Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 64 of 190
Found at i:18473869 original size:21 final size:21
Alignment explanation
Indices: 18473827--18473869 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
18473817 ACAGCAGAAC
*
18473827 AGGTTTTAGCGGCGTTTTTTT
1 AGGTTTTAGCGGCGTCTTTTT
18473848 AGGTCTTTAGCGGCG-CTTTTT
1 AGGT-TTTAGCGGCGTCTTTTT
18473869 A
1 A
18473870 ACGCCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.47
Consensus pattern (21 bp):
AGGTTTTAGCGGCGTCTTTTT
Found at i:18474145 original size:42 final size:42
Alignment explanation
Indices: 18473945--18474504 Score: 677
Period size: 43 Copynumber: 13.2 Consensus size: 42
18473935 ACTAACTTCT
*
18473945 GCGGCGCTTACGGAAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTA--GAAAAAAACGCCGCTAAAGATCATGCTCTTTA
18473989 GCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCTCTTTA
1 GCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGCTCTTTA
* *
18474032 GCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTA
1 GCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGCTCTTTA
*
18474075 GCGGCGCTTAG--AAAAACGCCCCTAAAGATCATGCTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
* *
18474115 GCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
* *
18474157 GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
* * ** * * * *
18474199 GCAGCGCTTTGGAAGGAAACGCCTCTAAA-AGTAATGTTCTATA
1 GCGGCGC-TTAGAAAAAAACGCCGCTAAAGA-TCATGCTCTTTA
*** * ***
18474242 GCGGCGCTTATTTCACAAACGTCACTG-TTTTGAT-ATGACT-TTTA
1 GCGGCGCTTA-GAAAAAAACG-C-C-GCTAAAGATCATG-CTCTTTA
18474286 GCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCTCTTTA
1 GCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGCTCTTTA
* *
18474329 GCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTA
1 GCGGCGCTTAGAAAA-AAACGCCGCTAAAGATCATGCTCTTTA
*
18474372 GCGGCGCTTAG--AAAAACGCCCCTAAAGATCATGCTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
* *
18474412 GCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
* *
18474454 GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTA
1 GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
18474496 GCGGCGCTT
1 GCGGCGCTT
18474505 TTTTCACAAA
Statistics
Matches: 454, Mismatches: 45, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
40 72 0.16
41 5 0.01
42 164 0.36
43 176 0.39
44 32 0.07
45 4 0.01
46 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (42 bp):
GCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGCTCTTTA
Found at i:18474316 original size:254 final size:253
Alignment explanation
Indices: 18473948--18474548 Score: 845
Period size: 254 Copynumber: 2.4 Consensus size: 253
18473938 AACTTCTGCG
* * **** *
18473948 GCGCTTACGGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAACAAACGCCG
1 GCGCTTA-GG-AAAAAACGCCGCTAAAGATAATGTTCTATAGCGGCGCTTATTTCACAAACGCCA
***
18474013 C--TAAAGATCATG-CTCTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTA
64 CTGTTTTGAT-ATGACT-TTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTA
* *
18474075 GCGGCGCTTAG-AA-AAACGCCCCTAAAGATCATGCTCTTTAGCGGCGCTTATAAAAAAACGCCG
127 GCGGCGCTTAGAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGC-T-TAAAAAAACGCCC
* *
18474138 CTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCA
190 CTAAAGATCATGCTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCA
* * * *
18474202 GCGCTTTGGAAGGAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATTTCACAAACGTCA
1 GCGCTTAGGAA-AAAACGCCGCTAAAGA-TAATGTTCTATAGCGGCGCTTATTTCACAAACGCCA
* *
18474266 CTGTTTTGATATGACTTTTAGCGGCGCTTAGAAAACAAACGCCGCTAAAGATCATGCTCTTTAGC
64 CTGTTTTGATATGACTTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGC
*
18474331 GGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAGAAAAACGCCCCTA
129 GGCGCTTAG-AAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAAAAAAACGCCCCTA
* *
18474396 AAGATCATGCTCTTTAGCGGCGCTTATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCG
193 AAGATCATGCTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCA
* * *
18474457 GCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTTCACAAACGCCACT
1 GCGCTTAGGAAAAAACGCCGCTAAAGATAATGTTCTATAGCGGCGCTTATTTCACAAACGCCACT
18474522 GTTTTGATATGACTTTTAGCGGCGCTT
66 GTTTTGATATGACTTTTAGCGGCGCTT
18474549 TTTAAAAAAA
Statistics
Matches: 308, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
252 3 0.01
253 43 0.14
254 138 0.45
255 88 0.29
256 3 0.01
257 33 0.11
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (253 bp):
GCGCTTAGGAAAAAACGCCGCTAAAGATAATGTTCTATAGCGGCGCTTATTTCACAAACGCCACT
GTTTTGATATGACTTTTAGCGGCGCTTAGAAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGG
CGCTTAGAAACAAACGCCCCTAAAGATCACGCTCTTTAGCGGCGCTTAAAAAAACGCCCCTAAAG
ATCATGCTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCA
Found at i:18474955 original size:12 final size:12
Alignment explanation
Indices: 18474925--18474984 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
18474915 TTTTGAACCT
* *
18474925 CTGCTTCTATTG
1 CTGCTTCTCTCG
*
18474937 CTTCTTCTCTCG
1 CTGCTTCTCTCG
18474949 CTGCTTCTCTCG
1 CTGCTTCTCTCG
**
18474961 CTGCGGC-CT--
1 CTGCTTCTCTCG
18474970 CTGCTTCTCTCG
1 CTGCTTCTCTCG
18474982 CTG
1 CTG
18474985 TGGCCTCTAC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 5 0.14
10 2 0.05
11 2 0.05
12 28 0.76
ACGTcount: A:0.02, C:0.38, G:0.18, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:18474975 original size:21 final size:21
Alignment explanation
Indices: 18474949--18475017 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
18474939 TCTTCTCTCG
18474949 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
*
18474970 CTGCTTCTCTCGCTGTGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
* * *
18474991 CTACTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCGGCCT
18475012 CTGCTT
1 CTGCTT
18475018 TAAGTTGCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.01, C:0.43, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGGCCT
Found at i:18498921 original size:17 final size:16
Alignment explanation
Indices: 18498899--18498932 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18498889 TTGACTACCC
18498899 AATTAAATTAATTCTAT
1 AATTAAATTAATT-TAT
*
18498916 AATTAATTTAATTTAT
1 AATTAAATTAATTTAT
18498932 A
1 A
18498933 TGACAACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAAATTAATTTAT
Found at i:18500967 original size:40 final size:40
Alignment explanation
Indices: 18500900--18500979 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
18500890 AAATAGTACG
*
18500900 AATTTCATGCAAGAAACAAGGGATTCATGCAAGAAAACAC
1 AATTTCATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
** *
18500940 AATTTCCATGCAAGAAGTAAGAG-TTCATGCAGGAAAACAC
1 AATTT-CATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
18500980 GTAAAATGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 21 0.60
41 14 0.40
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (40 bp):
AATTTCATGCAAGAAACAAGAGATTCATGCAAGAAAACAC
Found at i:18507231 original size:27 final size:27
Alignment explanation
Indices: 18507198--18507255 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
18507188 TTTGGTTAAA
*
18507198 AATTAACCGGATTACCTGAATTAACCG
1 AATTAACCGGATTACCCGAATTAACCG
18507225 AATTAACCGGATTACCCGAATTAACCG
1 AATTAACCGGATTACCCGAATTAACCG
18507252 AATT
1 AATT
18507256 GAATCACTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (27 bp):
AATTAACCGGATTACCCGAATTAACCG
Found at i:18507238 original size:18 final size:18
Alignment explanation
Indices: 18507198--18507255 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
18507188 TTTGGTTAAA
*
18507198 AATTAACCGGATT-ACCTG
1 AATTAACCGAATTAACC-G
18507216 AATTAACCGAATTAACCG
1 AATTAACCGAATTAACCG
* *
18507234 GATTACCCGAATTAACCG
1 AATTAACCGAATTAACCG
18507252 AATT
1 AATT
18507256 GAATCACTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 32 0.91
19 3 0.09
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTAACCG
Found at i:18509343 original size:8 final size:8
Alignment explanation
Indices: 18509330--18509365 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
18509320 CAAATATAAA
18509330 AAAAATAT
1 AAAAATAT
18509338 AAAAATAT
1 AAAAATAT
18509346 AAAAAATAT
1 -AAAAATAT
*
18509355 AAAAGTAT
1 AAAAATAT
18509363 AAA
1 AAA
18509366 GTATAAAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (8 bp):
AAAAATAT
Found at i:18509350 original size:9 final size:9
Alignment explanation
Indices: 18509321--18509358 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
18509311 TCACCTCAAC
18509321 AAATATAAA
1 AAATATAAA
*
18509330 AAAAATATAA
1 AAATATA-AA
18509340 AAATATAAA
1 AAATATAAA
18509349 AAATATAAA
1 AAATATAAA
18509358 A
1 A
18509359 GTATAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATATAAA
Found at i:18509351 original size:17 final size:17
Alignment explanation
Indices: 18509329--18509365 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18509319 ACAAATATAA
18509329 AAAAAATATAAAAATAT
1 AAAAAATATAAAAATAT
*
18509346 AAAAAATATAAAAGTAT
1 AAAAAATATAAAAATAT
18509363 AAA
1 AAA
18509366 GTATAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAAAATATAAAAATAT
Found at i:18521223 original size:2 final size:2
Alignment explanation
Indices: 18521216--18521247 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18521206 AATGATAATA
18521216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18521248 GTTTTTACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18527461 original size:53 final size:54
Alignment explanation
Indices: 18527388--18527501 Score: 194
Period size: 53 Copynumber: 2.1 Consensus size: 54
18527378 TGTTAAAATA
*
18527388 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAGATTCTTTAAATAATAG-T
1 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAATAATAGTT
* *
18527441 TTAAAAATAATATAATAATTTAAATAGTTAATTGAAATTCTTTAAATAATAGTT
1 TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAATAATAGTT
18527495 TTAAAAA
1 TTAAAAA
18527502 ATACTGTTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 49 0.86
54 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (54 bp):
TTAAAAATAAAATAAAAATTTAAATAGTTAATTGAAATTCTTTAAATAATAGTT
Found at i:18529295 original size:21 final size:20
Alignment explanation
Indices: 18529252--18529291 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
18529242 AGGTTAATGG
18529252 CCAAATTTAACTAAAAAATAA
1 CCAAA-TTAACTAAAAAATAA
18529273 CCAAATTAAC-AAAAAATAA
1 CCAAATTAACTAAAAAATAA
18529292 AACCTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.20
Consensus pattern (20 bp):
CCAAATTAACTAAAAAATAA
Found at i:18531971 original size:54 final size:54
Alignment explanation
Indices: 18531872--18532016 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 54
18531862 GTCACATGGT
*
18531872 CGTGTGACTCAAGTTAGAGAGTTACACGGGCTGACACGCGACCTAACACATGCC
1 CGTGTGACTCAAGTTAGAGAGTTACACGGGCTGACACGCGACCTAACACACGCC
* * * * * *
18531926 TGTGTGACTCAAGTTAGAGAGTTACATGGTCTGGCAC-CTGGCCTAACATACGCC
1 CGTGTGACTCAAGTTAGAGAGTTACACGGGCTGACACGC-GACCTAACACACGCC
* * * * * *
18531980 CGTGCGACTCAAGTCAAAGAGTTGCACAGTCTGACAC
1 CGTGTGACTCAAGTTAGAGAGTTACACGGGCTGACAC
18532017 ACGCCTATGT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 1 0.01
54 74 0.99
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (54 bp):
CGTGTGACTCAAGTTAGAGAGTTACACGGGCTGACACGCGACCTAACACACGCC
Found at i:18533645 original size:21 final size:22
Alignment explanation
Indices: 18533612--18533654 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
18533602 TTAGATTTGT
* *
18533612 AAAAATTATAAATAATTTAAAA
1 AAAAACTATAAATAATGTAAAA
*
18533634 AAAAACTA-AAATTATGTAAAA
1 AAAAACTATAAATAATGTAAAA
18533655 TATTTTTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAACTATAAATAATGTAAAA
Found at i:18536081 original size:12 final size:12
Alignment explanation
Indices: 18536064--18536128 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 12
18536054 TTAAACAAAA
18536064 TTAAAAAGTATT
1 TTAAAAAGTATT
**
18536076 TTAAAATAAAAATT
1 TT-AAA-AAGTATT
**
18536090 AAAAAAAGTATT
1 TTAAAAAGTATT
18536102 TTAAAAA-TATT
1 TTAAAAAGTATT
18536113 TT-AAAAGTA-T
1 TTAAAAAGTATT
18536123 TTAAAA
1 TTAAAA
18536129 TTTAAAAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
10 7 0.17
11 11 0.27
12 12 0.29
13 6 0.15
14 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (12 bp):
TTAAAAAGTATT
Found at i:18536125 original size:10 final size:11
Alignment explanation
Indices: 18536093--18536128 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
18536083 AAAAATTAAA
18536093 AAAAGTATTTT
1 AAAAGTATTTT
*
18536104 AAAAATATTTT
1 AAAAGTATTTT
18536115 AAAAGTA-TTT
1 AAAAGTATTTT
18536125 AAAA
1 AAAA
18536129 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.30
11 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:18536195 original size:60 final size:57
Alignment explanation
Indices: 18536083--18536196 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 57
18536073 ATTTTAAAAT
* ** *
18536083 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAGTATTTAAAATTTAAAAATTA
1 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAGAATAAAAAATATAAAAATTA
*
18536140 AAAAATTTAAAAAAGTAGTATTTTAAAAGTATTTTAAAA-AATAAAAAATAATAAAAA
1 AAAAA-TTAAAAAA--AGTATTTTAAAAATATTTTAAAAGAATAAAAAAT-ATAAAAA
18536197 ATATTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
57 5 0.10
58 8 0.17
59 7 0.15
60 28 0.58
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAGAATAAAAAATATAAAAATTA
Found at i:18536523 original size:23 final size:26
Alignment explanation
Indices: 18536496--18536576 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 26
18536486 TTTGTAAAAT
18536496 TAATGATACATAAAATATAAAT-A-A
1 TAATGATACATAAAATATAAATAATA
* * * *
18536520 -AATGATAAATGATATTTAAATTAATA
1 TAATGATACATAAAATATAAA-TAATA
* *
18536546 TAAAGATACATAAAATATAAATTAATT
1 TAATGATACATAAAATATAAA-TAATA
18536573 TAAT
1 TAAT
18536577 TATTATATGC
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
23 16 0.38
24 1 0.02
25 1 0.02
26 1 0.02
27 23 0.55
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (26 bp):
TAATGATACATAAAATATAAATAATA
Found at i:18536529 original size:12 final size:12
Alignment explanation
Indices: 18536497--18536529 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18536487 TTGTAAAATT
*
18536497 AATGATACATAA
1 AATGATAAATAA
18536509 AAT-ATAAATAA
1 AATGATAAATAA
18536520 AATGATAAAT
1 AATGATAAAT
18536530 GATATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (12 bp):
AATGATAAATAA
Found at i:18537944 original size:8 final size:8
Alignment explanation
Indices: 18537931--18537964 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
18537921 TTGGACGAGG
18537931 TTTTTAAT
1 TTTTTAAT
18537939 TTTTTAAT
1 TTTTTAAT
18537947 ATTTTATAAT
1 -TTTT-TAAT
18537957 TTTTTAAT
1 TTTTTAAT
18537965 AATTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 12 0.50
9 8 0.33
10 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTAAT
Found at i:18537958 original size:18 final size:18
Alignment explanation
Indices: 18537931--18537971 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
18537921 TTGGACGAGG
18537931 TTTT-TAATTTTTTAATA
1 TTTTATAATTTTTTAATA
18537948 TTTTATAATTTTTTAATA
1 TTTTATAATTTTTTAATA
*
18537966 ATTTAT
1 TTTTAT
18537972 TTAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTTTAATA
Found at i:18539286 original size:27 final size:27
Alignment explanation
Indices: 18539256--18539318 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
18539246 GGTAATGGAA
* *
18539256 TGGCGGCACCGGTGGTGCCTTTCTCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
18539283 TGGCGGCACCGGTGGTGCCATTCCCAT
1 TGGCGGCACCGGTGGTGCCATTCCCAT
18539310 TGGCGGCAC
1 TGGCGGCAC
18539319 AGGACTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.10, C:0.32, G:0.35, T:0.24
Consensus pattern (27 bp):
TGGCGGCACCGGTGGTGCCATTCCCAT
Found at i:18541193 original size:13 final size:12
Alignment explanation
Indices: 18541163--18541213 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
18541153 GTAAATAAAA
18541163 TTTTTTGTATAT
1 TTTTTTGTATAT
*
18541175 TATTTTGGTAT-T
1 T-TTTTTGTATAT
*
18541187 TTTTTT-TATCT
1 TTTTTTGTATAT
18541198 TTTTTTGTATTAT
1 TTTTTTGTA-TAT
18541211 TTT
1 TTT
18541214 AGTAAAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.09
11 11 0.34
12 5 0.16
13 13 0.41
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTGTATAT
Found at i:18541203 original size:23 final size:22
Alignment explanation
Indices: 18541163--18541213 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
18541153 GTAAATAAAA
18541163 TTTTTTGTATATTATTTTGGTAT
1 TTTTTTGTATATTATTTT-GTAT
* * *
18541186 TTTTTTTTATCTTTTTTTGTAT
1 TTTTTTGTATATTATTTTGTAT
*
18541208 TATTTT
1 TTTTTT
18541214 AGTAAAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.14, C:0.02, G:0.08, T:0.76
Consensus pattern (22 bp):
TTTTTTGTATATTATTTTGTAT
Found at i:18549037 original size:48 final size:48
Alignment explanation
Indices: 18548983--18549079 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
18548973 AGAAGCAATT
* *
18548983 ATACATAACATATAACACATACAAAGTCATATTAATTTACTCTTTTCA
1 ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
* *
18549031 ATACATAATATACATCACATACAAAGTCATATTAACTTACTCTTTTCA
1 ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
18549079 A
1 A
18549080 ATCATTCCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (48 bp):
ATACATAACATACAACACATACAAAGTCATATTAACTTACTCTTTTCA
Found at i:18549813 original size:2 final size:2
Alignment explanation
Indices: 18549806--18549831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18549796 GCTCACAGCT
18549806 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
18549832 GAACTAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18559202 original size:17 final size:18
Alignment explanation
Indices: 18559180--18559214 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18559170 TCTTTCTACA
*
18559180 TTTCTT-CATTTTTTTTC
1 TTTCTTCCATTTATTTTC
18559197 TTTCTTCCATTTATTTTC
1 TTTCTTCCATTTATTTTC
18559215 CTTGGCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTCCATTTATTTTC
Found at i:18565601 original size:19 final size:19
Alignment explanation
Indices: 18565548--18565607 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
18565538 TTGTACGGGA
* *
18565548 TTGCACTTCGGTGCCTCTG
1 TTGCACATCAGTGCCTCTG
* * *
18565567 ATTGCACATTATTGCCTTTG
1 -TTGCACATCAGTGCCTCTG
18565587 TTGCACATCAGTGCCTCTG
1 TTGCACATCAGTGCCTCTG
18565606 TT
1 TT
18565608 ACGCATCTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.13, C:0.27, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGCACATCAGTGCCTCTG
Found at i:18570114 original size:50 final size:50
Alignment explanation
Indices: 18569948--18570127 Score: 166
Period size: 50 Copynumber: 3.5 Consensus size: 50
18569938 AGTAAAGAGA
* * * * *
18569948 TCCCATGTAAGACCATGTCTGAGACATAGCATTGGCATCATTGAGACTATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAG---ATGAAAGG
* *
18570004 TCCCATGTAAGACCATGTCTGGGACATGGTATTGGCACCGAGATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAAAGG
* * *
18570054 TCCTC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAA-T
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGA-AAGG
* *
18570104 TCCCATGTAAGATCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
18570128 TATGACATTG
Statistics
Matches: 108, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
49 1 0.01
50 66 0.61
51 3 0.03
53 3 0.03
55 1 0.01
56 34 0.31
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAAAGG
Found at i:18571916 original size:2 final size:2
Alignment explanation
Indices: 18571909--18571934 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18571899 AGGAGGAGTA
18571909 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
18571935 GAATATTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18577591 original size:45 final size:44
Alignment explanation
Indices: 18577525--18577834 Score: 180
Period size: 45 Copynumber: 6.9 Consensus size: 44
18577515 AATTTATAGC
** * *
18577525 TTCAATCTATTCTACTACAACTTCAGGGAAATGAGATTTGCTATT
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTG-TATT
* * *
18577570 TTCAATTTGCTCTACTGCAACTTCAGGGAGATAAGACTTGTA--
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGTATT
* * * *
18577612 -T-GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTAT
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGT-A--T-T
** * *
18577658 AACTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATTTGCTATC
1 ---TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTG-TATT
* * * * *
18577706 TTCAGTCTGCTCCACTGCAACTTCAGGGAAATGAGATTCTTTATCC
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATT-TGTAT-T
* * * * * * * ***
18577752 TT-AGTTTACTCCACTGCAACTTCAAGGAGATAAGACTTGTGGC
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGTATT
* * * *
18577795 TTCAATCTGCCCCACTACAACTTCAGGGGAATAAGATTTG
1 TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTG
18577835 GCTTTGGTGA
Statistics
Matches: 207, Mismatches: 43, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
40 33 0.16
41 2 0.01
43 3 0.01
44 32 0.15
45 99 0.48
46 4 0.02
49 1 0.00
50 1 0.00
51 31 0.15
52 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
TTCAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTTGTATT
Found at i:18577620 original size:136 final size:137
Alignment explanation
Indices: 18577433--18577734 Score: 471
Period size: 136 Copynumber: 2.2 Consensus size: 137
18577423 GAATAGTAAT
* * * **
18577433 TTCAATCTACTTCACTGTAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTC
* * * *
18577498 AGAGATATAAGATCTGTAATTTATAGCTTCAATCTATTCTACTACAACTTCAGGGAAATGAGATT
66 AGAGAGATAAGATCTGTAATTTATAACTTCAATCTATTCCACTACAACTTCAGGGAAATAAGATT
*
18577563 TGCTATT
131 TGCTATC
* *
18577570 TTCAATTTGCTCTACTGCAACTTCAGGGAGATAAGACTTG-TATGATCTGCTCTACTGCAACTTC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTC
*
18577634 AGAGAGATAAGATCTGTAATTTATAACTTCAATCTATTCCACTGCAACTTCAGGGAAATAAGATT
66 AGAGAGATAAGATCTGTAATTTATAACTTCAATCTATTCCACTACAACTTCAGGGAAATAAGATT
18577699 TGCTATC
131 TGCTATC
*
18577706 TTCAGTCTGCTCCACTGCAACTTCAGGGA
1 TTCAATCTGCTCCACTGCAACTTCAGGGA
18577735 AATGAGATTC
Statistics
Matches: 149, Mismatches: 16, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
136 116 0.78
137 33 0.22
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (137 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATATGATCTGCTCTACTGCAACTTC
AGAGAGATAAGATCTGTAATTTATAACTTCAATCTATTCCACTACAACTTCAGGGAAATAAGATT
TGCTATC
Found at i:18578132 original size:143 final size:143
Alignment explanation
Indices: 18577898--18578209 Score: 364
Period size: 143 Copynumber: 2.2 Consensus size: 143
18577888 GTTTTAATTC
* * * *
18577898 GCTCAACTACAACTTTAAGGAGAT-AGGATTGGTGGCTTCAATCTACTTCATACAAATTCAGAAA
1 GCTCAACTGCAACTTTAGGGAGATAAGGATTGGTGGCTTCAATATACTCCATACAAATTCAGAAA
* * **
18577962 GATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCATTGTAACATTAGAGAAATAAGATTCG
66 GATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAAATAAGATTCG
*
18578027 -TGGTCTTCAGTCT
131 CT-ATCTTCAGTCT
* * ** *
18578040 GCTCCACTGCAACTTTAGGGAGATAAGG-TTGGTGGCTTCAATATGCTCCACTGTAACTTCAGAA
1 GCTCAACTGCAACTTTAGGGAGATAAGGATTGGTGGCTTCAATATACTCCA-TACAAATTCAGAA
* * * * *
18578104 AGATAAGCT-CTGGC-ATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAGTAAGAT
65 AGATAAGATCCT--CTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAAATAAGAT
18578167 TCGCTATCTTCAGTCT
128 TCGCTATCTTCAGTCT
* *
18578183 GCTCTACTGGAACTTTAGGGAGATAAG
1 GCTCAACTGCAACTTTAGGGAGATAAG
18578210 ACTTGTCACT
Statistics
Matches: 144, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
142 42 0.29
143 100 0.69
144 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (143 bp):
GCTCAACTGCAACTTTAGGGAGATAAGGATTGGTGGCTTCAATATACTCCATACAAATTCAGAAA
GATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAAATAAGATTCG
CTATCTTCAGTCT
Found at i:18578232 original size:143 final size:143
Alignment explanation
Indices: 18577954--18578253 Score: 338
Period size: 143 Copynumber: 2.1 Consensus size: 143
18577944 TTCATACAAA
* * **
18577954 TTCAGAAAGATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCATTGTAACATTAGAGAAAT
1 TTCAGAAAGATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAAAT
* * ** *
18578019 AAGATTCGTGGTCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGGTTGGTGGCTTCAATAT
66 AAGATTCGTGATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGCTTGGTCACTTCAACAT
* *
18578084 GCTCCACTGTAAC
131 ACTCCACTGCAAC
* * * *
18578097 TTCAGAAAGATAAGCT-CTGGC-ATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAA
1 TTCAGAAAGATAAGATCCT--CTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAA
* * *
18578160 GTAAGATTCGCT-ATCTTCAGTCTGCTCTACTGGAACTTTAGGGAGATAAGACTT-GTCACTTCA
64 ATAAGATTCG-TGATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAG-CTTGGTCACTTCA
* *
18578223 ACCTACTCCATTGCAAC
127 ACATACTCCACTGCAAC
**
18578240 TTCAGGGAGATAAG
1 TTCAGAAAGATAAG
18578254 GTTTGCTATG
Statistics
Matches: 131, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
142 2 0.02
143 125 0.95
144 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (143 bp):
TTCAGAAAGATAAGATCCTCTATAATTTGTAGCTTTAATCTATTCCACTGCAACACCAGAGAAAT
AAGATTCGTGATCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGCTTGGTCACTTCAACAT
ACTCCACTGCAAC
Found at i:18579708 original size:50 final size:44
Alignment explanation
Indices: 18579654--18579774 Score: 134
Period size: 45 Copynumber: 2.6 Consensus size: 44
18579644 GTCTAAAGGT
*
18579654 GCCCTTTGCTGGTTTTCGCCTTGGCCTCTCTCTTTTTTAGGACTCAAAGC
1 GCCCTTTGC-GGTTTTCACCTTGG----TCTC-TTTTTAGGACTCAAAGC
**
18579704 GCCCTTCACGGGTTTTCACCTTGGTCTCTTTTTAGGACTCAAAGC
1 GCCCTTTGC-GGTTTTCACCTTGGTCTCTTTTTAGGACTCAAAGC
*
18579749 ACCCTTTGCGAGTTTTCACCTTGGTC
1 GCCCTTTGCG-GTTTTCACCTTGGTC
18579775 CCTTCTCTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 38 0.60
46 4 0.06
50 20 0.32
ACGTcount: A:0.12, C:0.30, G:0.20, T:0.38
Consensus pattern (44 bp):
GCCCTTTGCGGTTTTCACCTTGGTCTCTTTTTAGGACTCAAAGC
Found at i:18579740 original size:45 final size:46
Alignment explanation
Indices: 18579682--18579774 Score: 143
Period size: 45 Copynumber: 2.0 Consensus size: 46
18579672 CCTTGGCCTC
* *
18579682 TCTCTTTTTTAGGACTCAAAGCGCCCTTCACGGGTTTTCACCTTGG
1 TCTCTTTTTTAGGACTCAAAGCACCCTTCACGAGTTTTCACCTTGG
**
18579728 TCTC-TTTTTAGGACTCAAAGCACCCTTTGCGAGTTTTCACCTTGG
1 TCTCTTTTTTAGGACTCAAAGCACCCTTCACGAGTTTTCACCTTGG
18579773 TC
1 TC
18579775 CCTTCTCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 39 0.91
46 4 0.09
ACGTcount: A:0.16, C:0.28, G:0.18, T:0.38
Consensus pattern (46 bp):
TCTCTTTTTTAGGACTCAAAGCACCCTTCACGAGTTTTCACCTTGG
Found at i:18587068 original size:19 final size:20
Alignment explanation
Indices: 18587044--18587090 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
18587034 TGGTGGACTT
* *
18587044 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
18587063 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
18587083 -AATGCAAA
1 TAATGCAAA
18587091 AAGGCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:18595472 original size:9 final size:9
Alignment explanation
Indices: 18595460--18595484 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18595450 GAAAGGGTTC
18595460 AAAGAAATA
1 AAAGAAATA
18595469 AAAGAAATA
1 AAAGAAATA
18595478 AAAGAAA
1 AAAGAAA
18595485 GGGCTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAAGAAATA
Found at i:18596268 original size:21 final size:21
Alignment explanation
Indices: 18596239--18596286 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
18596229 CAGAAAATTA
*
18596239 TTTATGAAAAATGACTTACTTT
1 TTTATGAAAAATGA-ATACTTT
*
18596261 TTTA-GAAAAATTAATACTTT
1 TTTATGAAAAATGAATACTTT
18596281 TTTATG
1 TTTATG
18596287 TTTGGGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 9 0.39
22 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (21 bp):
TTTATGAAAAATGAATACTTT
Found at i:18606182 original size:26 final size:27
Alignment explanation
Indices: 18606130--18606183 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
18606120 AAAATTTTAA
*
18606130 TAAATAAAATATATATTTATTAAATAT
1 TAAATAAAATATATATTAATTAAATAT
18606157 TAAATTAAAATA-ATA-TAATTAAATAT
1 TAAA-TAAAATATATATTAATTAAATAT
18606183 T
1 T
18606184 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
27 7 0.28
28 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATAAAATATATATTAATTAAATAT
Found at i:18607380 original size:16 final size:16
Alignment explanation
Indices: 18607355--18607385 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18607345 GTCTCCCACA
*
18607355 TTAGGTTTAGGGTTTT
1 TTAGGGTTAGGGTTTT
18607371 TTAGGGTTAGGGTTT
1 TTAGGGTTAGGGTTT
18607386 AAGGTTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (16 bp):
TTAGGGTTAGGGTTTT
Found at i:18607738 original size:125 final size:124
Alignment explanation
Indices: 18607533--18607970 Score: 653
Period size: 125 Copynumber: 3.5 Consensus size: 124
18607523 AAATCAAAGT
18607533 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACTCGCTTTTGCTACAGTAGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGA-TCGCTTTTGCTACAGTAGGT
* * *
18607598 ACTGAAAAAATAATTTTGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTCAAGC
65 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * * * * *
18607658 AGGATGCTTTATTAGAAGAATTTCTGAAATCGCGCTCATGTCGATGCGCTTTTACTACAATAGGT
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGAT-CGCTTTTGCTACAGTAGGT
18607723 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
65 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * *
18607783 AGGATGCTTTATCAGAAGAATTTCT-AAAGTCGCGCCCACGTGGACACGCTTTTGTTATAGTAGG
1 AGGATGCTTTATCAGAAGAATTTCTGAAA-TCGCGCCCACGTGGA-TCGCTTTTGCTACAGTAGG
18607847 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
64 TCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
* * * * * * *
18607908 AGAATGTTTTATCAGAAGAATTTATGAAATCGCTCCCTCGTGAACACGCTTTTGCTACAGTAG
1 AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGA-TCGCTTTTGCTACAGTAG
18607971 CATGTTTGGG
Statistics
Matches: 283, Mismatches: 26, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
124 4 0.01
125 276 0.98
126 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
AGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGATCGCTTTTGCTACAGTAGGTC
CTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAGC
Found at i:18609246 original size:28 final size:28
Alignment explanation
Indices: 18609197--18609251 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
18609187 TAAGTTAGAT
*
18609197 AAAAGAATTGACACAAGCAGAATCTAAG
1 AAAAGAATTGACACAAGCAGAAACTAAG
18609225 AAAAGAAATTGA-AC-AGCAAGAAACTAA
1 AAAAG-AATTGACACAAGC-AGAAACTAA
18609252 ATTAAAGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.12
28 15 0.62
29 6 0.25
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (28 bp):
AAAAGAATTGACACAAGCAGAAACTAAG
Found at i:18617440 original size:43 final size:43
Alignment explanation
Indices: 18617379--18617466 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
18617369 TTTCCAACAA
18617379 GGATGGTTTTATTGGTGCTTTGAAACAACATAGCATCAAAAAC
1 GGATGGTTTTATTGGTGCTTTGAAACAACATAGCATCAAAAAC
18617422 GGATGGTTTTATTGGTGCTTTGAAACAACATAGCATCAAAAAC
1 GGATGGTTTTATTGGTGCTTTGAAACAACATAGCATCAAAAAC
18617465 GG
1 GG
18617467 CGTTAACTAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (43 bp):
GGATGGTTTTATTGGTGCTTTGAAACAACATAGCATCAAAAAC
Found at i:18619569 original size:112 final size:111
Alignment explanation
Indices: 18619373--18619585 Score: 320
Period size: 112 Copynumber: 1.9 Consensus size: 111
18619363 ATATTTTTTT
**
18619373 GTACCAGTCAAAAATTTTGTAAAATCTGGCTGAATGTTAGTAAAATTATTAATTGCTAATTGTAT
1 GTACCAGTCAAAAATTTTGTAAAATCTAACTGAATGTTAGTAAAATTATTAATTGCTAATTGTAT
*
18619438 TAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTCTAG
66 TAATTGTTAGTAAAATTATCAAATCATATCAAATTATTAATTCTAG
** * *
18619484 GTACCAGTCAAAACATTTTGTAAAATCTAACAT-TTTGTTAGTCAAATTATTAATTGTTAATTGT
1 GTACCAGTCAAAA-ATTTTGTAAAATCTAAC-TGAATGTTAGTAAAATTATTAATTGCTAATTGT
* *
18619548 ATTAATTGTTAGTAAATTTATCAAATCATATCATATTA
64 ATTAATTGTTAGTAAAATTATCAAATCATATCAAATTA
18619586 GGGTTAGATT
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 13 0.14
112 77 0.85
113 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (111 bp):
GTACCAGTCAAAAATTTTGTAAAATCTAACTGAATGTTAGTAAAATTATTAATTGCTAATTGTAT
TAATTGTTAGTAAAATTATCAAATCATATCAAATTATTAATTCTAG
Found at i:18619652 original size:15 final size:15
Alignment explanation
Indices: 18619632--18619660 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18619622 GGGTTTTGGT
18619632 GTTTTTAAGTTAAGA
1 GTTTTTAAGTTAAGA
18619647 GTTTTTAAGTTAAG
1 GTTTTTAAGTTAAG
18619661 GGTTAGGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
GTTTTTAAGTTAAGA
Found at i:18619675 original size:21 final size:21
Alignment explanation
Indices: 18619647--18619821 Score: 287
Period size: 21 Copynumber: 8.2 Consensus size: 21
18619637 TAAGTTAAGA
18619647 GTTTTTAAGTTAAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGG
*
18619668 GGTTTTAAGTTAAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGG
18619689 GTTTTTAAGTTAAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGG
* *
18619710 GTTTTTAAATTAAGGGTTAGT
1 GTTTTTAAGTTAAGGGTTAGG
18619731 GTTTTTAAGTTAAGGGTTTAGG
1 GTTTTTAAGTTAAGGG-TTAGG
*
18619753 GTTTTTAAGTTAAGCGTTAGG
1 GTTTTTAAGTTAAGGGTTAGG
18619774 GTTTTTAAGTTAAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGG
*
18619795 GTTTTTAAGTTAAAGGTTATGG
1 GTTTTTAAGTTAAGGGTTA-GG
18619817 GTTTT
1 GTTTT
18619822 GTTAGGGTTT
Statistics
Matches: 143, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
21 117 0.82
22 26 0.18
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (21 bp):
GTTTTTAAGTTAAGGGTTAGG
Found at i:18619772 original size:85 final size:84
Alignment explanation
Indices: 18619647--18619813 Score: 289
Period size: 85 Copynumber: 2.0 Consensus size: 84
18619637 TAAGTTAAGA
*
18619647 GTTTTTAAGTTAAGGGTTAGGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
1 GTTTTTAAGTTAAGGGTTAGGGGTTTTAAGTTAAGCGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
*
18619712 TTTTAAATTAAGGGTTAGT
66 TTTTAAATTAAAGGTTAGT
*
18619731 GTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGCGTTAGGGTTTTTAAGTTAAGGGTTAGGG
1 GTTTTTAAGTTAAGGG-TTAGGGGTTTTAAGTTAAGCGTTAGGGTTTTTAAGTTAAGGGTTAGGG
*
18619796 TTTTTAAGTTAAAGGTTA
65 TTTTTAAATTAAAGGTTA
18619814 TGGGTTTTGT
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 16 0.21
85 62 0.79
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.44
Consensus pattern (84 bp):
GTTTTTAAGTTAAGGGTTAGGGGTTTTAAGTTAAGCGTTAGGGTTTTTAAGTTAAGGGTTAGGGT
TTTTAAATTAAAGGTTAGT
Found at i:18619780 original size:64 final size:63
Alignment explanation
Indices: 18619647--18619821 Score: 287
Period size: 64 Copynumber: 2.7 Consensus size: 63
18619637 TAAGTTAAGA
* *
18619647 GTTTTTAAGTTAAGGGTTAGGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGCGTTAGG
* *
18619710 GTTTTTAAATTAAGGGTTAGTGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGCGTTAGG
1 GTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGCGTTAGG
*
18619774 GTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAAGGTTATGGGTTTT
1 GTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTA-GGGTTTT
18619822 GTTAGGGTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
63 37 0.36
64 66 0.64
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (63 bp):
GTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGCGTTAGG
Found at i:18619852 original size:12 final size:12
Alignment explanation
Indices: 18619835--18619877 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
18619825 AGGGTTTGTC
18619835 AATTAAATTATA
1 AATTAAATTATA
18619847 AATTAAATTATA
1 AATTAAATTATA
18619859 AATTATAAATTTATA
1 AA-T-TAAA-TTATA
18619874 AATT
1 AATT
18619878 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 14 0.50
13 2 0.07
14 5 0.18
15 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:18619878 original size:8 final size:7
Alignment explanation
Indices: 18619838--18619877 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
18619828 GTTTGTCAAT
18619838 TAAATTA
1 TAAATTA
18619845 TAAA-T-
1 TAAATTA
18619850 TAAATTA
1 TAAATTA
18619857 TAAATTA
1 TAAATTA
18619864 TAAATTTA
1 TAAA-TTA
18619872 TAAATT
1 TAAATT
18619878 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAATTA
Found at i:18621074 original size:7 final size:7
Alignment explanation
Indices: 18621062--18621087 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18621052 TTATATGCAT
18621062 AATACTA
1 AATACTA
18621069 AATACTA
1 AATACTA
18621076 AATACTA
1 AATACTA
18621083 AATAC
1 AATAC
18621088 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:18622282 original size:29 final size:28
Alignment explanation
Indices: 18622250--18622305 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
18622240 GATTTAAGAG
*
18622250 AAATTTAATA-GGAAATTGAGAGCAAATTA
1 AAATTAAATATGG-AATTGAGAG-AAATTA
*
18622279 AAATTAAATATGGATTTGAGAGAAATT
1 AAATTAAATATGGAATTGAGAGAAATT
18622306 TGGAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 17 0.71
30 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (28 bp):
AAATTAAATATGGAATTGAGAGAAATTA
Found at i:18634136 original size:18 final size:18
Alignment explanation
Indices: 18634115--18634154 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18634105 TCTCTAGACT
18634115 TTTTAGGATTGT-TTTTGG
1 TTTTAGG-TTGTATTTTGG
*
18634133 TTTTAGGTTTTATTTTGG
1 TTTTAGGTTGTATTTTGG
18634151 TTTT
1 TTTT
18634155 CGAAGCGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.68
Consensus pattern (18 bp):
TTTTAGGTTGTATTTTGG
Found at i:18640907 original size:18 final size:18
Alignment explanation
Indices: 18640886--18640925 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18640876 TCTCCGGACT
18640886 TTTTGGGATTGT-TTTTGG
1 TTTTGGG-TTGTATTTTGG
*
18640904 TTTTGGGTTTTATTTTGG
1 TTTTGGGTTGTATTTTGG
18640922 TTTT
1 TTTT
18640926 CTAAGCGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.05, C:0.00, G:0.28, T:0.68
Consensus pattern (18 bp):
TTTTGGGTTGTATTTTGG
Found at i:18641862 original size:51 final size:51
Alignment explanation
Indices: 18641801--18641907 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
18641791 TTCTTTTTAT
* *
18641801 ATATTGATATATTAGCTCTTCTGGAGCTTTCAACTAATTTTGTATTACCAA
1 ATATTAATATATTAGCTCTTCTGGAGCTTTCAACTAATTTTGTACTACCAA
** * * *
18641852 ATATTAATATATTATTTCTTTTGGAGCTTTCGACTAATTTTTTACTACCAA
1 ATATTAATATATTAGCTCTTCTGGAGCTTTCAACTAATTTTGTACTACCAA
18641903 ATATT
1 ATATT
18641908 GTTATAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (51 bp):
ATATTAATATATTAGCTCTTCTGGAGCTTTCAACTAATTTTGTACTACCAA
Found at i:18652466 original size:26 final size:26
Alignment explanation
Indices: 18652395--18652482 Score: 95
Period size: 26 Copynumber: 3.3 Consensus size: 26
18652385 TAGAATAATT
* * *
18652395 TTAAAATAATTAATATATAAAACAAC
1 TTAAAATAAATAATATACAAAACAAG
* ** *
18652421 TAAAAATAAAATAATATACAAAGTAAT
1 TTAAAAT-AAATAATATACAAAACAAG
*
18652448 TTAAAATAAATAATTTACAAAACAAG
1 TTAAAATAAATAATATACAAAACAAG
18652474 TTAAAATAA
1 TTAAAATAA
18652483 CACATAATGA
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
26 30 0.60
27 20 0.40
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
TTAAAATAAATAATATACAAAACAAG
Found at i:18652540 original size:15 final size:16
Alignment explanation
Indices: 18652520--18652553 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18652510 AAAGGGAAAT
*
18652520 TTTAAA-ATAAATTAA
1 TTTAAAGATAAATAAA
18652535 TTTAAAGATAAATAAA
1 TTTAAAGATAAATAAA
18652551 TTT
1 TTT
18652554 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TTTAAAGATAAATAAA
Found at i:18656364 original size:4 final size:4
Alignment explanation
Indices: 18656355--18656380 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18656345 TCACTGGGAG
18656355 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
18656381 GTGTGTGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:18659238 original size:34 final size:34
Alignment explanation
Indices: 18659189--18659287 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 34
18659179 GAATAATTAA
18659189 TAAATTATTTATAAATATAATGATACATAAAATATTT
1 TAAA-TATTT-TAAATATAATGATACATAAAATA-TT
*
18659226 TAAA-ATTTTAAATATAAT-A-A-TTAATAATATT
1 TAAATATTTTAAATATAATGATACATAA-AATATT
* *
18659257 TAAATAATTT-AATATAATGATACACAAAATA
1 TAAATATTTTAAATATAATGATACATAAAATA
18659288 GAAATTAGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
31 17 0.32
32 10 0.19
33 6 0.11
34 12 0.23
35 4 0.08
37 4 0.08
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (34 bp):
TAAATATTTTAAATATAATGATACATAAAATATT
Found at i:18660507 original size:20 final size:20
Alignment explanation
Indices: 18660484--18660529 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
18660474 TGTTAATATT
*
18660484 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
18660504 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
18660524 TTGTTA
1 TTGTTA
18660530 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:18664018 original size:50 final size:50
Alignment explanation
Indices: 18663902--18664144 Score: 378
Period size: 50 Copynumber: 4.8 Consensus size: 50
18663892 GATAATGACA
* ** *
18663902 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTACTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATCTCGG
* **
18663953 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
18664003 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
18664053 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
18664103 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
18664145 TTACCCAAAT
Statistics
Matches: 176, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 142 0.81
51 34 0.19
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:18664453 original size:27 final size:27
Alignment explanation
Indices: 18664390--18664446 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
18664380 TTATTCTTTC
18664390 CTTTGTCTAACCTCGAGTTTCATTCTT
1 CTTTGTCTAACCTCGAGTTTCATTCTT
18664417 CTTTGTCTAACCTCGAGTTTCATTCTT
1 CTTTGTCTAACCTCGAGTTTCATTCTT
18664444 CTT
1 CTT
18664447 GATCTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.26, G:0.11, T:0.49
Consensus pattern (27 bp):
CTTTGTCTAACCTCGAGTTTCATTCTT
Found at i:18668840 original size:20 final size:20
Alignment explanation
Indices: 18668817--18668862 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
18668807 TGTTAATATT
*
18668817 TTGTTATTTATTCAAATAGG
1 TTGTTACTTATTCAAATAGG
*
18668837 TTGTTACTTATTTAAATAGG
1 TTGTTACTTATTCAAATAGG
18668857 TTGTTA
1 TTGTTA
18668863 AGCTTTACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (20 bp):
TTGTTACTTATTCAAATAGG
Found at i:18671303 original size:114 final size:114
Alignment explanation
Indices: 18671091--18671308 Score: 330
Period size: 114 Copynumber: 1.9 Consensus size: 114
18671081 ATTTATATTA
18671091 TTTATTAAGTATTTTACTAAGTTGGTGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTA
1 TTTATTAAGTATTTTACTAAGTTGGTGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTA
* *
18671156 CCAAAAAGTTAATTTATATACCAAGTAAATTATATGATTAAGTAGGCGT
66 CCAAAAAATTAATTTATATACCAAGCAAATTATATGATTAAGTAGGCGT
* * * *
18671205 TTTATTAAG-ATTTTTTCTAAGTTGGTGCCACCCATCAACTGAGTCCTAAGTCAATTAGGGAATT
1 TTTATTAAGTA-TTTTACTAAGTTGGTGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATT
* * * *
18671269 ACCAAAAAATTATTTTATATGCTAAGCAAGTTATATGATT
65 ACCAAAAAATTAATTTATATACCAAGCAAATTATATGATT
18671309 GAGTGTGTAA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
113 1 0.01
114 92 0.99
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (114 bp):
TTTATTAAGTATTTTACTAAGTTGGTGCCACCCATCAACCGAGTCCCAACTCAATTAGGGAATTA
CCAAAAAATTAATTTATATACCAAGCAAATTATATGATTAAGTAGGCGT
Found at i:18674913 original size:11 final size:11
Alignment explanation
Indices: 18674897--18674923 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18674887 TTAACGAGTG
18674897 TATTTTTTATA
1 TATTTTTTATA
18674908 TATTTTTTATA
1 TATTTTTTATA
18674919 TATTT
1 TATTT
18674924 GTGTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TATTTTTTATA
Found at i:18681744 original size:17 final size:17
Alignment explanation
Indices: 18681724--18681761 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
18681714 CTGTGAAATT
18681724 TAATCATTTT-ATTGAAA
1 TAAT-ATTTTAATTGAAA
*
18681741 TAATATTTTAATTGAGA
1 TAATATTTTAATTGAAA
18681758 TAAT
1 TAAT
18681762 TTTCATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (17 bp):
TAATATTTTAATTGAAA
Found at i:18695175 original size:26 final size:27
Alignment explanation
Indices: 18695146--18695280 Score: 106
Period size: 27 Copynumber: 5.1 Consensus size: 27
18695136 TCTATTGTAG
*
18695146 TTAAATA-ACTAG-TTTATTATACTGTT
1 TTAAATATA-TAGTTTTAATATACTGTT
*
18695172 TT-AATATATTGTTTTAATATACTGTT
1 TTAAATATATAGTTTTAATATACTGTT
* *
18695198 TT-AGTATACT-GTTATAAATATACTGTT
1 TTAAATATA-TAGTT-TTAATATACTGTT
*
18695225 TT-AATATA-ATGTTTTAATATATTGTT
1 TTAAATATATA-GTTTTAATATACTGTT
* *
18695251 ATAAATATACT-GTTTTAATATAATGTT
1 TTAAATATA-TAGTTTTAATATACTGTT
18695278 TTA
1 TTA
18695281 GTATACTGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
25 6 0.07
26 38 0.42
27 46 0.51
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (27 bp):
TTAAATATATAGTTTTAATATACTGTT
Found at i:18695179 original size:13 final size:13
Alignment explanation
Indices: 18695158--18695299 Score: 169
Period size: 13 Copynumber: 10.8 Consensus size: 13
18695148 AAATAACTAG
*
18695158 TTTATTATACTGT
1 TTTAATATACTGT
*
18695171 TTTAATATATTGT
1 TTTAATATACTGT
18695184 TTTAATATACTGT
1 TTTAATATACTGT
*
18695197 TTTAGTATACTGT
1 TTTAATATACTGT
*
18695210 TATAAATATACTGT
1 T-TTAATATACTGT
*
18695224 TTTAATATAATGT
1 TTTAATATACTGT
*
18695237 TTTAATATATTGT
1 TTTAATATACTGT
*
18695250 TATAAATATACTGT
1 T-TTAATATACTGT
*
18695264 TTTAATATAATGT
1 TTTAATATACTGT
*
18695277 TTTAGTATACTGT
1 TTTAATATACTGT
*
18695290 TATAA-ATACT
1 TTTAATATACT
18695300 ACACCTTAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
12 5 0.05
13 83 0.75
14 22 0.20
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (13 bp):
TTTAATATACTGT
Found at i:18695225 original size:53 final size:53
Alignment explanation
Indices: 18695163--18695290 Score: 132
Period size: 53 Copynumber: 2.4 Consensus size: 53
18695153 ACTAGTTTAT
* * * *
18695163 TATACTGTTTTAATATATTGTTTTAATATACTGTTTTAGTATACTGTTATAAA
1 TATACTGTTTAAATATACTGTTTTAATATAATGTTTTAATATACTGTTATAAA
* * * * *
18695216 TATACTGTTTTAATATAATGTTTTAATATATTGTTATAAATATACTGTT-TTAA
1 TATACTGTTTAAATATACTGTTTTAATATAATGTT-TTAATATACTGTTATAAA
* * *
18695269 TATAATGTTTTAGTATACTGTT
1 TATACTGTTTAAATATACTGTT
18695291 ATAAATACTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
53 55 0.83
54 11 0.17
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (53 bp):
TATACTGTTTAAATATACTGTTTTAATATAATGTTTTAATATACTGTTATAAA
Found at i:18695309 original size:40 final size:40
Alignment explanation
Indices: 18695158--18695297 Score: 219
Period size: 40 Copynumber: 3.5 Consensus size: 40
18695148 AAATAACTAG
* * * *
18695158 TTTATTATACTGTT-TTAATATATTGTTTTAATATACTGT
1 TTTAGTATACTGTTATAAATATACTGTTTTAATATAATGT
18695197 TTTAGTATACTGTTATAAATATACTGTTTTAATATAATGT
1 TTTAGTATACTGTTATAAATATACTGTTTTAATATAATGT
* *
18695237 TTTAATATATTGTTATAAATATACTGTTTTAATATAATGT
1 TTTAGTATACTGTTATAAATATACTGTTTTAATATAATGT
18695277 TTTAGTATACTGTTATAAATA
1 TTTAGTATACTGTTATAAATA
18695298 CTACACCTTA
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 13 0.14
40 79 0.86
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (40 bp):
TTTAGTATACTGTTATAAATATACTGTTTTAATATAATGT
Found at i:18695357 original size:22 final size:22
Alignment explanation
Indices: 18695331--18695372 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
18695321 TATACTGGTT
18695331 TAATATACTGTTATAAAATTTG
1 TAATATACTGTTATAAAATTTG
18695353 TAATATACTGTTATAAAATT
1 TAATATACTGTTATAAAATT
18695373 ACTCAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (22 bp):
TAATATACTGTTATAAAATTTG
Found at i:18704687 original size:21 final size:20
Alignment explanation
Indices: 18704663--18704701 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
18704653 AATTATATTT
*
18704663 AAATATTATTCTTCTAATAGG
1 AAATATTATTATT-TAATAGG
18704684 AAATATTATTATTTAATA
1 AAATATTATTATTTAATA
18704702 TTAAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (20 bp):
AAATATTATTATTTAATAGG
Found at i:18710521 original size:13 final size:13
Alignment explanation
Indices: 18710503--18710527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18710493 ATTTACAAGA
18710503 TTACATAATCAAT
1 TTACATAATCAAT
18710516 TTACATAATCAA
1 TTACATAATCAA
18710528 AACAAATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:18721971 original size:3 final size:3
Alignment explanation
Indices: 18721965--18722004 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18721955 ACTCTACTAC
18721965 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18722005 TTAAATGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18726288 original size:36 final size:36
Alignment explanation
Indices: 18726248--18726338 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 36
18726238 TGTTCAAGAT
***
18726248 CTTGGGATTGAGAAGACCTGATATTTTGTTCAGAAG
1 CTTGGGATTGAGAAGACCTGATATCGAGTTCAGAAG
* *
18726284 CTT--G---G-GAAGACTTGATATCGAGTTCAGGAG
1 CTTGGGATTGAGAAGACCTGATATCGAGTTCAGAAG
18726314 CTTGGGATTGAGAAGACCTGATATC
1 CTTGGGATTGAGAAGACCTGATATC
18726339 TCGTCCAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
30 23 0.53
31 1 0.02
32 1 0.02
34 1 0.02
35 1 0.02
36 16 0.37
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (36 bp):
CTTGGGATTGAGAAGACCTGATATCGAGTTCAGAAG
Found at i:18726302 original size:66 final size:66
Alignment explanation
Indices: 18726192--18726359 Score: 194
Period size: 66 Copynumber: 2.5 Consensus size: 66
18726182 CAAGAACTTA
* * * * ** *
18726192 AGAAGACCCGATATCTCGTTTAGGAGCTTTGGAAGACTCAATATCTTGTTCAAGATCTTGGGATT
1 AGAAGACCTGATATCTCGTTCAGAAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGGGATT
18726257 G
66 G
* * ** *
18726258 AGAAGACCTGATATTTTGTTCAGAAGCTTGGGAAGACTTGATATCGAGTTCAGGAGCTTGGGATT
1 AGAAGACCTGATATCTCGTTCAGAAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGGGATT
18726323 G
66 G
* *
18726324 AGAAGACCTGATATCTCGTCCA-AGAGTTTGGGAAGA
1 AGAAGACCTGATATCTCGTTCAGA-AGCTTGGGAAGA
18726360 TCTGATATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
65 1 0.01
66 84 0.99
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (66 bp):
AGAAGACCTGATATCTCGTTCAGAAGCTTGGGAAGACTCAATATCGAGTTCAAGAGCTTGGGATT
G
Found at i:18728198 original size:31 final size:31
Alignment explanation
Indices: 18728163--18728231 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
18728153 CTTAACAACC
*
18728163 CAGTGACTTAAA-CAAAAGCTTTTAAAT-GTTT
1 CAGTGACTTAAATCAAAA-CTTTCAAATAG-TT
* *
18728194 CAGTGATTTAAATGAAAACTTTCAAATAGTT
1 CAGTGACTTAAATCAAAACTTTCAAATAGTT
18728225 CAGTGAC
1 CAGTGAC
18728232 CAATTCTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (31 bp):
CAGTGACTTAAATCAAAACTTTCAAATAGTT
Found at i:18733044 original size:22 final size:22
Alignment explanation
Indices: 18733009--18733066 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
18732999 AAATGGTATC
* *
18733009 TACAAATTAAATCTT-TAAGAT
1 TACAAATCATATCTTCTAAGAT
18733030 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
18733053 TGCATATCATATCT
1 TACAAATCATATCT
18733067 AAGACTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 20 0.65
23 8 0.26
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:18734231 original size:5 final size:5
Alignment explanation
Indices: 18734221--18734253 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
18734211 AAAACTCATA
18734221 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
18734254 CTAGTCACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:18740046 original size:47 final size:49
Alignment explanation
Indices: 18739925--18740051 Score: 134
Period size: 49 Copynumber: 2.6 Consensus size: 49
18739915 GTTTTCACAT
* * *
18739925 TGCCATAGTCCA-ACTATGGTCTTACATGTAATCACATATCACATACCGA
1 TGCCATAGCCCAGA-TATGGTCTTACACGGAATCACATATCACATACCGA
* * *
18739974 TGCCATAGCCCAGCTATAGTCTTACACGGAATCACATATCACA-A-TGA
1 TGCCATAGCCCAGATATGGTCTTACACGGAATCACATATCACATACCGA
** * *
18740021 TGCCATATTCTAGATATGGTTTTACACGGAA
1 TGCCATAGCCCAGATATGGTCTTACACGGAA
18740052 ATTTCATAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 27 0.42
48 1 0.02
49 37 0.57
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (49 bp):
TGCCATAGCCCAGATATGGTCTTACACGGAATCACATATCACATACCGA
Found at i:18747242 original size:52 final size:53
Alignment explanation
Indices: 18747146--18747249 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
18747136 AAGCAAACGA
*
18747146 AAAAAAGTTTTGGGGTTTGGGGGAAGTAAAATTTTTGAGGGGGAAGTAAAAGC
1 AAAAAAGTTTTGGGGTTTGGGGGAAGTAAAATTTTTGAGAGGGAAGTAAAAGC
* *
18747199 AAAAAGGTTTTGGGGTTT-GGGGATTA-TAAAATTTTTTA-AGGGAAGTAAAAG
1 AAAAAAGTTTTGGGGTTTGGGGGA--AGTAAAATTTTTGAGAGGGAAGTAAAAG
18747250 TTTTAGGGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
52 17 0.37
53 28 0.61
54 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.33, T:0.30
Consensus pattern (53 bp):
AAAAAAGTTTTGGGGTTTGGGGGAAGTAAAATTTTTGAGAGGGAAGTAAAAGC
Found at i:18747302 original size:66 final size:65
Alignment explanation
Indices: 18747225--18747348 Score: 221
Period size: 66 Copynumber: 1.9 Consensus size: 65
18747215 TTGGGGATTA
* *
18747225 TAAAATTTTTTAAGGGAAGTAAAAGTTTTAGGGGGAAAGTAAAAGGAAAAAAGGTTTTAGGGAAT
1 TAAAATATTTTAAGGGAAGTAAAAGTTTAAGGGGGAAAGTAAAAGGAAAAAA-GTTTTAGGGAAT
18747290 G
65 G
18747291 TAAAATATTTTAAGGGAAGTAAAAGTTTAAGGGGGAAAGTAAAAGGAAAAAAGTTTTA
1 TAAAATATTTTAAGGGAAGTAAAAGTTTAAGGGGGAAAGTAAAAGGAAAAAAGTTTTA
18747349 AGGTTTGGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 6 0.11
66 50 0.89
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (65 bp):
TAAAATATTTTAAGGGAAGTAAAAGTTTAAGGGGGAAAGTAAAAGGAAAAAAGTTTTAGGGAATG
Found at i:18749194 original size:27 final size:27
Alignment explanation
Indices: 18749163--18749215 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
18749153 AAAGTGAACA
* * *
18749163 AAAAAGAGAAAAATAATAGAAAATATG
1 AAAAAGAAAAAAATAAAAAAAAATATG
*
18749190 AAAAATAAAAAAATAAAAAAAAATAT
1 AAAAAGAAAAAAATAAAAAAAAATAT
18749216 CATATGAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (27 bp):
AAAAAGAAAAAAATAAAAAAAAATATG
Found at i:18750178 original size:26 final size:26
Alignment explanation
Indices: 18750093--18750181 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
18750083 ATTTTATCAA
*
18750093 TAAATTATGGATATAGTTAAATATAT
1 TAAATAATGGATATAGTTAAATATAT
** * * * ** *
18750119 TACTTAATGAAAATTCAATTATTTATCAA
1 TAAATAATGGATA-T-AGTTAAATAT-AT
18750148 TAAATAATGGATATAGTTAAATATAT
1 TAAATAATGGATATAGTTAAATATAT
18750174 TAAATAAT
1 TAAATAAT
18750182 TAGAATTTTA
Statistics
Matches: 43, Mismatches: 17, Indels: 6
0.65 0.26 0.09
Matches are distributed among these distances:
26 17 0.40
27 8 0.19
28 8 0.19
29 10 0.23
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAATAATGGATATAGTTAAATATAT
Found at i:18756666 original size:51 final size:50
Alignment explanation
Indices: 18756539--18756679 Score: 162
Period size: 50 Copynumber: 2.8 Consensus size: 50
18756529 GTGAAAGTGA
* *
18756539 AAGTGATGGTCACGTGTGTAGTACTTTGTGCAGGCTACTACGCATACTAG
1 AAGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCATACTAG
* * * *
18756589 AA-AGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTACATGTAT-C-GG
1 AAGTGAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTAC--GCATACTAG
*
18756639 ATAGTGATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 A-AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
18756680 TGTGAACCTG
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
49 3 0.04
50 35 0.45
51 33 0.43
52 6 0.08
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
AAGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGCATACTAG
Found at i:18756926 original size:38 final size:38
Alignment explanation
Indices: 18756884--18756960 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
18756874 ATGTGTGGAA
* *
18756884 TTGAATTGAATATTGACTTGAAAATGGAAAAGT-GAATT
1 TTGAATTGAATAGTGA-TTGAAAATGAAAAAGTAGAATT
*
18756922 TTGAATTGAATAGTGATTGAAAGTGAAAAAGTAGAATT
1 TTGAATTGAATAGTGATTGAAAATGAAAAAGTAGAATT
18756960 T
1 T
18756961 GCAACAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 14 0.40
38 21 0.60
ACGTcount: A:0.43, C:0.01, G:0.22, T:0.34
Consensus pattern (38 bp):
TTGAATTGAATAGTGATTGAAAATGAAAAAGTAGAATT
Found at i:18770580 original size:5 final size:5
Alignment explanation
Indices: 18770570--18770612 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
18770560 ATTAGTTTAT
* *
18770570 AAATA AAATA AAATA AAA-A TATATA TAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAATA AAATA AAA
18770613 ATAGAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.03
5 30 0.94
6 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:18770603 original size:25 final size:24
Alignment explanation
Indices: 18770567--18770615 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
18770557 GGAATTAGTT
18770567 TATAAATAAAATAAAATAAAAATA
1 TATAAATAAAATAAAATAAAAATA
18770591 TATATAATAAAATAAAATAAAAATA
1 TATA-AATAAAATAAAATAAAAATA
18770616 GAATTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
TATAAATAAAATAAAATAAAAATA
Found at i:18779181 original size:42 final size:42
Alignment explanation
Indices: 18779104--18779302 Score: 201
Period size: 43 Copynumber: 4.7 Consensus size: 42
18779094 CTCGGTGGAT
* **
18779104 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGTGAA
1 TCAGCACATAGCAACCACCTTTACAA-TCAAAGATACGGTGAA
18779145 TCAGCACATAGCAACC-CCTTTCACAATCAAAGATACGGTGGAA
1 TCAGCACATAGCAACCACCTTT-ACAATCAAAGATACGGT-GAA
* * * **
18779188 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACTGG-GAA
1 TCAGCACATAGCAACCACCTTTACAATCAAAGATAC-GGTGAA
*
18779230 TCAGCACATAGCAACC-CCTTTCACAATCAAATATACGGTTGAA
1 TCAGCACATAGCAACCACCTTT-ACAATCAAAGATACGG-TGAA
* * *
18779273 TCAGCACTTAACAACCACCTTTAGAATCAA
1 TCAGCACATAGCAACCACCTTTACAATCAA
18779303 TAATTTGAGG
Statistics
Matches: 131, Mismatches: 17, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
40 2 0.02
41 24 0.18
42 39 0.30
43 54 0.41
44 12 0.09
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.24
Consensus pattern (42 bp):
TCAGCACATAGCAACCACCTTTACAATCAAAGATACGGTGAA
Found at i:18779193 original size:43 final size:43
Alignment explanation
Indices: 18779096--18779330 Score: 225
Period size: 42 Copynumber: 5.6 Consensus size: 43
18779086 ATCCATTACT
* **
18779096 CGGTGGATTCAGCACTTAGCAACCACC-TTA-AATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAA-TCAAAGATA
*
18779138 CGGT-GAATCAGCACATAGCAACC-CCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAAAGATA
* * **
18779180 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAAAGATA
* * *
18779223 CTG-GGAATCAGCACATAGCAACC-CCTTTCACAATCAAATATA
1 CGGTGGAATCAGCACTTAGCAACCACCTTT-ACAATCAAAGATA
* * *
18779265 CGGTTGAATCAGCACTTAACAACCACCTTTAGAATCAATA-AT-
1 CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAA-AGATA
** *
18779307 TTGAGGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
18779331 TCTCGGGGAA
Statistics
Matches: 158, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
40 2 0.01
41 24 0.15
42 64 0.41
43 57 0.36
44 11 0.07
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTACAATCAAAGATA
Found at i:18779242 original size:85 final size:85
Alignment explanation
Indices: 18779096--18779330 Score: 334
Period size: 85 Copynumber: 2.8 Consensus size: 85
18779086 ATCCATTACT
*
18779096 CGGTGGATTCAGCACTTAGCAACCACC-TTAAATTCAGTGATAC-GGTGAATCAGCACATAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACTGG-GAATCAGCACATAGCAA
18779159 CCCCTTTCACAATCAAAGATA
65 CCCCTTTCACAATCAAAGATA
*
18779180 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACTGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACTGGGAATCAGCACATAGCAAC
*
18779245 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * * * * *
18779265 CGGTTGAATCAGCACTTAACAACCACCTTTAGAA-TCAATAAT-TTGAGGAATCAGCACTTAGCA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAGTGATACTG-GGAATCAGCACATAGCA
18779328 ACC
64 ACC
18779331 TCTCGGGGAA
Statistics
Matches: 137, Mismatches: 10, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
84 28 0.20
85 106 0.77
86 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATACTGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:18779322 original size:42 final size:41
Alignment explanation
Indices: 18779104--18779330 Score: 178
Period size: 43 Copynumber: 5.4 Consensus size: 41
18779094 CTCGGTGGAT
* * *
18779104 TCAGCACTTAGCAACCACC-TTA-AATTCAGTGATACGGTGAA
1 TCAGCACTTAGCAACCACCTTTACAA-TCAATAATATGG-GAA
* *
18779145 TCAGCACATAGCAACC-CCTTTCACAATCAA-AGATACGGTGGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATA-ATA-TG-GGAA
* * * *
18779188 TCAGCACTTAGCAACCACCTTTATATTCAGTGATACTGGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATAATA-TGGGAA
* *
18779230 TCAGCACATAGCAACC-CCTTTCACAATCAA-ATATACGGTTGAA
1 TCAGCACTTAGCAACCACCTTT-ACAATCAATA-ATATGG--GAA
* * *
18779273 TCAGCACTTAACAACCACCTTTAGAATCAATAATTTGAGGAA
1 TCAGCACTTAGCAACCACCTTTACAATCAATAATATG-GGAA
18779315 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
18779331 TCTCGGGGAA
Statistics
Matches: 149, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
40 2 0.01
41 24 0.16
42 52 0.35
43 58 0.39
44 13 0.09
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.24
Consensus pattern (41 bp):
TCAGCACTTAGCAACCACCTTTACAATCAATAATATGGGAA
Found at i:18779733 original size:30 final size:30
Alignment explanation
Indices: 18779697--18779753 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
18779687 TCCTTAACTC
*
18779697 AAACTTTTGTAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
18779727 AAACTTTTGCATATTTACACTTTTGCC
1 AAACTTTTGCAAAATTACAATTTTGCC
18779754 TGAAAGCTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:18783552 original size:14 final size:14
Alignment explanation
Indices: 18783533--18783562 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18783523 TATGTGTATC
18783533 CATTTAACAATTAA
1 CATTTAACAATTAA
*
18783547 CATTTAACATTTAA
1 CATTTAACAATTAA
18783561 CA
1 CA
18783563 ATTTTCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (14 bp):
CATTTAACAATTAA
Found at i:18794573 original size:27 final size:27
Alignment explanation
Indices: 18794508--18794574 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
18794498 AAACACAAGA
**
18794508 TAGTCCACTGGGACATTAAAAACGGGG
1 TAGTCCACCAGGACATTAAAAACGGGG
* *
18794535 TAGTCCATCAGGACATTAAAAATGGGG
1 TAGTCCACCAGGACATTAAAAACGGGG
*
18794562 TAGTCCGCCAGGA
1 TAGTCCACCAGGA
18794575 AGTGAAACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.19
Consensus pattern (27 bp):
TAGTCCACCAGGACATTAAAAACGGGG
Found at i:18795885 original size:45 final size:45
Alignment explanation
Indices: 18795821--18795919 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 45
18795811 GTAACGGTAG
* *
18795821 CAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAAT-GTGTAA
1 CAGTAACAGAAACAGTATTCAACACACAAAGTGTC-GAATCG-ATAA
*
18795866 CAGTAACAGAAATAGTATTCAACACACAAAGTGTCGAATCGATAA
1 CAGTAACAGAAACAGTATTCAACACACAAAGTGTCGAATCGATAA
18795911 CAGTAACAG
1 CAGTAACAG
18795920 TAGTCGGCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.20
Consensus pattern (45 bp):
CAGTAACAGAAACAGTATTCAACACACAAAGTGTCGAATCGATAA
Found at i:18796168 original size:19 final size:19
Alignment explanation
Indices: 18796144--18796186 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
18796134 CAGTTCAATG
*
18796144 CAGTACACATAACAATATT
1 CAGTACACAAAACAATATT
*
18796163 CAGTACTCAAAACAATATT
1 CAGTACACAAAACAATATT
18796182 CAGTA
1 CAGTA
18796187 TTCCATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (19 bp):
CAGTACACAAAACAATATT
Found at i:18800496 original size:22 final size:22
Alignment explanation
Indices: 18800471--18800513 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
18800461 AAAAAATTAT
18800471 ATTTATA-AATATAAAAGTTTTC
1 ATTTATATAAT-TAAAAGTTTTC
* *
18800493 ATTTTTATAATTTAAAGTTTT
1 ATTTATATAATTAAAAGTTTT
18800514 AAAATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
ATTTATATAATTAAAAGTTTTC
Found at i:18800700 original size:29 final size:29
Alignment explanation
Indices: 18800658--18800715 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
18800648 TTAGATGTTA
18800658 GTAAAAAAAATTACATACTTGGTAAATGT
1 GTAAAAAAAATTACATACTTGGTAAATGT
*
18800687 GTAAAAATAATTACATACTTGGTAAATGT
1 GTAAAAAAAATTACATACTTGGTAAATGT
18800716 CATTTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.33
Consensus pattern (29 bp):
GTAAAAAAAATTACATACTTGGTAAATGT
Found at i:18801785 original size:28 final size:28
Alignment explanation
Indices: 18801754--18801848 Score: 77
Period size: 28 Copynumber: 3.2 Consensus size: 28
18801744 AGAGCTTTCA
18801754 AAATGAGAGTGTTTTGTAGTGTATCATC
1 AAATGAGAGTGTTTTGTAGTGTATCATC
** * * *
18801782 AAATGAGTTTTTTAAAATTG-AGAG-AGCCATC
1 AAATGAGAGTGTT----TTGTAGTGTA-TCATC
18801813 AAAATGAGAGTGTTTTGTAGTGTATCATC
1 -AAATGAGAGTGTTTTGTAGTGTATCATC
18801842 AAATGAG
1 AAATGAG
18801849 TTTTTTTGTA
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
28 20 0.41
29 7 0.14
30 2 0.04
31 7 0.14
32 13 0.27
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (28 bp):
AAATGAGAGTGTTTTGTAGTGTATCATC
Found at i:18801803 original size:60 final size:60
Alignment explanation
Indices: 18801739--18801854 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
18801729 ATTTTTTTTT
**
18801739 TTGAGAGAGCTTTCAAAATGAGAGTGTTTTGTAGTGTATCATCAAATGAGTTTTTTAAAA
1 TTGAGAGAGCCATCAAAATGAGAGTGTTTTGTAGTGTATCATCAAATGAGTTTTTTAAAA
18801799 TTGAGAGAGCCATCAAAATGAGAGTGTTTTGTAGTGTATCATCAAATGAGTTTTTT
1 TTGAGAGAGCCATCAAAATGAGAGTGTTTTGTAGTGTATCATCAAATGAGTTTTTT
18801855 TGTAATGGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (60 bp):
TTGAGAGAGCCATCAAAATGAGAGTGTTTTGTAGTGTATCATCAAATGAGTTTTTTAAAA
Found at i:18802225 original size:7 final size:7
Alignment explanation
Indices: 18802213--18802237 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18802203 TAATGTAGTC
18802213 GTTTAAG
1 GTTTAAG
18802220 GTTTAAG
1 GTTTAAG
18802227 GTTTAAG
1 GTTTAAG
18802234 GTTT
1 GTTT
18802238 CATTTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
GTTTAAG
Found at i:18802405 original size:90 final size:89
Alignment explanation
Indices: 18802294--18802547 Score: 384
Period size: 90 Copynumber: 2.8 Consensus size: 89
18802284 TTTGTATCTG
18802294 TAAATTTAATTTAGTTCGTATTATATGTAGTTTGAGTTTAAAATTTTCGTGTATTAATTTTACCC
1 TAAATTTAATTTAGTT-GTATTATATGTAGTTTGAGTTTAAAATTTTCGTGTATTAATTTTACCC
*
18802359 ATCTGTTTGTAGTTTGTTGGGTGTT
65 ATCTGTTTATAGTTTGTTGGGTGTT
* * * **
18802384 TAAATTTAATTTTGTATGTATTATATATAGTTTGAATTTAAAATTTTCGTGCGTTAATTTTACCC
1 TAAATTTAATTTAGT-TGTATTATATGTAGTTTGAGTTTAAAATTTTCGTGTATTAATTTTACCC
*
18802449 ATCTGTCTATAGTTTGTTGGGTGTT
65 ATCTGTTTATAGTTTGTTGGGTGTT
*
18802474 TAAATTTAATTTAGTCTGTATTATACGTAGTTTG-GATTTAAAATTTTCGTGTATTAATTTTACC
1 TAAATTTAATTTAGT-TGTATTATATGTAGTTTGAG-TTTAAAATTTTCGTGTATTAATTTTACC
*
18802538 CATTTGTTTA
64 CATCTGTTTA
18802548 ATATTCTAGA
Statistics
Matches: 146, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
90 145 0.99
91 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (89 bp):
TAAATTTAATTTAGTTGTATTATATGTAGTTTGAGTTTAAAATTTTCGTGTATTAATTTTACCCA
TCTGTTTATAGTTTGTTGGGTGTT
Found at i:18802684 original size:22 final size:20
Alignment explanation
Indices: 18802659--18802708 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
18802649 TTATTCAAAC
*
18802659 AAATAATTATTTTAGAAAAATT
1 AAATAATTATATTA-AAAAA-T
18802681 AAAT--TTATATTAAAAAAT
1 AAATAATTATATTAAAAAAT
18802699 AGAATAATTA
1 A-AATAATTA
18802709 CAAAATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 7 0.29
21 3 0.12
22 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
AAATAATTATATTAAAAAAT
Found at i:18805244 original size:22 final size:22
Alignment explanation
Indices: 18805217--18805264 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
18805207 TTTCCTTCAA
*
18805217 TTTCATTT-CATTTAAATTTTTT
1 TTTCATTTAAATTT-AATTTTTT
18805239 TTTCATTTAAATTTAATTTTTT
1 TTTCATTTAAATTTAATTTTTT
18805261 TTTC
1 TTTC
18805265 TCGTTTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCATTTAAATTTAATTTTTT
Found at i:18805258 original size:17 final size:17
Alignment explanation
Indices: 18805222--18805258 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
18805212 TTCAATTTCA
**
18805222 TTTCATTTAAATTTTTT
1 TTTCATTTAAATTTAAT
18805239 TTTCATTTAAATTTAAT
1 TTTCATTTAAATTTAAT
18805256 TTT
1 TTT
18805259 TTTTTCTCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCATTTAAATTTAAT
Found at i:18805379 original size:5 final size:5
Alignment explanation
Indices: 18805369--18805498 Score: 71
Period size: 5 Copynumber: 23.4 Consensus size: 5
18805359 TCATTTAAAC
* * *
18805369 TTTCA TTTCA TTTCA TAATCA TTACAAA ATTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA T-TTCA TTTC--A TTTCA TTTCA TTTCA TTTCA
* * * * *
18805417 TATTAA TTTAACA TTTCA TTTCA TTTGAA TATTCA TTACAAA TTACA TTACA
1 T-TTCA TTT--CA TTTCA TTTCA TTT-CA T-TTCA TTTC--A TTTCA TTTCA
18805469 TTTCA TATTCA TTTAACA TTTCA TTTCA TT
1 TTTCA T-TTCA TTT--CA TTTCA TTTCA TT
18805499 AGTTTTTTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
5 64 0.64
6 17 0.17
7 19 0.19
ACGTcount: A:0.33, C:0.16, G:0.01, T:0.50
Consensus pattern (5 bp):
TTTCA
Found at i:18805381 original size:23 final size:23
Alignment explanation
Indices: 18805333--18805381 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
18805323 TCAGTTTTTG
* * *
18805333 TTTTCATTTCAATTTATTATTTA
1 TTTTCATTTAAACTTATCATTTA
18805356 TTTTCATTTAAACTT-TCATTTCA
1 TTTTCATTTAAACTTATCATTT-A
18805379 TTT
1 TTT
18805382 CATAATCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTCATTTAAACTTATCATTTA
Found at i:18805391 original size:28 final size:29
Alignment explanation
Indices: 18805358--18805498 Score: 139
Period size: 28 Copynumber: 4.8 Consensus size: 29
18805348 ATTATTTATT
18805358 TTCATTTAAAC-TTTCATTTCATTTCATA
1 TTCATTTAAACATTTCATTTCATTTCATA
* *
18805386 ATCATTACAAAATTCATTTCATTTCATTTCATA
1 TTCATT--TAAA--CATTTCATTTCATTTCATA
* *
18805419 TTAATTT-AACATTTCATTTCATTTGAATA
1 TTCATTTAAACATTTCATTTCATTT-CATA
* *
18805448 TTCA-TTACAA-ATTACATTACATTTCATA
1 TTCATTTA-AACATTTCATTTCATTTCATA
18805476 TTCATTT-AACATTTCATTTCATT
1 TTCATTTAAACATTTCATTTCATT
18805499 AGTTTTTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.02
28 40 0.44
29 20 0.22
30 7 0.08
32 1 0.01
33 21 0.23
ACGTcount: A:0.33, C:0.16, G:0.01, T:0.50
Consensus pattern (29 bp):
TTCATTTAAACATTTCATTTCATTTCATA
Found at i:18805411 original size:33 final size:32
Alignment explanation
Indices: 18805369--18805480 Score: 115
Period size: 33 Copynumber: 3.5 Consensus size: 32
18805359 TCATTTAAAC
*
18805369 TTTCATTTCATTTCATAATCATTACAAAATTCA
1 TTTCATTTCATTTCATATTCATTAC-AAATTCA
* *
18805402 TTTCATTTCATTTCATATTAATT--TAA--CA
1 TTTCATTTCATTTCATATTCATTACAAATTCA
*
18805430 TTTCATTTCATTTGAATATTCATTACAAATTACA
1 TTTCATTTCATTT-CATATTCATTACAAATT-CA
*
18805464 TTACATTTCATATTCAT
1 TTTCATTTCAT-TTCAT
18805481 TTAACATTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
28 15 0.23
29 8 0.12
30 2 0.03
31 2 0.03
33 21 0.33
34 14 0.22
35 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.01, T:0.49
Consensus pattern (32 bp):
TTTCATTTCATTTCATATTCATTACAAATTCA
Found at i:18805488 original size:57 final size:59
Alignment explanation
Indices: 18805358--18805498 Score: 182
Period size: 57 Copynumber: 2.4 Consensus size: 59
18805348 ATTATTTATT
* *
18805358 TTCATTTAA-ACTTTCATTTCATTTCATAATCATTACAAAATTCATTTCATTTCATTTCATA
1 TTCATTTAACA-TTTCATTTCATTTAATAATCATTACAAAATTCA--TCATTACATTTCATA
* *
18805419 TTAATTTAACATTTCATTTCATTTGAATATTCATTAC-AAATT-A-CATTACATTTCATA
1 TTCATTTAACATTTCATTTCATTT-AATAATCATTACAAAATTCATCATTACATTTCATA
18805476 TTCATTTAACATTTCATTTCATT
1 TTCATTTAACATTTCATTTCATT
18805499 AGTTTTTTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
57 35 0.48
60 1 0.01
61 26 0.36
62 11 0.15
ACGTcount: A:0.33, C:0.16, G:0.01, T:0.50
Consensus pattern (59 bp):
TTCATTTAACATTTCATTTCATTTAATAATCATTACAAAATTCATCATTACATTTCATA
Found at i:18805601 original size:20 final size:20
Alignment explanation
Indices: 18805576--18805630 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
18805566 GTAGTCTCAT
18805576 TTCAATTTATTTTT-TTTCAA
1 TTCAATTT-TTTTTATTTCAA
*
18805596 TTCAATTTTTTTTCATTTCAT
1 TTCAATTTTTTTT-ATTTCAA
18805617 TTCATATTTTTTTT
1 TTCA-ATTTTTTTT
18805631 CATACTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.16
20 8 0.26
21 9 0.29
22 9 0.29
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCAATTTTTTTTATTTCAA
Found at i:18805605 original size:16 final size:16
Alignment explanation
Indices: 18805575--18805615 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
18805565 AGTAGTCTCA
*
18805575 TTTCAATT-TATTTTT
1 TTTCAATTCAATTTTT
18805590 TTTCAATTCAATTTTT
1 TTTCAATTCAATTTTT
*
18805606 TTTCATTTCA
1 TTTCAATTCA
18805616 TTTCATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTCAATTCAATTTTT
Found at i:18805620 original size:21 final size:21
Alignment explanation
Indices: 18805572--18805633 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
18805562 ACAAGTAGTC
18805572 TCATTTCAATTTATTTTT--TT
1 TCATTTCAATTT-TTTTTCATT
*
18805592 TCAATTCAATTTTTTTTCATT
1 TCATTTCAATTTTTTTTCATT
18805613 TCATTTCATATTTTTTTTCAT
1 TCATTTCA-ATTTTTTTTCAT
18805634 ACTAATTAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.14
20 11 0.30
21 9 0.24
22 12 0.32
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.66
Consensus pattern (21 bp):
TCATTTCAATTTTTTTTCATT
Found at i:18805706 original size:21 final size:21
Alignment explanation
Indices: 18805659--18805698 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18805649 TCTCAATTAC
18805659 ATTTTATTTAAATTTTTTCAT
1 ATTTTATTTAAATTTTTTCAT
*
18805680 ATTTTATTTAAACTTTTTC
1 ATTTTATTTAAATTTTTTC
18805699 TCAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTATTTAAATTTTTTCAT
Found at i:18806171 original size:29 final size:29
Alignment explanation
Indices: 18806070--18806172 Score: 138
Period size: 29 Copynumber: 3.6 Consensus size: 29
18806060 ATGGTAATTT
*
18806070 ATTTCAT-TTCAATTT-ATACTTTATTTTC
1 ATTTCATATTC-ATTTCATATTTTATTTTC
* *
18806098 ATTTCATATTCATTTAATATTTTAGTTTC
1 ATTTCATATTCATTTCATATTTTATTTTC
* *
18806127 ATTTCAAACTCATTTCATATTTTATTTTC
1 ATTTCATATTCATTTCATATTTTATTTTC
18806156 ATTTCATATTCATTTCA
1 ATTTCATATTCATTTCA
18806173 CTTTATTCAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.17
29 54 0.83
ACGTcount: A:0.27, C:0.15, G:0.01, T:0.57
Consensus pattern (29 bp):
ATTTCATATTCATTTCATATTTTATTTTC
Done.