Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012824.1 Corchorus capsularis cultivar CVL-1 contig12845, 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: 231002
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:628 original size:17 final size:16
Alignment explanation
Indices: 588--638 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
578 CATGTAATCT
*
588 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
604 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
621 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
638 T
1 T
639 GGGGGGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:2608 original size:1 final size:1
Alignment explanation
Indices: 2602--2647 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
2592 ACATGATCAG
2602 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2648 AATCTTTGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5624 original size:25 final size:25
Alignment explanation
Indices: 5590--5637 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
5580 GTTCCAATAA
5590 TTGGGAGAAACTCTAAAGGTGGATG
1 TTGGGAGAAACTCTAAAGGTGGATG
5615 TTGGGAGAAACTCTAAAGGTGGA
1 TTGGGAGAAACTCTAAAGGTGGA
5638 GCATCCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.35, T:0.23
Consensus pattern (25 bp):
TTGGGAGAAACTCTAAAGGTGGATG
Found at i:11912 original size:17 final size:17
Alignment explanation
Indices: 11890--11929 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
11880 TTAAGGTCAA
*
11890 TTTTTTCTTGTCGTCTT
1 TTTTTTCTTGTCGGCTT
*
11907 TTTTTTCTTGTCGGGTT
1 TTTTTTCTTGTCGGCTT
11924 TTTTTT
1 TTTTTT
11930 GAGAGATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.72
Consensus pattern (17 bp):
TTTTTTCTTGTCGGCTT
Found at i:14879 original size:52 final size:54
Alignment explanation
Indices: 14785--14893 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 54
14775 GTGAACAAAG
*
14785 TTTTGATTTAGAGATTATAATTAGTTTGGTTCGGGGTTTTCAAGTTTTTAAGGTC
1 TTTTGATTTAGAGATTATAA-TAGTTTGGTTCGGGGTTTTCAAGTTTTAAAGGTC
*
14840 TTTTGGTTTAGAGATTAT-A-AGTTTGGTTTC-GGGTTTTCAAGTTTTAAAGGTC
1 TTTTGATTTAGAGATTATAATAGTTTGG-TTCGGGGTTTTCAAGTTTTAAAGGTC
14892 TT
1 TT
14894 CAATCAGATC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
52 30 0.59
53 3 0.06
54 1 0.02
55 17 0.33
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.50
Consensus pattern (54 bp):
TTTTGATTTAGAGATTATAATAGTTTGGTTCGGGGTTTTCAAGTTTTAAAGGTC
Found at i:19791 original size:37 final size:37
Alignment explanation
Indices: 19747--19817 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
19737 CTTGATCAAC
* *
19747 ATACATGTCTTTTCATATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
19784 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
19818 ATAATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:21062 original size:31 final size:32
Alignment explanation
Indices: 21014--21075 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
21004 CATCATAGTG
21014 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
* *
21046 ATATATCTC-TTTGTTTCTTTAAGAAACCAA
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAA
21076 GACACCCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
Found at i:39537 original size:2 final size:2
Alignment explanation
Indices: 39532--39561 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
39522 CCAAAAAAGA
39532 AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39562 AACGATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46642 original size:11 final size:11
Alignment explanation
Indices: 46616--46648 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46606 CTTCCCTCTC
*
46616 TCTCTCT-CTC
1 TCTCTCTACTT
46626 TCTCTCTACTT
1 TCTCTCTACTT
46637 TCTCTCTACTT
1 TCTCTCTACTT
46648 T
1 T
46649 GGGTCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (11 bp):
TCTCTCTACTT
Found at i:53354 original size:1 final size:1
Alignment explanation
Indices: 53343--53372 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
53333 ACGTTTAAAG
*
53343 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
53373 CTTCTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:54649 original size:2 final size:2
Alignment explanation
Indices: 54642--54673 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54632 AAAGCAGAGC
54642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54674 GTCGAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55310 original size:14 final size:14
Alignment explanation
Indices: 55293--55327 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55283 AACGAGAACA
55293 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
55307 AGAGAGGGAGAAGG
1 AGAGAGGGAGAAGG
*
55321 GGAGAGG
1 AGAGAGG
55328 AGCGGCTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (14 bp):
AGAGAGGGAGAAGG
Found at i:64841 original size:2 final size:2
Alignment explanation
Indices: 64834--64880 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
64824 GGAGGAAAGT
**
64834 TA TA TA TA CC TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64875 TA TA TA
1 TA TA TA
64881 AATCCCCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:74377 original size:13 final size:13
Alignment explanation
Indices: 74359--74383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74349 GATACAGCTA
74359 TAAAAGAAAAGAT
1 TAAAAGAAAAGAT
74372 TAAAAGAAAAGA
1 TAAAAGAAAAGA
74384 AAAACACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
TAAAAGAAAAGAT
Found at i:76862 original size:13 final size:13
Alignment explanation
Indices: 76844--76872 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
76834 ACACGATTAG
76844 TTATTAATCGTGT
1 TTATTAATCGTGT
76857 TTATTAATCGTGT
1 TTATTAATCGTGT
76870 TTA
1 TTA
76873 CACGACTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (13 bp):
TTATTAATCGTGT
Found at i:77971 original size:12 final size:12
Alignment explanation
Indices: 77954--77981 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
77944 TATAGCTCTC
77954 TTTTTTCTTTTT
1 TTTTTTCTTTTT
77966 TTTTTTCTTTTT
1 TTTTTTCTTTTT
77978 TTTT
1 TTTT
77982 CCCTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:80413 original size:31 final size:31
Alignment explanation
Indices: 80378--80442 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
80368 TTGGGTTATC
*
80378 AGTCTCTAGATCTTTAGATCATGGATGTTTG
1 AGTCTCCAGATCTTTAGATCATGGATGTTTG
* *
80409 AGTCTCCGGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCATGGATGTTTG
80440 AGT
1 AGT
80443 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.20, C:0.14, G:0.25, T:0.42
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCATGGATGTTTG
Found at i:82038 original size:27 final size:25
Alignment explanation
Indices: 82003--82055 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
81993 CCTTTTTTTA
82003 AAATATATTTCTAA-ATTGCCATTATT
1 AAATATATTT-TAATATT-CCATTATT
82029 AAATAATATTTTAATTATTCCATTATT
1 AAAT-ATATTTTAA-TATTCCATTATT
82056 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATATATTTTAATATTCCATTATT
Found at i:82047 original size:19 final size:19
Alignment explanation
Indices: 82023--82069 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
82013 CTAAATTGCC
82023 ATTATTAAATAATATTTTA
1 ATTATTAAATAATATTTTA
** * *
82042 ATTATTCCATTATTTTTTA
1 ATTATTAAATAATATTTTA
82061 ATTA-TAAAT
1 ATTATTAAAT
82070 TATTCCATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTATTAAATAATATTTTA
Found at i:82085 original size:15 final size:15
Alignment explanation
Indices: 82039--82088 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
82029 AAATAATATT
82039 TTAATTATTCCATTA
1 TTAATTATTCCATTA
*
82054 TT--TT-TT-AATTA
1 TTAATTATTCCATTA
*
82065 TAAATTATTCCATTA
1 TTAATTATTCCATTA
82080 TTAATTATT
1 TTAATTATT
82089 AGATTATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
11 5 0.19
12 2 0.07
13 4 0.15
14 2 0.07
15 14 0.52
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAATTATTCCATTA
Found at i:82094 original size:15 final size:15
Alignment explanation
Indices: 82039--82100 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
82029 AAATAATATT
*
82039 TTAATTATTCCATTA
1 TTAATTATTACATTA
82054 TT--TT-TTA-ATTA
1 TTAATTATTACATTA
* *
82065 TAAATTATTCCATTA
1 TTAATTATTACATTA
*
82080 TTAATTATTAGATTA
1 TTAATTATTACATTA
82095 TATAAT
1 T-TAAT
82101 ACGTATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
11 5 0.14
12 2 0.06
13 4 0.11
14 2 0.06
15 19 0.53
16 4 0.11
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (15 bp):
TTAATTATTACATTA
Found at i:82231 original size:37 final size:37
Alignment explanation
Indices: 82136--82231 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
82126 AATTTGGCTT
*
82136 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTG
1 TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
* * ** *
82173 TTTGTTTCTAATCATTTTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTGCCTTTTGTC
*
82211 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
82232 GGTCTTATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
37 17 0.36
38 30 0.64
ACGTcount: A:0.15, C:0.18, G:0.10, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTGCCTTTTGTC
Found at i:83398 original size:20 final size:20
Alignment explanation
Indices: 83373--83418 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
83363 TGGAGTAATT
83373 AAAATTTCAGGGAGGATATC
1 AAAATTTCAGGGAGGATATC
83393 AAAA-TTCAGGGAGGATATC
1 AAAATTTCAGGGAGGATATC
83412 AAAATTT
1 AAAATTT
83419 TATATGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (20 bp):
AAAATTTCAGGGAGGATATC
Found at i:83436 original size:22 final size:22
Alignment explanation
Indices: 83408--83632 Score: 132
Period size: 22 Copynumber: 10.5 Consensus size: 22
83398 TCAGGGAGGA
83408 TATCAAAATTTTATATGAAGGT
1 TATCAAAATTTTATATGAAGGT
* *
83430 TATCAAAATTTCATAT-TA-GT
1 TATCAAAATTTTATATGAAGGT
* *
83450 TTTCAAAATTTCATAATG-AGGT
1 TATCAAAATTTTAT-ATGAAGGT
** * * * *
83472 TATCAAAAAATCATAGGGAGCT
1 TATCAAAATTTTATATGAAGGT
83494 TATCAAAA-TTT-T-T-AA--T
1 TATCAAAATTTTATATGAAGGT
* * * *
83510 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTTATATGAAGGT
83532 TATCAAAATTTTATA-GAAAGGTT
1 TATCAAAATTTTATATG-AAGG-T
* *
83555 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTTATATGAAG-GT
*
83578 TATCAAAATTTTATA-GCGAGGT
1 TATCAAAATTTTATATG-AAGGT
* * *
83600 TATCACAATTTTATATTG-TGAT
1 TATCAAAATTTTATA-TGAAGGT
83622 TATCAAAATTT
1 TATCAAAATTT
83633 CAGAGTGTGA
Statistics
Matches: 161, Mismatches: 25, Indels: 34
0.73 0.11 0.15
Matches are distributed among these distances:
16 8 0.05
17 2 0.01
18 2 0.01
20 18 0.11
21 8 0.05
22 84 0.52
23 37 0.23
24 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.40
Consensus pattern (22 bp):
TATCAAAATTTTATATGAAGGT
Found at i:94887 original size:45 final size:45
Alignment explanation
Indices: 94810--94896 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
94800 ATGATGTTGT
* * *
94810 CTTGGCTGGGGAAGTTGGCAGGGAAGCAGTGGTTACAACAGCAGG
1 CTTGGCTGGAGAAGATGGCAAGGAAGCAGTGGTTACAACAGCAGG
* * * *
94855 CTTGGCTGGAGAAGATGGCAATGACGCGGTGGTTGCAACAGC
1 CTTGGCTGGAGAAGATGGCAAGGAAGCAGTGGTTACAACAGC
94897 GGTCCTGACT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.40, T:0.18
Consensus pattern (45 bp):
CTTGGCTGGAGAAGATGGCAAGGAAGCAGTGGTTACAACAGCAGG
Found at i:102214 original size:11 final size:11
Alignment explanation
Indices: 102171--102208 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
102161 TTCCTATATA
*
102171 AAATAAATTAT
1 AAATTAATTAT
102182 CAAA-TAATTAT
1 -AAATTAATTAT
102193 AAATTAATTAT
1 AAATTAATTAT
102204 AAATT
1 AAATT
102209 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:113004 original size:2 final size:2
Alignment explanation
Indices: 112997--113022 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112987 AGTGTATGCA
112997 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
113023 GCATTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119528 original size:1 final size:1
Alignment explanation
Indices: 119522--119549 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
119512 GTAGTTAGGG
119522 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
119550 ACAGACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:134193 original size:7 final size:7
Alignment explanation
Indices: 134181--134217 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
134171 AAATTTCCTC
134181 TTCTTTT
1 TTCTTTT
134188 TTCTTTT
1 TTCTTTT
134195 TTCTTTT
1 TTCTTTT
*
134202 TTTTTTT
1 TTCTTTT
*
134209 TTATTTT
1 TTCTTTT
134216 TT
1 TT
134218 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (7 bp):
TTCTTTT
Found at i:134203 original size:9 final size:9
Alignment explanation
Indices: 134184--134225 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
134174 TTTCCTCTTC
134184 TTTTTTCTT-
1 TTTTTT-TTA
*
134193 TTTTCTTTTT
1 TTTT-TTTTA
134203 TTTTTTTTA
1 TTTTTTTTA
134212 TTTTTTTTA
1 TTTTTTTTA
134221 TTTTT
1 TTTTT
134226 AATTTGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:134219 original size:15 final size:15
Alignment explanation
Indices: 134183--134226 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
134173 ATTTCCTCTT
*
134183 CTTTTTTCTTTTTT-
1 CTTTTTTTTTTTTTA
134197 CTTTTTTTTTTTTTA
1 CTTTTTTTTTTTTTA
134212 -TTTTTTTTATTTTTA
1 CTTTTTTTT-TTTTTA
134227 ATTTGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (15 bp):
CTTTTTTTTTTTTTA
Found at i:134843 original size:22 final size:22
Alignment explanation
Indices: 134815--134856 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
134805 GTGCGCTCCC
134815 CTGAGCACGTGCAACTCACACG
1 CTGAGCACGTGCAACTCACACG
134837 CTGAGCACGTGCAACTCACA
1 CTGAGCACGTGCAACTCACA
134857 TGGGTACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (22 bp):
CTGAGCACGTGCAACTCACACG
Found at i:137431 original size:24 final size:24
Alignment explanation
Indices: 137404--137449 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
137394 ATGACCATCT
*
137404 CCAACAAGTCAAAAGGGTGAGCGA
1 CCAACAAGTCAAAAGGGCGAGCGA
137428 CCAACAAGTCAAAAGGGCGAGC
1 CCAACAAGTCAAAAGGGCGAGC
137450 AATTGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.24, G:0.28, T:0.07
Consensus pattern (24 bp):
CCAACAAGTCAAAAGGGCGAGCGA
Found at i:137618 original size:106 final size:106
Alignment explanation
Indices: 137434--137693 Score: 459
Period size: 106 Copynumber: 2.5 Consensus size: 106
137424 GCGACCAACA
* * *
137434 AGTCAAAAGGGCGAGCAATTGTAAA-ATTAGCTCTATACTTGACTTCAAGACCAAAGTTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
137498 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
* *
137539 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAGGACCAATGCTAATTGG
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
*
137604 CGAGCGATTGGTTTCACTATCCTCGACCTAATAAAAGCACG
66 CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
137645 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAA
1 AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAA
137694 AACTAAGGAT
Statistics
Matches: 147, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
105 24 0.16
106 123 0.84
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (106 bp):
AGTCAAAAGGGCGAGCAATCGTAAAGATTAGCTCTATACTTGACCTCAAGACCAAAGCTAATTGG
CGAGCGATTGGTTTCACTATCCTCGACCCAATAAAAGCACG
Found at i:138438 original size:119 final size:118
Alignment explanation
Indices: 138223--138539 Score: 418
Period size: 119 Copynumber: 2.7 Consensus size: 118
138213 GCATGATGAC
* *
138223 CAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCATCGGATGCTCCCCTGAACACGTGCAACTCT
1 CAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTC-
* *
138288 CCCAAGCACGTGA-AATCACCAATGCGGGAAAGAAGAGCGCTCAATGAAAAGTGA
65 CTCAAGCACGT-ACAATCACCAATGCGCGAAAGAAGAGCGCTCAATGAAAAGTGA
* * *
138342 CAACCGCGTGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTTAACATGTGCAACTCC
1 CAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCC
* * * *
138407 TCGAAGCACGTACAATCACCAATGTGCGAAAGAAGAGTGCTCAATGAAGAGTGC
66 TC-AAGCACGTACAATCACCAATGCGCGAAAGAAGAGCGCTCAATGAAAAGTGA
*
138461 CGACCGCGCGAGTGAAGAATGC----T----AGCACCGAATGCTCCCCTGAACACGTGCAACTCC
1 CAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACT-C
*
138518 CTCAAGCACGTGCAATCACCAA
65 CTCAAGCACGTACAATCACCAA
138540 CTTATTCATG
Statistics
Matches: 179, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
111 48 0.27
112 4 0.02
115 1 0.01
118 3 0.02
119 123 0.69
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (118 bp):
CAACCGCGCGAGTGAAGAATGCTTAATGAAGAGCACCGAATGCTCCCCTGAACACGTGCAACTCC
TCAAGCACGTACAATCACCAATGCGCGAAAGAAGAGCGCTCAATGAAAAGTGA
Found at i:141221 original size:5 final size:5
Alignment explanation
Indices: 141213--141251 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
141203 AAAGATAGGA
141213 ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
141252 ACATTAGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 28 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:144256 original size:24 final size:24
Alignment explanation
Indices: 144204--144250 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
144194 TGGTGCTGCT
* * *
144204 TATGAGAGGCGCAGGAGTCCTGAC
1 TATGGGAGGCACAGAAGTCCTGAC
144228 TATGGGAGGCACAGAAGTCCTGA
1 TATGGGAGGCACAGAAGTCCTGA
144251 GCATGGCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.36, T:0.17
Consensus pattern (24 bp):
TATGGGAGGCACAGAAGTCCTGAC
Found at i:145899 original size:2 final size:2
Alignment explanation
Indices: 145892--145920 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
145882 TTGGATTTGC
145892 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
145921 TTAAAATGGG
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:150707 original size:102 final size:103
Alignment explanation
Indices: 150449--150745 Score: 560
Period size: 102 Copynumber: 2.9 Consensus size: 103
150439 TTGAACATAC
*
150449 AAGTAGTATGTATTATGATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
1 AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
*
150514 GAGTGAGAGTTCTTCATTCCAATCTCTTGCAAAAAAAA
66 GAGTGAGAGTTCCTCATTCCAATCTCTTGCAAAAAAAA
*
150552 AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGCAGTTATGATTCTTAGTTTCTTA
1 AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
150617 GAGTGAGAGTTCCTCATTCCAATCTCTTGC-AAAAAAA
66 GAGTGAGAGTTCCTCATTCCAATCTCTTGCAAAAAAAA
150654 AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
1 AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
150719 GAGTGAGAGTTCCTCATTCCAATCTCT
66 GAGTGAGAGTTCCTCATTCCAATCTCT
150746 AGCTTTTTCC
Statistics
Matches: 190, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
102 98 0.52
103 92 0.48
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (103 bp):
AAGTAGTATGTATTATAATTACCTATATTGAACAGCTAGTTGTAGTTATGATTCTTAGTTTCTTA
GAGTGAGAGTTCCTCATTCCAATCTCTTGCAAAAAAAA
Found at i:166422 original size:27 final size:27
Alignment explanation
Indices: 166384--166436 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
166374 TGTCATGAAG
**
166384 CATATATTTATATACATGGGAATTTTC
1 CATATATTTATATACATAAGAATTTTC
166411 CATATATTTATATACATAAGAATTTT
1 CATATATTTATATACATAAGAATTTT
166437 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (27 bp):
CATATATTTATATACATAAGAATTTTC
Found at i:166449 original size:11 final size:11
Alignment explanation
Indices: 166431--166463 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
166421 TATACATAAG
166431 AATTTTTTTTT
1 AATTTTTTTTT
*
166442 -CTTTTTTTTT
1 AATTTTTTTTT
166452 AATTTTTTTTT
1 AATTTTTTTTT
166463 A
1 A
166464 TGAGAGCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:171980 original size:22 final size:22
Alignment explanation
Indices: 171939--171980 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
171929 ATTTTGTACT
*
171939 GTATATCTAGAATTTATGTGAA
1 GTATATCTAGAATCTATGTGAA
* *
171961 GTATATCTATAATCTGTGTG
1 GTATATCTAGAATCTATGTG
171981 CAAATGTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (22 bp):
GTATATCTAGAATCTATGTGAA
Found at i:195495 original size:7 final size:7
Alignment explanation
Indices: 195483--195510 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
195473 GCCAAGCTAA
195483 GTCTTCT
1 GTCTTCT
195490 GTCTTCT
1 GTCTTCT
195497 GTCTTCT
1 GTCTTCT
195504 GTCTTCT
1 GTCTTCT
195511 AGCTTTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.14, T:0.57
Consensus pattern (7 bp):
GTCTTCT
Found at i:202087 original size:2 final size:2
Alignment explanation
Indices: 202080--202107 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
202070 TTTTATAATC
202080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
202108 TATTATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203154 original size:3 final size:3
Alignment explanation
Indices: 203148--203184 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
203138 GTCGTCGTCG
203148 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
203185 TCTTTTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:205049 original size:21 final size:20
Alignment explanation
Indices: 205008--205049 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
204998 TTTTGGGTTC
*
205008 TACTCTCACGGAATGTGAGT
1 TACTCTCACGGAATATGAGT
205028 TACTCTCACGGAATTATGAGT
1 TACTCTCACGGAA-TATGAGT
205049 T
1 T
205050 TTCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
TACTCTCACGGAATATGAGT
Found at i:215806 original size:39 final size:39
Alignment explanation
Indices: 215749--215826 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
215739 CAGTAAACTT
* * **
215749 AGCCTTTGTATGTGATATAAATGCTTTCAATTAACTCAC
1 AGCCTTTCTATGTAATATAAATGCTTTCAAAGAACTCAC
215788 AGCCTTTCTATGTAATATAAATGCTTTCAAAGAACTCAC
1 AGCCTTTCTATGTAATATAAATGCTTTCAAAGAACTCAC
215827 CTTGGCCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (39 bp):
AGCCTTTCTATGTAATATAAATGCTTTCAAAGAACTCAC
Found at i:218238 original size:64 final size:64
Alignment explanation
Indices: 218159--218286 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
218149 CCGGGGTTCG
*
218159 ATTCCCCGGATGCGCAATTTTCTTTATTTTTCGCGTAAGTTTACTGGTAAACTTGGTAAGAAAT
1 ATTCCCCGGATGCGCAATTTTCTTTATTTTTCGCGTAAGGTTACTGGTAAACTTGGTAAGAAAT
*
218223 ATTCCCCGGATGCGCAATTTTCTTTATTTTTCGCGTAAGGTTACTTGTAAACTTGGTAAGAAAT
1 ATTCCCCGGATGCGCAATTTTCTTTATTTTTCGCGTAAGGTTACTGGTAAACTTGGTAAGAAAT
218287 TGTGTATCAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (64 bp):
ATTCCCCGGATGCGCAATTTTCTTTATTTTTCGCGTAAGGTTACTGGTAAACTTGGTAAGAAAT
Found at i:218571 original size:13 final size:13
Alignment explanation
Indices: 218553--218581 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
218543 CCTCGTATTG
218553 AAGTTCACCTTGT
1 AAGTTCACCTTGT
218566 AAGTTCACCTTGT
1 AAGTTCACCTTGT
218579 AAG
1 AAG
218582 AATGCGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (13 bp):
AAGTTCACCTTGT
Found at i:220514 original size:2 final size:2
Alignment explanation
Indices: 220507--220543 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
220497 TCACTTTCTC
220507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220544 GTATGTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:230352 original size:2 final size:2
Alignment explanation
Indices: 230347--230381 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
230337 GATTTAAAGG
230347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
230382 GTGATAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:230861 original size:10 final size:10
Alignment explanation
Indices: 230848--230873 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
230838 ATATCTCGAT
230848 ATATCCGTAA
1 ATATCCGTAA
230858 ATATCCGTAA
1 ATATCCGTAA
230868 ATATCC
1 ATATCC
230874 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Done.