Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006844.1 Corchorus capsularis cultivar CVL-1 contig06865, 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: 31489
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:2400 original size:33 final size:30
Alignment explanation
Indices: 2322--2402 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 30
2312 AGCCGCGCAA
2322 AACCGGCCACATGACCGGCCATCGCATGCGAC
1 AACCGGCCACA--ACCGGCCATCGCATGCGAC
* * *
2354 AATCGGCCGCAACCGGCCATCGCTTGGCGCACC
1 AACCGGCCACAACCGGCCATCGCAT-GCG-A-C
2387 AACCGGCCACAACCGG
1 AACCGGCCACAACCGG
2403 ACATAGATTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 13 0.32
31 3 0.07
32 10 0.24
33 15 0.37
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.09
Consensus pattern (30 bp):
AACCGGCCACAACCGGCCATCGCATGCGAC
Found at i:8360 original size:76 final size:76
Alignment explanation
Indices: 8165--8343 Score: 313
Period size: 76 Copynumber: 2.4 Consensus size: 76
8155 ACAAAGGCCT
*
8165 CGACTCCACCTGGGCGCGCACATGGTTGCCTTCAGCACCCATGTGGTTTGCTTGAAGAACCAGCT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTCAGCACCCATGTGGTTTGCTTGAAGAACCAGCT
8230 GAGTAGTGTCC
66 GAGTAGTGTCC
8241 CGACTCCACCTGGGCGCCCACATGGTTGCCTTCAGCACCCATGTGGTTTGCTTGAAGAACCAGCT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTCAGCACCCATGTGGTTTGCTTGAAGAACCAGCT
*
8306 GGGTAGTGTCC
66 GAGTAGTGTCC
* * *
8317 CGACTCTAGCTGGGTGCCCACATGGTT
1 CGACTCCACCTGGGCGCCCACATGGTT
8344 TGTCTGAGGA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 98 1.00
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTCAGCACCCATGTGGTTTGCTTGAAGAACCAGCT
GAGTAGTGTCC
Found at i:9380 original size:2 final size:2
Alignment explanation
Indices: 9373--9435 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
9363 TGGTAAACAA
9373 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
*
9415 GT GT GT GT GT GT GT GT TT GT G
1 GT GT GT GT GT GT GT GT GT GT G
9436 AGGATTTTCT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
GT
Found at i:10926 original size:22 final size:21
Alignment explanation
Indices: 10897--10983 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 21
10887 TTTATCAGAC
10897 CAAGTTCTGGGCAGAAGTTGT
1 CAAGTTCTGGGCAGAAGTTGT
**
10918 CTAAGTTCTGGGTGGAAGTTGT
1 C-AAGTTCTGGGCAGAAGTTGT
* *
10940 CCAAGTTCTGGACAGACGTTGT
1 -CAAGTTCTGGGCAGAAGTTGT
*
10962 ACAAGTTCT-GGCAGAACTTGT
1 -CAAGTTCTGGGCAGAAGTTGT
10983 C
1 C
10984 CTGTATTTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 10 0.19
22 42 0.78
23 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
CAAGTTCTGGGCAGAAGTTGT
Found at i:12014 original size:2 final size:2
Alignment explanation
Indices: 12007--12035 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11997 TAGTAAAGAA
12007 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
12036 AGGATCTTCT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:16966 original size:20 final size:20
Alignment explanation
Indices: 16938--16979 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
16928 TTATTTTAAA
16938 TTTTTTAA-TAAATGTGTAT
1 TTTTTTAATTAAATGTGTAT
16957 TTTTTATAATTAAATGTGTAT
1 TTTTT-TAATTAAATGTGTAT
16978 TT
1 TT
16980 AATATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTTTTAATTAAATGTGTAT
Found at i:16985 original size:21 final size:21
Alignment explanation
Indices: 16946--16985 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16936 AATTTTTTAA
**
16946 TAAATGTGTATTTTTTATAAT
1 TAAATGTGTATTTAATATAAT
16967 TAAATGTGTATTTAATATA
1 TAAATGTGTATTTAATATA
16986 TATTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TAAATGTGTATTTAATATAAT
Found at i:17021 original size:20 final size:20
Alignment explanation
Indices: 16989--17035 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
16979 TAATATATAT
16989 TTTTTAA-ATTA-TTTCTTA
1 TTTTTAATATTATTTTCTTA
*
17007 TTTTCTAATATTATTTTCTGA
1 TTTT-TAATATTATTTTCTTA
17028 TTTTTAAT
1 TTTTTAAT
17036 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 8 0.32
21 10 0.40
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTAATATTATTTTCTTA
Found at i:17382 original size:31 final size:31
Alignment explanation
Indices: 17347--17448 Score: 177
Period size: 31 Copynumber: 3.3 Consensus size: 31
17337 ATTGGGCGGG
* *
17347 TTCGGGTTCGGGTACTTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
17378 TTCGGGTTCGGGTATTTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTA-TTTCGGGTTCGGGTATT
17410 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
17441 TTCGGGTT
1 TTCGGGTT
17449 TGGGCTCGGG
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 39 0.57
32 29 0.43
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (31 bp):
TTCGGGTTCGGGTATTTCGGGTTCGGGTATT
Found at i:17383 original size:16 final size:16
Alignment explanation
Indices: 17347--17448 Score: 154
Period size: 16 Copynumber: 6.5 Consensus size: 16
17337 ATTGGGCGGG
*
17347 TTCGGGTTCGGGT-AC
1 TTCGGGTTCGGGTAAT
17362 TTCGGGTTCGGGTAAT
1 TTCGGGTTCGGGTAAT
*
17378 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTAAT
*
17394 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTAAT
17410 TTCGGGTTCGGGT-AT
1 TTCGGGTTCGGGTAAT
*
17425 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTAAT
17441 TTCGGGTT
1 TTCGGGTT
17449 TGGGCTCGGG
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
15 27 0.33
16 54 0.67
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (16 bp):
TTCGGGTTCGGGTAAT
Found at i:17427 original size:47 final size:47
Alignment explanation
Indices: 17347--17448 Score: 179
Period size: 47 Copynumber: 2.2 Consensus size: 47
17337 ATTGGGCGGG
17347 TTCGGGTTCGGGTACTTCGGGTTCGGGTAATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTACTTCGGGTTCGGGTAATTTCGGGTTCGGGTATT
*
17394 TTCGGGTTCGGGTATTTTCGGGTTCGGGT-ATTTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTA-CTTCGGGTTCGGGTAATTTCGGGTTCGGGTATT
17441 TTCGGGTT
1 TTCGGGTT
17449 TGGGCTCGGG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
47 40 0.75
48 13 0.25
ACGTcount: A:0.07, C:0.14, G:0.38, T:0.41
Consensus pattern (47 bp):
TTCGGGTTCGGGTACTTCGGGTTCGGGTAATTTCGGGTTCGGGTATT
Found at i:17470 original size:23 final size:23
Alignment explanation
Indices: 17441--17495 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
17431 TTCGGGTATT
* *
17441 TTCGGGTTTGGGCTCGGGTCGGG
1 TTCGGGTTTGGACCCGGGTCGGG
*
17464 TTCGGGTTCGGACCCGGGTCGGG
1 TTCGGGTTTGGACCCGGGTCGGG
17487 TTCGGGTTT
1 TTCGGGTTT
17496 ACTTTCGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.02, C:0.20, G:0.47, T:0.31
Consensus pattern (23 bp):
TTCGGGTTTGGACCCGGGTCGGG
Found at i:17474 original size:17 final size:17
Alignment explanation
Indices: 17442--17493 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17432 TCGGGTATTT
* *
17442 TCGGGTTTGGGCTCGGG
1 TCGGGTTCGGGTTCGGG
*
17459 TCGGGTTCGGGTTCGGAC
1 TCGGGTTCGGGTTCGG-G
*
17477 CCGGG-TCGGGTTCGGG
1 TCGGGTTCGGGTTCGGG
17493 T
1 T
17494 TTACTTTCGA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.02, C:0.21, G:0.50, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGGTTCGGG
Found at i:18279 original size:6 final size:6
Alignment explanation
Indices: 18238--18327 Score: 52
Period size: 6 Copynumber: 15.5 Consensus size: 6
18228 TTTTGATCTA
* *
18238 GGGTTC GGG-TC GGGTTT GGGTTC AGGTTC GGG--C GGGTTC GGGTT-
1 GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC
*
18282 --GTCTC GGGTTC GGGTATTTTC GGGTTC GGGTAC GGG--C GGGTTC GGG
1 GGGT-TC GGGTTC GGG----TTC GGGTTC GGGTTC GGGTTC GGGTTC GGG
18328 ACGTTGACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 26
0.68 0.05 0.27
Matches are distributed among these distances:
3 2 0.03
4 9 0.14
5 5 0.08
6 42 0.64
7 2 0.03
10 6 0.09
ACGTcount: A:0.03, C:0.16, G:0.50, T:0.31
Consensus pattern (6 bp):
GGGTTC
Found at i:18280 original size:22 final size:23
Alignment explanation
Indices: 18239--18281 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
18229 TTTGATCTAG
*
18239 GGTTCGGGTCGGGTTTGGGTTCA
1 GGTTCGGGTCGGGTTCGGGTTCA
18262 GGTTCGGG-CGGGTTCGGGTT
1 GGTTCGGGTCGGGTTCGGGTT
18282 GTCTCGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.02, C:0.14, G:0.51, T:0.33
Consensus pattern (23 bp):
GGTTCGGGTCGGGTTCGGGTTCA
Found at i:18289 original size:16 final size:16
Alignment explanation
Indices: 18270--18313 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
18260 CAGGTTCGGG
18270 CGGGTTCGGGT-TGTCT
1 CGGGTTCGGGTAT-TCT
*
18286 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTCT
18302 CGGGTTCGGGTA
1 CGGGTTCGGGTA
18314 CGGGCGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 25 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.16, G:0.43, T:0.36
Consensus pattern (16 bp):
CGGGTTCGGGTATTCT
Found at i:24651 original size:15 final size:15
Alignment explanation
Indices: 24631--24690 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
24621 TTTCATTTGG
*
24631 ATTATTTTAATATTT
1 ATTATTTAAATATTT
*
24646 ATTATTTAAATATTA
1 ATTATTTAAATATTT
*
24661 ATT-TATTATATATTT
1 ATTAT-TTAAATATTT
*
24676 TTTATGTTAAATATT
1 ATTAT-TTAAATATT
24691 ACAAAATTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 1 0.03
15 26 0.72
16 9 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
ATTATTTAAATATTT
Found at i:25349 original size:22 final size:22
Alignment explanation
Indices: 25324--25384 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
25314 TAATTATTAG
*
25324 TTACCATTTTATTCTTTACTGA
1 TTACCATTTTACTCTTTACTGA
25346 TTACCA--TTACGT-TTTACTGA
1 TTACCATTTTAC-TCTTTACTGA
*
25366 TTAACATTTTACTCTTTAC
1 TTACCATTTTACTCTTTAC
25385 CATTTTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 15 0.45
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.51
Consensus pattern (22 bp):
TTACCATTTTACTCTTTACTGA
Found at i:25435 original size:34 final size:34
Alignment explanation
Indices: 25336--25561 Score: 163
Period size: 34 Copynumber: 6.2 Consensus size: 34
25326 ACCATTTTAT
** *
25336 TCTTTACTGATTACCATTACGT-TTTACTGATTAAC
1 TCTTTACTCTTTACCATT-CTTCTTTACTGATT-AC
* *
25371 AT-TTTACTCTTTACCATTTTTTTCTTTACTGATTAT
1 -TCTTTACTCTTTACCA--TTCTTCTTTACTGATTAC
25407 TCTTTACTCTTTACCATTCTTCTTTACTGATTACCGATTAC
1 TCTTTACTCTTTACCATTCTTCTTTAC----T---GATTAC
*
25448 TCTTTACTCTTTACCACTT-TTCTTTACTAATTAC
1 TCTTTACTCTTTACCA-TTCTTCTTTACTGATTAC
* *
25482 TCTTCACTCTTTACCA-TCTTTCTTTATTGATTAC
1 TCTTTACTCTTTACCATTC-TTCTTTACTGATTAC
*
25516 TCTTTACCACTTTTCTTTACCATTTTTCTTTACTGATTAC
1 TCTTT---AC---TCTTTACCATTCTTCTTTACTGATTAC
25556 TCTTTA
1 TCTTTA
25562 TTTTTTTACC
Statistics
Matches: 155, Mismatches: 14, Indels: 41
0.74 0.07 0.20
Matches are distributed among these distances:
32 1 0.01
34 47 0.30
35 13 0.08
36 17 0.11
37 16 0.10
38 1 0.01
40 28 0.18
41 30 0.19
42 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (34 bp):
TCTTTACTCTTTACCATTCTTCTTTACTGATTAC
Found at i:25446 original size:41 final size:39
Alignment explanation
Indices: 25373--25555 Score: 147
Period size: 41 Copynumber: 4.8 Consensus size: 39
25363 TGATTAACAT
* *
25373 TTTACTCTTTACCATTTT-TTT-CT-TTACTGATTATTC
1 TTTACTCTTTACCATTTTCTTTACTATTACCGATTACTC
25409 TTTACTCTTTACCATTCTTCTTTACTGATTACCGATTACTC
1 TTTACTCTTTACCATT-TTCTTTACT-ATTACCGATTACTC
25450 TTTACTCTTTACCACTTTTCTTTAC---TA---ATTACTC
1 TTTACTCTTTACCA-TTTTCTTTACTATTACCGATTACTC
* * * *
25484 TTCACTCTTTACCATCTTTCTTTATTGATTACTC-TTTACCAC
1 TTTACTCTTTACCAT-TTTCTTTACT-ATTAC-CGATTA-CTC
25526 TTT--TCTTTACCATTTTTCTTTACTGATTAC
1 TTTACTCTTTACCA-TTTTCTTTACT-ATTAC
25556 TCTTTATTTT
Statistics
Matches: 123, Mismatches: 8, Indels: 28
0.77 0.05 0.18
Matches are distributed among these distances:
33 1 0.01
34 28 0.23
36 16 0.13
37 4 0.03
38 5 0.04
39 2 0.02
40 24 0.20
41 37 0.30
42 6 0.05
ACGTcount: A:0.19, C:0.25, G:0.03, T:0.54
Consensus pattern (39 bp):
TTTACTCTTTACCATTTTCTTTACTATTACCGATTACTC
Found at i:25481 original size:20 final size:20
Alignment explanation
Indices: 25402--25481 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
25392 TTCTTTACTG
*
25402 ATTATTCTTTACTCTTTACC
1 ATTATTCTTTACTCATTACC
* *
25422 ATTCTTCTTTACTGATTACC
1 ATTATTCTTTACTCATTACC
* *
25442 GATTACTCTTTACTCTTTACC
1 -ATTATTCTTTACTCATTACC
*
25463 ACTT-TTCTTTACTAATTAC
1 A-TTATTCTTTACTCATTAC
25482 TCTTCACTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.21, C:0.25, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTATTCTTTACTCATTACC
Found at i:25572 original size:75 final size:74
Alignment explanation
Indices: 25359--25561 Score: 232
Period size: 75 Copynumber: 2.7 Consensus size: 74
25349 CCATTACGTT
* * *
25359 TTACTGATTAACATTTTACTCTTTACCATTTTTTTCTTTACTGATTATTCTTTACTCTTTACCAT
1 TTACCGATT-ACACTTTA-TCTTTACCA--TTTTTCTTTACTGATTACTCTTTACTCTTTACCAT
25424 TCTTCTTTACTGA
62 TCTTCTTTACTGA
* * * *
25437 TTACCGATTACTCTTTACTCTTTACCACTTTTCTTTACTAATTACTCTTCACTCTTTACCA-TCT
1 TTACCGATTACACTTTA-TCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTC-
*
25501 TTCTTTATTGA
64 TTCTTTACTGA
*
25512 TTACTC-TTTACCACTTT-TCTTTACCATTTTTCTTTACTGATTACTCTTTA
1 TTAC-CGATTA-CACTTTATCTTTACCATTTTTCTTTACTGATTACTCTTTA
25562 TTTTTTTACC
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
74 32 0.29
75 47 0.43
76 6 0.06
77 16 0.15
78 8 0.07
ACGTcount: A:0.20, C:0.24, G:0.03, T:0.54
Consensus pattern (74 bp):
TTACCGATTACACTTTATCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACCATTCTT
CTTTACTGA
Found at i:25664 original size:21 final size:21
Alignment explanation
Indices: 25576--25775 Score: 224
Period size: 21 Copynumber: 9.5 Consensus size: 21
25566 TTTACCATTT
*
25576 TTACTGATTACCA-TTTCCT-
1 TTACTGATTACCATTTTACTC
* * *
25595 TTGCTGATTACCATGTGACTC
1 TTACTGATTACCATTTTACTC
* * *
25616 TTTTCTAATTACCATCTTACTCC
1 -TTACTGATTACCATTTTACT-C
*
25639 TTACTGATCACCATTTTACTC
1 TTACTGATTACCATTTTACTC
* *
25660 TTACTGATTACTATTTTACAC
1 TTACTGATTACCATTTTACTC
* *
25681 TTACTGATTATCTTTTTACTC
1 TTACTGATTACCATTTTACTC
*
25702 TTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTC
*
25723 TTACTGATTACTATTTTACTC
1 TTACTGATTACCATTTTACTC
* *
25744 TTACTGATTATCTTTTTACTC
1 TTACTGATTACCATTTTACTC
25765 TTACTGATTAC
1 TTACTGATTAC
25776 TATTACTCTT
Statistics
Matches: 151, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.08
20 3 0.02
21 103 0.68
22 32 0.21
23 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTC
Found at i:25773 original size:63 final size:63
Alignment explanation
Indices: 25632--25779 Score: 260
Period size: 63 Copynumber: 2.3 Consensus size: 63
25622 AATTACCATC
* *
25632 TTACTCCTTACTGATCACCATTTTACTCTTACTGATTACTATTTTACACTTACTGATTATCTTT
1 TTACT-CTTACTGATTACTATTTTACTCTTACTGATTACTATTTTACACTTACTGATTATCTTT
*
25696 TTACTCTTACTGATTACTATTTTACTCTTACTGATTACTATTTTACTCTTACTGATTATCTTT
1 TTACTCTTACTGATTACTATTTTACTCTTACTGATTACTATTTTACACTTACTGATTATCTTT
25759 TTACTCTTACTGATTACTATT
1 TTACTCTTACTGATTACTATT
25780 ACTCTTGTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 76 0.94
64 5 0.06
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (63 bp):
TTACTCTTACTGATTACTATTTTACTCTTACTGATTACTATTTTACACTTACTGATTATCTTT
Found at i:30912 original size:2 final size:2
Alignment explanation
Indices: 30905--30932 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30895 AACGTATGTG
30905 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
30933 TGCTTTAAGA
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
Done.