: 36, Mismatches: 6, Indels: 2 0.82 0.14 0.05 Matches are distributed among these distances: 38 4 0.11 39 32 0.89 ACGTcount: A:0.00, C:0.34, G:0.59, T:0.07 Consensus pattern (39 bp): GCGGGGCGGCCGGCCGCGGCGCCGGGGCGCGCCTGCGCG Found at i:123535 original size:18 final size:18 Alignment explanation
Indices: 123504--123554 Score: 75 Period size: 18 Copynumber: 2.8 Consensus size: 18 123494 GACCGCCGAT * 123504 GATCCGATGGGCTGAGCA 1 GATCCGACGGGCTGAGCA * * 123522 GATTCGACGGGCTGAGCG 1 GATCCGACGGGCTGAGCA 123540 GATCCGACGGGCTGA 1 GATCCGACGGGCTGA 123555 TCGGCCGCGG Statistics Matches: 29, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 29 1.00 ACGTcount: A:0.20, C:0.24, G:0.41, T:0.16 Consensus pattern (18 bp): GATCCGACGGGCTGAGCA Found at i:124798 original size:15 final size:15 Alignment explanation
Indices: 124774--124804 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 124764 GCCCCCATGA * 124774 CGGCGGCCGGGGCCG 1 CGGCGACCGGGGCCG 124789 CGGCGACCGGGGCCG 1 CGGCGACCGGGGCCG 124804 C 1 C 124805 CGGTGCGGCG 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:0.03, C:0.42, G:0.55, T:0.00 Consensus pattern (15 bp): CGGCGACCGGGGCCG Found at i:127531 original size:15 final size:15 Alignment explanation
Indices: 127511--127540 Score: 60 Period size: 15 Copynumber: 2.0 Consensus size: 15 127501 GCTGCGGTGT 127511 CTGGGACACATCATC 1 CTGGGACACATCATC 127526 CTGGGACACATCATC 1 CTGGGACACATCATC 127541 GGAGGACATC Statistics Matches: 15, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 15 1.00 ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20 Consensus pattern (15 bp): CTGGGACACATCATC Found at i:128932 original size:15 final size:15 Alignment explanation
Indices: 128912--128947 Score: 72 Period size: 15 Copynumber: 2.4 Consensus size: 15 128902 GCCTGACCGA 128912 CGGACACTCGAGCGG 1 CGGACACTCGAGCGG 128927 CGGACACTCGAGCGG 1 CGGACACTCGAGCGG 128942 CGGACA 1 CGGACA 128948 ATAGCCGAGC Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 21 1.00 ACGTcount: A:0.22, C:0.33, G:0.39, T:0.06 Consensus pattern (15 bp): CGGACACTCGAGCGG Found at i:131621 original size:18 final size:18 Alignment explanation
Indices: 131587--131621 Score: 52 Period size: 18 Copynumber: 1.9 Consensus size: 18 131577 CCGAGCCGGT * 131587 GGTGCCCGGTCACCCGCC 1 GGTGCCCGGTCAACCGCC * 131605 GGTGCCCGGTGAACCGC 1 GGTGCCCGGTCAACCGC 131622 GCGCCGCCGA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 15 1.00 ACGTcount: A:0.09, C:0.43, G:0.37, T:0.11 Consensus pattern (18 bp): GGTGCCCGGTCAACCGCC Found at i:152280 original size:21 final size:21 Alignment explanation
Indices: 152254--152298 Score: 90 Period size: 21 Copynumber: 2.1 Consensus size: 21 152244 GATGGTTCCT 152254 CGGTGTTCGGTGTCGCCCCGG 1 CGGTGTTCGGTGTCGCCCCGG 152275 CGGTGTTCGGTGTCGCCCCGG 1 CGGTGTTCGGTGTCGCCCCGG 152296 CGG 1 CGG 152299 CGGTGTTCGA Statistics Matches: 24, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 24 1.00 ACGTcount: A:0.00, C:0.33, G:0.44, T:0.22 Consensus pattern (21 bp): CGGTGTTCGGTGTCGCCCCGG Found at i:152304 original size:24 final size:22 Alignment explanation
Indices: 152254--152314 Score: 88 Period size: 24 Copynumber: 2.7 Consensus size: 22 152244 GATGGTTCCT 152254 CGGTGTTCGGTGTCG-CCCCGG 1 CGGTGTTCGGTGTCGCCCCCGG 152275 CGGTGTTCGGTGTCGCCCCGGCGG 1 CGGTGTTCGGTGTCGCCCC--CGG * 152299 CGGTGTTCGATGTCGC 1 CGGTGTTCGGTGTCGC 152315 GGAAGCGGTG Statistics Matches: 36, Mismatches: 1, Indels: 3 0.90 0.03 0.07 Matches are distributed among these distances: 21 15 0.42 22 3 0.08 24 18 0.50 ACGTcount: A:0.02, C:0.31, G:0.43, T:0.25 Consensus pattern (22 bp): CGGTGTTCGGTGTCGCCCCCGG Found at i:152305 original size:45 final size:45 Alignment explanation
Indices: 152254--152341 Score: 113 Period size: 45 Copynumber: 2.0 Consensus size: 45 152244 GATGGTTCCT * ** * 152254 CGGTGTTCGGTGTCGCCCCGGCGGTGTTCGGTGTCGCCCCGGCGG 1 CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGCGG ** * 152299 CGGTGTTCGATGTCGCGGAAGCGGTGTTCGATGTCGCCGCGGC 1 CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGC 152342 CGCGTCGAGG Statistics Matches: 36, Mismatches: 7, Indels: 0 0.84 0.16 0.00 Matches are distributed among these distances: 45 36 1.00 ACGTcount: A:0.05, C:0.30, G:0.43, T:0.23 Consensus pattern (45 bp): CGGTGTTCGATGTCGCCCAAGCGGTGTTCGATGTCGCCCCGGCGG Found at i:152339 original size:24 final size:22 Alignment explanation
Indices: 152254--152340 Score: 81 Period size: 21 Copynumber: 4.0 Consensus size: 22 152244 GATGGTTCCT * * 152254 CGGTGTTCGGTGTCGCC-CCGG 1 CGGTGTTCGATGTCGCCGCGGG * * 152275 CGGTGTTCGGTGTCGCCCCGGCGG 1 CGGTGTTCGATGTCGCCGC-G-GG * 152299 CGGTGTTCGATGTCG-CG-GAAG 1 CGGTGTTCGATGTCGCCGCG-GG 152320 CGGTGTTCGATGTCGCCGCGG 1 CGGTGTTCGATGTCGCCGCGG 152341 CCGCGTCGAG Statistics Matches: 55, Mismatches: 6, Indels: 9 0.79 0.09 0.13 Matches are distributed among these distances: 21 34 0.62 22 3 0.05 23 2 0.04 24 16 0.29 ACGTcount: A:0.05, C:0.29, G:0.44, T:0.23 Consensus pattern (22 bp): CGGTGTTCGATGTCGCCGCGGG Found at i:153109 original size:15 final size:15 Alignment explanation
Indices: 153089--153117 Score: 58 Period size: 15 Copynumber: 1.9 Consensus size: 15 153079 AGCTGGTCAA 153089 GTGGTAAGACCAATC 1 GTGGTAAGACCAATC 153104 GTGGTAAGACCAAT 1 GTGGTAAGACCAAT 153118 TGCTCGGCGA Statistics Matches: 14, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 15 14 1.00 ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21 Consensus pattern (15 bp): GTGGTAAGACCAATC Found at i:162219 original size:6 final size:6 Alignment explanation
Indices: 162167--162205 Score: 78 Period size: 6 Copynumber: 6.5 Consensus size: 6 162157 CAGGCTCGTT 162167 CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGG 1 CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGGAGC CGG 162206 GGAGGCCGGT Statistics Matches: 33, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 6 33 1.00 ACGTcount: A:0.15, C:0.33, G:0.51, T:0.00 Consensus pattern (6 bp): CGGAGC Found at i:165860 original size:15 final size:15 Alignment explanation
Indices: 165840--165899 Score: 75 Period size: 15 Copynumber: 4.0 Consensus size: 15 165830 TTGGACACCC 165840 TGCCCACGGAGACGG 1 TGCCCACGGAGACGG * 165855 TGCCCACGGAGACTG 1 TGCCCACGGAGACGG * * * 165870 TGCCCTCAGAGACCG 1 TGCCCACGGAGACGG * 165885 TGCCCTCGGAGACGG 1 TGCCCACGGAGACGG 165900 CGCCTTCGGA Statistics Matches: 39, Mismatches: 6, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 15 39 1.00 ACGTcount: A:0.18, C:0.35, G:0.35, T:0.12 Consensus pattern (15 bp): TGCCCACGGAGACGG Found at i:165916 original size:30 final size:30 Alignment explanation
Indices: 165848--165919 Score: 81 Period size: 30 Copynumber: 2.4 Consensus size: 30 165838 CCTGCCCACG * * * 165848 GAGACGGTGCCCACGGAGACTGTGCCCTCA 1 GAGACCGTGCCCACGGAGACGGCGCCCTCA * * * 165878 GAGACCGTGCCCTCGGAGACGGCGCCTTCG 1 GAGACCGTGCCCACGGAGACGGCGCCCTCA * 165908 GAGTCCGTGCCC 1 GAGACCGTGCCC 165920 CCGGGAACCG Statistics Matches: 35, Mismatches: 7, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 30 35 1.00 ACGTcount: A:0.15, C:0.36, G:0.35, T:0.14 Consensus pattern (30 bp): GAGACCGTGCCCACGGAGACGGCGCCCTCA Found at i:176574 original size:79 final size:79 Alignment explanation
Indices: 176438--176608 Score: 324 Period size: 79 Copynumber: 2.2 Consensus size: 79 176428 ATCGGCTGAG * * 176438 CCGGCTCGGGCGCGTCGGATACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGTAGCGCAGCGTCA 1 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA 176503 CCACGGAGGCCGCC 66 CCACGGAGGCCGCC 176517 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA 1 CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA 176582 CCACGGAGGCCGCC 66 CCACGGAGGCCGCC 176596 CCGGCTCGGGCGC 1 CCGGCTCGGGCGC 176609 AAATGGATAC Statistics Matches: 90, Mismatches: 2, Indels: 0 0.98 0.02 0.00 Matches are distributed among these distances: 79 90 1.00 ACGTcount: A:0.12, C:0.39, G:0.42, T:0.08 Consensus pattern (79 bp): CCGGCTCGGGCGCGTCGGACACCGCCTGAGCCGGGTCAGCGGCCGGAGGCGGCAGCGCAGCGTCA CCACGGAGGCCGCC Found at i:186573 original size:15 final size:15 Alignment explanation
Indices: 186555--186587 Score: 57 Period size: 15 Copynumber: 2.2 Consensus size: 15 186545 CCCCGGCGGC * 186555 CGAGGGCGCCGTGGG 1 CGAGGCCGCCGTGGG 186570 CGAGGCCGCCGTGGG 1 CGAGGCCGCCGTGGG 186585 CGA 1 CGA 186588 CGGTCCGCGC Statistics Matches: 17, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 17 1.00 ACGTcount: A:0.09, C:0.30, G:0.55, T:0.06 Consensus pattern (15 bp): CGAGGCCGCCGTGGG Found at i:193427 original size:79 final size:80 Alignment explanation
Indices: 193291--193467 Score: 320 Period size: 79 Copynumber: 2.2 Consensus size: 80 193281 CCCGATCGGT ** 193291 CTGACCCCGCTCAGGCTGTGTTTGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC 1 CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC 193356 TGCCGCCTCCGGCCG 66 TGCCGCCTCCGGCCG * 193371 CTGA-CCCGCTCAGGCTGTGTCGGATTTCGCCTGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC 1 CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC 193435 TGCCGCCTCCGGCCG 66 TGCCGCCTCCGGCCG 193450 CTGACCCCGCTCAGGCTG 1 CTGACCCCGCTCAGGCTG 193468 CTCAGGCGAG Statistics Matches: 93, Mismatches: 3, Indels: 2 0.95 0.03 0.02 Matches are distributed among these distances: 79 76 0.82 80 17 0.18 ACGTcount: A:0.07, C:0.36, G:0.37, T:0.20 Consensus pattern (80 bp): CTGACCCCGCTCAGGCTGTGTCGGATTTCGCCCGAGCGGGGGCGGCCTGCGTGGTGATGCTGCGC TGCCGCCTCCGGCCG Found at i:212338 original size:30 final size:30 Alignment explanation
Indices: 212304--212364 Score: 97 Period size: 30 Copynumber: 2.0 Consensus size: 30 212294 CAGCACGGAT * 212304 CCGAACGCCGCCGGTA-GTGACGCCGCCGCG 1 CCGAACGCCGCCGGCACG-GACGCCGCCGCG 212334 CCGAACGCCGCCGGCACGGACGCCGCCGCG 1 CCGAACGCCGCCGGCACGGACGCCGCCGCG 212364 C 1 C 212365 GGCGCGGCAC Statistics Matches: 29, Mismatches: 1, Indels: 2 0.91 0.03 0.06 Matches are distributed among these distances: 30 28 0.97 31 1 0.03 ACGTcount: A:0.13, C:0.48, G:0.36, T:0.03 Consensus pattern (30 bp): CCGAACGCCGCCGGCACGGACGCCGCCGCG Found at i:212341 original size:15 final size:16 Alignment explanation
Indices: 212323--212364 Score: 61 Period size: 15 Copynumber: 2.8 Consensus size: 16 212313 GCCGGTAGTG 212323 ACGCCGCCGCGC-CGA 1 ACGCCGCCGCGCACGA * 212338 ACGCCGCCG-GCACGG 1 ACGCCGCCGCGCACGA 212353 ACGCCGCCGCGC 1 ACGCCGCCGCGC 212365 GGCGCGGCAC Statistics Matches: 24, Mismatches: 1, Indels: 3 0.86 0.04 0.11 Matches are distributed among these distances: 14 2 0.08 15 20 0.83 16 2 0.08 ACGTcount: A:0.12, C:0.52, G:0.36, T:0.00 Consensus pattern (16 bp): ACGCCGCCGCGCACGA Found at i:221320 original size:18 final size:20 Alignment explanation
Indices: 221299--221336 Score: 53 Period size: 21 Copynumber: 1.9 Consensus size: 20 221289 CGATGCTGTC 221299 GCGGAA-GA-CGCCGAGGAA 1 GCGGAACGATCGCCGAGGAA 221317 GCGGAACGGATCGCCGAGGA 1 GCGGAAC-GATCGCCGAGGA 221337 TCTCGCCCAG Statistics Matches: 17, Mismatches: 0, Indels: 3 0.85 0.00 0.15 Matches are distributed among these distances: 18 6 0.35 20 2 0.12 21 9 0.53 ACGTcount: A:0.29, C:0.24, G:0.45, T:0.03 Consensus pattern (20 bp): GCGGAACGATCGCCGAGGAA Found at i:222448 original size:15 final size:15 Alignment explanation
Indices: 222430--222461 Score: 55 Period size: 15 Copynumber: 2.1 Consensus size: 15 222420 CGACCGTCGC 222430 CGGGTCGGTGATCGT 1 CGGGTCGGTGATCGT * 222445 CGGGTCGGTGGTCGT 1 CGGGTCGGTGATCGT 222460 CG 1 CG 222462 CCGAGTCGGC Statistics Matches: 16, Mismatches: 1, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 15 16 1.00 ACGTcount: A:0.03, C:0.22, G:0.50, T:0.25 Consensus pattern (15 bp): CGGGTCGGTGATCGT Found at i:222526 original size:12 final size:12 Alignment explanation
Indices: 222512--222556 Score: 63 Period size: 12 Copynumber: 3.8 Consensus size: 12 222502 GGTGGATGTG * 222512 GTGCCGGACGTG 1 GTGCCGGACGTC 222524 GTGCCGGACGTC 1 GTGCCGGACGTC * 222536 GTGTCGGACGTC 1 GTGCCGGACGTC * 222548 GTGTCGGAC 1 GTGCCGGAC 222557 TCGGAATCGC Statistics Matches: 31, Mismatches: 2, Indels: 0 0.94 0.06 0.00 Matches are distributed among these distances: 12 31 1.00 ACGTcount: A:0.09, C:0.27, G:0.44, T:0.20 Consensus pattern (12 bp): GTGCCGGACGTC Found at i:242414 original size:15 final size:15 Alignment explanation
Indices: 242391--242421 Score: 53 Period size: 15 Copynumber: 2.1 Consensus size: 15 242381 GCAGCGGTGA 242391 GGCGGCGGTGAGGTC 1 GGCGGCGGTGAGGTC * 242406 GGCGTCGGTGAGGTC 1 GGCGGCGGTGAGGTC 242421 G 1 G 242422 CGCACGGTCT 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:0.06, C:0.19, G:0.58, T:0.16 Consensus pattern (15 bp): GGCGGCGGTGAGGTC Found at i:246159 original size:18 final size:18 Alignment explanation
Indices: 246136--246173 Score: 67 Period size: 18 Copynumber: 2.1 Consensus size: 18 246126 GGCCTGGCCG 246136 AGCGCATCTGATCAGTCC 1 AGCGCATCTGATCAGTCC * 246154 AGCGCATCTGCTCAGTCC 1 AGCGCATCTGATCAGTCC 246172 AG 1 AG 246174 TGCGGTGAGC Statistics Matches: 19, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 19 1.00 ACGTcount: A:0.21, C:0.34, G:0.24, T:0.21 Consensus pattern (18 bp): AGCGCATCTGATCAGTCC Found at i:252719 original size:9 final size:9 Alignment explanation
Indices: 252705--252733 Score: 58 Period size: 9 Copynumber: 3.2 Consensus size: 9 252695 CCCCTATGCA 252705 TGAGCCGAC 1 TGAGCCGAC 252714 TGAGCCGAC 1 TGAGCCGAC 252723 TGAGCCGAC 1 TGAGCCGAC 252732 TG 1 TG 252734 GACGTGACCA Statistics Matches: 20, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 20 1.00 ACGTcount: A:0.21, C:0.31, G:0.34, T:0.14 Consensus pattern (9 bp): TGAGCCGAC Found at i:256041 original size:9 final size:9 Alignment explanation
Indices: 256029--256058 Score: 60 Period size: 9 Copynumber: 3.3 Consensus size: 9 256019 GGCCTATGCA 256029 TGGCCCAAC 1 TGGCCCAAC 256038 TGGCCCAAC 1 TGGCCCAAC 256047 TGGCCCAAC 1 TGGCCCAAC 256056 TGG 1 TGG 256059 AGCTGACCAG Statistics Matches: 21, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 9 21 1.00 ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13 Consensus pattern (9 bp): TGGCCCAAC Found at i:257053 original size:15 final size:15 Alignment explanation
Indices: 257027--257102 Score: 59 Period size: 15 Copynumber: 5.8 Consensus size: 15 257017 GGTGGGCTCG 257027 GTCGATGCTCGAGCAA 1 GTCGA-GCTCGAGCAA 257043 GTCGAGCTCGAG--A 1 GTCGAGCTCGAGCAA 257056 -T-G-GC-CGAGCAA 1 GTCGAGCTCGAGCAA 257067 GTCGAGCTCGAG--A 1 GTCGAGCTCGAGCAA 257080 -T-G-GC-CGAGCAA 1 GTCGAGCTCGAGCAA 257091 GTCGAGCTCGAG 1 GTCGAGCTCGAG 257103 ATGGCCGGCC Statistics Matches: 48, Mismatches: 0, Indels: 25 0.66 0.00 0.34 Matches are distributed among these distances: 9 8 0.17 10 4 0.08 11 4 0.08 12 4 0.08 13 4 0.08 14 4 0.08 15 15 0.31 16 5 0.10 ACGTcount: A:0.24, C:0.25, G:0.37, T:0.14 Consensus pattern (15 bp): GTCGAGCTCGAGCAA Found at i:257063 original size:24 final size:24 Alignment explanation
Indices: 257036--257109 Score: 148 Period size: 24 Copynumber: 3.1 Consensus size: 24 257026 GGTCGATGCT 257036 CGAGCAAGTCGAGCTCGAGATGGC 1 CGAGCAAGTCGAGCTCGAGATGGC 257060 CGAGCAAGTCGAGCTCGAGATGGC 1 CGAGCAAGTCGAGCTCGAGATGGC 257084 CGAGCAAGTCGAGCTCGAGATGGC 1 CGAGCAAGTCGAGCTCGAGATGGC 257108 CG 1 CG 257110 GCCGGGACAT Statistics Matches: 50, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 24 50 1.00 ACGTcount: A:0.24, C:0.26, G:0.38, T:0.12 Consensus pattern (24 bp): CGAGCAAGTCGAGCTCGAGATGGC Found at i:258616 original size:26 final size:26 Alignment explanation
Indices: 258572--258629 Score: 80 Period size: 26 Copynumber: 2.2 Consensus size: 26 258562 TGCCAGCCCC * 258572 GGTCTCGAGGGGACCTTCAACATGAA 1 GGTCTCGAGGAGACCTTCAACATGAA * * 258598 GGTCTCGAGGAGACGTTCAACTTGAA 1 GGTCTCGAGGAGACCTTCAACATGAA * 258624 CGTCTC 1 GGTCTC 258630 CCCCTCGGCC Statistics Matches: 28, Mismatches: 4, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 26 28 1.00 ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22 Consensus pattern (26 bp): GGTCTCGAGGAGACCTTCAACATGAA Found at i:258911 original size:24 final size:24 Alignment explanation
Indices: 258884--258934 Score: 84 Period size: 24 Copynumber: 2.1 Consensus size: 24 258874 AGCAAGTCAG * 258884 TCGGCCATCTCGAGCTCGACTTGC 1 TCGGCCATCCCGAGCTCGACTTGC * 258908 TCGGCCATCCCGGGCTCGACTTGC 1 TCGGCCATCCCGAGCTCGACTTGC 258932 TCG 1 TCG 258935 AGCATCGACC Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 24 25 1.00 ACGTcount: A:0.10, C:0.39, G:0.27, T:0.24 Consensus pattern (24 bp): TCGGCCATCCCGAGCTCGACTTGC Found at i:266024 original size:16 final size:17 Alignment explanation
Indices: 266003--266036 Score: 52 Period size: 18 Copynumber: 2.0 Consensus size: 17 265993 GCGCGGCGGT 266003 GAGCGG-CACCAGGATC 1 GAGCGGACACCAGGATC 266019 GAGCGGAACACCAGGATC 1 GAGCGG-ACACCAGGATC 266037 AGCAGCAGGA Statistics Matches: 16, Mismatches: 0, Indels: 2 0.89 0.00 0.11 Matches are distributed among these distances: 16 6 0.38 18 10 0.62 ACGTcount: A:0.29, C:0.29, G:0.35, T:0.06 Consensus pattern (17 bp): GAGCGGACACCAGGATC Found at i:268616 original size:17 final size:17 Alignment explanation
Indices: 268594--268628 Score: 70 Period size: 17 Copynumber: 2.1 Consensus size: 17 268584 ATAGCCGACA 268594 CCGCCGATACGCAACAC 1 CCGCCGATACGCAACAC 268611 CCGCCGATACGCAACAC 1 CCGCCGATACGCAACAC 268628 C 1 C 268629 TCAGGAGCCT Statistics Matches: 18, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 18 1.00 ACGTcount: A:0.29, C:0.49, G:0.17, T:0.06 Consensus pattern (17 bp): CCGCCGATACGCAACAC Found at i:275227 original size:15 final size:15 Alignment explanation
Indices: 275186--275227 Score: 57 Period size: 15 Copynumber: 2.8 Consensus size: 15 275176 GTACCCCCAG * * 275186 CAGCCCCCGCAATAC 1 CAGCCGCCGCAGTAC * 275201 CAGCAGCCGCAGTAC 1 CAGCCGCCGCAGTAC 275216 CAGCCGCCGCAG 1 CAGCCGCCGCAG 275228 CCGCAGTACC Statistics Matches: 23, Mismatches: 4, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 15 23 1.00 ACGTcount: A:0.24, C:0.48, G:0.24, T:0.05 Consensus pattern (15 bp): CAGCCGCCGCAGTAC Found at i:276164 original size:18 final size:18 Alignment explanation
Indices: 276150--276230 Score: 117 Period size: 18 Copynumber: 4.5 Consensus size: 18 276140 GCTGCTGTTC 276150 GCCGTACTGCGGCTGCTG 1 GCCGTACTGCGGCTGCTG * 276168 GCCGTACTGGGGCTGCTG 1 GCCGTACTGCGGCTGCTG ** * 276186 GCCGTAGGGCGGCTGCTC 1 GCCGTACTGCGGCTGCTG * 276204 GCCGTACTGGGGCTGCTG 1 GCCGTACTGCGGCTGCTG 276222 GCCGTACTG 1 GCCGTACTG 276231 AGGCGGTTGC Statistics Matches: 54, Mismatches: 9, Indels: 0 0.86 0.14 0.00 Matches are distributed among these distances: 18 54 1.00 ACGTcount: A:0.06, C:0.31, G:0.42, T:0.21 Consensus pattern (18 bp): GCCGTACTGCGGCTGCTG Found at i:276198 original size:36 final size:36 Alignment explanation
Indices: 276158--276227 Score: 131 Period size: 36 Copynumber: 1.9 Consensus size: 36 276148 TCGCCGTACT * 276158 GCGGCTGCTGGCCGTACTGGGGCTGCTGGCCGTAGG 1 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTAGG 276194 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTA 1 GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTA 276228 CTGAGGCGGT Statistics Matches: 33, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 36 33 1.00 ACGTcount: A:0.06, C:0.30, G:0.44, T:0.20 Consensus pattern (36 bp): GCGGCTGCTCGCCGTACTGGGGCTGCTGGCCGTAGG Found at i:286329 original size:78 final size:78 Alignment explanation
Indices: 286200--286413 Score: 401 Period size: 78 Copynumber: 2.7 Consensus size: 78 286190 GGTCGGGTAG * 286200 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGACTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG 1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG * 286265 TTTGTGCCTGAGT 66 TTTGTGCCTGAGC 286278 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG 1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG 286343 TTTGTGCCTGAGC 66 TTTGTGCCTGAGC 286356 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGGCGCTGACCCGCTCAGGC 1 GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCC-GGGCGCTGACCCGCTCAGGC 286414 GACGCAGAAC Statistics Matches: 133, Mismatches: 2, Indels: 1 0.98 0.01 0.01 Matches are distributed among these distances: 78 113 0.85 79 20 0.15 ACGTcount: A:0.06, C:0.34, G:0.39, T:0.21 Consensus pattern (78 bp): GGGGCGCCCTGCGTGGTGACGCTGCGCTGCCGCCTCCGGGCGCTGACCCGCTCAGGCTGTGTTTG TTTGTGCCTGAGC Found at i:297621 original size:21 final size:21 Alignment explanation
Indices: 297597--297639 Score: 68 Period size: 21 Copynumber: 2.0 Consensus size: 21 297587 CCCCGCCAGC * * 297597 CCCGGCTTCGCGGCCAACCTG 1 CCCGCCTTCCCGGCCAACCTG 297618 CCCGCCTTCCCGGCCAACCTG 1 CCCGCCTTCCCGGCCAACCTG 297639 C 1 C 297640 GCAAGCAGCT Statistics Matches: 20, Mismatches: 2, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 21 20 1.00 ACGTcount: A:0.09, C:0.53, G:0.23, T:0.14 Consensus pattern (21 bp): CCCGCCTTCCCGGCCAACCTG Found at i:309254 original size:18 final size:18 Alignment explanation
Indices: 309231--309267 Score: 65 Period size: 18 Copynumber: 2.1 Consensus size: 18 309221 CCGGTCGGCA 309231 CCGCACCGTAGGCGGGCG 1 CCGCACCGTAGGCGGGCG * 309249 CCGCACCGTGGGCGGGCG 1 CCGCACCGTAGGCGGGCG 309267 C 1 C 309268 TGTGACGTGG Statistics Matches: 18, Mismatches: 1, Indels: 0 0.95 0.05 0.00 Matches are distributed among these distances: 18 18 1.00 ACGTcount: A:0.08, C:0.41, G:0.46, T:0.05 Consensus pattern (18 bp): CCGCACCGTAGGCGGGCG Found at i:309276 original size:18 final size:18 Alignment explanation
Indices: 309255--309299 Score: 65 Period size: 17 Copynumber: 2.6 Consensus size: 18 309245 GGCGCCGCAC 309255 CGTGGGCGGGCGCTGTGA 1 CGTGGGCGGGCGCTGTGA * * 309273 CGTGGGC-GGCGTTGTGC 1 CGTGGGCGGGCGCTGTGA 309290 CGTGGGCGGG 1 CGTGGGCGGG 309300 TGTTGCCCCG Statistics Matches: 24, Mismatches: 2, Indels: 2 0.86 0.07 0.07 Matches are distributed among these distances: 17 15 0.62 18 9 0.38 ACGTcount: A:0.02, C:0.22, G:0.58, T:0.18 Consensus pattern (18 bp): CGTGGGCGGGCGCTGTGA Found at i:322119 original size:24 final size:24 Alignment explanation
Indices: 322083--322153 Score: 96 Period size: 24 Copynumber: 3.1 Consensus size: 24 322073 GAATGCCCGG * 322083 GCGGCATGT-GCGGCTGCCCGTACT 1 GCGGC-TGTGGCGGCTGCCCGAACT 322107 GCGGCTGTGGCGGCTGCCCGAACT 1 GCGGCTGTGGCGGCTGCCCGAACT 322131 GCGGC--TGG-GGCTGCCCGAACT 1 GCGGCTGTGGCGGCTGCCCGAACT 322152 GC 1 GC 322154 TGCGGCGGCT Statistics Matches: 45, Mismatches: 1, Indels: 5 0.88 0.02 0.10 Matches are distributed among these distances: 21 15 0.33 22 3 0.07 23 3 0.07 24 24 0.53 ACGTcount: A:0.08, C:0.34, G:0.41, T:0.17 Consensus pattern (24 bp): GCGGCTGTGGCGGCTGCCCGAACT Found at i:322156 original size:24 final size:24 Alignment explanation
Indices: 322094--322179 Score: 69 Period size: 21 Copynumber: 3.8 Consensus size: 24 322084 CGGCATGTGC * * * 322094 GGCTGCCCGTACTGCGGCTG-TGG 1 GGCTGCCCGAACTGCTGCGGCTGG 322117 CGGCTGCCCGAA---CTGCGGCTGG 1 -GGCTGCCCGAACTGCTGCGGCTGG 322139 GGCTGCCCGAACTGCTGCGGC--- 1 GGCTGCCCGAACTGCTGCGGCTGG * * 322160 GGCTGGCCGTACTGCTGCGG 1 GGCTGCCCGAACTGCTGCGG 322180 TCCACCCGGC Statistics Matches: 53, Mismatches: 5, Indels: 11 0.77 0.07 0.16 Matches are distributed among these distances: 21 33 0.62 22 3 0.06 24 17 0.32 ACGTcount: A:0.07, C:0.34, G:0.42, T:0.17 Consensus pattern (24 bp): GGCTGCCCGAACTGCTGCGGCTGG Found at i:322175 original size:21 final size:21 Alignment explanation
Indices: 322110--322179 Score: 88 Period size: 21 Copynumber: 3.3 Consensus size: 21 322100 CCGTACTGCG * 322110 GCTGTGGCGGCTGCCCGAACT 1 GCTGCGGCGGCTGCCCGAACT * 322131 GCGGCTGG-GGCTGCCCGAACT 1 GCTGC-GGCGGCTGCCCGAACT * * 322152 GCTGCGGCGGCTGGCCGTACT 1 GCTGCGGCGGCTGCCCGAACT 322173 GCTGCGG 1 GCTGCGG 322180 TCCACCCGGC Statistics Matches: 42, Mismatches: 5, Indels: 4 0.82 0.10 0.08 Matches are distributed among these distances: 20 2 0.05 21 38 0.90 22 2 0.05 ACGTcount: A:0.07, C:0.33, G:0.43, T:0.17 Consensus pattern (21 bp): GCTGCGGCGGCTGCCCGAACT Found at i:361961 original size:24 final size:24 Alignment explanation
Indices: 361934--361982 Score: 64 Period size: 24 Copynumber: 2.0 Consensus size: 24 361924 CGCCCAGCAC 361934 ACCAGC-CCGCCCTCGGCGTGCCCG 1 ACCAGCACCG-CCTCGGCGTGCCCG * * 361958 ACCAGCACCGCCTCGGTGTGGCCG 1 ACCAGCACCGCCTCGGCGTGCCCG 361982 A 1 A 361983 GCGCCCGGAT Statistics Matches: 22, Mismatches: 2, Indels: 2 0.85 0.08 0.08 Matches are distributed among these distances: 24 19 0.86 25 3 0.14 ACGTcount: A:0.12, C:0.47, G:0.31, T:0.10 Consensus pattern (24 bp): ACCAGCACCGCCTCGGCGTGCCCG Found at i:374012 original size:27 final size:27 Alignment explanation
Indices: 373970--374161 Score: 233 Period size: 27 Copynumber: 7.1 Consensus size: 27 373960 TCTGCCTTCC * * 373970 GTCTCGGCACTGGCCACAACACCGGAG 1 GTCTCGGCACCGGCCACAACGCCGGAG * * 373997 GTCGCGGCACCGGCCACAACGCCGGGG 1 GTCTCGGCACCGGCCACAACGCCGGAG * 374024 GTCTCGGCACC-GCCGACAACGCCGGGG 1 GTCTCGGCACCGGCC-ACAACGCCGGAG 374051 GTCTCGGCACCGGCCACAACGCCGGAG 1 GTCTCGGCACCGGCCACAACGCCGGAG * * * * 374078 GTCTTGGCGCCGGCCACAGCACCGGAG 1 GTCTCGGCACCGGCCACAACGCCGGAG * * 374105 GTCGCGGCACCGGCCACAACGCCGGGG 1 GTCTCGGCACCGGCCACAACGCCGGAG * * * * 374132 GTCTTGGCGCCGGCCACGACACCGGAG 1 GTCTCGGCACCGGCCACAACGCCGGAG 374159 GTC 1 GTC 374162 GCGCTCGACG Statistics Matches: 141, Mismatches: 22, Indels: 4 0.84 0.13 0.02 Matches are distributed among these distances: 26 3 0.02 27 135 0.96 28 3 0.02 ACGTcount: A:0.16, C:0.39, G:0.36, T:0.08 Consensus pattern (27 bp): GTCTCGGCACCGGCCACAACGCCGGAG Found at i:374028 original size:54 final size:54 Alignment explanation
Indices: 373970--374164 Score: 275 Period size: 54 Copynumber: 3.6 Consensus size: 54 373960 TCTGCCTTCC * 373970 GTCTCGGCACTGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG * * * * 374024 GTCTCGGCACC-GCCGACAACGCCGGGGGTCTCGGCACCGGCCACAACGCCGGAG 1 GTCTCGGCACCGGCC-ACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG * * * 374078 GTCTTGGCGCCGGCCACAGCACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG * * * 374132 GTCTTGGCGCCGGCCACGACACCGGAGGTCGCG 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCG 374165 CTCGACGGGG Statistics Matches: 125, Mismatches: 14, Indels: 4 0.87 0.10 0.03 Matches are distributed among these distances: 53 3 0.02 54 119 0.95 55 3 0.02 ACGTcount: A:0.16, C:0.39, G:0.37, T:0.08 Consensus pattern (54 bp): GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGG Found at i:374113 original size:81 final size:81 Alignment explanation
Indices: 373970--374164 Score: 266 Period size: 81 Copynumber: 2.4 Consensus size: 81 373960 TCTGCCTTCC * * * * 373970 GTCTCGGCACTGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACGCCGGGGGTCTCGGCACC 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC 374035 -GCCGACAACGCCGGGG 66 GGCC-ACAACGCCGGGG * ** * * 374051 GTCTCGGCACCGGCCACAACGCCGGAGGTCTTGGCGCCGGCCACAGCACCGGAGGTCGCGGCACC 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC 374116 GGCCACAACGCCGGGG 66 GGCCACAACGCCGGGG * * * 374132 GTCTTGGCGCCGGCCACGACACCGGAGGTCGCG 1 GTCTCGGCACCGGCCACAACACCGGAGGTCGCG 374165 CTCGACGGGG Statistics Matches: 98, Mismatches: 15, Indels: 2 0.85 0.13 0.02 Matches are distributed among these distances: 81 95 0.97 82 3 0.03 ACGTcount: A:0.16, C:0.39, G:0.37, T:0.08 Consensus pattern (81 bp): GTCTCGGCACCGGCCACAACACCGGAGGTCGCGGCACCGGCCACAACACCGGAGGTCGCGGCACC GGCCACAACGCCGGGG Found at i:375019 original size:16 final size:16 Alignment explanation
Indices: 375017--375163 Score: 71 Period size: 17 Copynumber: 8.8 Consensus size: 16 375007 GTGGTCCAGC 375017 GGCCCAGCGGCCCGGT 1 GGCCCAGCGGCCCGGT * 375033 GGCCTCAGCGGCCGGGT 1 GGCC-CAGCGGCCCGGT * * 375050 GGTCCAGTGGCCCGGT 1 GGCCCAGCGGCCCGGT * * * 375066 AGGCCATAGCGGCTCAGT 1 -GGCC-CAGCGGCCCGGT * ** * 375084 GGCCATAGCGGCCTAGC 1 GGCC-CAGCGGCCCGGT * 375101 GG-CCATTGTGGCCCGGT 1 GGCCCA--GCGGCCCGGT * * * 375118 GGCCATAGCGGCCCAGC 1 GGCC-CAGCGGCCCGGT * * 375135 GGCCCAGCGGCCCAGC 1 GGCCCAGCGGCCCGGT * 375151 GGCCCAGCAGCCC 1 GGCCCAGCGGCCC 375164 AGCAGCGGCC Statistics Matches: 101, Mismatches: 23, Indels: 14 0.73 0.17 0.10 Matches are distributed among these distances: 15 1 0.01 16 38 0.38 17 52 0.51 18 9 0.09 19 1 0.01 ACGTcount: A:0.12, C:0.38, G:0.39, T:0.11 Consensus pattern (16 bp): GGCCCAGCGGCCCGGT Found at i:375027 original size:24 final size:25 Alignment explanation
Indices: 374995--375045 Score: 68 Period size: 24 Copynumber: 2.1 Consensus size: 25 374985 GCCCGGTGGC * * 374995 CCCAACGGCCGGGTGGTC-CAGCGG 1 CCCAACGGCCCGGTGGCCTCAGCGG * 375019 CCCAGCGGCCCGGTGGCCTCAGCGG 1 CCCAACGGCCCGGTGGCCTCAGCGG 375044 CC 1 CC 375046 GGGTGGTCCA Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 24 15 0.65 25 8 0.35 ACGTcount: A:0.10, C:0.43, G:0.39, T:0.08 Consensus pattern (25 bp): CCCAACGGCCCGGTGGCCTCAGCGG Found at i:375031 original size:41 final size:41 Alignment explanation
Indices: 374983--375062 Score: 133 Period size: 41 Copynumber: 2.0 Consensus size: 41 374973 CAGTGACCAA 374983 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG 1 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG * * * 375024 CGGCCCGGTGGCCTCAGCGGCCGGGTGGTCCAGTGGCCC 1 CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCC 375063 GGTAGGCCAT Statistics Matches: 36, Mismatches: 3, Indels: 0 0.92 0.08 0.00 Matches are distributed among these distances: 41 36 1.00 ACGTcount: A:0.07, C:0.40, G:0.42, T:0.10 Consensus pattern (41 bp): CGGCCCGGTGGCCCCAACGGCCGGGTGGTCCAGCGGCCCAG Found at i:375086 original size:26 final size:25 Alignment explanation
Indices: 375053--375139 Score: 74 Period size: 25 Copynumber: 3.4 Consensus size: 25 375043 GCCGGGTGGT 375053 CCAGTGGCCCGGTAGGCCATAGCGG 1 CCAGTGGCCCGGTAGGCCATAGCGG * 375078 CTCAGTGG-CC-ATAGCGGCC-TAGCGG 1 C-CAGTGGCCCGGTA--GGCCATAGCGG 375103 CCATTGTGGCCCGGT-GGCCATAGCGG 1 CCA--GTGGCCCGGTAGGCCATAGCGG * 375129 CCCAGCGGCCC 1 -CCAGTGGCCC 375140 AGCGGCCCAG Statistics Matches: 50, Mismatches: 3, Indels: 18 0.70 0.04 0.25 Matches are distributed among these distances: 24 4 0.08 25 20 0.40 26 20 0.40 27 5 0.10 28 1 0.02 ACGTcount: A:0.14, C:0.36, G:0.37, T:0.14 Consensus pattern (25 bp): CCAGTGGCCCGGTAGGCCATAGCGG Found at i:375104 original size:17 final size:17 Alignment explanation
Indices: 375067--375154 Score: 97 Period size: 17 Copynumber: 5.2 Consensus size: 17 375057 TGGCCCGGTA * * 375067 GGCCATAGCGGCTCAGT 1 GGCCATAGCGGCCCAGC * 375084 GGCCATAGCGGCCTAGC 1 GGCCATAGCGGCCCAGC * * * * 375101 GGCCATTGTGGCCCGGT 1 GGCCATAGCGGCCCAGC 375118 GGCCATAGCGGCCCAGC 1 GGCCATAGCGGCCCAGC * 375135 GGCC-CAGCGGCCCAGC 1 GGCCATAGCGGCCCAGC 375151 GGCC 1 GGCC 375155 CAGCAGCCCA Statistics Matches: 58, Mismatches: 13, Indels: 1 0.81 0.18 0.01 Matches are distributed among these distances: 16 15 0.26 17 43 0.74 ACGTcount: A:0.14, C:0.38, G:0.38, T:0.11 Consensus pattern (17 bp): GGCCATAGCGGCCCAGC Found at i:375135 original size:8 final size:8 Alignment explanation
Indices: 375124--375190 Score: 80 Period size: 8 Copynumber: 8.0 Consensus size: 8 375114 CGGTGGCCAT 375124 AGCGGCCC 1 AGCGGCCC 375132 AGCGGCCC 1 AGCGGCCC 375140 AGCGGCCC 1 AGCGGCCC 375148 AGCGGCCC 1 AGCGGCCC * 375156 AGCAGCCCAGC 1 AGC-GGCC--C 375167 AGCGGCCC 1 AGCGGCCC * * 375175 AGCGACCT 1 AGCGGCCC 375183 AGCGGCCC 1 AGCGGCCC 375191 GGTGGCACGT Statistics Matches: 50, Mismatches: 6, Indels: 6 0.81 0.10 0.10 Matches are distributed among these distances: 8 40 0.80 9 3 0.06 10 3 0.06 11 4 0.08 ACGTcount: A:0.16, C:0.48, G:0.34, T:0.01 Consensus pattern (8 bp): AGCGGCCC Found at i:375190 original size:27 final size:27 Alignment explanation
Indices: 375139--375190 Score: 77 Period size: 27 Copynumber: 1.9 Consensus size: 27 375129 CCCAGCGGCC * 375139 CAGCGGCCCAGCGGCCCAGCAGCCCAG 1 CAGCGGCCCAGCGACCCAGCAGCCCAG * * 375166 CAGCGGCCCAGCGACCTAGCGGCCC 1 CAGCGGCCCAGCGACCCAGCAGCCC 375191 GGTGGCACGT Statistics Matches: 22, Mismatches: 3, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 27 22 1.00 ACGTcount: A:0.17, C:0.48, G:0.33, T:0.02 Consensus pattern (27 bp): CAGCGGCCCAGCGACCCAGCAGCCCAG Found at i:382655 original size:15 final size:15 Alignment explanation
Indices: 382637--382719 Score: 76 Period size: 15 Copynumber: 5.5 Consensus size: 15 382627 CGCCGCCAAG * 382637 AAGACCACCGCGACC 1 AAGACGACCGCGACC * 382652 AAGACGGCCGCGACC 1 AAGACGACCGCGACC * * 382667 AAGACGGCGGCGACC 1 AAGACGACCGCGACC * * ** 382682 AAGACCACGGCGAAG 1 AAGACGACCGCGACC ** 382697 AAGACGACCGCGAAG 1 AAGACGACCGCGACC 382712 AAGACGAC 1 AAGACGAC 382720 GGCCGCGAAG Statistics Matches: 59, Mismatches: 9, Indels: 0 0.87 0.13 0.00 Matches are distributed among these distances: 15 59 1.00 ACGTcount: A:0.35, C:0.34, G:0.31, T:0.00 Consensus pattern (15 bp): AAGACGACCGCGACC Found at i:382705 original size:18 final size:16 Alignment explanation
Indices: 382691--382731 Score: 57 Period size: 15 Copynumber: 2.5 Consensus size: 16 382681 CAAGACCACG 382691 GCGAAGAAGACGA-CC 1 GCGAAGAAGACGACCC 382706 GCGAAGAAGACGACGGCC 1 GCGAAGAAGACGAC--CC 382724 GCGAAGAA 1 GCGAAGAA 382732 AACCGCGGCC Statistics Matches: 23, Mismatches: 0, Indels: 3 0.88 0.00 0.12 Matches are distributed among these distances: 15 13 0.57 18 10 0.43 ACGTcount: A:0.39, C:0.24, G:0.37, T:0.00 Consensus pattern (16 bp): GCGAAGAAGACGACCC Found at i:382716 original size:45 final size:45 Alignment explanation
Indices: 382637--382722 Score: 109 Period size: 45 Copynumber: 1.9 Consensus size: 45 382627 CGCCGCCAAG * * * * 382637 AAGACCACCGCGACCAAGACGGCCGCGACCAAGACGGCGGCGACC 1 AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGCGACC * * * 382682 AAGACCACGGCGAAGAAGACGACCGCGAAGAAGACGACGGC 1 AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGC 382723 CGCGAAGAAA Statistics Matches: 34, Mismatches: 7, Indels: 0 0.83 0.17 0.00 Matches are distributed among these distances: 45 34 1.00 ACGTcount: A:0.34, C:0.34, G:0.33, T:0.00 Consensus pattern (45 bp): AAGACCACCGCGAACAAGACGACCGCGAACAAGACGACGGCGACC Found at i:382741 original size:18 final size:18 Alignment explanation
Indices: 382699--382734 Score: 54 Period size: 18 Copynumber: 2.0 Consensus size: 18 382689 CGGCGAAGAA * * 382699 GACGACCGCGAAGAAGAC 1 GACGGCCGCGAAGAAAAC 382717 GACGGCCGCGAAGAAAAC 1 GACGGCCGCGAAGAAAAC 382735 CGCGGCCAAG Statistics Matches: 16, Mismatches: 2, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 18 16 1.00 ACGTcount: A:0.39, C:0.28, G:0.33, T:0.00 Consensus pattern (18 bp): GACGGCCGCGAAGAAAAC Found at i:390602 original size:15 final size:15 Alignment explanation
Indices: 390574--390614 Score: 59 Period size: 15 Copynumber: 2.9 Consensus size: 15 390564 CGCTATCTGG 390574 TGTTCT-GA-GCGCA 1 TGTTCTCGACGCGCA 390587 TGTTCTCGACGCGCA 1 TGTTCTCGACGCGCA * 390602 TGTCCTCGACGCG 1 TGTTCTCGACGCG 390615 GCGCCCGACA Statistics Matches: 25, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 13 6 0.24 14 2 0.08 15 17 0.68 ACGTcount: A:0.12, C:0.32, G:0.29, T:0.27 Consensus pattern (15 bp): TGTTCTCGACGCGCA Found at i:391998 original size:17 final size:17 Alignment explanation
Indices: 391979--392038 Score: 84 Period size: 17 Copynumber: 3.5 Consensus size: 17 391969 GAATTTGTCG * 391979 CCCATCAGCACTTCTCG 1 CCCATCAGCACTTCTCA 391996 CCCATCAGCACTTCTCA 1 CCCATCAGCACTTCTCA * * 392013 CCCCTCACCACTTCTCA 1 CCCATCAGCACTTCTCA * 392030 CCCCTCAGC 1 CCCATCAGC 392039 GCTCGCATCC Statistics Matches: 39, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 17 39 1.00 ACGTcount: A:0.18, C:0.53, G:0.07, T:0.22 Consensus pattern (17 bp): CCCATCAGCACTTCTCA Found at i:396158 original size:13 final size:13 Alignment explanation
Indices: 396136--396175 Score: 62 Period size: 13 Copynumber: 3.1 Consensus size: 13 396126 CGGGACGTGG * 396136 CCGGTGAGCAGGC 1 CCGGTCAGCAGGC 396149 CCGGTCAGCAGGC 1 CCGGTCAGCAGGC * 396162 CCGGTCAGGAGGC 1 CCGGTCAGCAGGC 396175 C 1 C 396176 GAGGCGACCG Statistics Matches: 25, Mismatches: 2, Indels: 0 0.93 0.07 0.00 Matches are distributed among these distances: 13 25 1.00 ACGTcount: A:0.15, C:0.35, G:0.42, T:0.07 Consensus pattern (13 bp): CCGGTCAGCAGGC Found at i:409946 original size:22 final size:21 Alignment explanation
Indices: 409899--409946 Score: 53 Period size: 22 Copynumber: 2.2 Consensus size: 21 409889 GGTGCGCGGA * 409899 TCGGGGGCGGCGACCGTGGTG 1 TCGGGGGCGGCGACCGTGGCG * 409920 TCGGGCGGCGGCGGAGCGTGGCG 1 TCGGG-GGCGGC-GACCGTGGCG 409943 -CGGG 1 TCGGG 409947 TCCGGTGCGG Statistics Matches: 23, Mismatches: 2, Indels: 3 0.82 0.07 0.11 Matches are distributed among these distances: 21 5 0.22 22 10 0.43 23 8 0.35 ACGTcount: A:0.04, C:0.25, G:0.60, T:0.10 Consensus pattern (21 bp): TCGGGGGCGGCGACCGTGGCG Found at i:424203 original size:18 final size:20 Alignment explanation
Indices: 424152--424198 Score: 67 Period size: 21 Copynumber: 2.2 Consensus size: 20 424142 GCGAATGCTT * 424152 CCGCCACAGGATCGAATCCCG 1 CCGCCAC-GGGTCGAATCCCG 424173 CCGCCAGCGGGTCGAATCCCG 1 CCGCCA-CGGGTCGAATCCCG 424194 CCGCC 1 CCGCC 424199 GGGTCCAGCA Statistics Matches: 24, Mismatches: 1, Indels: 2 0.89 0.04 0.07 Matches are distributed among these distances: 21 23 0.96 22 1 0.04 ACGTcount: A:0.17, C:0.47, G:0.28, T:0.09 Consensus pattern (20 bp): CCGCCACGGGTCGAATCCCG Found at i:424215 original size:21 final size:21 Alignment explanation
Indices: 424191--424239 Score: 98 Period size: 21 Copynumber: 2.3 Consensus size: 21 424181 GGGTCGAATC 424191 CCGCCGCCGGGTCCAGCACTG 1 CCGCCGCCGGGTCCAGCACTG 424212 CCGCCGCCGGGTCCAGCACTG 1 CCGCCGCCGGGTCCAGCACTG 424233 CCGCCGC 1 CCGCCGC 424240 GCGTACGGGC Statistics Matches: 28, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 21 28 1.00 ACGTcount: A:0.08, C:0.51, G:0.33, T:0.08 Consensus pattern (21 bp): CCGCCGCCGGGTCCAGCACTG Found at i:424490 original size:54 final size:54 Alignment explanation
Indices: 424359--424496 Score: 136 Period size: 54 Copynumber: 2.5 Consensus size: 54 424349 GCCGCGGGTT ** * * * 424359 CGGGTGCCACCGGTTCCGGCACGGCCGCTGGTTCCGGTGTGGCGACCGGTCCAGG 1 CGGG-GCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTGCCGACCGGTCCAGG * * * * * * 424414 CAGGGCGACTGGTACCGACGTGGCCGCTGATCCCGGTGTGCCCG-CCGCTTCC-GG 1 CGGGGCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTG-CCGACCG-GTCCAGG 424468 CGGGGCCACCGGTTCCGGCGTGGCCGCTG 1 CGGGGCCACCGGTTCCGGCGTGGCCGCTG 424497 CTTCGGGCGC Statistics Matches: 65, Mismatches: 16, Indels: 5 0.76 0.19 0.06 Matches are distributed among these distances: 54 57 0.88 55 8 0.12 ACGTcount: A:0.07, C:0.36, G:0.41, T:0.16 Consensus pattern (54 bp): CGGGGCCACCGGTTCCGGCGTGGCCGCTGATCCCGGTGTGCCGACCGGTCCAGG Found at i:440618 original size:17 final size:17 Alignment explanation
Indices: 440596--440631 Score: 72 Period size: 17 Copynumber: 2.1 Consensus size: 17 440586 GAGCACCCGG 440596 CGATCGGGTGCGAATGT 1 CGATCGGGTGCGAATGT 440613 CGATCGGGTGCGAATGT 1 CGATCGGGTGCGAATGT 440630 CG 1 CG 440632 TTGCCGGGTC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 17 19 1.00 ACGTcount: A:0.17, C:0.19, G:0.42, T:0.22 Consensus pattern (17 bp): CGATCGGGTGCGAATGT Found at i:441244 original size:11 final size:12 Alignment explanation
Indices: 441230--441267 Score: 51 Period size: 12 Copynumber: 3.2 Consensus size: 12 441220 GGCGCCGGTT 441230 CGGCGGGGGTC- 1 CGGCGGGGGTCG * 441241 CGGCGCGGGTCG 1 CGGCGGGGGTCG * 441253 CGGCGGGGCTCG 1 CGGCGGGGGTCG 441265 CGG 1 CGG 441268 TCGTGCCGGG Statistics Matches: 23, Mismatches: 3, Indels: 1 0.85 0.11 0.04 Matches are distributed among these distances: 11 10 0.43 12 13 0.57 ACGTcount: A:0.00, C:0.32, G:0.61, T:0.08 Consensus pattern (12 bp): CGGCGGGGGTCG Found at i:443248 original size:18 final size:18 Alignment explanation
Indices: 443225--443282 Score: 89 Period size: 18 Copynumber: 3.2 Consensus size: 18 443215 GAAAGCGCCC 443225 TGCCGACGAGAAGAGCGG 1 TGCCGACGAGAAGAGCGG * 443243 TGCCGACGAGAAGAACGG 1 TGCCGACGAGAAGAGCGG * 443261 TGCCGACGAGAAAGGGCGG 1 TGCCGACGAG-AAGAGCGG 443280 TGC 1 TGC 443283 GGTCCGGGGA Statistics Matches: 36, Mismatches: 3, Indels: 1 0.90 0.07 0.03 Matches are distributed among these distances: 18 27 0.75 19 9 0.25 ACGTcount: A:0.28, C:0.22, G:0.43, T:0.07 Consensus pattern (18 bp): TGCCGACGAGAAGAGCGG Found at i:446494 original size:12 final size:12 Alignment explanation
Indices: 446477--446510 Score: 68 Period size: 12 Copynumber: 2.8 Consensus size: 12 446467 CCGCCGCCGT 446477 CGCCCACCTGCG 1 CGCCCACCTGCG 446489 CGCCCACCTGCG 1 CGCCCACCTGCG 446501 CGCCCACCTG 1 CGCCCACCTG 446511 TCGATCCGCC Statistics Matches: 22, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 12 22 1.00 ACGTcount: A:0.09, C:0.59, G:0.24, T:0.09 Consensus pattern (12 bp): CGCCCACCTGCG Found at i:509158 original size:15 final size:15 Alignment explanation
Indices: 509140--509177 Score: 51 Period size: 15 Copynumber: 2.5 Consensus size: 15 509130 CCGGTGCGTG 509140 GTGGACC-GTGCCTTC 1 GTGGACCGGT-CCTTC 509155 GTGGACCGGTCCTTC 1 GTGGACCGGTCCTTC * 509170 GTGCACCG 1 GTGGACCG 509178 CCCCACGATG Statistics Matches: 21, Mismatches: 1, Indels: 2 0.88 0.04 0.08 Matches are distributed among these distances: 15 19 0.90 16 2 0.10 ACGTcount: A:0.08, C:0.34, G:0.34, T:0.24 Consensus pattern (15 bp): GTGGACCGGTCCTTC Found at i:528163 original size:27 final size:27 Alignment explanation
Indices: 528147--528201 Score: 83 Period size: 27 Copynumber: 2.0 Consensus size: 27 528137 GGCCGGGTCG 528147 CTCCGCCAACTCGACCGGTGCCGGGAA 1 CTCCGCCAACTCGACCGGTGCCGGGAA * * * 528174 CTCCGCCAACTCCAACGGCGCCGGGAA 1 CTCCGCCAACTCGACCGGTGCCGGGAA 528201 C 1 C 528202 CAGACGGGAA Statistics Matches: 25, Mismatches: 3, Indels: 0 0.89 0.11 0.00 Matches are distributed among these distances: 27 25 1.00 ACGTcount: A:0.20, C:0.44, G:0.27, T:0.09 Consensus pattern (27 bp): CTCCGCCAACTCGACCGGTGCCGGGAA Found at i:528646 original size:33 final size:33 Alignment explanation
Indices: 528609--528679 Score: 101 Period size: 33 Copynumber: 2.2 Consensus size: 33 528599 TCGGCGCCGT * 528609 CCTCGGCACCGGGTCGGCCGGG-CT-GGGCCTCGG 1 CCTCGGCACCGGCTCGG-CGGGTCTCGGG-CTCGG 528642 CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG 1 CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG 528675 CCTCG 1 CCTCG 528680 CGACGGGTTC Statistics Matches: 35, Mismatches: 1, Indels: 4 0.88 0.03 0.10 Matches are distributed among these distances: 32 4 0.11 33 28 0.80 34 3 0.09 ACGTcount: A:0.03, C:0.41, G:0.42, T:0.14 Consensus pattern (33 bp): CCTCGGCACCGGCTCGGCGGGTCTCGGGCTCGG Found at i:528758 original size:15 final size:14 Alignment explanation
Indices: 528740--528841 Score: 60 Period size: 15 Copynumber: 6.9 Consensus size: 14 528730 GGTGCCGCGC 528740 TCGGTTCCGCGGCGG 1 TCGGTTCCGCGGC-G * * 528755 TCGGCTCGGCAGGCG 1 TCGGTTCCGC-GGCG * 528770 TCGGTTCCGCCGCCG 1 TCGGTTCCG-CGGCG * 528785 TCGGTTCCGCCGGGG 1 TCGGTTCCG-CGGCG * * 528800 TGGGTTCGGCGGGCG 1 TCGGTTCCGC-GGCG * * * 528815 TCGGCTCGGCCGGTG 1 TCGGTTCCG-CGGCG * 528830 TCGGATCCGCGG 1 TCGGTTCCGCGG 528842 GTGTCGGTCT Statistics Matches: 68, Mismatches: 15, Indels: 9 0.74 0.16 0.10 Matches are distributed among these distances: 14 4 0.06 15 59 0.87 16 5 0.07 ACGTcount: A:0.02, C:0.33, G:0.46, T:0.19 Consensus pattern (14 bp): TCGGTTCCGCGGCG Found at i:528774 original size:30 final size:30 Alignment explanation
Indices: 528740--528860 Score: 109 Period size: 30 Copynumber: 4.0 Consensus size: 30 528730 GGTGCCGCGC * 528740 TCGGTTCCGC-GGCGGTCGGCTCGGCAGGCG 1 TCGGTTCCGCGGGC-GTCGGCTCGGCCGGCG * * * * * 528770 TCGGTTCCGCCGCCGTCGGTTCCGCCGGGG 1 TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG * * * 528800 TGGGTTCGGCGGGCGTCGGCTCGGCCGGTG 1 TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG * * 528830 TCGGATCCGCGGGTGTCGGTCTCGGCTCGGC 1 TCGGTTCCGCGGGCGTCGG-CTCGGC-CGGC 528861 CGGTGCCGGT Statistics Matches: 71, Mismatches: 17, Indels: 4 0.77 0.18 0.04 Matches are distributed among these distances: 30 60 0.85 31 8 0.11 32 3 0.04 ACGTcount: A:0.02, C:0.33, G:0.45, T:0.20 Consensus pattern (30 bp): TCGGTTCCGCGGGCGTCGGCTCGGCCGGCG Found at i:528782 original size:45 final size:45 Alignment explanation
Indices: 528740--528855 Score: 119 Period size: 45 Copynumber: 2.6 Consensus size: 45 528730 GGTGCCGCGC 528740 TCGGTTCCG-CGGCGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG 1 TCGGTTCCGCCGG-GGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG * * * * * ** 528785 TCGGTTCCGCCGGGGTGGGTTCGGCGGGCGTCGGCTCGGCCGGTG 1 TCGGTTCCGCCGGGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG * 528830 TCGGATCCG-CGGGTGTCGGTCTCGGC 1 TCGGTTCCGCCGGG-GTCGG-CTCGGC 528856 TCGGCCGGTG Statistics Matches: 58, Mismatches: 10, Indels: 5 0.79 0.14 0.07 Matches are distributed among these distances: 44 4 0.07 45 46 0.79 46 8 0.14 ACGTcount: A:0.02, C:0.33, G:0.46, T:0.20 Consensus pattern (45 bp): TCGGTTCCGCCGGGGTCGGCTCGGCAGGCGTCGGTTCCGCCGCCG Found at i:528864 original size:15 final size:15 Alignment explanation
Indices: 528846--528892 Score: 60 Period size: 15 Copynumber: 3.1 Consensus size: 15 528836 CCGCGGGTGT 528846 CGGTCTCGGCTCGGC 1 CGGTCTCGGCTCGGC * 528861 CGGTGC-CGGTTCGGC 1 CGGT-CTCGGCTCGGC * 528876 CGGACTCGGCTCGGC 1 CGGTCTCGGCTCGGC 528891 CG 1 CG 528893 CGGTGGGTTC Statistics Matches: 27, Mismatches: 3, Indels: 4 0.79 0.09 0.12 Matches are distributed among these distances: 14 1 0.04 15 25 0.93 16 1 0.04 ACGTcount: A:0.02, C:0.38, G:0.43, T:0.17 Consensus pattern (15 bp): CGGTCTCGGCTCGGC Found at i:528914 original size:30 final size:29 Alignment explanation
Indices: 528850--528907 Score: 82 Period size: 30 Copynumber: 1.9 Consensus size: 29 528840 GGGTGTCGGT 528850 CTCGGCTCGGCCGGTGCCGGTTCGGCCGGA 1 CTCGGCTCGGCCGGTG-CGGTTCGGCCGGA 528880 CTCGGCTCGGCCGCGGTG-GGTTCGGCCG 1 CTCGGCTCGG-C-CGGTGCGGTTCGGCCG 528908 CGCTCGGTTC Statistics Matches: 26, Mismatches: 0, Indels: 4 0.87 0.00 0.13 Matches are distributed among these distances: 30 20 0.77 31 1 0.04 32 5 0.19 ACGTcount: A:0.02, C:0.36, G:0.45, T:0.17 Consensus pattern (29 bp): CTCGGCTCGGCCGGTGCGGTTCGGCCGGA Found at i:528916 original size:15 final size:15 Alignment explanation
Indices: 528867--528917 Score: 59 Period size: 15 Copynumber: 3.4 Consensus size: 15 528857 CGGCCGGTGC 528867 CGGTTCGGCCG-GACT 1 CGGTTCGGCCGCG-CT * * 528882 CGGCTCGGCCGCGGT 1 CGGTTCGGCCGCGCT * 528897 GGGTTCGGCCGCGCT 1 CGGTTCGGCCGCGCT 528912 CGGTTC 1 CGGTTC 528918 CGCCTCACCG Statistics Matches: 29, Mismatches: 6, Indels: 2 0.78 0.16 0.05 Matches are distributed among these distances: 15 28 0.97 16 1 0.03 ACGTcount: A:0.02, C:0.35, G:0.43, T:0.20 Consensus pattern (15 bp): CGGTTCGGCCGCGCT Found at i:529117 original size:27 final size:26 Alignment explanation
Indices: 529083--529139 Score: 73 Period size: 27 Copynumber: 2.2 Consensus size: 26 529073 CGATCGCCGT ** 529083 CGCCGCACCGGAGGCGCCCGCACCCG 1 CGCCGCACCCCAGGCGCCCGCACCCG 529109 CGCCGGCACCCCAGGCGCCCGC-CCC- 1 CGCC-GCACCCCAGGCGCCCGCACCCG 529134 CGCCGC 1 CGCCGC 529140 GCCGTCGGCC Statistics Matches: 28, Mismatches: 2, Indels: 4 0.82 0.06 0.12 Matches are distributed among these distances: 24 2 0.07 25 4 0.14 26 7 0.25 27 15 0.54 ACGTcount: A:0.09, C:0.60, G:0.32, T:0.00 Consensus pattern (26 bp): CGCCGCACCCCAGGCGCCCGCACCCG Found at i:547201 original size:20 final size:20 Alignment explanation
Indices: 547168--547216 Score: 75 Period size: 18 Copynumber: 2.5 Consensus size: 20 547158 GTTCCGGTGG * 547168 GGGCCGAGCCGTGTGTGT-- 1 GGGCGGAGCCGTGTGTGTGC 547186 GGGCGGAGCCGTGTGTGTGC 1 GGGCGGAGCCGTGTGTGTGC 547206 GGGCGGAGCCG 1 GGGCGGAGCCG 547217 AGGGCTCAGG Statistics Matches: 28, Mismatches: 1, Indels: 2 0.90 0.03 0.06 Matches are distributed among these distances: 18 17 0.61 20 11 0.39 ACGTcount: A:0.06, C:0.22, G:0.55, T:0.16 Consensus pattern (20 bp): GGGCGGAGCCGTGTGTGTGC Found at i:550851 original size:14 final size:14 Alignment explanation
Indices: 550832--550864 Score: 66 Period size: 14 Copynumber: 2.4 Consensus size: 14 550822 CGGCGTCCGC 550832 GCTGACCGAACTCG 1 GCTGACCGAACTCG 550846 GCTGACCGAACTCG 1 GCTGACCGAACTCG 550860 GCTGA 1 GCTGA 550865 GCGGATCGGC Statistics Matches: 19, Mismatches: 0, Indels: 0 1.00 0.00 0.00 Matches are distributed among these distances: 14 19 1.00 ACGTcount: A:0.21, C:0.33, G:0.30, T:0.15 Consensus pattern (14 bp): GCTGACCGAACTCG Found at i:553062 original size:24 final size:22 Alignment explanation
Indices: 553017--553063 Score: 60 Period size: 24 Copynumber: 2.0 Consensus size: 22 553007 GCGGCTTCAC 553017 CAGGACCGCGACGGTGCTGGTG 1 CAGGACCGCGACGGTGCTGGTG 553039 CAGGCACCGCGCAGCGGT-CTGGTG 1 CAGG-ACCGCG-A-CGGTGCTGGTG 553063 C 1 C 553064 TCGACCCCGA Statistics Matches: 22, Mismatches: 0, Indels: 4 0.85 0.00 0.15 Matches are distributed among these distances: 22 4 0.18 23 6 0.27 24 8 0.36 25 4 0.18 ACGTcount: A:0.13, C:0.32, G:0.43, T:0.13 Consensus pattern (22 bp): CAGGACCGCGACGGTGCTGGTG Found at i:560262 original size:18 final size:18 Alignment explanation
Indices: 560254--560321 Score: 100 Period size: 18 Copynumber: 3.8 Consensus size: 18 560244 CGATGCCGCG * * 560254 GGTTCGACCAAGGCTGCG 1 GGTTCGACCGAGGCTGCC * 560272 GGTTCGACGGAGGCTGCC 1 GGTTCGACCGAGGCTGCC * 560290 GGTTCGACCCAGGCTGCC 1 GGTTCGACCGAGGCTGCC 560308 GGTTCGACCGAGGC 1 GGTTCGACCGAGGC 560322 CGTGGGGCAG Statistics Matches: 44, Mismatches: 6, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 18 44 1.00 ACGTcount: A:0.13, C:0.31, G:0.40, T:0.16 Consensus pattern (18 bp): GGTTCGACCGAGGCTGCC Found at i:560337 original size:18 final size:18 Alignment explanation
Indices: 560315--560362 Score: 62 Period size: 18 Copynumber: 2.7 Consensus size: 18 560305 GCCGGTTCGA * 560315 CCGAGGCCGTGGGGCAGAG 1 CCGAGGCCGCGGGGCAG-G * 560334 -CGAGGCCGCGGGGGAGG 1 CCGAGGCCGCGGGGCAGG 560351 CCGAGGCCGCGG 1 CCGAGGCCGCGG 560363 AGGCGGTGTC Statistics Matches: 26, Mismatches: 2, Indels: 3 0.84 0.06 0.10 Matches are distributed among these distances: 17 1 0.04 18 25 0.96 ACGTcount: A:0.12, C:0.29, G:0.56, T:0.02 Consensus pattern (18 bp): CCGAGGCCGCGGGGCAGG Found at i:560460 original size:15 final size:16 Alignment explanation
Indices: 560416--560462 Score: 53 Period size: 15 Copynumber: 3.1 Consensus size: 16 560406 CAGCCTGGCC * 560416 AAGTCCGGTTTGTCG- 1 AAGTCCGGTCTGTCGA * * 560431 AAGTCCGGCCCGTCGA 1 AAGTCCGGTCTGTCGA 560447 AAG-CCGGTCTGTCGA 1 AAGTCCGGTCTGTCGA 560462 A 1 A 560463 GGACGGGCCG Statistics Matches: 26, Mismatches: 5, Indels: 2 0.79 0.15 0.06 Matches are distributed among these distances: 15 23 0.88 16 3 0.12 ACGTcount: A:0.19, C:0.28, G:0.32, T:0.21 Consensus pattern (16 bp): AAGTCCGGTCTGTCGA Found at i:568369 original size:20 final size:22 Alignment explanation
Indices: 568346--568387 Score: 61 Period size: 22 Copynumber: 2.0 Consensus size: 22 568336 GGGCCCTGGC 568346 GCGGCT-CGGCG-ACAGCGCGG 1 GCGGCTACGGCGCACAGCGCGG * 568366 GCGGCTACGGCGCACTGCGCGG 1 GCGGCTACGGCGCACAGCGCGG 568388 CGTCGCGCGC Statistics Matches: 19, Mismatches: 1, Indels: 2 0.86 0.05 0.09 Matches are distributed among these distances: 20 6 0.32 21 5 0.26 22 8 0.42 ACGTcount: A:0.10, C:0.36, G:0.48, T:0.07 Consensus pattern (22 bp): GCGGCTACGGCGCACAGCGCGG Found at i:569785 original size:22 final size:23 Alignment explanation
Indices: 569760--569803 Score: 63 Period size: 22 Copynumber: 2.0 Consensus size: 23 569750 CTGCGAACGG * 569760 CGGGTGAACGGG-CCCGTCCGGC 1 CGGGCGAACGGGACCCGTCCGGC * 569782 CGGGCGAACGGGAGCCGTCCGG 1 CGGGCGAACGGGACCCGTCCGG 569804 AAGGCCGATG Statistics Matches: 19, Mismatches: 2, Indels: 1 0.86 0.09 0.05 Matches are distributed among these distances: 22 11 0.58 23 8 0.42 ACGTcount: A:0.11, C:0.34, G:0.48, T:0.07 Consensus pattern (23 bp): CGGGCGAACGGGACCCGTCCGGC Found at i:585107 original size:77 final size:77 Alignment explanation
Indices: 584984--585242 Score: 443 Period size: 77 Copynumber: 3.4 Consensus size: 77 584974 GCTCGTCACC 584984 GCCTGACC-GGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC 1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC * 585048 GCATCGGATACC 66 GCATCGGATACA * * 585060 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTCACCACGCAGGCCGCCCCGGTCGGGC 1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC * 585125 GCAAAT-GG-CACA 66 GC--ATCGGATACA 585137 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC 1 GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC 585202 GCATCGGATACA 66 GCATCGGATACA 585214 GCCTGACCGGGTCAGCGGCCGGAGGCGGT 1 GCCTGACCGGGTCAGCGGCCGGAGGCGGT 585243 GGTCTCTACC Statistics Matches: 171, Mismatches: 7, Indels: 9 0.91 0.04 0.05 Matches are distributed among these distances: 75 2 0.01 76 10 0.06 77 155 0.91 78 2 0.01 79 2 0.01 ACGTcount: A:0.15, C:0.34, G:0.42, T:0.08 Consensus pattern (77 bp): GCCTGACCGGGTCAGCGGCCGGAGGCGGTAGCGGAGCGTGACCACGCAGGCCGCCCCGGGCGGGC GCATCGGATACA Found at i:586998 original size:17 final size:17 Alignment explanation
Indices: 586966--586999 Score: 50 Period size: 17 Copynumber: 2.0 Consensus size: 17 586956 CGGCGTCCGA * * 586966 ATTGTCCGGTGGGTGCC 1 ATTGTCCGGCGAGTGCC 586983 ATTGTCCGGCGAGTGCC 1 ATTGTCCGGCGAGTGCC 587000 GGTCGGGTGA Statistics Matches: 15, Mismatches: 2, Indels: 0 0.88 0.12 0.00 Matches are distributed among these distances: 17 15 1.00 ACGTcount: A:0.09, C:0.26, G:0.38, T:0.26 Consensus pattern (17 bp): ATTGTCCGGCGAGTGCC Done.