Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 87 of 290
Found at i:29216829 original size:54 final size:54
Alignment explanation
Indices: 29216766--29216916 Score: 176
Period size: 54 Copynumber: 2.8 Consensus size: 54
29216756 CATCCTACAA
* * * * *** *
29216766 GGGTGTTTTGGTAAATCTACAAATTAAGGGTATTTCTGTAATTTTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
*
29216820 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
* * * * *
29216874 TGGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTGGTAATT
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATT
29216917 CTACCCTATA
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 82 1.00
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAG
Found at i:29216978 original size:27 final size:27
Alignment explanation
Indices: 29216948--29217039 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
29216938 ATAATTTCAT
*** *
29216948 AATCGAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACAATAATTCTGTA
29216975 AATC-AGGGGTAAAACAATAATTCTGTA
1 AATCGA-GGGTAAAACAATAATTCTGTA
* *
29217002 AATTGAGGGTAAAACAATAATTCTATA
1 AATCGAGGGTAAAACAATAATTCTGTA
29217029 AATCGAGGGTA
1 AATCGAGGGTA
29217040 CTTTGGTAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACAATAATTCTGTA
Found at i:29217049 original size:27 final size:27
Alignment explanation
Indices: 29217019--29217242 Score: 105
Period size: 27 Copynumber: 8.2 Consensus size: 27
29217009 GGTAAAACAA
* *
29217019 TAATTCTATAAATCGAGGGTACTTTGG
1 TAATTTTATAAATCGAGGGTAATTTGG
* *
29217046 TAATTTT-TACAAGTCAAGGGT-ATTTCAG
1 TAATTTTATA-AA-TCGAGGGTAATTT-GG
* * *
29217074 TAATTTTACAAATC-AGGAGGTATTTTAG
1 TAATTTTATAAATCGA-G-GGTAATTTGG
* * * *
29217102 TAATTTTACAAA-CCAGGGGTATTTTAG
1 TAATTTTATAAATCGA-GGGTAATTTGG
* * ***
29217129 TAATTTTGTAAATTGAGGGTAAAACGG
1 TAATTTTATAAATCGAGGGTAATTTGG
* * **
29217156 TAATTCTATAAATCAAGGGTAAAATGG
1 TAATTTTATAAATCGAGGGTAATTTGG
* ****
29217183 TAATTCTATAAATCGAGGGTAGGACGG
1 TAATTTTATAAATCGAGGGTAATTTGG
* * * *
29217210 TAATTTTGTAAATTGGGGGTACTTTGG
1 TAATTTTATAAATCGAGGGTAATTTGG
29217237 TAATTT
1 TAATTT
29217243 GGTAAACTAA
Statistics
Matches: 156, Mismatches: 32, Indels: 18
0.76 0.16 0.09
Matches are distributed among these distances:
26 3 0.02
27 111 0.71
28 38 0.24
29 4 0.03
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (27 bp):
TAATTTTATAAATCGAGGGTAATTTGG
Found at i:29217066 original size:28 final size:27
Alignment explanation
Indices: 29217019--29217135 Score: 126
Period size: 28 Copynumber: 4.3 Consensus size: 27
29217009 GGTAAAACAA
* * * * *
29217019 TAATTCTATAAATCGAGGGTACTTTGG
1 TAATTTTACAAATCAAGGGTATTTTAG
* *
29217046 TAATTTTTACAAGTCAAGGGTATTTCAG
1 TAA-TTTTACAAATCAAGGGTATTTTAG
*
29217074 TAATTTTACAAATCAGGAGGTATTTTAG
1 TAATTTTACAAATCAAG-GGTATTTTAG
* *
29217102 TAATTTTACAAACCAGGGGTATTTTAG
1 TAATTTTACAAATCAAGGGTATTTTAG
29217129 TAATTTT
1 TAATTTT
29217136 GTAAATTGAG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 32 0.42
28 45 0.58
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.40
Consensus pattern (27 bp):
TAATTTTACAAATCAAGGGTATTTTAG
Found at i:29217087 original size:55 final size:54
Alignment explanation
Indices: 29217019--29217149 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 54
29217009 GGTAAAACAA
* * **
29217019 TAATTCTATAAATCGAGGGTACTTTGGTAATTTTTACAAGTCAAGGGTATTTCAG
1 TAATTTTATAAATCGAGGGTACTTTAGTAA-TTTTACAAACCAAGGGTATTTCAG
* * * *
29217074 TAATTTTACAAATC-AGGAGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTAG
1 TAATTTTATAAATCGA-G-GGTACTTTAGTAATTTTACAAACCAAGGGTATTTCAG
* *
29217129 TAATTTTGTAAATTGAGGGTA
1 TAATTTTATAAATCGAGGGTA
29217150 AAACGGTAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
54 5 0.08
55 45 0.73
56 12 0.19
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (54 bp):
TAATTTTATAAATCGAGGGTACTTTAGTAATTTTACAAACCAAGGGTATTTCAG
Found at i:29223988 original size:25 final size:25
Alignment explanation
Indices: 29223889--29223994 Score: 101
Period size: 25 Copynumber: 4.3 Consensus size: 25
29223879 TACCCGTTTT
* * *
29223889 TGGCTCGCATGAGCTTCCTGAT-TA
1 TGGCTCGAATAAGCTTCCTGTTATA
* * *
29223913 TGGCTCTAATGAGCTTCTTGTTATA
1 TGGCTCGAATAAGCTTCCTGTTATA
** *
29223938 CCGCTCGAATAAGCTTCCCGTTATA
1 TGGCTCGAATAAGCTTCCTGTTATA
29223963 TGGCTC-ACATAAGCTTCCTGTTATA
1 TGGCTCGA-ATAAGCTTCCTGTTATA
29223988 T-GCTCGA
1 TGGCTCGA
29223995 GAAAGTAATT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
24 23 0.35
25 43 0.65
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (25 bp):
TGGCTCGAATAAGCTTCCTGTTATA
Found at i:29225300 original size:20 final size:19
Alignment explanation
Indices: 29225240--29225312 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
29225230 TACATAATAA
*
29225240 ATAATTAATAATAAAATGAT
1 ATAA-TAATAATAAAAAGAT
* *
29225260 ATAGTAA-AATAAAAATAAT
1 ATAATAATAATAAAAA-GAT
29225279 ATAATGAATAATAAAAAGAT
1 ATAAT-AATAATAAAAAGAT
29225299 ATAATATATAATAA
1 ATAATA-ATAATAA
29225313 TTTTTACATA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.16
19 10 0.23
20 19 0.43
21 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAATAATAATAAAAAGAT
Found at i:29225604 original size:6 final size:6
Alignment explanation
Indices: 29225593--29225618 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29225583 GGTCAGGGCC
29225593 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
29225619 TGAAACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:29228638 original size:39 final size:40
Alignment explanation
Indices: 29228593--29228764 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
29228583 GCTCCTCGTT
* * *
29228593 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
29228633 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
29228672 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29228712 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
29228752 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29228765 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29228693 original size:40 final size:39
Alignment explanation
Indices: 29228595--29228817 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
29228585 TCCTCGTTCA
* * * *
29228595 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
29228634 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
29228673 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
29228713 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
29228753 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
29228794 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
29228818 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:29228777 original size:80 final size:79
Alignment explanation
Indices: 29228593--29228817 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
29228583 GCTCCTCGTT
* * * * *
29228593 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
29228657 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
29228672 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
29228737 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
29228752 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
29228816 GA
63 GA
29228818 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:29228826 original size:41 final size:41
Alignment explanation
Indices: 29228749--29228826 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29228739 TTTGTATCTC
* * *
29228749 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29228790 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29228827 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:29234412 original size:14 final size:14
Alignment explanation
Indices: 29234393--29234422 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29234383 ATGCTGTAAG
29234393 TAATACATTGAGTT
1 TAATACATTGAGTT
29234407 TAATACATTGAGTT
1 TAATACATTGAGTT
29234421 TA
1 TA
29234423 GTTGCGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (14 bp):
TAATACATTGAGTT
Found at i:29235043 original size:61 final size:61
Alignment explanation
Indices: 29234971--29235221 Score: 493
Period size: 61 Copynumber: 4.1 Consensus size: 61
29234961 GCATAATAAG
*
29234971 CAAGCCATTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
1 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
29235032 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
1 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
29235093 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
1 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
29235154 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
1 CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
29235215 CAAGCCT
1 CAAGCCT
29235222 ATACATGCCA
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 189 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (61 bp):
CAAGCCTTTTTCGCATGGCTTTAAATACATATACAAATTTCAAAACCAAATATATATAAAA
Found at i:29235601 original size:26 final size:26
Alignment explanation
Indices: 29235571--29235624 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
29235561 CTAAATATAC
29235571 ATAAACTCATATACATATATTCATGG
1 ATAAACTCATATACATATATTCATGG
*
29235597 ATAAACTTATATACATATATTCATGG
1 ATAAACTCATATACATATATTCATGG
29235623 AT
1 AT
29235625 CATTCCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (26 bp):
ATAAACTCATATACATATATTCATGG
Found at i:29236239 original size:56 final size:56
Alignment explanation
Indices: 29236156--29236290 Score: 216
Period size: 56 Copynumber: 2.4 Consensus size: 56
29236146 GTGACCACAT
* *
29236156 ATATCGATGCCAACGTATTAGACGTGGTCTTACACGCACACATATATCGGAATCAC
1 ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCAC
* * *
29236212 ATATCGAAGCTAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCAC
1 ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCAC
*
29236268 ATATCGATGCCAACATATTAAAC
1 ATATCGATGCCAACGTATTAAAC
29236291 TCGGAATCAC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (56 bp):
ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCAC
Found at i:29236328 original size:145 final size:145
Alignment explanation
Indices: 29236156--29236435 Score: 454
Period size: 145 Copynumber: 1.9 Consensus size: 145
29236146 GTGACCACAT
* *
29236156 ATATCGATGCCAACGTATTAGACGTGGTCTTACACGCACACATATATCGGAATCACATATCGA-A
1 ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCACATATCGATA
* *
29236220 GCTAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATA
66 -CCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCAATGCCAACATA
29236285 TTAAACTCGGAATCAC
130 TTAAACTCGGAATCAC
* *
29236301 ATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAGAATCACATATCGATA
1 ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCACATATCGATA
* * * *
29236366 CCAACGTATTAAATGTTGTCTTACTCGCACACATATATCGGAATCACATATCAATGCCAACGTAT
66 CCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCAATGCCAACATAT
29236431 TAAAC
131 TAAAC
29236436 GTGATCTTAA
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
145 123 0.99
146 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (145 bp):
ATATCGATGCCAACGTATTAAACGTGGTCTTACACGCACACATATATCAGAATCACATATCGATA
CCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCACATATCAATGCCAACATAT
TAAACTCGGAATCAC
Found at i:29236353 original size:89 final size:89
Alignment explanation
Indices: 29236202--29236378 Score: 309
Period size: 89 Copynumber: 2.0 Consensus size: 89
29236192 CACACATATA
*
29236202 TCGGAATCACATATCGAAGCTAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCA
1 TCGGAATCACATATCGAAGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCA
*
29236267 CATATCGATGCCAACATATTAAAC
66 CATATCGATACCAACATATTAAAC
* *
29236291 TCGGAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCAGAATCA
1 TCGGAATCACATATCGAAGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCA
*
29236356 CATATCGATACCAACGTATTAAA
66 CATATCGATACCAACATATTAAA
29236379 TGTTGTCTTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (89 bp):
TCGGAATCACATATCGAAGCCAACGTATTAAACGTGGTCTTACTCGCACACATATATCAGAATCA
CATATCGATACCAACATATTAAAC
Found at i:29236370 original size:56 final size:56
Alignment explanation
Indices: 29236294--29236444 Score: 248
Period size: 56 Copynumber: 2.7 Consensus size: 56
29236284 ATTAAACTCG
29236294 GAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
1 GAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
* * *
29236350 GAATCACATATCGATACCAACGTATTAAATGTTGTCTTACTCGCACACATATATCG
1 GAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
* * *
29236406 GAATCACATATCAATGCCAACGTATTAAACGTGATCTTA
1 GAATCACATATCGATGCCAACGTATTAAATGTGGTCTTA
29236445 ATCACAAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 87 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (56 bp):
GAATCACATATCGATGCCAACGTATTAAATGTGGTCTTACTCGCACACATATATCA
Found at i:29238343 original size:23 final size:23
Alignment explanation
Indices: 29238302--29238354 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
29238292 AAGCTCCTTC
*
29238302 GAGCTG-AACAGTAAGCTCTATT
1 GAGCTGAAACAGTAACCTCTATT
*
29238324 GAGCTGAAATAGTAACCTCTATT
1 GAGCTGAAACAGTAACCTCTATT
29238347 GAGCTGAA
1 GAGCTGAA
29238355 CGGTCTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (23 bp):
GAGCTGAAACAGTAACCTCTATT
Found at i:29238368 original size:19 final size:19
Alignment explanation
Indices: 29238340--29238377 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29238330 AAATAGTAAC
*
29238340 CTCTATTGAGCTGAACGGT
1 CTCTAATGAGCTGAACGGT
29238359 CTCTAATGAGCTGAACGGT
1 CTCTAATGAGCTGAACGGT
29238378 AAGCTCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (19 bp):
CTCTAATGAGCTGAACGGT
Found at i:29239905 original size:53 final size:53
Alignment explanation
Indices: 29239825--29240020 Score: 149
Period size: 53 Copynumber: 3.6 Consensus size: 53
29239815 TTCCTTTTTA
* * * *
29239825 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
* * * *
29239878 AACTCACCATTGTCATGCCTTGGCATGGTCTTACATGGGATCTTTGTCTTATCG
1 AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G
** * * * * * * *** * *
29239932 TAGTTTATCAATGCCATGTCTTCATATGGTCTTACATGATTTCCTTGCCTTGTAA
1 -AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTAT-G
* * *
29239987 AACTTACCAATGCCATGCCTTGGCATGGTCTTAC
1 AACTCACCATTGCCATGCCTTGACATGGTCTTAC
29240021 TTGTTATCCT
Statistics
Matches: 108, Mismatches: 33, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
53 44 0.41
54 28 0.26
55 36 0.33
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (53 bp):
AACTCACCATTGCCATGCCTTGACATGGTCTTACATGGGATCCTTGCCTTATG
Found at i:29250467 original size:212 final size:212
Alignment explanation
Indices: 29250100--29250512 Score: 745
Period size: 212 Copynumber: 1.9 Consensus size: 212
29250090 ATGTAAAACC
* *
29250100 TAGCTATGGTTGATTTTTCTTTCTCAATTTCGGCAAGAGATGGATTGAAAAATGTGATTTTGATT
1 TAGCTATGGCTGATTTTTATTTCTCAATTTCGGCAAGAGATGGATTGAAAAATGTGATTTTGATT
*
29250165 TTGTTTTTATTATTATTAACTTAATAAGACATTTACAAAAATAACATTTATTTAAAGATATAATA
66 TTGTTTTTATTATTATTAACTTAATAAGACATTTACAAAAATAACATTTATTTAAACATATAATA
*
29250230 ACCATGCTAATTATGAACATAAATGTCCACTAACATTAATTAAGGTATATTATCAACTTAGGGAC
131 ACCATGCTAATTATGAACATAAATGTCCACTAACATTAATTAAGGTATATTATCAACTCAGGGAC
29250295 CTCCAATATAAATTTCA
196 CTCCAATATAAATTTCA
* *
29250312 TAGCTATGGCTGATTTTTATTTCTTAATTTCGGCAAGAGATGGATTGAATAATGTGATTTTGATT
1 TAGCTATGGCTGATTTTTATTTCTCAATTTCGGCAAGAGATGGATTGAAAAATGTGATTTTGATT
* *
29250377 TTGTTTTTATTATTATTAACTTAATAAGCCATTTACAAAAATAACCTTTATTTAAACATATAATA
66 TTGTTTTTATTATTATTAACTTAATAAGACATTTACAAAAATAACATTTATTTAAACATATAATA
*
29250442 ACCATGCTAATTATGGACATAAATGTCCACTAACATTAATTAAGGTATATTATCAACTCAGGGAC
131 ACCATGCTAATTATGAACATAAATGTCCACTAACATTAATTAAGGTATATTATCAACTCAGGGAC
29250507 CTCCAA
196 CTCCAA
29250513 CTAATAGAAC
Statistics
Matches: 192, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
212 192 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (212 bp):
TAGCTATGGCTGATTTTTATTTCTCAATTTCGGCAAGAGATGGATTGAAAAATGTGATTTTGATT
TTGTTTTTATTATTATTAACTTAATAAGACATTTACAAAAATAACATTTATTTAAACATATAATA
ACCATGCTAATTATGAACATAAATGTCCACTAACATTAATTAAGGTATATTATCAACTCAGGGAC
CTCCAATATAAATTTCA
Found at i:29252971 original size:61 final size:60
Alignment explanation
Indices: 29252823--29253000 Score: 257
Period size: 61 Copynumber: 3.0 Consensus size: 60
29252813 CAACAAATTT
* * * * *
29252823 AATATTAAATTAAATTTAATATTTATCTATATAGTATTTTATTAAATTAACATTACTTGA
1 AATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAATTGA
*
29252883 AATTTTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAATATGA
1 AATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAAT-TGA
* * * *
29252944 GATATTAAAATAAATTAAATATTTATCTTGATAATATTTTATTAATTTAATATTAAT
1 AATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAAT
29253001 GTGATTAATT
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
60 51 0.48
61 55 0.52
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (60 bp):
AATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAATTGA
Found at i:29256422 original size:22 final size:22
Alignment explanation
Indices: 29256373--29256415 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29256363 TAACATGTGT
*
29256373 CACATATA-TCATGAGCTTAGAC
1 CACATA-ACTCATGAGCTCAGAC
29256395 CACATAACTCATGAGCTCAGA
1 CACATAACTCATGAGCTCAGA
29256416 TCGCATAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (22 bp):
CACATAACTCATGAGCTCAGAC
Found at i:29258814 original size:269 final size:269
Alignment explanation
Indices: 29258335--29258875 Score: 1073
Period size: 269 Copynumber: 2.0 Consensus size: 269
29258325 GCAGGTCCTA
29258335 GATTTGGCAGGTAAGTCGAGAGTAACCTTAGTGGTGTAGTGCTATCCACCCAATTGTTGTTCTAG
1 GATTTGGCAGGTAAGTCGAGAGTAACCTTAGTGGTGTAGTGCTATCCACCCAATTGTTGTTCTAG
*
29258400 TGTAAAGATCGAATGCCTAGTATGTATCAGATTATTAAGCGAGGGTTTTTCTTAAAATGTATTAA
66 TGTAAAGATCGAACGCCTAGTATGTATCAGATTATTAAGCGAGGGTTTTTCTTAAAATGTATTAA
29258465 GTTATAAAGAAGAAGAGATTTAGTAAGAGTGTTGAGAACCTTATAAGTAGGGGTTATTGACAAAG
131 GTTATAAAGAAGAAGAGATTTAGTAAGAGTGTTGAGAACCTTATAAGTAGGGGTTATTGACAAAG
29258530 GTATTGTACGCCCAATATATTGAGTTATTGTGCTAGTTACATTCTAAAGAGGTAGTTGGAAATAA
196 GTATTGTACGCCCAATATATTGAGTTATTGTGCTAGTTACATTCTAAAGAGGTAGTTGGAAATAA
29258595 ACAAGGGAT
261 ACAAGGGAT
29258604 GATTTGGCAGGTAAGTCGAGAGTAACCTTAGTGGTGTAGTGCTATCCACCCAATTGTTGTTCTAG
1 GATTTGGCAGGTAAGTCGAGAGTAACCTTAGTGGTGTAGTGCTATCCACCCAATTGTTGTTCTAG
29258669 TGTAAAGATCGAACGCCTAGTATGTATCAGATTATTAAGCGAGGGTTTTTCTTAAAATGTATTAA
66 TGTAAAGATCGAACGCCTAGTATGTATCAGATTATTAAGCGAGGGTTTTTCTTAAAATGTATTAA
29258734 GTTATAAAGAAGAAGAGATTTAGTAAGAGTGTTGAGAACCTTATAAGTAGGGGTTATTGACAAAG
131 GTTATAAAGAAGAAGAGATTTAGTAAGAGTGTTGAGAACCTTATAAGTAGGGGTTATTGACAAAG
29258799 GTATTGTACGCCCAATATATTGAGTTATTGTGCTAGTTACATTCTAAAGAGGTAGTTGGAAATAA
196 GTATTGTACGCCCAATATATTGAGTTATTGTGCTAGTTACATTCTAAAGAGGTAGTTGGAAATAA
29258864 ACAAGGGAT
261 ACAAGGGAT
29258873 GAT
1 GAT
29258876 CCAGGAATAT
Statistics
Matches: 271, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
269 271 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.32
Consensus pattern (269 bp):
GATTTGGCAGGTAAGTCGAGAGTAACCTTAGTGGTGTAGTGCTATCCACCCAATTGTTGTTCTAG
TGTAAAGATCGAACGCCTAGTATGTATCAGATTATTAAGCGAGGGTTTTTCTTAAAATGTATTAA
GTTATAAAGAAGAAGAGATTTAGTAAGAGTGTTGAGAACCTTATAAGTAGGGGTTATTGACAAAG
GTATTGTACGCCCAATATATTGAGTTATTGTGCTAGTTACATTCTAAAGAGGTAGTTGGAAATAA
ACAAGGGAT
Found at i:29260579 original size:41 final size:41
Alignment explanation
Indices: 29260524--29260641 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 41
29260514 GTTAGAGCTA
* ** *
29260524 TAGCGACGATTATGATAAAAACACCGTAAAAGGT-TGAGCAT
1 TAGCGACGTTTATGATAAAAACACCACAAAAGGTCAG-GCAT
* *
29260565 TAGC-AGCGTTTATGAGAAAAACGCCACAAAAGGTCAGGCAT
1 TAGCGA-CGTTTATGATAAAAACACCACAAAAGGTCAGGCAT
** *
29260606 TAGCGACGTTTATGATAAAAATGCTACAAAAGGTCA
1 TAGCGACGTTTATGATAAAAACACCACAAAAGGTCA
29260642 AGTAGTTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 1 0.02
41 62 0.95
42 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (41 bp):
TAGCGACGTTTATGATAAAAACACCACAAAAGGTCAGGCAT
Found at i:29260729 original size:15 final size:15
Alignment explanation
Indices: 29260709--29260848 Score: 76
Period size: 15 Copynumber: 9.6 Consensus size: 15
29260699 GTTTAAAGTA
29260709 TATGGTTTAGGGTTT
1 TATGGTTTAGGGTTT
29260724 TATGGTTTAGGG-TT
1 TATGGTTTAGGGTTT
** **
29260738 TATTATTTTTGG-TT
1 TATGGTTTAGGGTTT
* *
29260752 TATGGTTTTGTGTTT
1 TATGGTTTAGGGTTT
** *
29260767 TAAAGTTTATGG-TT
1 TATGGTTTAGGGTTT
* * *
29260781 TAGGGTTAAGTGTTT
1 TATGGTTTAGGGTTT
*
29260796 TATAG-TTAGGGTTT
1 TATGGTTTAGGGTTT
29260810 TA-GTGTTTAGGGTTT
1 TATG-GTTTAGGGTTT
* *
29260825 TAAAGG-TTAGGGTAT
1 T-ATGGTTTAGGGTTT
*
29260840 TAGGGTTTA
1 TATGGTTTA
29260849 AAGGTAAGGG
Statistics
Matches: 93, Mismatches: 25, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
14 42 0.45
15 48 0.52
16 2 0.02
17 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
TATGGTTTAGGGTTT
Found at i:29260757 original size:7 final size:7
Alignment explanation
Indices: 29260709--29260787 Score: 52
Period size: 7 Copynumber: 11.0 Consensus size: 7
29260699 GTTTAAAGTA
29260709 TATGGTT
1 TATGGTT
*
29260716 TAGGGTTT
1 TATGG-TT
29260724 TATGGTT
1 TATGGTT
*
29260731 TAGGGTT
1 TATGGTT
**
29260738 TATTATT
1 TATGGTT
*
29260745 TTTGGTT
1 TATGGTT
29260752 TATGGTT
1 TATGGTT
29260759 T-TGTGTTT
1 TATG-G-TT
**
29260767 TAAAGTT
1 TATGGTT
29260774 TATGGTT
1 TATGGTT
*
29260781 TAGGGTT
1 TATGGTT
29260788 AAGTGTTTTA
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
6 2 0.04
7 41 0.77
8 10 0.19
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.57
Consensus pattern (7 bp):
TATGGTT
Found at i:29260779 original size:29 final size:29
Alignment explanation
Indices: 29260747--29260846 Score: 85
Period size: 29 Copynumber: 3.4 Consensus size: 29
29260737 TTATTATTTT
* **
29260747 TGGTTTATGGTTTTGTGTTTTAAAGTTTA
1 TGGTTTAGGGTTAAGTGTTTTAAAGTTTA
*
29260776 TGGTTTAGGGTTAAGTGTTTTATAG-TTA
1 TGGTTTAGGGTTAAGTGTTTTAAAGTTTA
* * * * *
29260804 GGGTTTTAGTGTTTAGGGTTTTAAAGGTTA
1 TGG-TTTAGGGTTAAGTGTTTTAAAGTTTA
*
29260834 GGGTATTAGGGTT
1 TGGT-TTAGGGTT
29260847 TAAAGGTAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
28 5 0.09
29 40 0.69
30 13 0.22
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (29 bp):
TGGTTTAGGGTTAAGTGTTTTAAAGTTTA
Found at i:29260818 original size:21 final size:21
Alignment explanation
Indices: 29260771--29260818 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
29260761 GTGTTTTAAA
*
29260771 GTTTATGGTTTAGGGTTAAGT
1 GTTTATAGTTTAGGGTTAAGT
*
29260792 GTTTTATAG-TTAGGGTTTTAGT
1 G-TTTATAGTTTAGGG-TTAAGT
29260814 GTTTA
1 GTTTA
29260819 GGGTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (21 bp):
GTTTATAGTTTAGGGTTAAGT
Found at i:29260842 original size:23 final size:22
Alignment explanation
Indices: 29260816--29260858 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
29260806 GTTTTAGTGT
*
29260816 TTAGGGTTTTAAAGGTTAGGGTA
1 TTAGGG-TTTAAAGGTAAGGGTA
29260839 TTAGGGTTTAAAGGTAAGGG
1 TTAGGGTTTAAAGGTAAGGG
29260859 ATTTTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (22 bp):
TTAGGGTTTAAAGGTAAGGGTA
Found at i:29261060 original size:7 final size:7
Alignment explanation
Indices: 29260988--29261066 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
29260978 TTAAGAAGTA
29260988 AGGGTTT
1 AGGGTTT
*
29260995 AGCGTTT
1 AGGGTTT
29261002 AGGGTTT
1 AGGGTTT
* *
29261009 AAGATTT
1 AGGGTTT
* *
29261016 ATGATTT
1 AGGGTTT
*
29261023 AGAGTTT
1 AGGGTTT
29261030 AGGGTTT
1 AGGGTTT
* *
29261037 ATGATTT
1 AGGGTTT
*
29261044 AGGGTCT
1 AGGGTTT
29261051 AGGGTTT
1 AGGGTTT
*
29261058 AGGCTTT
1 AGGGTTT
29261065 AG
1 AG
29261067 TTTAGGGGTG
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 56 1.00
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:29261066 original size:21 final size:21
Alignment explanation
Indices: 29260999--29261058 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
29260989 GGGTTTAGCG
* *
29260999 TTTAGGGTTTAAGATTTATGA
1 TTTAGGGTTTAGGGTTTATGA
*
29261020 TTTAGAGTTTAGGGTTTATGA
1 TTTAGGGTTTAGGGTTTATGA
*
29261041 TTTAGGGTCTAGGGTTTA
1 TTTAGGGTTTAGGGTTTA
29261059 GGCTTTAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATGA
Found at i:29269123 original size:37 final size:37
Alignment explanation
Indices: 29269073--29269160 Score: 158
Period size: 37 Copynumber: 2.4 Consensus size: 37
29269063 GTACTACTTG
29269073 GAGTGTAGGGATGGGTGGGTGTTTTAAACCCCACATA
1 GAGTGTAGGGATGGGTGGGTGTTTTAAACCCCACATA
*
29269110 GAGTGTAGGGATGGGTGGGTGTTTTAAACCCCACATG
1 GAGTGTAGGGATGGGTGGGTGTTTTAAACCCCACATA
*
29269147 GAGTGTAGGAATGG
1 GAGTGTAGGGATGG
29269161 ACGGAGATGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.24, C:0.11, G:0.39, T:0.26
Consensus pattern (37 bp):
GAGTGTAGGGATGGGTGGGTGTTTTAAACCCCACATA
Found at i:29274480 original size:40 final size:39
Alignment explanation
Indices: 29274417--29274502 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 39
29274407 TAACGACTTA
**
29274417 TCGGCTAAAATAGCACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGCTAAAATAGCACTTAGTGTGCAATTCGAAATAGCT
* * * *
29274456 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TAGCACTTAGTGTGCAATTCGAAATAGCT
29274496 TCGGCTA
1 TCGGCTA
29274503 TATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 10 0.25
40 30 0.75
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (39 bp):
TCGGCTAAAATAGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:29277303 original size:50 final size:50
Alignment explanation
Indices: 29277239--29277373 Score: 148
Period size: 50 Copynumber: 2.7 Consensus size: 50
29277229 CAATACATGT
* *
29277239 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAG-CAC-AAAAAGAGGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAA-A-GA
* * * * * * *
29277289 GAGCCAGTGTAAGACCATGTCTGGGATATGACGTCGGCCTCGATATAAGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAAAGA
*
29277339 GAGTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC
29277374 GACTCGATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
50 64 0.91
51 3 0.04
52 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (50 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAAAAAAGA
Found at i:29277473 original size:43 final size:43
Alignment explanation
Indices: 29277346--29277489 Score: 132
Period size: 43 Copynumber: 3.3 Consensus size: 43
29277336 AGAGAGTCAG
29277346 TGTAAGACCATGTCTGGGACA-TGGCATCGACTCGATATGTGATTAAA
1 TGTAAGACCATGTCTGGGACAGTGG---C-A-TCGATATGTGATTAAA
* * * ***
29277393 TGTAATACCATGTCTGGGACATTGGCATTG-TATTGTGATTTTG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATA-TGTGATTAAA
* *
29277436 TGTAAGACCCTGTGTGGGACAGTGGCATCGATATGTGA-TAACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTAA-A
29277479 TGTAAGACCAT
1 TGTAAGACCAT
29277490 ATCTAGGATA
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
42 3 0.04
43 49 0.62
44 3 0.04
45 1 0.01
47 20 0.25
48 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATGTGATTAAA
Found at i:29281445 original size:40 final size:39
Alignment explanation
Indices: 29281367--29281445 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
29281357 TTAATGACTT
**
29281367 ATCAGCTAAAATGGCACTTAGTGTGCGGTTCGAAATAGC
1 ATCAGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGC
* * *
29281406 ATCAGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGC
1 ATCAGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGC
29281446 TTCGGCTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 11 0.32
40 23 0.68
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (39 bp):
ATCAGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGC
Found at i:29281527 original size:40 final size:40
Alignment explanation
Indices: 29281472--29281551 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
29281462 TAAATGGAAA
29281472 TGTGACAGCCCTAAATTGACCCTAGTCGGGAAGTGGTTTC
1 TGTGACAGCCCTAAATTGACCCTAGTCGGGAAGTGGTTTC
*
29281512 TGTGACAGCCCTAAATTGACCCTAGTTGGGAAGTGGTTTC
1 TGTGACAGCCCTAAATTGACCCTAGTCGGGAAGTGGTTTC
29281552 GGGGCCGCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TGTGACAGCCCTAAATTGACCCTAGTCGGGAAGTGGTTTC
Found at i:29283228 original size:39 final size:40
Alignment explanation
Indices: 29283131--29283228 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
29283121 CGGATGATAA
* *
29283131 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
29283171 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTA-CTATAT
*
29283211 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29283229 TACTTGGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.31
40 37 0.69
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.21
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
Found at i:29291126 original size:39 final size:40
Alignment explanation
Indices: 29291029--29291126 Score: 146
Period size: 40 Copynumber: 2.5 Consensus size: 40
29291019 CGGATGATAA
* *
29291029 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
29291069 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTA-CTATAT
*
29291109 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29291127 TACTTGGTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.31
40 37 0.69
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.21
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAGTTACTATAT
Found at i:29294316 original size:32 final size:32
Alignment explanation
Indices: 29294275--29294339 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29294265 CACGGGTGTG
29294275 TGACCCTATTTCATGATGAAATTTTCTAAGTT
1 TGACCCTATTTCATGATGAAATTTTCTAAGTT
29294307 TGACCCTATTTCATGATGAAATTTTCTAAGTT
1 TGACCCTATTTCATGATGAAATTTTCTAAGTT
29294339 T
1 T
29294340 TCTAAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (32 bp):
TGACCCTATTTCATGATGAAATTTTCTAAGTT
Found at i:29294593 original size:25 final size:25
Alignment explanation
Indices: 29294560--29294608 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29294550 TACAAGTATA
29294560 ATTTATATTTTTTGTTTTTGGTTGG
1 ATTTATATTTTTTGTTTTTGGTTGG
*
29294585 ATTTGTATTTTTTGTTTTTGGTTG
1 ATTTATATTTTTTGTTTTTGGTTG
29294609 TTACAGGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.69
Consensus pattern (25 bp):
ATTTATATTTTTTGTTTTTGGTTGG
Found at i:29294845 original size:86 final size:86
Alignment explanation
Indices: 29294750--29295020 Score: 290
Period size: 86 Copynumber: 3.2 Consensus size: 86
29294740 ACACGACATT
* * ** * * * *
29294750 TAGCGGCATTTTTAGTAAAAGCATCACTAAAGGTCATGTTCTATAGCAACGTTTGTTGGACAAGC
1 TAGCGGCATTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGTTTGTGGGAAAAGC
* *
29294815 GCCACTAAAGGTCATGTTCTT
66 GCTACTAAAGGTCATGTTCTA
* * * * * *
29294836 TAGCGGCATTTGTGGGAGAAGCGCCGCTAAATGTCATGTTCTTTAGCGGCATTTGTGGGAAAAGC
1 TAGCGGCATTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGTTTGTGGGAAAAGC
*
29294901 GCTACTAAAGGTCTTGTTCTA
66 GCTACTAAAGGTCATGTTCTA
* * * * * *
29294922 TAGTGGCGTTTTTGGGAAAGGCGCCGCTAAAGCTCATGTTCTATAACAGTGTTTGTGGGAAAAGC
1 TAGCGGCATTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGTTTGTGGGAAAAGC
** *
29294987 ATTGCTAAAGGTCATGTTCTA
66 GCTACTAAAGGTCATGTTCTA
* *
29295008 TAGAGGCGTTTTT
1 TAGCGGCATTTTT
29295021 TCAAATAAAC
Statistics
Matches: 151, Mismatches: 34, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 151 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (86 bp):
TAGCGGCATTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCAGCGTTTGTGGGAAAAGC
GCTACTAAAGGTCATGTTCTA
Found at i:29294848 original size:43 final size:43
Alignment explanation
Indices: 29294748--29294963 Score: 211
Period size: 43 Copynumber: 5.0 Consensus size: 43
29294738 GAACACGACA
* **
29294748 TTTAGCGGCATTT-TTAGTAAAAGCATCACTAAAGGTCATGTTC
1 TTTAGCGGCATTTGTT-GGAAAAGCGCCACTAAAGGTCATGTTC
* ** * *
29294791 TATAGCAACGTTTGTTGGACAAGCGCCACTAAAGGTCATGTTC
1 TTTAGCGGCATTTGTTGGAAAAGCGCCACTAAAGGTCATGTTC
* * * *
29294834 TTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAATGTCATGTTC
1 TTTAGCGGCATTTGTTGGAAAAGCGCCACTAAAGGTCATGTTC
* * *
29294877 TTTAGCGGCATTTGTGGGAAAAGCGCTACTAAAGGTCTTGTTC
1 TTTAGCGGCATTTGTTGGAAAAGCGCCACTAAAGGTCATGTTC
* * * * * *
29294920 TATAGTGGCGTTT-TTGGGAAAGGCGCCGCTAAAGCTCATGTTC
1 TTTAGCGGCATTTGTT-GGAAAAGCGCCACTAAAGGTCATGTTC
29294963 T
1 T
29294964 ATAACAGTGT
Statistics
Matches: 141, Mismatches: 30, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
42 1 0.01
43 138 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCATTTGTTGGAAAAGCGCCACTAAAGGTCATGTTC
Found at i:29294964 original size:43 final size:42
Alignment explanation
Indices: 29294776--29295018 Score: 243
Period size: 43 Copynumber: 5.7 Consensus size: 42
29294766 AAAAGCATCA
** * *
29294776 CTAAAGGTCATGTTCTATAGCAACGTTTGTTGGACAAGCGCCA
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGA-AAGCGCCG
* *
29294819 CTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGAGAAGCGCCG
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGA-AAGCGCCG
* * * **
29294862 CTAAATGTCATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCTA
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGG-AAAGCGCCG
* * *
29294905 CTAAAGGTCTTGTTCTATAGTGGCGTTTTTGGGAAAGGCGCCG
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAA-GCGCCG
* * * * ***
29294948 CTAAAGCTCATGTTCTATAACAGTGTTTGTGGGAAAAGCATTG
1 CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGG-AAAGCGCCG
*
29294991 CTAAAGGTCATGTTCTATAGAGGCGTTT
1 CTAAAGGTCATGTTCTATAGCGGCGTTT
29295019 TTTCAAATAA
Statistics
Matches: 164, Mismatches: 33, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
42 3 0.02
43 157 0.96
44 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
CTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAGCGCCG
Found at i:29294978 original size:129 final size:129
Alignment explanation
Indices: 29294748--29295006 Score: 290
Period size: 129 Copynumber: 2.0 Consensus size: 129
29294738 GAACACGACA
* *
29294748 TTTAGCGGCATTTTTAGTAAAAGCATCACTAAAGGTCATGTTCTATAGCAACGTTTGTTGGACAA
1 TTTAGCGGCATTTGTAGGAAAAGCATCACTAAAGGTCATGTTCTATAGCAACGTTTGTTGGACAA
* * * * * * *
29294813 GCGCCACTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAATGTCATGTTC
66 GCGCCACTAAAGCTCATGTTCTATAACAGCATTTGTGGGAAAAGCACCGCTAAAGGTCATGTTC
* * * ***
29294877 TTTAGCGGCATTTGTGGGAAAAGC-GCTACTAAAGGTCTTGTTCTATAGTGGCGTTT-TTGGGA-
1 TTTAGCGGCATTTGTAGGAAAAGCATC-ACTAAAGGTCATGTTCTATAGCAACGTTTGTT-GGAC
* ** **
29294939 AAGGCGCCGCTAAAGCTCATGTTCTATAACAGTGTTTGTGGGAAAAGCATTGCTAAAGGTCATGT
64 AA-GCGCCACTAAAGCTCATGTTCTATAACAGCATTTGTGGGAAAAGCACCGCTAAAGGTCATGT
29295004 TC
128 TC
29295006 T
1 T
29295007 ATAGAGGCGT
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
128 5 0.05
129 102 0.95
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (129 bp):
TTTAGCGGCATTTGTAGGAAAAGCATCACTAAAGGTCATGTTCTATAGCAACGTTTGTTGGACAA
GCGCCACTAAAGCTCATGTTCTATAACAGCATTTGTGGGAAAAGCACCGCTAAAGGTCATGTTC
Found at i:29298227 original size:93 final size:93
Alignment explanation
Indices: 29298120--29298290 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
29298110 GCCCCTAAGT
* *
29298120 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29298185 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
29298213 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29298278 CGAGTTCGGATGC
66 CGAGTTCGGATGC
29298291 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:29298287 original size:46 final size:46
Alignment explanation
Indices: 29298115--29298287 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
29298105 AACCCGCCCC
* * *
29298115 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
29298161 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
29298209 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
29298254 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29298288 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:29298743 original size:30 final size:30
Alignment explanation
Indices: 29298709--29298768 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
29298699 CCTTAATACG
29298709 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
29298739 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
29298769 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:29300896 original size:21 final size:20
Alignment explanation
Indices: 29300872--29300910 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
29300862 GAGTATTTTG
29300872 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAG-TTATGA
29300893 ATGTTTGATGATAGTTAT
1 ATGTTTGATGATAGTTAT
29300911 ACAAGTTTTG
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:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (20 bp):
ATGTTTGATGATAGTTATGA
Found at i:29300920 original size:21 final size:21
Alignment explanation
Indices: 29300872--29300918 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29300862 GAGTATTTTG
*
29300872 ATGTTTGATGATAGATTATGA
1 ATGTTTGATGATAGATTATCA
29300893 ATGTTTGATGATAG-TTATACA
1 ATGTTTGATGATAGATTAT-CA
29300914 A-GTTT
1 ATGTTT
29300919 TGTTAAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (21 bp):
ATGTTTGATGATAGATTATCA
Found at i:29306997 original size:27 final size:27
Alignment explanation
Indices: 29306944--29307002 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
29306934 TAATGGATGG
* *
29306944 AAATTACCGTAATGCCTTCGTAAGGTA
1 AAATGACCGTAATGCCCTCGTAAGGTA
*
29306971 AAATGACCGTAATGCCC-CTGTAGGGTA
1 AAATGACCGTAATGCCCTC-GTAAGGTA
29306998 AAATG
1 AAATG
29307003 GCAAGTATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
AAATGACCGTAATGCCCTCGTAAGGTA
Found at i:29308540 original size:27 final size:27
Alignment explanation
Indices: 29308510--29308687 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
29308500 ATATTGAGCC
* * * *
29308510 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
29308537 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29308564 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
29308592 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
29308619 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
29308646 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
29308673 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29308688 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:29308649 original size:82 final size:81
Alignment explanation
Indices: 29308531--29308686 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
29308521 TGCTATATAA
* *
29308531 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
29308596 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
29308613 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
29308677 CACTTAGTGC
65 CACTTAGTGC
29308687 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:29318298 original size:27 final size:27
Alignment explanation
Indices: 29318268--29318444 Score: 144
Period size: 27 Copynumber: 6.5 Consensus size: 27
29318258 ATATTGAGCC
* * *
29318268 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCCACATAATCAACT
* * *
29318295 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCCACATAATCAACT
* *
29318322 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCCACATAAT-CAACT
* ** *
29318350 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCCACATAATCAACT
* **
29318377 CGCACACTTAGTG-CATCATATTCATTT
1 CGCACACTTAGTGCCA-CATAATCAACT
* *
29318404 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCCACATAA-TCA-ACT
29318431 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29318445 TGTACAATTT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
26 3 0.02
27 95 0.78
28 24 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCCACATAATCAACT
Found at i:29320925 original size:14 final size:14
Alignment explanation
Indices: 29320906--29320933 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29320896 AAGGGTTTTA
29320906 AGTTAATTTCGAAT
1 AGTTAATTTCGAAT
29320920 AGTTAATTTCGAAT
1 AGTTAATTTCGAAT
29320934 TTCTAACGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
AGTTAATTTCGAAT
Found at i:29321331 original size:48 final size:48
Alignment explanation
Indices: 29321193--29321371 Score: 183
Period size: 48 Copynumber: 3.9 Consensus size: 48
29321183 GGTTATGTGC
* *
29321193 GATCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* **** * *
29321241 AATTTTGTGTAAGACCATAGT-TGGG-C-T---ATCGGCATCGCTATGT
1 GATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGT
*
29321284 GCTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * *
29321332 GATCCCATGTAAGCCCATATCT-GGATATGGCATTGGCATC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
29321372 CTACCATGTG
Statistics
Matches: 105, Mismatches: 19, Indels: 15
0.76 0.14 0.11
Matches are distributed among these distances:
42 2 0.02
43 29 0.28
44 1 0.01
45 1 0.01
46 1 0.01
47 18 0.17
48 51 0.49
49 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:29323031 original size:27 final size:27
Alignment explanation
Indices: 29322995--29323607 Score: 442
Period size: 27 Copynumber: 22.8 Consensus size: 27
29322985 TACCCCTGAT
** *
29322995 TTGTAAAATTATCGAAATATACTCGGA
1 TTGTAAAATTATCGAAATACCCTCAGA
* * *
29323022 TTGTAAAATTACCAAAATACCC-CTGA
1 TTGTAAAATTATCGAAATACCCTCAGA
*
29323048 TTTGTAAAATTATCGAAATACCCTTAGA
1 -TTGTAAAATTATCGAAATACCCTCAGA
*
29323076 TTGTAAAATTATCGAAATACCC-CTAGT
1 TTGTAAAATTATCGAAATACCCTC-AGA
* * *
29323103 TTGTAGAATTATCGAAATACCCTCGGC
1 TTGTAAAATTATCGAAATACCCTCAGA
*
29323130 TTGTAAAATTAAT-GAAATACCC-CCGA
1 TTGTAAAATT-ATCGAAATACCCTCAGA
* * * *
29323156 TTTGTAAAATTACCAAAACACCCTTAGA
1 -TTGTAAAATTATCGAAATACCCTCAGA
* *
29323184 TTGTAAAATTATCGAAATACCCCCAGT
1 TTGTAAAATTATCGAAATACCCTCAGA
29323211 TTGTAAAATTA-CAGAAATACCC-CA-A
1 TTGTAAAATTATC-GAAATACCCTCAGA
*
29323236 TTTGTAAAATTATCGAAATACCCT-TGA
1 -TTGTAAAATTATCGAAATACCCTCAGA
* * * *
29323263 TTTGTAAAACTACCAAAATACCCTCAGT
1 -TTGTAAAATTATCGAAATACCCTCAGA
* * *
29323291 TTATAAAATTACCAAAATACCC-CTA-A
1 TTGTAAAATTATCGAAATACCCTC-AGA
* * *
29323317 TTTGTAAAATTACCGAAATACCCCCAGT
1 -TTGTAAAATTATCGAAATACCCTCAGA
* * *
29323345 TTGTAAAATTACCAAAATACCC-CCGA
1 TTGTAAAATTATCGAAATACCCTCAGA
* * * * *
29323371 TTTATAAAATTAT-TAAAAACCC-CTGGT
1 -TTGTAAAATTATCGAAATACCCTC-AGA
*
29323398 TTGTAAAATTATCAAAATACCC-CTA-A
1 TTGTAAAATTATCGAAATACCCTC-AGA
*
29323424 TTTGTAAAATTATCAAAATACCC-CTA-A
1 -TTGTAAAATTATCGAAATACCCTC-AGA
* * *
29323451 TTTGTAAAAGTACCAAAATACCCTCA-A
1 -TTGTAAAATTATCGAAATACCCTCAGA
*
29323478 TTTGTAAAATTA-CTAAAATACCCTCAGA
1 -TTGTAAAATTATC-GAAATACCCTCAGA
* *
29323506 TTATAAAATTATCGAAATA-CCTCTGA
1 TTGTAAAATTATCGAAATACCCTCAGA
* * * *
29323532 TTTATAAAATTACCGAAATACCCTCGGT
1 -TTGTAAAATTATCGAAATACCCTCAGA
*
29323560 TTGTAAAATTATCGAAATACCCT-TGTA
1 TTGTAAAATTATCGAAATACCCTCAG-A
*
29323587 GTGTAAAATTATCG-AATACCC
1 TTGTAAAATTATCGAAATACCC
29323608 CTGTAGGGTA
Statistics
Matches: 488, Mismatches: 69, Indels: 59
0.79 0.11 0.10
Matches are distributed among these distances:
26 66 0.14
27 405 0.83
28 17 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
TTGTAAAATTATCGAAATACCCTCAGA
Found at i:29323067 original size:54 final size:54
Alignment explanation
Indices: 29322978--29323607 Score: 586
Period size: 54 Copynumber: 11.7 Consensus size: 54
29322968 ATCTCTGTTA
* ** *
29322978 ATCAAACTACCCCTGATTTGTAAAATTATCGAAATATACTCGGATTGTAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* *
29323032 ACCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTTAGATTGTAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* * * *
29323086 ATCGAAATACCCCT-AGTTTGTAGAATTATCGAAATACCCTCGGCTTGTAAAATT
1 ATCAAAATACCCCTGA-TTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* * * * * *
29323140 AAT-GAAATACCCCCGATTTGTAAAATTACCAAAACACCCTTAGATTGTAAAATT
1 -ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* *
29323194 ATCGAAATACCCC-CAGTTTGTAAAATTA-CAGAAATACCC-CA-ATTTGTAAAATT
1 ATCAAAATACCCCTGA-TTTGTAAAATTATC-GAAATACCCTCAGA-TTGTAAAATT
* * * * * * *
29323247 ATCGAAATACCCTTGATTTGTAAAACTACCAAAATACCCTCAGTTTATAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* * * * *
29323301 ACCAAAATACCCCTAATTTGTAAAATTACCGAAATACCCCCAGTTTGTAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* * * * * * *
29323355 ACCAAAATACCCCCGATTTATAAAATTAT-TAAAAACCC-CTGGTTTGTAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTC-AGATTGTAAAATT
* * *
29323408 ATCAAAATACCCCTAATTTGTAAAATTATCAAAATACCC-CTA-ATTTGTAAAAGT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTC-AGA-TTGTAAAATT
* * * *
29323462 ACCAAAATA-CCCTCAATTTGTAAAATTA-CTAAAATACCCTCAGATTATAAAATT
1 ATCAAAATACCCCT-GATTTGTAAAATTATC-GAAATACCCTCAGATTGTAAAATT
* * * * * *
29323516 ATCGAAATACCTCTGATTTATAAAATTACCGAAATACCCTCGGTTTGTAAAATT
1 ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
* * *
29323570 ATCGAAATACCCTTG-TAGTGTAAAATTATCG-AATACCC
1 ATCAAAATACCCCTGAT-TTGTAAAATTATCGAAATACCC
29323608 CTGTAGGGTA
Statistics
Matches: 484, Mismatches: 71, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
52 2 0.00
53 104 0.21
54 369 0.76
55 9 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.30
Consensus pattern (54 bp):
ATCAAAATACCCCTGATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATT
Found at i:29323093 original size:81 final size:82
Alignment explanation
Indices: 29322992--29323610 Score: 549
Period size: 81 Copynumber: 7.7 Consensus size: 82
29322982 AACTACCCCT
** * *
29322992 GATTTGTAAAATTATCGAAATATACTCGGATTGTAAAATTACCAAAATACCCCTGATTTGTAAAA
1 GATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATTATCAAAATACCCCTGATTTGTAAAA
* *
29323057 TTATCGAAATACCCTTA
66 TTACCGAAATACCCTCA
* * * **
29323074 GA-TTGTAAAATTATCGAAATACCC-CTAGTTTGTAGAATTATCGAAATA-CCCTCGGCTTGTAA
1 GATTTGTAAAATTATCGAAATACCCTC-AGATTGTAAAATTATCAAAATACCCCT-GATTTGTAA
** *
29323136 AATTAATGAAATACCC-CC
64 AATTACCGAAATACCCTCA
* * * * * *
29323154 GATTTGTAAAATTACCAAAACACCCTTAGATTGTAAAATTATCGAAATACCCC-CAGTTTGTAAA
1 GATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATTATCAAAATACCCCTGA-TTTGTAAA
*
29323218 ATTACAGAAATACCC-CA
65 ATTACCGAAATACCCTCA
* * * * *
29323235 -ATTTGTAAAATTATCGAAATACCCT-TGATTTGTAAAACTACCAAAATA-CCCTCAGTTTATAA
1 GATTTGTAAAATTATCGAAATACCCTCAGA-TTGTAAAATTATCAAAATACCCCTGA-TTTGTAA
*
29323297 AATTACCAAAATACCC-CTA
64 AATTACCGAAATACCCTC-A
* * * * * *
29323316 -ATTTGTAAAATTACCGAAATACCCCCAGTTTGTAAAATTACCAAAATACCCCCGATTTATAAAA
1 GATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATTATCAAAATACCCCTGATTTGTAAAA
** * *
29323380 TTA-TTAAAAACCC-CT
66 TTACCGAAATACCCTCA
* * *
29323395 GGTTTGTAAAATTATCAAAATACCC-CTA-ATTTGTAAAATTATCAAAATACCCCTAATTTGTAA
1 GATTTGTAAAATTATCGAAATACCCTC-AGA-TTGTAAAATTATCAAAATACCCCTGATTTGTAA
* *
29323458 AAGTACCAAAATACCCTCA
64 AATTACCGAAATACCCTCA
* * * * *
29323477 -ATTTGTAAAATTA-CTAAAATACCCTCAGATTATAAAATTATCGAAATACCTCTGATTTATAAA
1 GATTTGTAAAATTATC-GAAATACCCTCAGATTGTAAAATTATCAAAATACCCCTGATTTGTAAA
29323540 ATTACCGAAATACCCTC-
65 ATTACCGAAATACCCTCA
* * * *
29323557 GGTTTGTAAAATTATCGAAATACCCT-TGTAGTGTAAAATTATC-GAATACCCCTG
1 GATTTGTAAAATTATCGAAATACCCTCAG-ATTGTAAAATTATCAAAATACCCCTG
29323611 TAGGGTAAAA
Statistics
Matches: 441, Mismatches: 74, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
79 6 0.01
80 143 0.32
81 278 0.63
82 14 0.03
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (82 bp):
GATTTGTAAAATTATCGAAATACCCTCAGATTGTAAAATTATCAAAATACCCCTGATTTGTAAAA
TTACCGAAATACCCTCA
Found at i:29324004 original size:22 final size:22
Alignment explanation
Indices: 29323976--29324023 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
29323966 TCTGATTATG
29323976 GCCAACCTAAATATGGCTTTGT
1 GCCAACCTAAATATGGCTTTGT
29323998 GCCAACCTAAATATGGCTTTGT
1 GCCAACCTAAATATGGCTTTGT
29324020 GCCA
1 GCCA
29324024 TCTTGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (22 bp):
GCCAACCTAAATATGGCTTTGT
Found at i:29324158 original size:32 final size:32
Alignment explanation
Indices: 29324113--29324185 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
29324103 ATATTTACCC
* *
29324113 ATGGCTGTATGCCGGTCATATTACAGCTACTG
1 ATGGCTGTATGCCGATCAAATTACAGCTACTG
* * * *
29324145 ATGGCTTTGTGCCGATCAAATTACCGCTATTG
1 ATGGCTGTATGCCGATCAAATTACAGCTACTG
29324177 ATGGCTGTA
1 ATGGCTGTA
29324186 AGGCGTGTAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (32 bp):
ATGGCTGTATGCCGATCAAATTACAGCTACTG
Found at i:29324463 original size:28 final size:28
Alignment explanation
Indices: 29324417--29324472 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
29324407 TTTATTCTGA
* *
29324417 TACTGTATTGGACTTAGGCCCACACTGT
1 TACTATATTGGACTAAGGCCCACACTGT
*
29324445 TACTATATTGGGCTAAGGCCCACACTGT
1 TACTATATTGGACTAAGGCCCACACTGT
29324473 GCTGTTACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (28 bp):
TACTATATTGGACTAAGGCCCACACTGT
Found at i:29325832 original size:42 final size:42
Alignment explanation
Indices: 29325770--29325859 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
29325760 ATCCTAATTG
29325770 GAAATATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
1 GAAA-ATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
* *
29325813 GAAAATAGTTCCCTTATTCTAATCAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
*
29325855 TAAAA
1 GAAAA
29325860 ATGTTCCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 40 0.91
43 4 0.09
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
Found at i:29330572 original size:42 final size:42
Alignment explanation
Indices: 29330510--29330590 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
29330500 TAATTGGGAA
*
29330510 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAG
1 AATAGTTCCCTTATTATAATAAACTACTAAAACATAAAAGAG
*
29330552 AATAGTTCCCTTATTATAATAAACTACTAAAAGATAAAA
1 AATAGTTCCCTTATTATAATAAACTACTAAAACATAAAA
29330591 TAAAAAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (42 bp):
AATAGTTCCCTTATTATAATAAACTACTAAAACATAAAAGAG
Found at i:29336057 original size:48 final size:48
Alignment explanation
Indices: 29335866--29336093 Score: 189
Period size: 48 Copynumber: 4.9 Consensus size: 48
29335856 GGTTATGGAA
* * *
29335866 GATCCCATGTAAGACCATGTCTGGAACATGGCTTTGGCATCAATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* ** * * * * *
29335914 AATTTCGTGTAAAACCATAG-CTAGG-C-T---ATTGACATTGATATGT
1 GATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGT
* * * ** **
29335957 GATCCCATGTAAGACCATTTCTAGGACATGGCATTGGCATTGACCTAC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
*
29336005 GATCCCATGTAATACCATGTCTGGGACATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
* * * * *
29336053 GATCCCATGTGAGACCATATCCGGGATATGGCATTGACATC
1 GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
29336094 CTACCATGTG
Statistics
Matches: 137, Mismatches: 36, Indels: 14
0.73 0.19 0.07
Matches are distributed among these distances:
43 30 0.22
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 102 0.74
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (48 bp):
GATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGT
Found at i:29336810 original size:154 final size:153
Alignment explanation
Indices: 29336611--29336907 Score: 497
Period size: 154 Copynumber: 1.9 Consensus size: 153
29336601 GAGACACGGC
*
29336611 CGTGTGTCTCAGTCGTGTGAAGTCTGCACTTGATTTTTGGAATTTAATTCACCACACGGCCTAAG
1 CGTGTGTCTCAGCCGTGTGAAGTCTGCACTTGATTTTTGGAATTTAATTCACCACACGGCCTAAG
*
29336676 CACATAGACGTGTGACTTGGCCATGTGACCCTAATTATGTTGATGACGTCACAAATAGAGAGTTA
66 CACATAGACGTGTGACTTGGCCATGTGACCCTAATTATGTTGATGACGTCACAAACAGAGAGTTA
29336741 CACGCGCTGAGGAAGCCACATGGA
131 CACGCGCTG-GGAAGCCACATGGA
*
29336765 CGTGTGTCT-AGGCCGTGTGAAGTCTGCACTTGATTTTTGGAATTTAATTCGCCACACGGCCTAA
1 CGTGTGTCTCA-GCCGTGTGAAGTCTGCACTTGATTTTTGGAATTTAATTCACCACACGGCCTAA
* * * *
29336829 GCACATGGATGTGTGACTTGGCCATGTGACCCTAATTGTGTTGATGACGTCATAAACAGAGAGTT
65 GCACATAGACGTGTGACTTGGCCATGTGACCCTAATTATGTTGATGACGTCACAAACAGAGAGTT
*
29336894 ACGCGCGCTGGGAA
130 ACACGCGCTGGGAA
29336908 CTATGTCCCA
Statistics
Matches: 134, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
153 5 0.04
154 129 0.96
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (153 bp):
CGTGTGTCTCAGCCGTGTGAAGTCTGCACTTGATTTTTGGAATTTAATTCACCACACGGCCTAAG
CACATAGACGTGTGACTTGGCCATGTGACCCTAATTATGTTGATGACGTCACAAACAGAGAGTTA
CACGCGCTGGGAAGCCACATGGA
Found at i:29336936 original size:20 final size:20
Alignment explanation
Indices: 29336911--29336953 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
29336901 CTGGGAACTA
*
29336911 TGTCCCAAGCCACATGGTCG
1 TGTCCCAAGCCACATGGACG
29336931 TGTCCCAAGCCACATGGACG
1 TGTCCCAAGCCACATGGACG
29336951 TGT
1 TGT
29336954 GTAACCACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (20 bp):
TGTCCCAAGCCACATGGACG
Found at i:29349115 original size:18 final size:19
Alignment explanation
Indices: 29349092--29349142 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
29349082 TTTAAGGACT
29349092 AAATTTA-ATAAAAACGTA
1 AAATTTAGATAAAAACGTA
* *
29349110 AAATTTAGGCTAAAAATGTA
1 AAATTTA-GATAAAAACGTA
*
29349130 AAATTTTGATAAA
1 AAATTTAGATAAA
29349143 GTGTTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.26
19 5 0.19
20 15 0.56
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (19 bp):
AAATTTAGATAAAAACGTA
Found at i:29349781 original size:13 final size:14
Alignment explanation
Indices: 29349765--29349801 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
29349755 GAAAAATAAA
29349765 TATATGAAAT-GGT
1 TATATGAAATCGGT
29349778 TATATG-AATCGGT
1 TATATGAAATCGGT
29349791 TATATGGAAAT
1 TATAT-GAAAT
29349802 AGATATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 1 0.05
15 3 0.14
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (14 bp):
TATATGAAATCGGT
Found at i:29352363 original size:232 final size:232
Alignment explanation
Indices: 29351957--29352420 Score: 910
Period size: 232 Copynumber: 2.0 Consensus size: 232
29351947 GGTTTCCAAC
*
29351957 CTAAGCCAATACATATGGCCAAACCTCAGTGACCCAAAATAATAAAGTCTAAGTCCTATACATGC
1 CTAAGCCAATACATATGGCCAAACCTCAGTGACACAAAATAATAAAGTCTAAGTCCTATACATGC
29352022 CATATTCAAAAATATAAATCCAACTATACCAAATGCTTCAGTTGAGAGTGTGATCGATATATCTG
66 CATATTCAAAAATATAAATCCAACTATACCAAATGCTTCAGTTGAGAGTGTGATCGATATATCTG
29352087 ACTTCCGGTAATCCTTGAGCTAGTTAGGCGGCACTGTAAGGAAATGAAAAGGGAAGGGAGTAAGC
131 ACTTCCGGTAATCCTTGAGCTAGTTAGGCGGCACTGTAAGGAAATGAAAAGGGAAGGGAGTAAGC
29352152 ATAACAACTTAGTAAGTTGCATATAAGTAAGTATACA
196 ATAACAACTTAGTAAGTTGCATATAAGTAAGTATACA
29352189 CTAAGCCAATACATATGGCCAAACCTCAGTGACACAAAATAATAAAGTCTAAGTCCTATACATGC
1 CTAAGCCAATACATATGGCCAAACCTCAGTGACACAAAATAATAAAGTCTAAGTCCTATACATGC
29352254 CATATTCAAAAATATAAATCCAACTATACCAAATGCTTCAGTTGAGAGTGTGATCGATATATCTG
66 CATATTCAAAAATATAAATCCAACTATACCAAATGCTTCAGTTGAGAGTGTGATCGATATATCTG
*
29352319 ACTTCCGGTGATCCTTGAGCTAGTTAGGCGGCACTGTAAGGAAATGAAAAGGGAAGGGAGTAAGC
131 ACTTCCGGTAATCCTTGAGCTAGTTAGGCGGCACTGTAAGGAAATGAAAAGGGAAGGGAGTAAGC
29352384 ATAACAACTTAGTAAGTTGCATATAAGTAAGTATACA
196 ATAACAACTTAGTAAGTTGCATATAAGTAAGTATACA
29352421 ACAACAATTT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 230 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (232 bp):
CTAAGCCAATACATATGGCCAAACCTCAGTGACACAAAATAATAAAGTCTAAGTCCTATACATGC
CATATTCAAAAATATAAATCCAACTATACCAAATGCTTCAGTTGAGAGTGTGATCGATATATCTG
ACTTCCGGTAATCCTTGAGCTAGTTAGGCGGCACTGTAAGGAAATGAAAAGGGAAGGGAGTAAGC
ATAACAACTTAGTAAGTTGCATATAAGTAAGTATACA
Found at i:29352770 original size:47 final size:47
Alignment explanation
Indices: 29352664--29352929 Score: 190
Period size: 46 Copynumber: 5.7 Consensus size: 47
29352654 AGGGTAAGGT
* *
29352664 GCCGATGCCATGTCCTGGACATGGTCTTACACTGGCTCAT-ATCTCAA
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCT-ATCATCTCGA
** * * *
29352711 GTTGATGCCATGTTCTAGACATGGTATTACACTGACTATCATCTCGTA
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTCG-A
*
29352759 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGA
1 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTAT-CATCTCGA
* * * * ** * *
29352804 GGCCGATG-CATGCCCCAAACAT-GTCTTATACTGGCCCTCGTCTCAA
1 -GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTCGA
* * * * * * *
29352850 TGTCGATGCTATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT-GTG
1 -GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCAT-CTCG-A
*
29352899 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCTAGACATGGTCTTACACT
29352930 AGCTCACACA
Statistics
Matches: 176, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
45 2 0.01
46 73 0.41
47 73 0.41
48 27 0.15
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTATCATCTCGA
Found at i:29352802 original size:46 final size:47
Alignment explanation
Indices: 29352664--29352929 Score: 199
Period size: 47 Copynumber: 5.7 Consensus size: 47
29352654 AGGGTAAGGT
** * *
29352664 GCCGATGCCATGTCCTGGACATGGTCTTACACTGGCTCATATCTC-AA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAA
** * * * * *
29352711 GTTGATGCCATGTTCTAGACATGGTATTACACTGAC-TATCATCTCGTA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTGGCTTA-CATCTCGAA
*
29352759 GCCGATGCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAA
* * * * *
29352805 GCCGATGCATGCCCCAAACAT-GTCTTATACTGGCCCT-CGTCTC-AA
1 GCCGATGCATGTCCCAGACATGGTCTTACACTGG-CTTACATCTCGAA
* * * **
29352850 TGTCGATGCTATGTCCCAGACATGGCCTTACACTGGCTCT-CATAAT-GTG
1 -GCCGATGC-ATGTCCCAGACATGGTCTTACACTGGCT-TACAT-CTCGAA
29352899 GCCGATGCATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCATGTCCCAGACATGGTCTTACACT
29352930 AGCTCACACA
Statistics
Matches: 174, Mismatches: 35, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 70 0.40
47 76 0.44
48 26 0.15
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGAA
Found at i:29359984 original size:21 final size:21
Alignment explanation
Indices: 29359958--29360001 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
29359948 AGTGTTAGAG
29359958 AACTTAGGCTCTAACACCACT
1 AACTTAGGCTCTAACACCACT
*
29359979 AACTTAGGCTCTAATACCACT
1 AACTTAGGCTCTAACACCACT
29360000 AA
1 AA
29360002 ATGAAACACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (21 bp):
AACTTAGGCTCTAACACCACT
Found at i:29360472 original size:21 final size:21
Alignment explanation
Indices: 29360448--29360489 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29360438 TACATACATT
29360448 TTAA-CATCGATGTATCAATAC
1 TTAAGCATCGA-GTATCAATAC
* *
29360469 TTAAGCCTCGAGTATCGATAC
1 TTAAGCATCGAGTATCAATAC
29360490 CTCTGTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (21 bp):
TTAAGCATCGAGTATCAATAC
Found at i:29377800 original size:14 final size:14
Alignment explanation
Indices: 29377781--29377812 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
29377771 CCATAACAAG
*
29377781 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTAC
29377795 TTTTTTTCTTTTAC
1 TTTTTTTCTTTTAC
29377809 TTTT
1 TTTT
29377813 GAAAATCGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTTTAC
Found at i:29377947 original size:15 final size:15
Alignment explanation
Indices: 29377909--29377941 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29377899 GCTATATTTA
*
29377909 TTAAAAGTTTTGTAT
1 TTAAAAATTTTGTAT
29377924 TTAAAAATTTT-TAT
1 TTAAAAATTTTGTAT
29377938 TTAA
1 TTAA
29377942 GTAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTAAAAATTTTGTAT
Found at i:29378411 original size:12 final size:11
Alignment explanation
Indices: 29378378--29378417 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29378368 TAAAATATTC
*
29378378 TTATATTAATT
1 TTATAATAATT
29378389 TTATAATAATT
1 TTATAATAATT
*
29378400 TATATTATAATT
1 T-TATAATAATT
29378412 TTATAA
1 TTATAA
29378418 ATATATTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATAATAATT
Found at i:29381045 original size:45 final size:45
Alignment explanation
Indices: 29380980--29381070 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
29380970 CCTGTCTTAA
* * *
29380980 AAGCTTGGTAAATATAGAAGGTGATCTTCAAATATATGCGATCCT
1 AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
* * *
29381025 AAGCTTGGCAAATATGGAAGGTGATCTTTAAAGATATATGATCCT
1 AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
29381070 A
1 A
29381071 GACATTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (45 bp):
AAGCTTGGCAAATATAGAAGGTGATCTTCAAAGATATACGATCCT
Found at i:29385282 original size:55 final size:55
Alignment explanation
Indices: 29385215--29385323 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
29385205 ATATGTGTAT
29385215 TAGCCGAAATGGAACTTGAATAATGATTTGAGCTCAATGTGTTGTATTGATATTC
1 TAGCCGAAATGGAACTTGAATAATGATTTGAGCTCAATGTGTTGTATTGATATTC
*
29385270 TAGCCGAGATGGAACTTGAATAATGATTTGAGCTCAATGTGTTGTATTGATATT
1 TAGCCGAAATGGAACTTGAATAATGATTTGAGCTCAATGTGTTGTATTGATATT
29385324 ATGTTTAAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (55 bp):
TAGCCGAAATGGAACTTGAATAATGATTTGAGCTCAATGTGTTGTATTGATATTC
Found at i:29386144 original size:40 final size:40
Alignment explanation
Indices: 29386100--29386258 Score: 207
Period size: 40 Copynumber: 4.0 Consensus size: 40
29386090 TCGATATATT
29386100 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
*
29386140 GTATA-CTCGGGTTAAATCCCGCAGGCTTCGTACTGGTAAA
1 GTATATC-CGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
* *
29386180 GTATATCCGGGTTAATTCCCGCAGGCTTAGTGCTGGT--A
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
* * * *
29386218 CTATATCCGGGCCTAAAGTCCCGCAGGCTTTGTGCTAGTAA
1 GTATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAA
29386259 CTGGATTCGG
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
38 11 0.11
39 4 0.04
40 88 0.85
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
Found at i:29393948 original size:40 final size:40
Alignment explanation
Indices: 29393904--29394062 Score: 196
Period size: 40 Copynumber: 4.0 Consensus size: 40
29393894 TCGATATATT
29393904 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
*
29393944 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAG
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
* * * *
29393984 GTATATCCGGGTTAATTCCCGTAGGCTTAGTGTTGGT--A
1 GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
* * * * *
29394022 CTATATCCGGGCCTAAAGTCCCGCAGGTTTTGTGCTAGTAA
1 GTATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAA
29394063 TTGGATTCGG
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 10 0.10
39 3 0.03
40 88 0.87
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (40 bp):
GTATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAAA
Found at i:29395413 original size:13 final size:14
Alignment explanation
Indices: 29395389--29395419 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
29395379 CCAGAATTGA
29395389 AGAAGAAAAAGAAG
1 AGAAGAAAAAGAAG
29395403 AGAAG-AAAAGAAG
1 AGAAGAAAAAGAAG
29395416 AGAA
1 AGAA
29395420 AGAATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAGAAG
Found at i:29396851 original size:44 final size:43
Alignment explanation
Indices: 29396803--29396960 Score: 164
Period size: 43 Copynumber: 3.7 Consensus size: 43
29396793 ATGTGATTTC
29396803 GTGTAAGACCACGTCTGGGACATTGGCATCGATTTGAGATTTAT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATTT-AGATTTAT
* * *
29396847 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGATTT-C
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATTTA-GATTTAT
* * **
29396889 GTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATTTGATAACAT
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTAGAT-TTAT
*
29396934 -T-TAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
29396961 TGTACAAGTT
Statistics
Matches: 95, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
42 29 0.31
43 33 0.35
44 33 0.35
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATTTAGATTTAT
Found at i:29404061 original size:30 final size:30
Alignment explanation
Indices: 29404005--29404061 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
29403995 ATTGACACAC
*
29404005 TTTTGCAAAATTTACAATTTTGCCCCTCTA
1 TTTTGCAAAATTTACAAATTTGCCCCTCTA
29404035 TTTTGTCAAAA-TTACCAAATTT-CCCCT
1 TTTTG-CAAAATTTA-CAAATTTGCCCCT
29404062 AGGCACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.28, C:0.25, G:0.05, T:0.42
Consensus pattern (30 bp):
TTTTGCAAAATTTACAAATTTGCCCCTCTA
Found at i:29423415 original size:47 final size:47
Alignment explanation
Indices: 29423357--29423466 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
29423347 TGGCCACGGA
* * * * * *
29423357 CCATGGTATAGGTATTTAGAGAGGAGTTACCTTGATTTGGCTACGTG
1 CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
* * *
29423404 CCATGGTATAGGTACTCCGAGATAAGTTACCTTGGTTTGACTAAGGG
1 CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
29423451 CCATGGTATAGGTACT
1 CCATGGTATAGGTACT
29423467 TATCGATTGT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (47 bp):
CCATGGTATAGGTACTCAGAGAGAAGTTACCTTGATTTGACTAAGGG
Found at i:29424764 original size:27 final size:27
Alignment explanation
Indices: 29424734--29424950 Score: 272
Period size: 27 Copynumber: 8.0 Consensus size: 27
29424724 TAGAATACTT
** *
29424734 TAGTTTACCAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
29424761 TAGTTTAAAAAATTACCAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
29424788 TGGTTTAAAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* * * *
29424815 TGGTTTGTAAAATTACTAAAATACCCT
1 TAGTTTATAAAATTACCAAAATACCCC
* *
29424842 TTGTTTATAAAATTACTAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
29424869 TGGTTTGTAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
* *
29424896 TAGTTTGTAAAATTATCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
*
29424923 TAGTTTGTAAAATTACCAAAATACCCC
1 TAGTTTATAAAATTACCAAAATACCCC
29424950 T
1 T
29424951 GATTTGTGAA
Statistics
Matches: 173, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 173 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (27 bp):
TAGTTTATAAAATTACCAAAATACCCC
Found at i:29424881 original size:81 final size:81
Alignment explanation
Indices: 29424743--29424975 Score: 324
Period size: 81 Copynumber: 2.9 Consensus size: 81
29424733 TTAGTTTACC
* * * **
29424743 AAATTACCAAAATACCCTTAGTTTAAAAAATTACCAAAATACCCTTGGTTTAAAAAATTACCAAA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
*
29424808 ATACCCCTGGTTTGTA
66 ATACCCCTAGTTTGTA
* *
29424824 AAATTACTAAAATACCCTTTGTTTATAAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAA
1 AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
29424889 ATACCCCTAGTTTGTA
66 ATACCCCTAGTTTGTA
* * * * **
29424905 AAATTA-TCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGA
1 AAATTACT-AAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAA
29424969 AATACCC
65 AATACCC
29424976 TCGACCTGTA
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
80 1 0.01
81 134 0.99
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATTACTAAAATACCCTTAGTTTATAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAA
ATACCCCTAGTTTGTA
Found at i:29424956 original size:27 final size:27
Alignment explanation
Indices: 29424743--29425035 Score: 267
Period size: 27 Copynumber: 10.9 Consensus size: 27
29424733 TTAGTTTACC
* **
29424743 AAATTACCAAAATA-CCCTTAGTTTAAA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* * **
29424770 AAATTACCAAAATACCCTTGGTTTAAA
1 AAATTACCAAAATACCCCTGATTTGTA
*
29424797 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
29424824 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCC-CTGATTTGTA
* *
29424851 AAATTACTAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
29424878 AAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
29424905 AAATTATCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
*
29424932 AAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
** **
29424959 AAATTACTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*** *
29424986 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*
29425013 AAATTACCAAAGTA-CCCTGATTT
1 AAATTACCAAAATACCCCTGATTT
29425036 ACAGAATTAC
Statistics
Matches: 232, Mismatches: 28, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
26 10 0.04
27 216 0.93
28 6 0.03
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:29424986 original size:81 final size:80
Alignment explanation
Indices: 29424743--29425035 Score: 295
Period size: 81 Copynumber: 3.6 Consensus size: 80
29424733 TTAGTTTACC
* * * * * **
29424743 AAATTACCAAAATACCCTTAGTTTAAAAAATTACCAAAATACCCTTGGTTTAAAAAATTACCAAA
1 AAATTATCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
*
29424808 ATACCCCTGGTTTGTA
66 ATACCCC-GATTTGTA
* * * *
29424824 AAATTA-CTAAAATACCCTTTGTTTATAAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAA
1 AAATTATC-AAAATACCCCTAGTTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAA
*
29424888 AATACCCCTAGTTTGTA
65 AATACCCCGA-TTTGTA
* * **
29424905 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAA
1 AAATTATCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
**
29424970 ATACCCTCGACCTGTA
66 ATACCC-CGATTTGTA
** * * * *
29424986 AAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTA-CCCTGATTT
1 AAATTATCAAAATACCCCTAG-TTTATAAAATTACCAAAATACCCCTGATTT
29425036 ACAGAATTAC
Statistics
Matches: 183, Mismatches: 24, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
80 15 0.08
81 165 0.90
82 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (80 bp):
AAATTATCAAAATACCCCTAGTTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
ATACCCCGATTTGTA
Found at i:29425073 original size:80 final size:79
Alignment explanation
Indices: 29424904--29425152 Score: 194
Period size: 81 Copynumber: 3.1 Consensus size: 79
29424894 CCTAGTTTGT
** * * **
29424904 AAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTT-GTGAAATTACTG
1 AAAATTATTGAAATA-CCCTCGATTGTAAAATTACCAAAATA-CCCTGATTTACAG-AATTACTG
*** * **
29424968 AAATACCCTCGACCTGT
63 TTTTACCCTCGACTTAA
* *
29424985 AAAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTGATTTACAGAATTACCGTT
1 AAAATTATTGAAATACCCTCGA-TTGTAAAATTACCAAAATACCCTGATTTACAGAATTACTGTT
29425050 TTACCCTCGACTTAA
65 TTACCCTCGACTTAA
*** * ***** *
29425065 AAAATTATTGTTTTACCCTCGATTGATAGAATTACTGTTTTACCCTCGATTTACAAAATTACTGT
1 AAAATTATTGAAATACCCTCGATTG-TAAAATTACCAAAATACCCT-GATTTACAGAATTACTGT
* * *
29425130 TTTACCCTTGATTTAC
64 TTTACCCTCGACTTAA
29425146 AAAATTA
1 AAAATTA
29425153 CTGTTTTATC
Statistics
Matches: 136, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
79 3 0.02
80 65 0.48
81 68 0.50
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (79 bp):
AAAATTATTGAAATACCCTCGATTGTAAAATTACCAAAATACCCTGATTTACAGAATTACTGTTT
TACCCTCGACTTAA
Found at i:29425077 original size:27 final size:27
Alignment explanation
Indices: 29425025--29425217 Score: 244
Period size: 27 Copynumber: 7.2 Consensus size: 27
29425015 ATTACCAAAG
* *
29425025 TACCCT-GATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29425051 TACCCTCGACTTAAAAAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29425078 TACCCTCGATTGATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
29425105 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
29425132 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
29425159 TATCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * **
29425186 TACCCTAGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
29425213 TACCC
1 TACCC
29425218 CTAGGGTGTT
Statistics
Matches: 143, Mismatches: 23, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
26 6 0.04
27 137 0.96
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:29425152 original size:81 final size:80
Alignment explanation
Indices: 29425025--29425217 Score: 269
Period size: 81 Copynumber: 2.4 Consensus size: 80
29425015 ATTACCAAAG
* *
29425025 TACCCTGATTTACAGAATTACCGTTTTACCCTCGACTTAAAAAATTATTGTTTTACCCTCGATTG
1 TACCCTGATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTGTTTTACCCTCGATTG
*
29425090 ATAGAATTACTGTTT
66 ACAGAATTACTGTTT
* * * * *
29425105 TACCCTCGATTTACAAAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTATCCTCGATT
1 TACCCT-GATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTGTTTTACCCTCGATT
*
29425170 TACAGAATTACTGTTT
65 GACAGAATTACTGTTT
* *
29425186 TACCCTAGATTTATAAAATTACCATTTTACCC
1 TACCCT-GATTTACAAAATTACCGTTTTACCC
29425218 CTAGGGTGTT
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
80 6 0.06
81 93 0.94
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.41
Consensus pattern (80 bp):
TACCCTGATTTACAAAATTACCGTTTTACCCTCGACTTAAAAAATTACTGTTTTACCCTCGATTG
ACAGAATTACTGTTT
Found at i:29425573 original size:26 final size:27
Alignment explanation
Indices: 29425544--29425603 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
29425534 CCACATATAT
*
29425544 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
29425570 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
29425597 ATATCTG
1 ATATCTG
29425604 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:29425789 original size:6 final size:6
Alignment explanation
Indices: 29425778--29425818 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
29425768 GTGTCACCTA
* *
29425778 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCT
29425819 AGTTTTGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.54
Consensus pattern (6 bp):
ATTCTG
Found at i:29430655 original size:38 final size:38
Alignment explanation
Indices: 29430612--29430690 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
29430602 ACCTACTAGT
29430612 TCATCTACACAACATTTACATACTCATGCAAACATATA
1 TCATCTACACAACATTTACATACTCATGCAAACATATA
*
29430650 TCATCTACACAACATTTACATACTCATGCAAGCATATA
1 TCATCTACACAACATTTACATACTCATGCAAACATATA
29430688 TCA
1 TCA
29430691 CATTTCACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.29
Consensus pattern (38 bp):
TCATCTACACAACATTTACATACTCATGCAAACATATA
Found at i:29432586 original size:48 final size:48
Alignment explanation
Indices: 29432491--29432740 Score: 387
Period size: 48 Copynumber: 5.2 Consensus size: 48
29432481 CCCAGACGGA
* * *
29432491 GTCTTACACGGGCACACATATCATCGT-GATGCCATGTCCCAGACATG
1 GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
* *
29432538 GT-TTGACACAGGCACATATATCATCGTCAATGCCATGTCCTAGGCATG
1 GTCTT-ACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
*
29432586 GTCTTACACAGGCACATATATCATCGCCGATGCCATGTCCTAGACATG
1 GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
* * *
29432634 GTCTTACAGAGGCACATTTATCATTGTCGATGCCATGTCCTAGACATG
1 GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
*
29432682 GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCCAGACATG
1 GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
29432730 GTCTTACACAG
1 GTCTTACACAG
29432741 ACATATTAGC
Statistics
Matches: 184, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
46 2 0.01
47 22 0.12
48 158 0.86
49 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (48 bp):
GTCTTACACAGGCACATATATCATCGTCGATGCCATGTCCTAGACATG
Found at i:29439143 original size:35 final size:35
Alignment explanation
Indices: 29439104--29439175 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
29439094 GTCTAGGATC
*
29439104 GCATATCTTTGAAGATCCCGTTCCATATTTGCCAA
1 GCATATCTTTGAAGATCACGTTCCATATTTGCCAA
* * *
29439139 GCATATCTTTGAAGATTACTTTCCATATTTTCCAA
1 GCATATCTTTGAAGATCACGTTCCATATTTGCCAA
29439174 GC
1 GC
29439176 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (35 bp):
GCATATCTTTGAAGATCACGTTCCATATTTGCCAA
Found at i:29446310 original size:48 final size:48
Alignment explanation
Indices: 29446025--29446310 Score: 391
Period size: 48 Copynumber: 6.0 Consensus size: 48
29446015 ATGAATCCAC
*
29446025 ATATCATCGCCGATGCCATGTCCCAGAC--GGTCTTACACT-GGCACAC
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACA-TAGGCACAT
* *
29446071 ATATCATCGCTGATGCCATGTCCCAGACATGGTCTTACACT-GGCACAC
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACA-TAGGCACAT
* * *
29446119 ATATCATCGCTGATGCCATGTCCTAGACATTGTCTTACATAGGCACAT
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAT
* *
29446167 ATATCATCGCCGATGCCATGTCCCAAACATGGTCTTACACAGGCACAT
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAT
* * * *
29446215 ATATCATCGCCGATGCCATGTCCAAGACATGGTATTACACAGACACAT
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAT
* * *
29446263 ATATCATCACCGATGTCATATCCCAGACATGGTCTTACATAGGCACAT
1 ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAT
29446311 TAGCACGGTG
Statistics
Matches: 217, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
46 27 0.12
47 1 0.00
48 189 0.87
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (48 bp):
ATATCATCGCCGATGCCATGTCCCAGACATGGTCTTACATAGGCACAT
Found at i:29454302 original size:24 final size:24
Alignment explanation
Indices: 29454260--29454319 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
29454250 TAAATTTGTG
*
29454260 AAATTA-AATAT-ATAATACCTTA
1 AAATTATAATATAATAATACCTAA
29454282 AAATT-TAGATATAATAATACCTAA
1 AAATTATA-ATATAATAATACCTAA
29454306 AAATTATAATATAA
1 AAATTATAATATAA
29454320 CATCTTTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 21 0.64
25 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATTATAATATAATAATACCTAA
Found at i:29459952 original size:44 final size:44
Alignment explanation
Indices: 29459879--29459985 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
29459869 TCTCAGATAG
* **
29459879 GGTCCTACTCGCACACATATATCGGAGTCACATATTGATGCCAT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAT
* *
29459923 GGTCTTACTTGCACACATATATCGGAGTCACATATCAATGCCCT
1 GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAT
*
29459967 GGTCTTACTCGTACACATA
1 GGTCTTACTCGCACACATA
29459986 AATTGGAATC
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (44 bp):
GGTCTTACTCGCACACATATATCGGAGTCACATATCAATGCCAT
Found at i:29464103 original size:22 final size:22
Alignment explanation
Indices: 29464075--29464121 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
29464065 ACTTGAAGAA
29464075 ATAGATTGACAAATATATATAT
1 ATAGATTGACAAATATATATAT
*
29464097 ATAGATTGACTAATATATATAT
1 ATAGATTGACAAATATATATAT
29464119 ATA
1 ATA
29464122 TATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (22 bp):
ATAGATTGACAAATATATATAT
Found at i:29464575 original size:22 final size:20
Alignment explanation
Indices: 29464549--29464591 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
29464539 AAATAACACA
29464549 AATATGAAAGCAATACAAAAAT
1 AATATGAAA--AATACAAAAAT
*
29464571 AATATTAAAAATACAAAAAT
1 AATATGAAAAATACAAAAAT
29464591 A
1 A
29464592 TAAGACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (20 bp):
AATATGAAAAATACAAAAAT
Found at i:29464601 original size:20 final size:20
Alignment explanation
Indices: 29464560--29464603 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29464550 ATATGAAAGC
**
29464560 AATACAAAAATAATATTAAA
1 AATACAAAAATAATAAGAAA
29464580 AATACAAAAAT-ATAAGACAA
1 AATACAAAAATAATAAGA-AA
29464600 AATA
1 AATA
29464604 ATACAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.20
Consensus pattern (20 bp):
AATACAAAAATAATAAGAAA
Found at i:29467605 original size:43 final size:43
Alignment explanation
Indices: 29467558--29467670 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
29467548 CCATATAACG
29467558 ATGCCAATGTCCTAGACATGGTCTTACATGTAATCA-CAATA-CA
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAT-ATC-ATACCA
* *
29467601 ATGCCAATGTCCCA-AGCATGGTCTTACATGTAATATCATACCG
1 ATGCCAATGTCCTAGA-CATGGTCTTACATGTAATATCATACCA
* *
29467644 ATGCC-ATATCCTAGATATGGTCTTACA
1 ATGCCAATGTCCTAGACATGGTCTTACA
29467671 CGTATTCTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
42 22 0.36
43 39 0.64
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGTAATATCATACCA
Found at i:29469000 original size:23 final size:25
Alignment explanation
Indices: 29468974--29469020 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29468964 TACCAAGCTT
29468974 TAAGCTAAAC-A-CATACCAAACAC
1 TAAGCTAAACTATCATACCAAACAC
*
29468997 TAAGCTAAGCTATCATACCAAACA
1 TAAGCTAAACTATCATACCAAACA
29469021 TAGCCTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.49, C:0.28, G:0.06, T:0.17
Consensus pattern (25 bp):
TAAGCTAAACTATCATACCAAACAC
Found at i:29471529 original size:34 final size:32
Alignment explanation
Indices: 29471491--29471556 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
29471481 ATTATTTCAA
29471491 TCATTGTAAAACGCAATCCAAA-TATATAAACAAT
1 TCATT-TAAAAC-CAA-CCAAATTATATAAACAAT
* *
29471525 TCATTTTAAACCAACCAAATTATATTAACAAT
1 TCATTTAAAACCAACCAAATTATATAAACAAT
29471557 ATAAGCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 14 0.48
33 5 0.17
34 5 0.17
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (32 bp):
TCATTTAAAACCAACCAAATTATATAAACAAT
Found at i:29472168 original size:56 final size:56
Alignment explanation
Indices: 29472082--29472211 Score: 260
Period size: 56 Copynumber: 2.3 Consensus size: 56
29472072 TCTTACATGT
29472082 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGG
1 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGG
29472138 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGG
1 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGG
29472194 AATCACATATCGATGCCA
1 AATCACATATCGATGCCA
29472212 TGGTCTTACT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (56 bp):
AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGG
Found at i:29477357 original size:42 final size:41
Alignment explanation
Indices: 29477299--29477391 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 41
29477289 TACTGAGTGA
* *
29477299 TCTCTTACGCGAGTCTCTAGCTTCAAAATCAGCTTTTCTCT
1 TCTCTTTCCCGAGTCTCTAGCTTCAAAATCAGCTTTTCTCT
*
29477340 TCTCTTTCCCNGAGTCTCTAGCTTCAAAATCAGCTTTTCTTT
1 TCTCTTTCCC-GAGTCTCTAGCTTCAAAATCAGCTTTTCTCT
29477382 TCTCTTTCCC
1 TCTCTTTCCC
29477392 TAGCTCTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 8 0.17
42 40 0.83
ACGTcount: A:0.16, C:0.31, G:0.10, T:0.42
Consensus pattern (41 bp):
TCTCTTTCCCGAGTCTCTAGCTTCAAAATCAGCTTTTCTCT
Found at i:29479121 original size:34 final size:32
Alignment explanation
Indices: 29479083--29479148 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
29479073 ATTATTTCAA
29479083 TCATTGTAAAACGCAATCCAAA-TATATAAACAAT
1 TCATT-TAAAAC-CAA-CCAAATTATATAAACAAT
* *
29479117 TCATTTTAAACCAACCAAATTATATTAACAAT
1 TCATTTAAAACCAACCAAATTATATAAACAAT
29479149 ATAAGCTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 14 0.48
33 5 0.17
34 5 0.17
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (32 bp):
TCATTTAAAACCAACCAAATTATATAAACAAT
Found at i:29479762 original size:56 final size:56
Alignment explanation
Indices: 29479676--29479805 Score: 260
Period size: 56 Copynumber: 2.3 Consensus size: 56
29479666 TCTTACATGT
29479676 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGA
1 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGA
29479732 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGA
1 AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGA
29479788 AATCACATATCGATGCCA
1 AATCACATATCGATGCCA
29479806 TGGTCTTACT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (56 bp):
AATCACATATCGATGCCACTGTCCCAGACAAGGTCTTACTCGCTCATATATGTCGA
Found at i:29480161 original size:23 final size:23
Alignment explanation
Indices: 29480131--29480199 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
29480121 CTTGATATAA
29480131 AAATATTCAAATTAAGATCATTC
1 AAATATTCAAATTAAGATCATTC
**
29480154 AAATATTC---TT--GAT-ATAA
1 AAATATTCAAATTAAGATCATTC
29480171 AAATATTCAAATTAAGATCATTC
1 AAATATTCAAATTAAGATCATTC
29480194 AAATAT
1 AAATAT
29480200 ATTTTCATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 10 0.28
18 3 0.08
20 4 0.11
22 3 0.08
23 16 0.44
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.36
Consensus pattern (23 bp):
AAATATTCAAATTAAGATCATTC
Found at i:29480163 original size:40 final size:40
Alignment explanation
Indices: 29480119--29480199 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
29480109 ATTTCTTTTG
29480119 TTCTTGATATAAAAATATTCAAATTAAGATCATTCAAATA
1 TTCTTGATATAAAAATATTCAAATTAAGATCATTCAAATA
29480159 TTCTTGATATAAAAATATTCAAATTAAGATCATTCAAATA
1 TTCTTGATATAAAAATATTCAAATTAAGATCATTCAAATA
29480199 T
1 T
29480200 ATTTTCATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (40 bp):
TTCTTGATATAAAAATATTCAAATTAAGATCATTCAAATA
Found at i:29481056 original size:13 final size:13
Alignment explanation
Indices: 29481022--29481047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29481012 ATATAAGTTC
29481022 ATAGAAAATAATT
1 ATAGAAAATAATT
29481035 ATAGAAAATAATT
1 ATAGAAAATAATT
29481048 TTTGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATAGAAAATAATT
Found at i:29483712 original size:80 final size:79
Alignment explanation
Indices: 29483555--29483714 Score: 207
Period size: 80 Copynumber: 2.0 Consensus size: 79
29483545 TGGATGATAA
* * * *
29483555 CCGGGCTAAGTCCGAAGGCATTTGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGTCCGAAGGCATTGGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTCGA
29483620 GCGAGTTACTATAT
66 GCGAGTTACTATAT
* * *
29483634 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTA-TATCCGGGCTATGTCCCGAAGGCATTC
1 CCGGGCTAAGT-CCGAAGGCATTGGCGCGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTC
*
29483698 GAGCTAG-TAGCTATAT
64 GAGCGAGTTA-CTATAT
29483714 C
1 C
29483715 TGGTGAAATC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 14 0.20
80 56 0.80
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGTCCGAAGGCATTGGCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTCGA
GCGAGTTACTATAT
Found at i:29483714 original size:40 final size:40
Alignment explanation
Indices: 29483555--29483696 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
29483545 TGGATGATAA
* * *
29483555 CCGGGCTAAGT-CCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
29483594 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29483634 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
29483674 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
29483697 CGAGCTAGTA
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 12 0.12
40 84 0.88
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:29491335 original size:31 final size:31
Alignment explanation
Indices: 29491294--29491465 Score: 154
Period size: 31 Copynumber: 5.6 Consensus size: 31
29491284 TAAGGTGTCC
29491294 ATCACCGGTACATAGTACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* *
29491325 ATCACTGGTACATAATACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* * * * * *
29491356 AACACTGGCATATAGTGCATGAT-AGAATATA
1 ATCACCGGTACATAGTACCTGATAAG-ATATA
* * * *
29491387 AACATCGGTATAAAGTACCTGAT-A-ATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
* * * *
29491416 GTCACCAGTATATAATACCTGATAAGATATA
1 ATCACCGGTACATAGTACCTGATAAGATATA
*
29491447 ATCACCGGCACATA-TACCT
1 ATCACCGGTACATAGTACCT
29491466 AATACTTTAA
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
29 22 0.19
30 8 0.07
31 84 0.74
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.27
Consensus pattern (31 bp):
ATCACCGGTACATAGTACCTGATAAGATATA
Found at i:29493191 original size:57 final size:57
Alignment explanation
Indices: 29493096--29493227 Score: 187
Period size: 57 Copynumber: 2.3 Consensus size: 57
29493086 AGTATTTTTA
*
29493096 ATTTTTCATTTTCATTTTGGAGAAAACCACATTAATTTCCAAATGATTT-CATTTCTCC
1 ATTTTT-ATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATG-TTTCCATTTCTCC
* *
29493154 ATTTTTATTTTCATTTTGGTA-AAAACCATAATCATTTCCAAATGTTTCCATTTCTCC
1 ATTTTTATTTTCATTTTGG-AGAAAACCACAATAATTTCCAAATGTTTCCATTTCTCC
*
29493211 ATTTTCATTTTCATTTT
1 ATTTTTATTTTCATTTT
29493228 CATTCTCATT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
56 3 0.04
57 58 0.85
58 7 0.10
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.49
Consensus pattern (57 bp):
ATTTTTATTTTCATTTTGGAGAAAACCACAATAATTTCCAAATGTTTCCATTTCTCC
Done.