Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009431.1 Corchorus capsularis cultivar CVL-1 contig09452, whole genome shotgun sequence
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: 57802
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:7864 original size:109 final size:108
Alignment explanation
Indices: 7729--7927 Score: 344
Period size: 109 Copynumber: 1.8 Consensus size: 108
7719 TTTTTTTTGA
* *
7729 CAAAAACGCCACCATATAGTGGTGTTTCTTGTTTAAAATGCCGCTAAGTGTAAAAATTAAATAAA
1 CAAAAACACCACCATATAGTGGTGTTTCTTGTTTAAAACGCCGCTAAGTGTAAAAA-TAAATAAA
* *
7794 TAAAATAGGGGAATTAGTAAAGCATAGCTAGCTGCGTTTTAAGT
65 TAAAATAGGGCAATTAGTAAAACATAGCTAGCTGCGTTTTAAGT
*
7838 CAAAAACACCACCATATAGTGGTGTTTCTTGTTTAAAACGCCTCTAAGTGTAAAAATAAATAAAT
1 CAAAAACACCACCATATAGTGGTGTTTCTTGTTTAAAACGCCGCTAAGTGTAAAAATAAATAAAT
7903 AAAATAGGGCAATTAGTAAAACATA
66 AAAATAGGGCAATTAGTAAAACATA
7928 TTTAGCGGCA
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
108 32 0.38
109 53 0.62
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (108 bp):
CAAAAACACCACCATATAGTGGTGTTTCTTGTTTAAAACGCCGCTAAGTGTAAAAATAAATAAAT
AAAATAGGGCAATTAGTAAAACATAGCTAGCTGCGTTTTAAGT
Found at i:11287 original size:16 final size:16
Alignment explanation
Indices: 11264--11350 Score: 99
Period size: 16 Copynumber: 5.6 Consensus size: 16
11254 CCCGACCCGG
11264 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
11280 CACC-AACCCG-AAATA
1 C-CCGAACCCGAAAATA
* * **
11295 CTCGAACCCGACAGGA
1 CCCGAACCCGAAAATA
11311 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
11327 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
11342 CCCGAACCC
1 CCCGAACCC
11351 AAACCTGCCC
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
14 1 0.02
15 25 0.42
16 31 0.53
17 2 0.03
ACGTcount: A:0.38, C:0.41, G:0.15, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:11303 original size:31 final size:32
Alignment explanation
Indices: 11264--11367 Score: 92
Period size: 31 Copynumber: 3.3 Consensus size: 32
11254 CCCGACCCGG
*
11264 CCCGAACCCGAAAATACACC-AACCCG-AAATA
1 CCCGAACCCGAAAAGAC-CCGAACCCGAAAATA
* * *
11295 CTCGAACCCGACAGGACCCGAACCCGAAAATA
1 CCCGAACCCGAAAAGACCCGAACCCGAAAATA
* *
11327 CCCGAACCCG--AAGTACCCGAACCC-AAACCTG
1 CCCGAACCCGAAAAG-ACCCGAACCCGAAA-ATA
11358 CCCGAACCCG
1 CCCGAACCCG
11368 CCCAATTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
30 7 0.11
31 40 0.66
32 14 0.23
ACGTcount: A:0.37, C:0.42, G:0.15, T:0.06
Consensus pattern (32 bp):
CCCGAACCCGAAAAGACCCGAACCCGAAAATA
Found at i:11315 original size:47 final size:47
Alignment explanation
Indices: 11247--11367 Score: 149
Period size: 47 Copynumber: 2.6 Consensus size: 47
11237 TCGAAAGTGA
*
11247 ACCCGAACCCGACCCGGCCCGAACCCGAAAATACACC-AACCCGAAAT
1 ACCCGAACCCGACCAGGCCCGAACCCGAAAATAC-CCGAACCCGAAAT
* *
11294 ACTCGAACCCGA-CAGGACCCGAACCCGAAAATACCCGAACCCGAAGT
1 ACCCGAACCCGACCAGG-CCCGAACCCGAAAATACCCGAACCCGAAAT
* *
11341 ACCCGAACCCAAACC-TGCCCGAACCCG
1 ACCCGAACCC-GACCAGGCCCGAACCCG
11368 CCCAATTGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
46 5 0.08
47 56 0.88
48 2 0.03
49 1 0.02
ACGTcount: A:0.35, C:0.44, G:0.17, T:0.05
Consensus pattern (47 bp):
ACCCGAACCCGACCAGGCCCGAACCCGAAAATACCCGAACCCGAAAT
Found at i:13722 original size:31 final size:31
Alignment explanation
Indices: 13686--13745 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
13676 TGTTCATAAG
*
13686 TGAACAATTATGAAAAGATTTATTTGTCTTA
1 TGAACAATTATGAAAAGACTTATTTGTCTTA
*
13717 TGAACAATTATGAAGAGACTTATTTGTCT
1 TGAACAATTATGAAAAGACTTATTTGTCT
13746 ATAATAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (31 bp):
TGAACAATTATGAAAAGACTTATTTGTCTTA
Found at i:13816 original size:37 final size:37
Alignment explanation
Indices: 13774--13844 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
13764 ACATGATTAT
* * *
13774 TCATAAATTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
13811 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACATGTAT
13845 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (37 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGTATTGA
Found at i:15059 original size:31 final size:32
Alignment explanation
Indices: 15021--15084 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
15011 TAGTGGGGTG
15021 TGTTGGTTTCTTAAAGAAAC-AAAGAGATATA
1 TGTTGGTTTCTTAAAGAAACAAAAGAGATATA
* *
15052 TGTTGGTTTCTTAGAGAAACAAAAGAGTTATA
1 TGTTGGTTTCTTAAAGAAACAAAAGAGATATA
15084 T
1 T
15085 TACTATGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (32 bp):
TGTTGGTTTCTTAAAGAAACAAAAGAGATATA
Found at i:16263 original size:31 final size:31
Alignment explanation
Indices: 16227--16286 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
16217 TGTTCATAAG
* *
16227 TGAACAATTATGAAAATATTTATTTGTCTTA
1 TGAACAATTATGAAAAGACTTATTTGTCTTA
*
16258 TGAACAATTATGAAGAGACTTATTTGTCT
1 TGAACAATTATGAAAAGACTTATTTGTCT
16287 ATAATAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (31 bp):
TGAACAATTATGAAAAGACTTATTTGTCTTA
Found at i:16357 original size:37 final size:36
Alignment explanation
Indices: 16304--16384 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
16294 ATATCTTTAT
* * *
16304 GACATG-ATTATTCATAAAGTTATGTCTATTTGGAAA
1 GACATGTATTAATCATAAAG-TATGTCTATATGAAAA
16340 GACATGTATTAATCATAAAGTATGTCTATATGAAAA
1 GACATGTATTAATCATAAAGTATGTCTATATGAAAA
16376 GACATGTAT
1 GACATGTAT
16385 CATGTATGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 29 0.71
37 12 0.29
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (36 bp):
GACATGTATTAATCATAAAGTATGTCTATATGAAAA
Found at i:17396 original size:16 final size:15
Alignment explanation
Indices: 17375--17416 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
17365 GTTTTTTTGG
17375 TTTTTTGCTTTTGTT
1 TTTTTTGCTTTTGTT
17390 TTGTTTT-CATTTTGTT
1 TT-TTTTGC-TTTTGTT
*
17406 TTTATTGCTTT
1 TTTTTTGCTTT
17417 GTTAATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.05, C:0.07, G:0.12, T:0.76
Consensus pattern (15 bp):
TTTTTTGCTTTTGTT
Found at i:17426 original size:31 final size:30
Alignment explanation
Indices: 17369--17427 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
17359 GTTTTCGTTT
*
17369 TTTTGGTTTTTTGCTTTTGTTTTGTTTTCA
1 TTTTGGTTTTTTGCTTTTGTTATGTTTTCA
*
17399 TTTTGTTTTTATTGC-TTTGTTAATGTTTT
1 TTTTGGTTTT-TTGCTTTTGTT-ATGTTTT
17428 AAAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.07, C:0.05, G:0.15, T:0.73
Consensus pattern (30 bp):
TTTTGGTTTTTTGCTTTTGTTATGTTTTCA
Found at i:19076 original size:1 final size:1
Alignment explanation
Indices: 19072--19101 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
19062 TGATTTTTAC
19072 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19102 TTGAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19852 original size:57 final size:57
Alignment explanation
Indices: 19740--19856 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 57
19730 GGGCATATAT
* * ** **
19740 CGGTGGTTAAAGCTTGAGACTTTTAGTTGAGGTCCCAAGTTTGAATGTTGTGATGGC
1 CGGTGGTTAAAACTTGAGACTTTTAGTGGAGGTCCCAAGTTTGAATACTACGATGGC
19797 CGGTGGTTAAAACTTGAGACTTTTAGTGGAGGTCCCAAGTTTGAATACTACGATGGC
1 CGGTGGTTAAAACTTGAGACTTTTAGTGGAGGTCCCAAGTTTGAATACTACGATGGC
19854 CGG
1 CGG
19857 GGTGGGATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.32
Consensus pattern (57 bp):
CGGTGGTTAAAACTTGAGACTTTTAGTGGAGGTCCCAAGTTTGAATACTACGATGGC
Found at i:20685 original size:107 final size:104
Alignment explanation
Indices: 20401--20677 Score: 386
Period size: 107 Copynumber: 2.7 Consensus size: 104
20391 ATTTTTCTAA
* ** * *
20401 CCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAATG-AATTAGTTATATATTTTATTT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
*
20465 CTAAAACCCTATAACAATATTAATAATTATGGAATTTAC
66 CTAAAACCCTATAACAATATTAATAATTATGAAATTTAC
* *
20504 CCTTAAAAT--AAA-AAAA--TTAATTTGGGGTTAAACTTAGTGAAATTAGTTTTGTATTTTATT
1 CCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
* *
20564 TCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTTAC
65 TCTAAAACCCTATAACAAT--ATTAATAATTATGAAATTTAC
20606 CCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTATATTTTATT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAAATTAGTTTTATATTTTATT
20671 TCTAAAA
65 TCTAAAA
20678 TTCTATAATA
Statistics
Matches: 152, Mismatches: 12, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
98 7 0.05
99 13 0.09
100 39 0.26
101 2 0.01
102 27 0.18
103 9 0.06
104 3 0.02
105 4 0.03
106 3 0.02
107 45 0.30
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (104 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTT
CTAAAACCCTATAACAATATTAATAATTATGAAATTTAC
Found at i:22256 original size:12 final size:12
Alignment explanation
Indices: 22215--22257 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
22205 CATCGATACC
22215 TCGATATATCCG
1 TCGATATATCCG
* *
22227 ACGATATATCCA
1 TCGATATATCCG
22239 TCGATATATCCG
1 TCGATATATCCG
*
22251 TGGATAT
1 TCGATAT
22258 CTATATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:22566 original size:1 final size:1
Alignment explanation
Indices: 22560--22598 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
22550 AGAAAGAAAG
**
22560 AAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
22599 CTTTGACAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:23155 original size:29 final size:30
Alignment explanation
Indices: 23087--23158 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
23077 GAGTTTTTTA
23087 CCAAATTATAACACTTGAAAAACTTATTTC
1 CCAAATTATAACACTTGAAAAACTTATTTC
* * *
23117 TC-AATATATAATA-TTGTAAAACTTATTTC
1 CCAAAT-TATAACACTTGAAAAACTTATTTC
23146 CCAAATTATAACA
1 CCAAATTATAACA
23159 ATTTTTGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (30 bp):
CCAAATTATAACACTTGAAAAACTTATTTC
Found at i:24576 original size:22 final size:22
Alignment explanation
Indices: 24539--24603 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
24529 TACTTTCTTA
*
24539 GTTATAATAAACTAATAATCTAC
1 GTTATTAT-AACTAATAATCTAC
* *
24562 GTTATTATAACTAAT-ATATAT
1 GTTATTATAACTAATAATCTAC
*
24583 GATAATTA-AACTAATAATCTA
1 G-TTATTATAACTAATAATCTA
24604 AGTTTAATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
21 12 0.34
22 16 0.46
23 7 0.20
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (22 bp):
GTTATTATAACTAATAATCTAC
Found at i:25004 original size:2 final size:2
Alignment explanation
Indices: 24997--25025 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24987 TCATCATTAT
24997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25026 TCCCATCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26465 original size:8 final size:8
Alignment explanation
Indices: 26454--26488 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
26444 AATAAAAAAC
26454 AAAAAATT
1 AAAAAATT
26462 -AAAAATT
1 AAAAAATT
26469 AAAAAATT
1 AAAAAATT
26477 AAAAAAATT
1 -AAAAAATT
26486 AAA
1 AAA
26489 TATTTCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.28
8 10 0.40
9 8 0.32
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:26466 original size:15 final size:15
Alignment explanation
Indices: 26446--26482 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
26436 TTTAGTGAAA
26446 TAAAAAACAAAAAAT
1 TAAAAAACAAAAAAT
**
26461 TAAAAATTAAAAAAT
1 TAAAAAACAAAAAAT
26476 TAAAAAA
1 TAAAAAA
26483 ATTAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAAAACAAAAAAT
Found at i:28306 original size:25 final size:25
Alignment explanation
Indices: 28272--28322 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
28262 TAGGATCTAC
28272 TAAACATATTTTGCCATACAAGAAA
1 TAAACATATTTTGCCATACAAGAAA
28297 TAAACATATTTTGCCATACAAGAAA
1 TAAACATATTTTGCCATACAAGAAA
28322 T
1 T
28323 TATGGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (25 bp):
TAAACATATTTTGCCATACAAGAAA
Found at i:28719 original size:13 final size:13
Alignment explanation
Indices: 28701--28760 Score: 88
Period size: 12 Copynumber: 4.8 Consensus size: 13
28691 ATATCGACGA
28701 ATATATCGAACAG
1 ATATATCGAACAG
**
28714 ATATATCG-ATGG
1 ATATATCGAACAG
28726 ATATATCGAACAG
1 ATATATCGAACAG
28739 ATATATCG-ACAG
1 ATATATCGAACAG
28751 ATATATCGAA
1 ATATATCGAA
28761 TGAATATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
12 22 0.54
13 19 0.46
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (13 bp):
ATATATCGAACAG
Found at i:28722 original size:25 final size:25
Alignment explanation
Indices: 28691--28784 Score: 111
Period size: 25 Copynumber: 3.8 Consensus size: 25
28681 TTTAATCCAG
28691 ATATCGACGAATATATCGAACAGAT
1 ATATCGACGAATATATCGAACAGAT
* *
28716 ATATCGATGGATATATCGAACAGAT
1 ATATCGACGAATATATCGAACAGAT
*
28741 ATATCGAC-AGATATATCGAA-TGAAT
1 ATATCGACGA-ATATATCGAACAG-AT
* *
28766 ATATTGACGGATATATCGA
1 ATATCGACGAATATATCGA
28785 GGTATCGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.02
25 58 0.98
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (25 bp):
ATATCGACGAATATATCGAACAGAT
Found at i:28769 original size:13 final size:12
Alignment explanation
Indices: 28691--28784 Score: 73
Period size: 12 Copynumber: 7.6 Consensus size: 12
28681 TTTAATCCAG
*
28691 ATATCGACGAAT
1 ATATCGAAGAAT
*
28703 ATATCGAACAGAT
1 ATATCGAAGA-AT
* *
28716 ATATCGATGGAT
1 ATATCGAAGAAT
*
28728 ATATCGAACAGAT
1 ATATCGAAGA-AT
28741 ATATCGACAG-AT
1 ATATCGA-AGAAT
28753 ATATCGAATGAAT
1 ATATCGAA-GAAT
* * *
28766 ATATTGACGGAT
1 ATATCGAAGAAT
28778 ATATCGA
1 ATATCGA
28785 GGTATCGATA
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
11 1 0.02
12 36 0.56
13 26 0.41
14 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (12 bp):
ATATCGAAGAAT
Found at i:29256 original size:31 final size:31
Alignment explanation
Indices: 29212--29296 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
29202 TCCATTTTGT
* *
29212 AAAATTAC-CAATTTGAGCCTAAACCTTTCA
1 AAAATTGCTCAATTTGAGCCTAAACATTTCA
* *
29242 AAAGTTGCTTAATTTGAGCCTAAACATTTCA
1 AAAATTGCTCAATTTGAGCCTAAACATTTCA
*
29273 AAAATTGCTCAATTTGAGTCTAAA
1 AAAATTGCTCAATTTGAGCCTAAA
29297 AACAGAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 6 0.13
31 41 0.87
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (31 bp):
AAAATTGCTCAATTTGAGCCTAAACATTTCA
Found at i:30998 original size:24 final size:24
Alignment explanation
Indices: 30964--31012 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
30954 AATTTGAAAA
*
30964 CCCATGGCTCATGGCAACCAAGTC
1 CCCATGACTCATGGCAACCAAGTC
30988 CCCATGACTCATGGCAACCAAGTC
1 CCCATGACTCATGGCAACCAAGTC
31012 C
1 C
31013 ATGGCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.16
Consensus pattern (24 bp):
CCCATGACTCATGGCAACCAAGTC
Found at i:31017 original size:15 final size:15
Alignment explanation
Indices: 30997--31027 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30987 CCCCATGACT
*
30997 CATGGCAACCAAGTC
1 CATGGCAACAAAGTC
31012 CATGGCAACAAAGTC
1 CATGGCAACAAAGTC
31027 C
1 C
31028 CCATGACTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.13
Consensus pattern (15 bp):
CATGGCAACAAAGTC
Found at i:31027 original size:39 final size:39
Alignment explanation
Indices: 30973--31051 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
30963 ACCCATGGCT
*
30973 CATGGCAACCAAGTCCCCATGACTCATGGCAACCAAGTC
1 CATGGCAACAAAGTCCCCATGACTCATGGCAACCAAGTC
31012 CATGGCAACAAAGTCCCCATGACTCATGGCAACCAAGTC
1 CATGGCAACAAAGTCCCCATGACTCATGGCAACCAAGTC
31051 C
1 C
31052 CCATGGCTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (39 bp):
CATGGCAACAAAGTCCCCATGACTCATGGCAACCAAGTC
Found at i:31043 original size:63 final size:63
Alignment explanation
Indices: 30964--31096 Score: 230
Period size: 63 Copynumber: 2.1 Consensus size: 63
30954 AATTTGAAAA
*
30964 CCCATGGCTCATGGCAACCAAGTCCCCATGACTCATGGCAACCAAGTCCATGGCAACAAAGTC
1 CCCATGACTCATGGCAACCAAGTCCCCATGACTCATGGCAACCAAGTCCATGGCAACAAAGTC
* *
31027 CCCATGACTCATGGCAACCAAGTCCCCATGGCTCATGGCAACCAAGTCCATGGCAACTAAGTC
1 CCCATGACTCATGGCAACCAAGTCCCCATGACTCATGGCAACCAAGTCCATGGCAACAAAGTC
31090 CCACATG
1 CC-CATG
31097 GTATATGGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
63 62 0.94
64 4 0.06
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (63 bp):
CCCATGACTCATGGCAACCAAGTCCCCATGACTCATGGCAACCAAGTCCATGGCAACAAAGTC
Found at i:31044 original size:24 final size:24
Alignment explanation
Indices: 31012--31075 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
31002 CAACCAAGTC
*
31012 CATGGCAACAAAGTCCCCATGACT
1 CATGGCAACCAAGTCCCCATGACT
*
31036 CATGGCAACCAAGTCCCCATGGCT
1 CATGGCAACCAAGTCCCCATGACT
31060 CATGGCAACCAAGTCC
1 CATGGCAACCAAGTCC
31076 ATGGCAACTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.30, C:0.36, G:0.19, T:0.16
Consensus pattern (24 bp):
CATGGCAACCAAGTCCCCATGACT
Found at i:31080 original size:15 final size:15
Alignment explanation
Indices: 31060--31090 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31050 CCCCATGGCT
31060 CATGGCAACCAAGTC
1 CATGGCAACCAAGTC
*
31075 CATGGCAACTAAGTC
1 CATGGCAACCAAGTC
31090 C
1 C
31091 CACATGGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.16
Consensus pattern (15 bp):
CATGGCAACCAAGTC
Found at i:34936 original size:491 final size:492
Alignment explanation
Indices: 33980--34963 Score: 1776
Period size: 491 Copynumber: 2.0 Consensus size: 492
33970 ATTCCCTTTC
*
33980 CTCTTTGTTTCGCTTAGAAATACCAATTGGGGGCGGTGTTTATTCAACACCTTTAAAACATTCGG
1 CTCTTTGTTTCGCTTAGAAATACCAATTGGGGGCGGTGTTTATTCAACACCTCTAAAACATTCGG
*
34045 AATTGCCTAGGGTGCCCCCAATCCCTGGCAATTCCAAGCTAGAATACTCATGATTCTTAGCGGGG
66 AATTGCCTAGGGTGCCCCAAATCCCTGGCAATTCCAAGCTAGAATACTCATGATTCTTAGCGGGG
*
34110 TTGGCTATTGAGACCAACCTCCGCCATTTTAGGAGTATGAAATTCAGATATACTATCAGACTCAA
131 TTGGCTATTGAGACAAACCTCCGCCATTTTAGGAGTATGAAATTCAGATATACTATCAGACTCAA
*
34175 GCTCACCATCTTCTCTACTCTTCTTCCTTCCACCCGCCCCCATTCCTTTTGATCCAGCTCTCTTT
196 GCTCACCATCTTCTCTACTCTTCTTCCTTCCACCCGCCCCCATTCCTTTTGATCCAACTCTCTTT
34240 GCACCTGATATCTTCATAGGGTGAGAAGTTCTATTCAAATCATTGTTACTCTGTGCTGCTCTCTT
261 GCACCTGATATCTTCATAGGGTGAGAAGTTCTATTCAAATCATTGTTACTCTGTGCTGCTCTCTT
* *
34305 CCAACGTTTGCCACTTTGACTTTCACCACTATTATTTGAGATATTTTGTGCCTTGAAAGTAAATG
326 CCAACGTTTGCCACTCTAACTTTCACCACTATTATTTGAGATATTTTGTGCCTTGAAAGTAAATG
*
34370 GTTGCCCCTTCGACATTTCCTGTTCCCTAGTTAAATTCCGATTTATGCAAGTATCAGTTTTTGGC
391 GTTGCCCCTTCGACATTTCCTGTTCCCCAGTTAAATTCCGATTTATGCAAGTATCAGTTTTTGGC
34435 ACAATAGACAACAGCCCCGTTTTCTCCTTCTCTACTT
456 ACAATAGACAACAGCCCCGTTTTCTCCTTCTCTACTT
*
34472 CTCTTTGTTTCGCTTAGAAATACCAATT-GGGGTGGTGTTTATTCAACACCTCTAAAACATTCGG
1 CTCTTTGTTTCGCTTAGAAATACCAATTGGGGGCGGTGTTTATTCAACACCTCTAAAACATTCGG
*
34536 AATTGCC-CGTGGTGCCCCAAATCCCTGGCAATTCCAAGCTAGAATACTCATGATTCTT-GCTGG
66 AATTGCCTAG-GGTGCCCCAAATCCCTGGCAATTCCAAGCTAGAATACTCATGATTCTTAGC-GG
*
34599 GGTTGGCTATTGAGACAAACCTCCGCCATTTTAGGAGTATGAAATTCATATATACTATCAGACTC
129 GGTTGGCTATTGAGACAAACCTCCGCCATTTTAGGAGTATGAAATTCAGATATACTATCAGACTC
* *
34664 AAGCTCACCATCTTCTTTACTCTTCTTCCTTCCACCTGCCCCCATTCCTTTTGATCCAACTCTCT
194 AAGCTCACCATCTTCTCTACTCTTCTTCCTTCCACCCGCCCCCATTCCTTTTGATCCAACTCTCT
*
34729 TTGCACCTGATATCTTCATAGGGTGAGAAGTTCTATTCGAATCATTGTTACTCTGTGCTGCTCTC
259 TTGCACCTGATATCTTCATAGGGTGAGAAGTTCTATTCAAATCATTGTTACTCTGTGCTGCTCTC
*
34794 TTCCAACGTTTGTCACTCTAACTTTCACCACTATTATTTGAGATATTTTGTGCCTTGAAAGTAAA
324 TTCCAACGTTTGCCACTCTAACTTTCACCACTATTATTTGAGATATTTTGTGCCTTGAAAGTAAA
* * *
34859 TGGTTGCCTCTTCGACATTTTCTGTTCCCCAGTTAAATTCCGATTTATGCAAGTATCGGTTTTTG
389 TGGTTGCCCCTTCGACATTTCCTGTTCCCCAGTTAAATTCCGATTTATGCAAGTATCAGTTTTTG
34924 GCACAATAGACAACAGCCCCGTTTTCTCCTTCTCTACTT
454 GCACAATAGACAACAGCCCCGTTTTCTCCTTCTCTACTT
34963 C
1 C
34964 GGTATCCATC
Statistics
Matches: 473, Mismatches: 17, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
490 3 0.01
491 442 0.93
492 28 0.06
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (492 bp):
CTCTTTGTTTCGCTTAGAAATACCAATTGGGGGCGGTGTTTATTCAACACCTCTAAAACATTCGG
AATTGCCTAGGGTGCCCCAAATCCCTGGCAATTCCAAGCTAGAATACTCATGATTCTTAGCGGGG
TTGGCTATTGAGACAAACCTCCGCCATTTTAGGAGTATGAAATTCAGATATACTATCAGACTCAA
GCTCACCATCTTCTCTACTCTTCTTCCTTCCACCCGCCCCCATTCCTTTTGATCCAACTCTCTTT
GCACCTGATATCTTCATAGGGTGAGAAGTTCTATTCAAATCATTGTTACTCTGTGCTGCTCTCTT
CCAACGTTTGCCACTCTAACTTTCACCACTATTATTTGAGATATTTTGTGCCTTGAAAGTAAATG
GTTGCCCCTTCGACATTTCCTGTTCCCCAGTTAAATTCCGATTTATGCAAGTATCAGTTTTTGGC
ACAATAGACAACAGCCCCGTTTTCTCCTTCTCTACTT
Found at i:37463 original size:16 final size:15
Alignment explanation
Indices: 37439--37495 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
37429 TTGGACGGGC
*
37439 TCGGATTCGGGTTTAT
1 TCGGGTTCGGGTTT-T
*
37455 TCGGGTTCGGGTTCTG
1 TCGGGTTCGGGTT-TT
*
37471 TCAGGTTCGGGTATTT
1 TCGGGTTCGGGT-TTT
37487 TCGGGTTCG
1 TCGGGTTCG
37496 ATCTCGGGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 32 0.94
17 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.37, T:0.40
Consensus pattern (15 bp):
TCGGGTTCGGGTTTT
Found at i:38255 original size:2 final size:2
Alignment explanation
Indices: 38248--38272 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38238 TGCTTTAAGT
38248 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38273 TTAGTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38371 original size:14 final size:14
Alignment explanation
Indices: 38354--38412 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
38344 ATTGTGATCA
38354 TTATTATATAAATT
1 TTATTATATAAATT
* *
38368 TTATTATATGTAGTT
1 TTATTATAT-AAATT
38383 TTATTTAATATAAATT
1 TTA-TT-ATATAAATT
38399 ATTATTAT-TAAATT
1 -TTATTATATAAATT
38413 CAAATTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 15 0.41
15 8 0.22
16 7 0.19
17 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (14 bp):
TTATTATATAAATT
Found at i:43093 original size:2 final size:2
Alignment explanation
Indices: 43086--43133 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
43076 ATCCTCACAA
43086 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
43128 GT GT GT
1 GT GT GT
43134 TTATACCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:46787 original size:36 final size:36
Alignment explanation
Indices: 46747--46815 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
46737 AACACACTTA
46747 ATCATAAATATAAAAATAGTAAATTACAAAAAAAGG
1 ATCATAAATATAAAAATAGTAAATTACAAAAAAAGG
46783 ATCATAAATATAAAAATAGTAAATTACAAAAAA
1 ATCATAAATATAAAAATAGTAAATTACAAAAAA
46816 GGGCAGCAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (36 bp):
ATCATAAATATAAAAATAGTAAATTACAAAAAAAGG
Found at i:47796 original size:13 final size:13
Alignment explanation
Indices: 47778--47805 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47768 CCATGGTAGT
47778 TAAAAATAATATA
1 TAAAAATAATATA
47791 TAAAAATAATATA
1 TAAAAATAATATA
47804 TA
1 TA
47806 GTATATATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATAATATA
Found at i:48686 original size:438 final size:435
Alignment explanation
Indices: 48159--49162 Score: 1270
Period size: 438 Copynumber: 2.3 Consensus size: 435
48149 TTTTTTTTTC
* * * *
48159 TATTTGTCCGATTAAGGTGATTCAAGTGTCTACTAAAAGGTAATTTCATGATCTACAATTTTCAT
1 TATTTGTCCAATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
* * * *
48224 GAAGAACTCAAAAGGCAATTTTTATGTTTTGATTCTAAAAAATGCTTCCGAAATTTTGTGATTTT
66 GAA-AACTCAAAA-GCAATTTTTATGTTTTAATTCTAAAAAATACTTTCGAAATTTTGTGATTTC
* * * * * * *
48289 GATTGCCAGT-TAATTTAATATCGTATAATTTTTTG-TTCACATGTCCGATTAAGGTTATTGAAG
129 GATTGCCAGTCT-ATTTAATACCATATAA-TTTTCGATCCACATATCCGATTAAAGTTATTCAAG
* * * **
48352 TGTCAGG-TAAAAGGTTATTGTATGATTTATGACATTCATGAAGGACCC-GAAAGTTAAATTTGA
192 TGTC-GGTTAAAAGGTTACTGTATGATCTACGACATTCATGAACAACCCAG-AAGTT-AATTTGA
* * * *
48415 TCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGCTTCTAGATCTCTATTAAC-AAACA
254 TCTACGAGTTTCATGAAGGGTTCAAAAGCGAATTTTTATGCTTCAAGATATCCATT-ACGAAACA
* * * * *
48479 TTTTCTTATTTGGATTATTTATCAAATGACCCTCATATTTTTCTACTTTATACTACTTAGTCCTT
318 TTTTCTTATTTGAATTAGTTATCAAATGACCCTCATAGTTTTCTACTTTAAACTACTTAGTCATT
*
48544 TACAAATTCTATCTTAATCTAATGTTTAAGATT-TATTTTTTTA-TTCTTTGTTT
383 TACAAATTCTATCTT-ATCTAAT-TTTAAGATTATATTTTTTTATTTCTTTGTTA
* * * *
48597 TATTTGTCCAATTAAGTTGATTCATGTATCTATTCAAAGGTAATTTCATGATCTACAACTTTCAT
1 TATTTGTCCAATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
*
48662 GAATAACTCAAAAGCAAATTTTTATGTTTTAATTC-AAAAGAATACTTTCTAAATTTTGTCG-TT
66 GAA-AACTCAAAAGC-AATTTTTATGTTTTAATTCTAAAA-AATACTTTCGAAATTTTGT-GATT
***
48725 TCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATATCCGATTAAAGTTATTCAAG
127 TCGATTGCCAGTCTATTTAATACCATATAATTTTCGATCCACATATCCGATTAAAGTTATTCAAG
*
48790 TGTCGGTTAAAAGGTTACTGTATGATCTACGACTTTCATGAACAACCCAGAAGTTAATTTGATCT
192 TGTCGGTTAAAAGGTTACTGTATGATCTACGACATTCATGAACAACCCAGAAGTTAATTTGATCT
* *
48855 ACGAGTTTCATGAAGGGTTCAAAAGCGAATTTTTATGTTTCAAGATATCCATTACGAAATATTTT
257 ACGAGTTTCATGAAGGGTTCAAAAGCGAATTTTTATGCTTCAAGATATCCATTACGAAACATTTT
*
48920 CTTATTTGAATTAGTTATCAAATGACCCTCATAGTTTTCTATTTTAAACTACTTAGTCATTTACA
322 CTTATTTGAATTAGTTATCAAATGACCCTCATAGTTTTCTACTTTAAACTACTTAGTCATTTACA
* * * * *
48985 AATTCTATCTTATTTGATTTTACGCTTATTTTTTTTTATTTTCTTTGTTA
387 AATTCTATCTTATCTAATTTTAAGATTATATTTTTTTA-TTTCTTTGTTA
* * * * ** *
49035 TATTTATGCAATTAAGATAATTCAGGTGTCTATTAAAAGGTAATTTTGTGATCTACAACTTTTAT
1 TATTTGTCCAATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
* * * *
49100 GAAAGACTAAAAAGCTAATTTTCATGTTTCAATTCTAAAAAATACTTTTGAAATTTTGTGATT
66 GAAA-ACTCAAAAGC-AATTTTTATGTTTTAATTCTAAAAAATACTTTCGAAATTTTGTGATT
49163 CCAATTGACA
Statistics
Matches: 489, Mismatches: 63, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
435 7 0.01
436 16 0.03
437 151 0.31
438 308 0.63
439 7 0.01
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (435 bp):
TATTTGTCCAATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCAT
GAAAACTCAAAAGCAATTTTTATGTTTTAATTCTAAAAAATACTTTCGAAATTTTGTGATTTCGA
TTGCCAGTCTATTTAATACCATATAATTTTCGATCCACATATCCGATTAAAGTTATTCAAGTGTC
GGTTAAAAGGTTACTGTATGATCTACGACATTCATGAACAACCCAGAAGTTAATTTGATCTACGA
GTTTCATGAAGGGTTCAAAAGCGAATTTTTATGCTTCAAGATATCCATTACGAAACATTTTCTTA
TTTGAATTAGTTATCAAATGACCCTCATAGTTTTCTACTTTAAACTACTTAGTCATTTACAAATT
CTATCTTATCTAATTTTAAGATTATATTTTTTTATTTCTTTGTTA
Found at i:57194 original size:1 final size:1
Alignment explanation
Indices: 57188--57223 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
57178 TACTTAAGTC
57188 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
57224 CATCTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.