Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 136 of 240
Found at i:42279053 original size:25 final size:25
Alignment explanation
Indices: 42279004--42279054 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
42278994 CTTTCTATTC
* *
42279004 AAAAAATGGATAAATTAATTAATAT
1 AAAAAATAGATAAAATAATTAATAT
* *
42279029 AAAAAATAGATAAAATAGTTCATAT
1 AAAAAATAGATAAAATAATTAATAT
42279054 A
1 A
42279055 GGTTACATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AAAAAATAGATAAAATAATTAATAT
Found at i:42279115 original size:23 final size:23
Alignment explanation
Indices: 42279086--42279131 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
42279076 TTTTTTTTGC
*
42279086 TAAAAATTTCATTTATTTATGTTG
1 TAAAATTTTCATTT-TTTATGTTG
*
42279110 TAAAATTTTCATTTTTTTTGTT
1 TAAAATTTTCATTTTTTATGTT
42279132 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (23 bp):
TAAAATTTTCATTTTTTATGTTG
Found at i:42280360 original size:16 final size:17
Alignment explanation
Indices: 42280339--42280394 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
42280329 TTTAAAAAAC
42280339 ATTTTTAATATTTTAT-
1 ATTTTTAATATTTTATA
* *
42280355 ATTTTTAATAATTCATA
1 ATTTTTAATATTTTATA
*
42280372 ATTTTTATATATTTTAAA
1 ATTTTTA-ATATTTTATA
42280390 ATTTT
1 ATTTT
42280395 AAAAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
16 14 0.42
17 7 0.21
18 12 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTTAATATTTTATA
Found at i:42280379 original size:25 final size:26
Alignment explanation
Indices: 42280344--42280392 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
42280334 AAAACATTTT
42280344 TAATATTTTATAT-TTTTAATAATTCA
1 TAATATTTTATATATTTTAA-AATTCA
42280370 TAAT-TTTTATATATTTTAAAATT
1 TAATATTTTATATATTTTAAAATT
42280393 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TAATATTTTATATATTTTAAAATTCA
Found at i:42285239 original size:23 final size:23
Alignment explanation
Indices: 42285213--42285258 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42285203 AAATTGGTTT
42285213 GGCACACTAAAAAATTTAAAATA
1 GGCACACTAAAAAATTTAAAATA
42285236 GGCACACTAAAAAATTTAAAATA
1 GGCACACTAAAAAATTTAAAATA
42285259 AGTAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.57, C:0.13, G:0.09, T:0.22
Consensus pattern (23 bp):
GGCACACTAAAAAATTTAAAATA
Found at i:42288671 original size:31 final size:32
Alignment explanation
Indices: 42288585--42288664 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 32
42288575 CCTGTTAAAA
*
42288585 TTACTCCTAAAATCATACCACAAACACTTAAC
1 TTACTCCTAAAATCATGCCACAAACACTTAAC
42288617 TTACTCCTAAAATCATGCCACAAACACTTAAC
1 TTACTCCTAAAATCATGCCACAAACACTTAAC
42288649 TTACT-CTAAAATCATG
1 TTACTCCTAAAATCATG
42288665 TAACAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 11 0.23
32 36 0.77
ACGTcount: A:0.41, C:0.29, G:0.03, T:0.28
Consensus pattern (32 bp):
TTACTCCTAAAATCATGCCACAAACACTTAAC
Found at i:42291399 original size:15 final size:15
Alignment explanation
Indices: 42291379--42291408 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42291369 TTAGTAAAAA
42291379 CACTCATCTCCTTTT
1 CACTCATCTCCTTTT
*
42291394 CACTCATTTCCTTTT
1 CACTCATCTCCTTTT
42291409 TAATTTCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.37, G:0.00, T:0.50
Consensus pattern (15 bp):
CACTCATCTCCTTTT
Found at i:42295156 original size:27 final size:27
Alignment explanation
Indices: 42295112--42295197 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
42295102 AGCAAATCGG
*
42295112 TACCCTTCAAGGGTATTTCGGTAATTT
1 TACCCTTCAGGGGTATTTCGGTAATTT
* *
42295139 TATCCTTCAGGGGCATTTCGGTAATTT
1 TACCCTTCAGGGGTATTTCGGTAATTT
**
42295166 TACCCTT-AGAGGGTATTTTAGTAATTT
1 TACCCTTCAG-GGGTATTTCGGTAATTT
42295193 TACCC
1 TACCC
42295198 ATCGAGTCGC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.04
27 49 0.96
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (27 bp):
TACCCTTCAGGGGTATTTCGGTAATTT
Found at i:42295504 original size:44 final size:44
Alignment explanation
Indices: 42295439--42295526 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
42295429 CAAATTCAGC
* * *
42295439 ACAAGCATACTCCATATGGCACACAACTCTTCCTTTCCCACAAA
1 ACAAGCATACTCCATACGGCACACAACTCCTCCTCTCCCACAAA
42295483 ACAAGCATACTCCATACGGCACACAACTCCTCCTCTCCCACAAA
1 ACAAGCATACTCCATACGGCACACAACTCCTCCTCTCCCACAAA
42295527 CTCCTTGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.34, C:0.40, G:0.07, T:0.19
Consensus pattern (44 bp):
ACAAGCATACTCCATACGGCACACAACTCCTCCTCTCCCACAAA
Found at i:42298232 original size:50 final size:53
Alignment explanation
Indices: 42298157--42298297 Score: 207
Period size: 56 Copynumber: 2.7 Consensus size: 53
42298147 ACATGTCAAA
*
42298157 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-GTCTC-GG-TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATGCCAAT
42298207 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--AATCTC-AGGATGCCAAT
* *
42298263 GTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42298298 TTGCCCAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
50 36 0.44
53 4 0.05
55 2 0.02
56 40 0.49
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (53 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAATCTCAGGATGCCAAT
Found at i:42301660 original size:8 final size:8
Alignment explanation
Indices: 42301647--42301673 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
42301637 AATTAAAAAG
42301647 TATAAGAA
1 TATAAGAA
42301655 TATAAGAA
1 TATAAGAA
42301663 TATAAGAA
1 TATAAGAA
42301671 TAT
1 TAT
42301674 TTTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (8 bp):
TATAAGAA
Found at i:42304165 original size:3 final size:3
Alignment explanation
Indices: 42304147--42304196 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
42304137 AGGTCAAACC
* * *
42304147 TCA TCA TAA TCT TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
42304195 TC
1 TC
42304197 TTCAATATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:42305441 original size:15 final size:14
Alignment explanation
Indices: 42305399--42305441 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
42305389 TTACAAAAAG
*
42305399 AAAAAAAAATCCCA
1 AAAAAAAAATCCCC
42305413 AAAAAAAAATCCCC
1 AAAAAAAAATCCCC
42305427 AAAAAAAAAGTCCCC
1 AAAAAAAAA-TCCCC
42305442 CCTTTTAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.65, C:0.26, G:0.02, T:0.07
Consensus pattern (14 bp):
AAAAAAAAATCCCC
Found at i:42306532 original size:30 final size:30
Alignment explanation
Indices: 42306489--42306554 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
42306479 TTAAATTTTT
* * *
42306489 TATAAAAATTAAATTTTTAATTTTTTTAAA
1 TATAAAAACTAAATTTTAAATTTTATTAAA
*
42306519 TATAAGAACTAAATTTTAAATTTTATTAAA
1 TATAAAAACTAAATTTTAAATTTTATTAAA
42306549 T-TAAAA
1 TATAAAA
42306555 GGATTAACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TATAAAAACTAAATTTTAAATTTTATTAAA
Found at i:42306830 original size:32 final size:32
Alignment explanation
Indices: 42306787--42306850 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
42306777 GCAAAAAAAA
* * * *
42306787 CTTGTTGTTTTTTATTATTTTGTTGCTATTTT
1 CTTGTTATTTTTTACTATTTTGCTACTATTTT
42306819 CTTGTTATTTTTTACTATTTTGCTACTATTTT
1 CTTGTTATTTTTTACTATTTTGCTACTATTTT
42306851 AATATTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.69
Consensus pattern (32 bp):
CTTGTTATTTTTTACTATTTTGCTACTATTTT
Found at i:42306859 original size:32 final size:32
Alignment explanation
Indices: 42306794--42306861 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
42306784 AAACTTGTTG
* * * ** *
42306794 TTTTTTATTATTTTGTTGCTATTTTCTTGTTA
1 TTTTTTACTATTTTGCTACTATTTTAATATTA
42306826 TTTTTTACTATTTTGCTACTATTTTAATATTA
1 TTTTTTACTATTTTGCTACTATTTTAATATTA
42306858 TTTT
1 TTTT
42306862 GTTGTTATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.18, C:0.07, G:0.06, T:0.69
Consensus pattern (32 bp):
TTTTTTACTATTTTGCTACTATTTTAATATTA
Found at i:42306869 original size:11 final size:11
Alignment explanation
Indices: 42306794--42306870 Score: 50
Period size: 11 Copynumber: 7.2 Consensus size: 11
42306784 AAACTTGTTG
42306794 TTTT-TTATTA
1 TTTTGTTATTA
**
42306804 TTTTGTTGCTA
1 TTTTGTTATTA
* *
42306815 TTTTCTTGTTA
1 TTTTGTTATTA
*
42306826 TTTT-TTACTA
1 TTTTGTTATTA
* *
42306836 TTTTGCTACTA
1 TTTTGTTATTA
**
42306847 TTTTAATATTA
1 TTTTGTTATTA
*
42306858 TTTTGTTGTTA
1 TTTTGTTATTA
42306869 TT
1 TT
42306871 GTTTGAATAT
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
10 12 0.23
11 40 0.77
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTGTTATTA
Found at i:42306870 original size:22 final size:21
Alignment explanation
Indices: 42306812--42306870 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
42306802 TATTTTGTTG
* *
42306812 CTATTTTCTTGTTATTTTTTA
1 CTATTTTGTTGTTATTTTATA
* **
42306833 CTATTTTGCTACTATTTTAATA
1 CTATTTTGTTGTTATTTT-ATA
*
42306855 TTATTTTGTTGTTATT
1 CTATTTTGTTGTTATT
42306871 GTTTGAATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.19, C:0.08, G:0.07, T:0.66
Consensus pattern (21 bp):
CTATTTTGTTGTTATTTTATA
Found at i:42307051 original size:14 final size:14
Alignment explanation
Indices: 42307014--42307052 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
42307004 TATATTTTTT
42307014 AAAAAATT-ATATA
1 AAAAAATTAATATA
42307027 AAAATAA-TAATATA
1 AAAA-AATTAATATA
42307041 AAAAAATTAATA
1 AAAAAATTAATA
42307053 CAGCCAGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAATTAATATA
Found at i:42309538 original size:84 final size:84
Alignment explanation
Indices: 42309378--42309540 Score: 208
Period size: 84 Copynumber: 1.9 Consensus size: 84
42309368 TGATAAAAAG
* *
42309378 GCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAGTTTAGAGCATGAGGAAGCAGA
1 GCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAGTTTAGAGCATGAAGAACCAGA
*
42309443 AGCAAGTTCAAATAAAATT
66 AGCAAGATCAAATAAAATT
* * *
42309462 GCCAAAGGTGTCACTGAGGACAATGAAACTGAATG-G-ATTATGAGTTT-GAAGTATGAAGAACC
1 GCCAAAGGTGTCACTGAGGACAAGGAAACTGAA-GAGAATT-CGAGTTTAG-AGCATGAAGAACC
42309524 AGAAGCACA-ATCAAATA
63 AGAAGCA-AGATCAAATA
42309541 CATTCACTGC
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
83 4 0.06
84 63 0.91
85 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (84 bp):
GCCAAAGGTGTCACTGAGGACAAGGAAACTGAAGAGAATTCGAGTTTAGAGCATGAAGAACCAGA
AGCAAGATCAAATAAAATT
Found at i:42315604 original size:19 final size:19
Alignment explanation
Indices: 42315568--42315605 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42315558 TCAAGATCTT
*
42315568 TCAATAAAATACTGTTTAA
1 TCAATAAAATACTATTTAA
*
42315587 TCAATAAAATATTATTTAA
1 TCAATAAAATACTATTTAA
42315606 AATTTAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (19 bp):
TCAATAAAATACTATTTAA
Found at i:42325205 original size:6 final size:6
Alignment explanation
Indices: 42325194--42325244 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
42325184 AGAGATATAT
* * *
42325194 AAAATA AAAATAGA AAAATA GAAA-A ATAATG AAAATA AAAATA AAAATA
1 AAAATA AAAAT--A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
42325243 AA
1 AA
42325245 TTTAAGAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
5 3 0.08
6 27 0.75
8 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:42326371 original size:25 final size:25
Alignment explanation
Indices: 42326343--42326394 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
42326333 TTAGGGCAGA
*
42326343 GTTGTTTGAGGT-TTGGGCTGTTTGG
1 GTTGTTTG-GGTATTAGGCTGTTTGG
42326368 GTTGTTTGGGTATTAGGCTGTTTGG
1 GTTGTTTGGGTATTAGGCTGTTTGG
42326393 GT
1 GT
42326395 ATTGGGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.06, C:0.04, G:0.42, T:0.48
Consensus pattern (25 bp):
GTTGTTTGGGTATTAGGCTGTTTGG
Found at i:42326490 original size:22 final size:21
Alignment explanation
Indices: 42326448--42326490 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42326438 GGACTGAACT
*
42326448 TTTATTTATTTTTTTACTTGG
1 TTTATTTATTTTTTTAATTGG
*
42326469 TTTATTTTTTTTATTTAATTGG
1 TTTATTTATTTT-TTTAATTGG
42326491 GCCTGAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.72
Consensus pattern (21 bp):
TTTATTTATTTTTTTAATTGG
Found at i:42326882 original size:98 final size:98
Alignment explanation
Indices: 42326724--42326955 Score: 302
Period size: 98 Copynumber: 2.4 Consensus size: 98
42326714 GCTCCGTTGT
* * ** * * * *
42326724 AACTTTAGGGAGATAAGCCTGGTGGCTTCAAGGTGCTCCACTGCAACTTTAGAAAAATAAGATCC
1 AACTTCAGGGAGATAAGCTTGGTGGCTTCAATCTGCTCAACTGAAACTTCAGAAAAATAAGACCC
42326789 GCCATAATTTGTAGCTTTAATCTGTTCCACTGC
66 GCCATAATTTGTAGCTTTAATCTGTTCCACTGC
* * *
42326822 AACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTGCTCAACTGAAACTTCAGGAAGATAAGACCC
1 AACTTCAGGGAGATAAGCTTGGTGGCTTCAATCTGCTCAACTGAAACTTCAGAAAAATAAGACCC
42326887 GCCATAATTTGTAGCTTTAATCTGTTCCACTGC
66 GCCATAATTTGTAGCTTTAATCTGTTCCACTGC
** * * * *
42326920 AACGCCAGGGAAATAAGATTTGGTGTCTTCAGTCTG
1 AACTTCAGGGAGATAAG-CTTGGTGGCTTCAATCTG
42326956 TTCCGCTGCA
Statistics
Matches: 116, Mismatches: 17, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
98 101 0.87
99 15 0.13
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (98 bp):
AACTTCAGGGAGATAAGCTTGGTGGCTTCAATCTGCTCAACTGAAACTTCAGAAAAATAAGACCC
GCCATAATTTGTAGCTTTAATCTGTTCCACTGC
Found at i:42326992 original size:143 final size:143
Alignment explanation
Indices: 42326809--42327180 Score: 609
Period size: 143 Copynumber: 2.6 Consensus size: 143
42326799 GTAGCTTTAA
* * * *
42326809 TCTGTTCCACTGCAACTTCAGGGAGATAAGGTTGGTGGCTTCAATCTGCTCAACTGAAACTTCAG
1 TCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGAAACTTCAG
*
42326874 GAAGATAAGACCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGAT
66 GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGAT
* * *
42326939 TTGGTGTCTTCAG
131 TCGCTATCTTCAG
* *
42326952 TCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATGTGCTCCACTGCAACTTCAG
1 TCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGAAACTTCAG
* *
42327017 AAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCTACTGCAACGCCAGGGAAATAAGAT
66 GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGAT
42327082 TCGCTATCTTCAG
131 TCGCTATCTTCAG
* * *
42327095 TCTGCTCCGCTGCAACTTTAGGGAGATAAGGCTGGTAGCTTCAATCTGCTCCACTGTAACTTCAG
1 TCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGAAACTTCAG
42327160 GAAGATAAGATCCGCCATAAT
66 GAAGATAAGATCCGCCATAAT
42327181 GACTTCAATC
Statistics
Matches: 212, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
143 212 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (143 bp):
TCTGTTCCGCTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGAAACTTCAG
GAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGAT
TCGCTATCTTCAG
Found at i:42336442 original size:322 final size:321
Alignment explanation
Indices: 42335855--42336483 Score: 1003
Period size: 322 Copynumber: 2.0 Consensus size: 321
42335845 CTTCATTAGC
*
42335855 AAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTTAAGAAAA
1 AAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAA
*
42335920 TCAAGAAACCAAATCTTGGCCCAATTTTGTTATTTGAGCGATTTCAAGAATCAAGAAAATTAAGA
66 TCAAGAAACCAAATCTTGGCCCAATTTTGTTATTTGAGCGATTTCAAGAATCAAGAAAATCAAGA
* **
42335985 TTTCAAATCTTGGAAATCTTGGCCCAAGAAACTGAATCTTGCAGTTAAAGCGCATTGGATCTAAG
131 TTTCAAATCTTAGAAATCTTGGCCCAAGAAACTGAATCTTGCAACTAAAGCGCATTGGATCTAAG
* ** * *
42336050 TTACGAGCATCAAGGAACCAATTTTGGGAGAGAACAGATTACAAGCCCAAGTTCTTGAAGATACG
196 TTACGAGCATCAAGCAACCAATTTCAGGAGAGAACAGATTACAAGCCCAAGTTCTTGAAGACAAG
42336115 GCCCAATAAGATGTTCCAAGCCCAA-CCAAGAAGTTTAAATTAGACTTTGATACGAGTCACA
261 GCCCAATAAGATGTTCCAAGCCCAATCC-AGAAGTTTAAATTAGACTTTGATACGAGTCACA
* * *
42336176 AAGGCCTTAGATGCGTATACAAAGGAAAAAGGAAATCAAGATTCACTTTCTTGTTTTCAAGAAAA
1 AAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAA
* * * *
42336241 TCAAGAAACCGAATCTTTGTCCAATTTTGTTGTTTTGAGCGATTTCAAGAATCAAGAAAATCAAG
66 TCAAGAAACCAAATCTTGGCCCAATTTTGTT-ATTTGAGCGATTTCAAGAATCAAGAAAATCAAG
* * *
42336306 ATTTCAAATCTTAGAAATCTTGGTCCAAGAAA-TCGAATCTTGCAACTAAGGCGCATTGGATCTT
130 ATTTCAAATCTTAGAAATCTTGGCCCAAGAAACT-GAATCTTGCAACTAAAGCGCATTGGATCTA
* *
42336370 AGTTACGAGCATTAA-CAAGCCAATTTCAGGAGAGAACGGATTACAAGCCCAAGTTCTTGAAGAC
194 AGTTACGAGCATCAAGCAA-CCAATTTCAGGAGAGAACAGATTACAAGCCCAAGTTCTTGAAGAC
42336434 AAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAGTTTAAATTAGACTT
258 AAGGCCCAATAAGATGTTCCAAGCCCAATCCAGAAGTTTAAATTAGACTT
42336484 AGCTGAAAAT
Statistics
Matches: 282, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
321 92 0.33
322 188 0.67
323 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (321 bp):
AAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAGAAAA
TCAAGAAACCAAATCTTGGCCCAATTTTGTTATTTGAGCGATTTCAAGAATCAAGAAAATCAAGA
TTTCAAATCTTAGAAATCTTGGCCCAAGAAACTGAATCTTGCAACTAAAGCGCATTGGATCTAAG
TTACGAGCATCAAGCAACCAATTTCAGGAGAGAACAGATTACAAGCCCAAGTTCTTGAAGACAAG
GCCCAATAAGATGTTCCAAGCCCAATCCAGAAGTTTAAATTAGACTTTGATACGAGTCACA
Found at i:42341909 original size:21 final size:21
Alignment explanation
Indices: 42341885--42341928 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
42341875 AAGTTTATAG
42341885 TTATAGATATGAAACACTCAC
1 TTATAGATATGAAACACTCAC
42341906 TTATAGATATGAAACACTCAC
1 TTATAGATATGAAACACTCAC
42341927 TT
1 TT
42341929 TGTGAATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (21 bp):
TTATAGATATGAAACACTCAC
Found at i:42345479 original size:9 final size:9
Alignment explanation
Indices: 42345465--42345489 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42345455 TGGTATCAGA
42345465 TTTTGGGCG
1 TTTTGGGCG
42345474 TTTTGGGCG
1 TTTTGGGCG
42345483 TTTTGGG
1 TTTTGGG
42345490 TTGATTTCTA
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:0.00, C:0.08, G:0.44, T:0.48
Consensus pattern (9 bp):
TTTTGGGCG
Found at i:42348263 original size:40 final size:40
Alignment explanation
Indices: 42348219--42348481 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
42348209 GCTCCTCGTT
* *
42348219 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
42348259 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42348299 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42348338 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42348377 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * * *
42348416 CAAATTCCTTC-GGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGT-ATC-TCGCA
42348457 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42348482 CATCACTCAA
Statistics
Matches: 202, Mismatches: 12, Indels: 17
0.87 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 113 0.56
40 73 0.36
41 14 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:42353982 original size:39 final size:39
Alignment explanation
Indices: 42353865--42354127 Score: 302
Period size: 39 Copynumber: 6.6 Consensus size: 39
42353855 GCTCCTCGTT
* *
42353865 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
42353905 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
42353945 CAAATGCCTTCGGGCTTAGCCCGGAATTAGCATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
42353984 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
*
42354023 CAAATGCCTTCGGGCTTAGCCCAGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * * *
42354062 CAAATGCCTTCGGATCTTAGTCCGG-ATATGGTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAAT-TAGT-ATC-TCGCA
42354103 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
42354128 CATCACTCAA
Statistics
Matches: 197, Mismatches: 18, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
39 111 0.56
40 75 0.38
41 11 0.06
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:42359254 original size:22 final size:22
Alignment explanation
Indices: 42359224--42359267 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42359214 TTTGGTATTT
42359224 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
* *
42359246 GGGATTTGGTATGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
42359268 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:42361580 original size:11 final size:11
Alignment explanation
Indices: 42361564--42361596 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42361554 AAGAGGAAAT
42361564 TCGAAAAAAAA
1 TCGAAAAAAAA
42361575 TCGAAAAAAAA
1 TCGAAAAAAAA
*
42361586 T-TAAAAAAAA
1 TCGAAAAAAAA
42361596 T
1 T
42361597 TTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (11 bp):
TCGAAAAAAAA
Found at i:42361608 original size:12 final size:12
Alignment explanation
Indices: 42361578--42361609 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42361568 AAAAAAATCG
42361578 AAAAAAAA--TT
1 AAAAAAAATTTT
42361588 AAAAAAAATTTT
1 AAAAAAAATTTT
42361600 AAAAAAAATT
1 AAAAAAAATT
42361610 CGAAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAAAAAATTTT
Found at i:42365902 original size:11 final size:11
Alignment explanation
Indices: 42365886--42365927 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
42365876 AAGTGGAAAT
42365886 TCGAAAAAAAA
1 TCGAAAAAAAA
42365897 TCG-AAAAAAA
1 TCGAAAAAAAA
*
42365907 -CTAAAAAAAA
1 TCGAAAAAAAA
*
42365917 TTGAAAAAAAA
1 TCGAAAAAAAA
42365928 AATTTCGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 1 0.04
10 14 0.54
11 11 0.42
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (11 bp):
TCGAAAAAAAA
Found at i:42365912 original size:20 final size:20
Alignment explanation
Indices: 42365889--42365926 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42365879 TGGAAATTCG
42365889 AAAAAAAATCGAAAAAAACT
1 AAAAAAAATCGAAAAAAACT
*
42365909 AAAAAAAATTGAAAAAAA
1 AAAAAAAATCGAAAAAAA
42365927 AAATTTCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAAAAAATCGAAAAAAACT
Found at i:42373463 original size:31 final size:28
Alignment explanation
Indices: 42373418--42373490 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 28
42373408 CTCGCAAGAC
*
42373418 TTTTCAC--TTTTTTTTAACTTGATTTT
1 TTTTCACTTTTTTTTTTAACTCGATTTT
**
42373444 TTTGGTCACCTTTTTTTTTTTGCTCGATTTT
1 TTT--TCA-CTTTTTTTTTTAACTCGATTTT
42373475 TTTTCACTTTTTTTTT
1 TTTTCACTTTTTTTTT
42373491 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 3 0.08
28 13 0.33
29 4 0.10
31 19 0.49
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.70
Consensus pattern (28 bp):
TTTTCACTTTTTTTTTTAACTCGATTTT
Found at i:42373486 original size:12 final size:12
Alignment explanation
Indices: 42373471--42373539 Score: 61
Period size: 12 Copynumber: 5.5 Consensus size: 12
42373461 TTTTGCTCGA
*
42373471 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
42373483 TTTTTTTTGAAT
1 TTTTTTTTCAAT
42373495 TTTTTTTTCAAT
1 TTTTTTTTCAAT
42373507 CAAATTTTTTTTCGAAT
1 ----TTTTTTTTC-AAT
42373524 TTTTTTTT--AT
1 TTTTTTTTCAAT
42373534 TTTTTT
1 TTTTTT
42373540 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
10 8 0.16
12 21 0.43
13 8 0.16
16 9 0.18
17 3 0.06
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:42377476 original size:28 final size:26
Alignment explanation
Indices: 42377442--42377512 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 26
42377432 CTCGCAAGAC
*
42377442 TTTTCACTTTTTTTTAACTTGATTTT
1 TTTTCACTTTTTTTTAACTCGATTTT
**
42377468 TTTGGTCACCTTTTTTTTTTGCTCGATTTT
1 TTT--TCA-C-TTTTTTTTAACTCGATTTT
42377498 TTTTCACTTTTTTTT
1 TTTTCACTTTTTTTT
42377513 TTGAATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
26 11 0.29
27 1 0.03
28 6 0.16
29 1 0.03
30 19 0.50
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (26 bp):
TTTTCACTTTTTTTTAACTCGATTTT
Found at i:42377510 original size:13 final size:13
Alignment explanation
Indices: 42377494--42377555 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
42377484 TTTTGCTCGA
*
42377494 TTTTTTTTCACTT
1 TTTTTTTTCAATT
*
42377507 TTTTTTTTGAATT
1 TTTTTTTTCAATT
42377520 TTTTTTTTCAATCAAAT
1 TTTTTTTTCAAT----T
*
42377537 TTTTTTTTGAATT
1 TTTTTTTTCAATT
42377550 TTTTTT
1 TTTTTT
42377556 GATTTTTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 29 0.71
17 12 0.29
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:42380026 original size:13 final size:13
Alignment explanation
Indices: 42379980--42380026 Score: 71
Period size: 12 Copynumber: 3.8 Consensus size: 13
42379970 TTGAAATTCG
*
42379980 AAAAAAAATCG-A
1 AAAAAAAATTGAA
42379992 AAAAAAAATT-AA
1 AAAAAAAATTGAA
42380004 AAAAAAAATTGAA
1 AAAAAAAATTGAA
42380017 AAAAAAAATT
1 AAAAAAAATT
42380027 TCGAAGTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:42387521 original size:68 final size:68
Alignment explanation
Indices: 42387412--42387550 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
42387402 TATTAAAGAG
*
42387412 TTATATAATGATGATGCTGAATTCGGCTATATCTATAGTAATTATGGAAATACTACTTTTGAGAA
1 TTATATAATGATGATGCTGAATTCGGCCATATCTATAGTAATTATGGAAATACTACTTTTGAGAA
42387477 GTT
66 GTT
42387480 TTATATAATGATGATGCTGAATTCGGCCATATCTATAGTAATTATGGAAATACTACTTTTGAGAA
1 TTATATAATGATGATGCTGAATTCGGCCATATCTATAGTAATTATGGAAATACTACTTTTGAGAA
42387545 GTT
66 GTT
42387548 TTA
1 TTA
42387551 CCTTGTAGAT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (68 bp):
TTATATAATGATGATGCTGAATTCGGCCATATCTATAGTAATTATGGAAATACTACTTTTGAGAA
GTT
Found at i:42389620 original size:33 final size:34
Alignment explanation
Indices: 42389569--42389643 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
42389559 AGATTTAAAC
*
42389569 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42389603 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42389636 AATTTAAT
1 AAATTAAT
42389644 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:42390889 original size:18 final size:17
Alignment explanation
Indices: 42390866--42390904 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
42390856 CTCTTTTTGC
42390866 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
42390884 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
42390902 TCT
1 TCT
42390905 ATCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:42393752 original size:54 final size:54
Alignment explanation
Indices: 42393689--42393797 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
42393679 CCACGAACTA
*
42393689 AGAAAGGAAGAGATAGTATATTTGTTGTTGTTGACAGGTTTTCCAAGATGGCAC
1 AGAAAGGAAGAGATAGTATATCTGTTGTTGTTGACAGGTTTTCCAAGATGGCAC
42393743 AGAAAGGAAGAGATAGTATATCTGTTGTTGTTGACAGGTTTTCCAAGATGGCAC
1 AGAAAGGAAGAGATAGTATATCTGTTGTTGTTGACAGGTTTTCCAAGATGGCAC
42393797 A
1 A
42393798 TTTTATTCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (54 bp):
AGAAAGGAAGAGATAGTATATCTGTTGTTGTTGACAGGTTTTCCAAGATGGCAC
Found at i:42398921 original size:12 final size:12
Alignment explanation
Indices: 42398904--42398928 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42398894 CTATCTCTAG
42398904 TTACACATGATT
1 TTACACATGATT
42398916 TTACACATGATT
1 TTACACATGATT
42398928 T
1 T
42398929 GATGACACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TTACACATGATT
Found at i:42405295 original size:10 final size:10
Alignment explanation
Indices: 42405280--42405328 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
42405270 TTGGGTTAAG
42405280 ATTGAGCTGA
1 ATTGAGCTGA
42405290 ATTGAGCTCGA
1 ATTGAGCT-GA
42405301 A-TGAGCTGA
1 ATTGAGCTGA
* *
42405310 CTTGAGCTCA
1 ATTGAGCTGA
*
42405320 AGTGAGCTG
1 ATTGAGCTG
42405329 GAAACAAGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:42405305 original size:20 final size:20
Alignment explanation
Indices: 42405282--42405328 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
42405272 GGGTTAAGAT
42405282 TGAGCTGAATTGAGCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
42405302 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
42405322 TGAGCTG
1 TGAGCTG
42405329 GAAACAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:42407574 original size:22 final size:22
Alignment explanation
Indices: 42407546--42407589 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
42407536 TTTTGAACCA
42407546 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
42407568 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
42407590 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:42408617 original size:11 final size:11
Alignment explanation
Indices: 42408601--42408630 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
42408591 TATTAAACTT
42408601 ATTAAACACTA
1 ATTAAACACTA
42408612 ATTAAACACTA
1 ATTAAACACTA
42408623 ATTAAACA
1 ATTAAACA
42408631 TGTAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (11 bp):
ATTAAACACTA
Found at i:42412582 original size:23 final size:23
Alignment explanation
Indices: 42412552--42412614 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
42412542 TTTGAACCAT
**
42412552 TACCATTTCGTACCAAATCGTAA
1 TACCATTTCGTACCAAATCACAA
* *
42412575 TACCATTTCGAACCAAATCACAT
1 TACCATTTCGTACCAAATCACAA
*
42412598 TACCATTTCGTAACAAA
1 TACCATTTCGTACCAAA
42412615 CCTAAACCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (23 bp):
TACCATTTCGTACCAAATCACAA
Found at i:42415148 original size:19 final size:18
Alignment explanation
Indices: 42415106--42415181 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 18
42415096 CAAATGAGAG
42415106 AAAAAGAAAAGAGCGAAAATA
1 AAAAAGAAAAGA---AAAATA
42415127 AAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAAT-A
*
42415146 AAAAA-AGAAAGAAAATTCA
1 AAAAAGA-AAAGAAAAAT-A
42415165 AAAAATGAAAATGAAAA
1 AAAAA-GAAAA-GAAAA
42415182 GAAAGCGAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.12
19 21 0.44
20 3 0.06
21 18 0.38
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.08
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATA
Found at i:42415149 original size:20 final size:20
Alignment explanation
Indices: 42415126--42415181 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
42415116 GAGCGAAAAT
*
42415126 AAAAAAGAAAAGAAAAATGA
1 AAAAAAGAAAAGAAAAATCA
*
42415146 AAAAAAG-AAAGAAAATTCA
1 AAAAAAGAAAAGAAAAATCA
*
42415165 AAAAATGAAAATGAAAA
1 AAAAAAGAAAA-GAAAA
42415182 GAAAGCGAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 10 0.32
21 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (20 bp):
AAAAAAGAAAAGAAAAATCA
Found at i:42419351 original size:23 final size:23
Alignment explanation
Indices: 42419321--42419383 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
42419311 TTTGAACCAT
**
42419321 TACCATTTCGTACCAAATCGTAA
1 TACCATTTCGTACCAAATCACAA
*
42419344 TACCATTTC-TAACCAAATCACAT
1 TACCATTTCGT-ACCAAATCACAA
*
42419367 TACCATTTCGTAACAAA
1 TACCATTTCGTACCAAA
42419384 CCTAAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (23 bp):
TACCATTTCGTACCAAATCACAA
Found at i:42423124 original size:17 final size:18
Alignment explanation
Indices: 42423104--42423139 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
42423094 CACATTCATT
42423104 TTCTCAATGTTTTT-TTC
1 TTCTCAATGTTTTTCTTC
*
42423121 TTCTCCATGTTTTTCTTC
1 TTCTCAATGTTTTTCTTC
42423139 T
1 T
42423140 ATTGTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.08, C:0.22, G:0.06, T:0.64
Consensus pattern (18 bp):
TTCTCAATGTTTTTCTTC
Found at i:42429048 original size:33 final size:34
Alignment explanation
Indices: 42428997--42429071 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
42428987 AGATTCAAAC
*
42428997 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42429031 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
42429064 AATTTAAT
1 AAATTAAT
42429072 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:42429711 original size:12 final size:12
Alignment explanation
Indices: 42429694--42429724 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42429684 GAGGAAATTC
42429694 AAAAAAAATCGA
1 AAAAAAAATCGA
*
42429706 AAAAAAAATTGA
1 AAAAAAAATCGA
42429718 AAAAAAA
1 AAAAAAA
42429725 TTTCGAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:42429725 original size:11 final size:11
Alignment explanation
Indices: 42429688--42429726 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42429678 TTTGAAGAGG
*
42429688 AAATTCAAAAA
1 AAATTGAAAAA
*
42429699 AAATCGAAAAAA
1 AAATTG-AAAAA
42429711 AAATTGAAAAA
1 AAATTGAAAAA
42429722 AAATT
1 AAATT
42429727 TCGAAGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (11 bp):
AAATTGAAAAA
Found at i:42437638 original size:19 final size:18
Alignment explanation
Indices: 42437602--42437641 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42437592 TTTCCACTCG
*
42437602 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
42437620 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
42437639 TTT
1 TTT
42437642 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:42438718 original size:15 final size:14
Alignment explanation
Indices: 42438698--42438735 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
42438688 AACTAGCTTC
42438698 TTTTTTTTCACGAT
1 TTTTTTTTCACGAT
*
42438712 TTTTTTTTCACGAA
1 TTTTTTTTCACGAT
42438726 TTTTTTTTCA
1 TTTTTTTTCA
42438736 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.16, C:0.13, G:0.05, T:0.66
Consensus pattern (14 bp):
TTTTTTTTCACGAT
Found at i:42438805 original size:12 final size:13
Alignment explanation
Indices: 42438778--42438810 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42438768 AACCAAATTT
*
42438778 TTTTTTTTGAATA
1 TTTTTTTTCAATA
42438791 TTTTTTTTCAA-A
1 TTTTTTTTCAATA
42438803 TTTTTTTT
1 TTTTTTTT
42438811 TGAAGAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCAATA
Found at i:42442390 original size:27 final size:27
Alignment explanation
Indices: 42442359--42442536 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42442349 TAAATTGTAC
42442359 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42442386 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42442412 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42442440 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42442468 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42442495 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42442522 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42442537 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42442473 original size:82 final size:81
Alignment explanation
Indices: 42442360--42442515 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42442350 AAATTGTACA
* *
42442360 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42442424 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42442441 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42442506 TGCGAGTTGA
65 TGCGAATTGA
42442516 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42442527 original size:82 final size:81
Alignment explanation
Indices: 42442356--42442536 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42442346 GATTAAATTG
* *
42442356 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42442421 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42442437 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42442501 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42442519 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42442537 GGCTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42442547 original size:27 final size:27
Alignment explanation
Indices: 42442441--42442547 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
42442431 TGACCATGCG
* * * *
42442441 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
42442469 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
42442496 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
42442523 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
42442548 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:42445495 original size:18 final size:18
Alignment explanation
Indices: 42445451--42445498 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
42445441 CTTTCTCCAA
42445451 TCTTTTCTCTTTTTCAATT
1 TCTTTT-TCTTTTTCAATT
**
42445470 T-TTATTTCTTTTTCGGTT
1 TCTT-TTTCTTTTTCAATT
42445488 TCTTTTTCTTT
1 TCTTTTTCTTT
42445499 CGTCACTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (18 bp):
TCTTTTTCTTTTTCAATT
Found at i:42446441 original size:14 final size:14
Alignment explanation
Indices: 42446422--42446457 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
42446412 TAGCTTCTTC
42446422 TTTTTTCACGATTT
1 TTTTTTCACGATTT
42446436 TTTTTTCACGATTT
1 TTTTTTCACGATTT
42446450 TTTTTTCA
1 TTTTTTCA
42446458 ACTTGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTTTCACGATTT
Found at i:42446516 original size:13 final size:12
Alignment explanation
Indices: 42446498--42446533 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
42446488 GAAACCAAAT
42446498 TTTTTTTTGAATA
1 TTTTTTTTGAA-A
*
42446511 TTTTTTTCGAAA
1 TTTTTTTTGAAA
42446523 TTTTTTTTGAA
1 TTTTTTTTGAA
42446534 GAAACTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.22, C:0.03, G:0.08, T:0.67
Consensus pattern (12 bp):
TTTTTTTTGAAA
Found at i:42450385 original size:18 final size:18
Alignment explanation
Indices: 42450362--42450400 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42450352 CCCTTTTTCC
42450362 TCTTTT-TCATTCTCTTTT
1 TCTTTTCTCATT-TCTTTT
*
42450380 TCTTTTCTGATTTCTTTT
1 TCTTTTCTCATTTCTTTT
42450398 TCT
1 TCT
42450401 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTCTCATTTCTTTT
Found at i:42457714 original size:20 final size:20
Alignment explanation
Indices: 42457691--42457736 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42457681 CCAGCTCGAA
*
42457691 TTAGCTCACATGAGCTTAAT
1 TTAGCTCACATGAGCTCAAT
***
42457711 TTAGCTCGTTTGAGCTCAAT
1 TTAGCTCACATGAGCTCAAT
42457731 TTAGCT
1 TTAGCT
42457737 TACTTTAGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (20 bp):
TTAGCTCACATGAGCTCAAT
Found at i:42457718 original size:30 final size:30
Alignment explanation
Indices: 42457683--42457756 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
42457673 AGTTTTTCCC
42457683 AGCTCGAATT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-ATTGAGCTCA-ATTGAGCTTAATTT
* * *
42457713 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGATTGAGCTCAATTGAGCTTAATTT
*
42457743 AGCTCGTTTGAGCT
1 AGCTCGATTGAGCT
42457757 TGGCTTAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 36 0.92
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (30 bp):
AGCTCGATTGAGCTCAATTGAGCTTAATTT
Found at i:42459395 original size:12 final size:13
Alignment explanation
Indices: 42459377--42459411 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
42459367 ATTTTGATTG
42459377 AAAAAAAAAATTC
1 AAAAAAAAAATTC
* *
42459390 AAAAAAAAAAGTG
1 AAAAAAAAAATTC
42459403 AAAAAAAAA
1 AAAAAAAAA
42459412 TCGAGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.06, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:42460518 original size:18 final size:18
Alignment explanation
Indices: 42460495--42460547 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
42460485 GAAAGAAAAC
*
42460495 AAAAAGAAAACGAAGAAG
1 AAAAAGAAATCGAAGAAG
*
42460513 AAAAAGAAATTGCAA-AAG
1 AAAAAGAAATCG-AAGAAG
42460531 AAAAA-AAATCGAAGAAG
1 AAAAAGAAATCGAAGAAG
42460548 TGAGAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.07
17 8 0.27
18 18 0.60
19 2 0.07
ACGTcount: A:0.70, C:0.06, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAAGAAATCGAAGAAG
Found at i:42460590 original size:12 final size:12
Alignment explanation
Indices: 42460553--42460613 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
42460543 AGAAGTGAGA
*
42460553 GAAAAAGAAAAT
1 GAAAAAGAAATT
42460565 GAAGAAAAGAAAATT
1 G-A-AAAAG-AAATT
42460580 GAAAAAGAAATT
1 GAAAAAGAAATT
* **
42460592 GAAAGAGAGCTT
1 GAAAAAGAAATT
42460604 G-AAAAGAAAT
1 GAAAAAGAAAT
42460614 CAAGTGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.15
12 16 0.41
13 6 0.15
14 6 0.15
15 5 0.13
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:42460633 original size:33 final size:33
Alignment explanation
Indices: 42460592--42460654 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
42460582 AAAAGAAATT
42460592 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
42460625 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
42460655 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:42462521 original size:30 final size:30
Alignment explanation
Indices: 42462485--42462545 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
42462475 CCGACACTTC
42462485 TACATTTGATCCCGGCATTGGATTATGCAT
1 TACATTTGATCCCGGCATTGGATTATGCAT
42462515 TACATTTGATCCCGGCATTGGATTATGCAT
1 TACATTTGATCCCGGCATTGGATTATGCAT
42462545 T
1 T
42462546 CTAATTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (30 bp):
TACATTTGATCCCGGCATTGGATTATGCAT
Found at i:42483165 original size:109 final size:109
Alignment explanation
Indices: 42482974--42483193 Score: 413
Period size: 109 Copynumber: 2.0 Consensus size: 109
42482964 ATGAGGCCTA
*
42482974 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAGATTTGT
1 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
*
42483039 TTAAGTGTAGAATTCTCTTTTAGTTTTTCTCCAAGAATTCTCTC
66 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
*
42483083 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAATCAAAAAATTTCAAATTTGT
1 TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
42483148 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
66 TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
42483192 TT
1 TT
42483194 GAGTTTTCTT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 108 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (109 bp):
TTTAAATGATGGCCGGCCACCCCTTGTATTCACTTCTCAATTAAAACAAAAAATTTCAAATTTGT
TTAAGTGTAGAATTCTCTTTGAGTTTTTCTCCAAGAATTCTCTC
Found at i:42492072 original size:30 final size:32
Alignment explanation
Indices: 42492038--42492099 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
42492028 TTAGGACTTA
42492038 TCTTTT-AATT-T-CTTGCTGTCAATTTTTATT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTTATT
*
42492068 TCTTTTAAATTCTGCTTGTGTCGATTTTTATT
1 TCTTTTAAATTCTGCTTGTGTCAATTTTTATT
42492100 AGCTAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 4 0.14
32 14 0.50
33 4 0.14
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (32 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTTATT
Found at i:42495084 original size:27 final size:27
Alignment explanation
Indices: 42495053--42495227 Score: 208
Period size: 27 Copynumber: 6.4 Consensus size: 27
42495043 TAAATTGTAC
42495053 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42495080 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42495106 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42495134 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
42495162 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42495189 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42495216 AGCACTGAGTGT
1 AGCACTAAGTGT
42495228 ACGGACTCAA
Statistics
Matches: 128, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42495167 original size:82 final size:81
Alignment explanation
Indices: 42495054--42495209 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
42495044 AAATTGTACA
*
42495054 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
42495118 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42495135 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
42495200 TGCGAGTTGA
65 TGCGAATTGA
42495210 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42495221 original size:82 final size:81
Alignment explanation
Indices: 42495050--42495227 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 81
42495040 GATTAAATTG
*
42495050 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
42495115 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42495131 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
42495195 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42495213 TATAGCACTGAGTGT
1 TACAGCACTAAGTGT
42495228 ACGGACTCAA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42503161 original size:27 final size:27
Alignment explanation
Indices: 42503130--42503307 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
42503120 TAAATTGTAC
42503130 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42503157 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42503183 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42503211 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
42503239 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42503266 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42503293 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42503308 GACTCAATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42503244 original size:82 final size:81
Alignment explanation
Indices: 42503131--42503286 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
42503121 AAATTGTACA
*
42503131 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
42503195 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42503212 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
42503277 TGCGAGTTGA
65 TGCGAATTGA
42503287 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42503298 original size:82 final size:81
Alignment explanation
Indices: 42503127--42503307 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
42503117 GATTAAATTG
*
42503127 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
42503192 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42503208 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
42503272 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42503290 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42503308 GACTCAATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42518288 original size:21 final size:21
Alignment explanation
Indices: 42518245--42518307 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
42518235 TTTGAACCAT
* *
42518245 TACCAATTCGTACCCAATACCA
1 TACCATTTCGTA-CCAATTCCA
42518267 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
*
42518288 TACCATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
42518308 CAAATACCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:42526690 original size:11 final size:11
Alignment explanation
Indices: 42526674--42526703 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
42526664 ACGGTATTGT
42526674 AAAAAAATCGA
1 AAAAAAATCGA
42526685 AAAAAAATCGA
1 AAAAAAATCGA
42526696 AAAAAAAT
1 AAAAAAAT
42526704 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (11 bp):
AAAAAAATCGA
Found at i:42537444 original size:80 final size:79
Alignment explanation
Indices: 42537222--42537481 Score: 244
Period size: 79 Copynumber: 3.3 Consensus size: 79
42537212 TTGAATGATG
* * * * * *
42537222 TCCGGGCTAAGTCCCGAAGGCT--TTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGG-TAATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCA
*
42537284 TTTGTGCGAGATACTAAT
63 TTTGTGCGAG-TACTAAA
* * * * * *
42537302 TCCGGGCTAAG-CCCGCAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
42537366 GTGCGAGTTACTAAA
66 GTGCGAG-TACTAAA
*
42537381 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
** *
42537445 TGAACGAGTAGCTATA
65 TGTGCGAGTA-CTAAA
* *
42537461 TCC-GGTTAAATTCCGAAGGTA
1 TCCGGGTTAAGTCCCGAAGGTA
42537482 CGTGATTTGG
Statistics
Matches: 151, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 75 0.50
80 73 0.48
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTACTAAA
Found at i:42537460 original size:40 final size:40
Alignment explanation
Indices: 42537222--42537446 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
42537212 TTGAATGATG
* * * *
42537222 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
42537262 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42537302 TCCGGGCTAAG-CCCGCAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42537341 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
42537381 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42537422 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42537447 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.21
40 115 0.72
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42545260 original size:80 final size:79
Alignment explanation
Indices: 42545029--42545286 Score: 256
Period size: 79 Copynumber: 3.3 Consensus size: 79
42545019 TTGAATGATG
* * * * * * * *
42545029 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CTGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
42545092 TTGTGCGAGATACTAAT
64 TTGTGCGAG-TACTAAA
* * * *
42545109 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCTGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
42545173 GTGCGAGTTACTAAA
66 GTGCGAG-TACTAAA
*
42545188 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
** *
42545252 TGAACGAGTAGCTATA
65 TGTGCGAGTA-CTAAA
* *
42545268 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42545287 TACGTGATTT
Statistics
Matches: 155, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 76 0.49
80 76 0.49
81 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGTACTAAA
Found at i:42545267 original size:40 final size:40
Alignment explanation
Indices: 42545029--42545253 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
42545019 TTGAATGATG
* * * *
42545029 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
42545069 TCCGGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
42545109 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42545148 TCCGGGTTAAGTCCTGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
42545188 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42545229 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42545254 AACGAGTAGC
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.21
40 117 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42548015 original size:37 final size:37
Alignment explanation
Indices: 42547965--42548043 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
42547955 TTATTACGAA
* * *
42547965 GTCTTACACGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACACGGACAAAATCCCCACACGAAGTCATCGG
* *
42548002 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACACGGACAAAATCCCCACACGAAGTCATCGG
42548039 GTCTT
1 GTCTT
42548044 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACACGGACAAAATCCCCACACGAAGTCATCGG
Found at i:42548312 original size:47 final size:47
Alignment explanation
Indices: 42548162--42548681 Score: 844
Period size: 47 Copynumber: 11.1 Consensus size: 47
42548152 CCCTTCGGGA
* * * * * * *
42548162 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42548209 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42548255 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42548302 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42548349 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42548396 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42548443 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
42548490 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42548537 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42548584 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42548631 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42548678 CTTA
1 CTTA
42548682 CTATCATTTC
Statistics
Matches: 452, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
46 40 0.09
47 412 0.91
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42561363 original size:22 final size:22
Alignment explanation
Indices: 42561332--42561396 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
42561322 ACCTTTTTGA
*
42561332 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
42561355 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
42561377 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
42561397 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:42562448 original size:19 final size:20
Alignment explanation
Indices: 42562401--42562438 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42562391 AACATTTTCG
42562401 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATTCGAGCTCA
42562421 ATTCAGCTCATT-GAGCTC
1 ATTCAGCTCATTCGAGCTC
42562439 GTATTAGCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (20 bp):
ATTCAGCTCATTCGAGCTCA
Found at i:42566099 original size:11 final size:11
Alignment explanation
Indices: 42566059--42566098 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
42566049 TACGAGATTG
42566059 TAAAAAAATTC
1 TAAAAAAATTC
42566070 TAAAAAAATTC
1 TAAAAAAATTC
42566081 TAAAAAAATTC
1 TAAAAAAATTC
42566092 -AAAAAAA
1 TAAAAAAA
42566099 AAGTTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 7 0.24
11 22 0.76
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAAAAAATTC
Found at i:42569405 original size:79 final size:81
Alignment explanation
Indices: 42569222--42569444 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 81
42569212 TTGAATGATG
* * *
42569222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATATCCGGGCTAAGACCCGAAGGCAT
*
42569284 TTGTGCGAGATACTAAT
65 TTGTGCGAGATACTAAA
*
42569301 TTCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGATACTAAT-TCCGGGCTAAG-CCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATATCCGGGCTAAGACCCGAAGGCAT
*
42569362 TTGTGCGAGTTACTAAA
65 TTGTGCGAGATACTAAA
* * * * * *
42569379 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
42569443 TG
66 TG
42569445 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
78 45 0.36
79 54 0.44
80 25 0.20
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:42569406 original size:40 final size:40
Alignment explanation
Indices: 42569222--42569444 Score: 253
Period size: 39 Copynumber: 5.7 Consensus size: 40
42569212 TTGAATGATG
* *
42569222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
42569261 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
42569301 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
42569340 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
42569379 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42569420 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42569445 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 91 0.56
40 61 0.38
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42569466 original size:79 final size:79
Alignment explanation
Indices: 42569222--42569477 Score: 199
Period size: 79 Copynumber: 3.3 Consensus size: 79
42569212 TTGAATGATG
* * * *
42569222 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
42569283 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* * *
42569301 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
42569365 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
42569379 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCAT
*
42569442 TTGAACGAG-GAGCTATA
63 TTGAACGAGTGA-CTAAA
* *
42569459 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
42569478 TACGTGATTT
Statistics
Matches: 150, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
77 1 0.01
78 45 0.30
79 67 0.45
80 36 0.24
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:42571398 original size:15 final size:14
Alignment explanation
Indices: 42571371--42571413 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
42571361 TCTATTGAGC
42571371 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
42571385 AAGAAAAAGAAAAA
1 AAGAAAAAGAAAAA
* *
42571399 GAGTGAAAAGAAAAA
1 AAG-AAAAAGAAAAA
42571414 GAAAGAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:42571414 original size:15 final size:14
Alignment explanation
Indices: 42571375--42571425 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
42571365 TTGAGCAAGA
* *
42571375 AAAAGAAAAAAAGA
1 AAAAGAAAAAGAGG
42571389 AAAAGAAAAAGAGTG
1 AAAAGAAAAAGAG-G
*
42571404 AAAAGAAAAAGAAAG
1 AAAAGAAAAAG-AGG
42571419 AAAAGAA
1 AAAAGAA
42571426 TGAGGAGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.38
15 19 0.59
16 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAGAGG
Found at i:42574046 original size:11 final size:11
Alignment explanation
Indices: 42574030--42574072 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
42574020 TAGTAGTTTC
42574030 TTCAAAAAAAA
1 TTCAAAAAAAA
42574041 TTCAAAATAAAA
1 TTCAAAA-AAAA
*
42574053 AT--AAAAAAA
1 TTCAAAAAAAA
42574062 TTCAAAAAAAA
1 TTCAAAAAAAA
42574073 AATTTGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.19
10 3 0.11
11 14 0.52
12 5 0.19
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:42574060 original size:21 final size:21
Alignment explanation
Indices: 42574034--42574075 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42574024 AGTTTCTTCA
*
42574034 AAAAAAATTCAAAATAAAAAT
1 AAAAAAATTCAAAAAAAAAAT
42574055 AAAAAAATTCAAAAAAAAAAT
1 AAAAAAATTCAAAAAAAAAAT
42574076 TTGGTTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAAAATTCAAAAAAAAAAT
Found at i:42574143 original size:16 final size:15
Alignment explanation
Indices: 42574116--42574170 Score: 83
Period size: 16 Copynumber: 3.5 Consensus size: 15
42574106 TATCAAGTTG
*
42574116 AAAAAAATTTCGTGA
1 AAAAAAAATTCGTGA
42574131 AAAGAAAAATTCGTGAA
1 AAA-AAAAATTCGTG-A
42574148 AAAAAAAATTCGTGA
1 AAAAAAAATTCGTGA
42574163 AAAAAAAA
1 AAAAAAAA
42574171 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
15 12 0.32
16 21 0.57
17 4 0.11
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (15 bp):
AAAAAAAATTCGTGA
Found at i:42587067 original size:56 final size:56
Alignment explanation
Indices: 42586962--42587068 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
42586952 ATTAATGCCG
* * * * *
42586962 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGTCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
42587018 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
42587069 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
Found at i:42587717 original size:20 final size:20
Alignment explanation
Indices: 42587692--42587746 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
42587682 ACGAGTTAAA
* *
42587692 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
42587712 TTGAGCTCGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
42587732 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
42587747 TTGAACCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:42589678 original size:13 final size:13
Alignment explanation
Indices: 42589660--42589687 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42589650 AGTGGATGTT
42589660 TTTGACCATTCGG
1 TTTGACCATTCGG
42589673 TTTGACCATTCGG
1 TTTGACCATTCGG
42589686 TT
1 TT
42589688 ACCTTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (13 bp):
TTTGACCATTCGG
Found at i:42590234 original size:16 final size:15
Alignment explanation
Indices: 42590208--42590237 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42590198 TTTCAATCCA
42590208 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
42590223 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
42590238 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:42591562 original size:21 final size:21
Alignment explanation
Indices: 42591536--42591598 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
42591526 TTGGTATTTG
42591536 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
42591557 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
42591578 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
42591599 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:42592692 original size:10 final size:10
Alignment explanation
Indices: 42592677--42592718 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
42592667 TTTGCAAGTT
42592677 TTGAGCTAAA
1 TTGAGCTAAA
* *
42592687 TTGAGCTGAT
1 TTGAGCTAAA
*
42592697 TTGAGCT-CA
1 TTGAGCTAAA
42592706 TTGAGCTAAA
1 TTGAGCTAAA
42592716 TTG
1 TTG
42592719 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:42598531 original size:19 final size:18
Alignment explanation
Indices: 42598491--42598535 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
42598481 ACCTTCTCTT
*
42598491 TTTTTTTTAATTTCAAAT
1 TTTTTTTTAATTTCAAAC
* *
42598509 TTTTTTTTACTTCTGAAAC
1 TTTTTTTTAATT-TCAAAC
42598528 TTTTTTTT
1 TTTTTTTT
42598536 CTCTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTTTTAATTTCAAAC
Found at i:42598646 original size:8 final size:9
Alignment explanation
Indices: 42598621--42598645 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42598611 TTTTTCGAAT
42598621 TTTTTTTTA
1 TTTTTTTTA
42598630 TTTTTTTTA
1 TTTTTTTTA
42598639 TTTTTTT
1 TTTTTTT
42598646 ACAATACCGA
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:42613224 original size:83 final size:80
Alignment explanation
Indices: 42613078--42613238 Score: 223
Period size: 81 Copynumber: 2.0 Consensus size: 80
42613068 TTTTGCTTCC
* * * *
42613078 CTTTAAATACCGTTCCATGCATGGGAACATCTCCTTATGCATGTTTCCTTTGCCATTAAGTAGCC
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTATGCATGTCTCCTTAGCCATTAAGTAGCC
42613143 GAATTTCAATGACCTT
66 GAA-TTCAATGACCTT
* * **
42613159 CTTTAAATGCCGTTCCTTGCATGTTAACAGCACCTTAAATGCATGTCTCCTTAGCCATTAAGTAG
1 CTTTAAATACCGTTCCATGCATGGGAACAGCACCTT--ATGCATGTCTCCTTAGCCATTAAGTAG
42613224 CCGAATTCAATGACC
64 CCGAATTCAATGACC
42613239 CGCAGACACA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 30 0.43
82 10 0.14
83 30 0.43
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (80 bp):
CTTTAAATACCGTTCCATGCATGGGAACAGCACCTTATGCATGTCTCCTTAGCCATTAAGTAGCC
GAATTCAATGACCTT
Found at i:42617535 original size:29 final size:29
Alignment explanation
Indices: 42617472--42617539 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
42617462 TAATCAACCG
*
42617472 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42617501 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42617530 CGCACACTTA
1 CGCACACTTA
42617540 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42617709 original size:29 final size:29
Alignment explanation
Indices: 42617646--42617713 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
42617636 TAATCAACCG
*
42617646 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
42617675 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
42617704 CGCACACTTA
1 CGCACACTTA
42617714 CGTTTTTCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:42617856 original size:29 final size:28
Alignment explanation
Indices: 42617822--42617890 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
42617812 ATCAACCGCG
*
42617822 CACACTTAGTGCCATGTAC-TTTAAACTCA
1 CACACTTAGTG-C-TGTACATTTAAACCCA
*
42617851 CACACTTAGTGCTGTACAATTTAAACCCG
1 CACACTTAGTGCTGTAC-ATTTAAACCCA
42617880 CACACTTAGTG
1 CACACTTAGTG
42617891 TCAATCTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 30 0.83
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (28 bp):
CACACTTAGTGCTGTACATTTAAACCCA
Found at i:42617887 original size:174 final size:174
Alignment explanation
Indices: 42617361--42617862 Score: 959
Period size: 174 Copynumber: 2.9 Consensus size: 174
42617351 AACTCAAGGT
* *
42617361 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42617426 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42617491 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
42617535 ACTTACCTTTTCCGCTATCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42617600 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42617665 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
* *
42617709 ACTTACGTTTTTCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
42617774 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42617839 ACTTTAAACTCACACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
42617863 TGTACAATTT
Statistics
Matches: 322, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 322 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42626768 original size:20 final size:20
Alignment explanation
Indices: 42626722--42626768 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
42626712 AGCTCGTTTC
*
42626722 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
42626742 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
42626762 CAGCTCA
1 CAGCTCA
42626769 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:42632404 original size:23 final size:22
Alignment explanation
Indices: 42632352--42632404 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42632342 TCCACGTCTT
*
42632352 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42632374 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42632397 TTTCTTTT
1 TTTCTTTT
42632405 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42636179 original size:23 final size:22
Alignment explanation
Indices: 42636127--42636179 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42636117 TCCACGTCTT
*
42636127 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42636149 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42636172 TTTCTTTT
1 TTTCTTTT
42636180 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:42649381 original size:24 final size:25
Alignment explanation
Indices: 42649354--42649407 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
42649344 ATGAGTGATA
*
42649354 AAAAAAGAGA-GAGTGATTCAAAA-G
1 AAAAAAGAAACGAGTGA-TCAAAATG
*
42649378 -AAAAAGAAACGAGTGATGAAAATG
1 AAAAAAGAAACGAGTGATCAAAATG
42649402 AAAAAA
1 AAAAAA
42649408 AGAATTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 5 0.20
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (25 bp):
AAAAAAGAAACGAGTGATCAAAATG
Done.