Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007215.1 Corchorus capsularis cultivar CVL-1 contig07236, 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: 55027
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:3283 original size:11 final size:12
Alignment explanation
Indices: 3256--3289 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3246 CACTATTATA
3256 TTAATTAATCAC
1 TTAATTAATCAC
3268 TTAATTAATC-C
1 TTAATTAATCAC
*
3279 TTAATCAATCA
1 TTAATTAATCA
3290 TTATCTCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAATTAATCAC
Found at i:3913 original size:29 final size:31
Alignment explanation
Indices: 3831--3913 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 31
3821 CAATTAAACG
* *
3831 GAGGGACTAAATTGATCATTTTCCAATAGTA
1 GAGGGACTAAATTGATCATTTTTCAATAATA
* **
3862 GAGGAACTAAATTGA-CAGATTTC-ATAATA
1 GAGGGACTAAATTGATCATTTTTCAATAATA
*
3891 GAGGGACTAAAATGATC-TTTTTC
1 GAGGGACTAAATTGATCATTTTTC
3914 TGATAGTACA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
29 22 0.52
30 6 0.14
31 14 0.33
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (31 bp):
GAGGGACTAAATTGATCATTTTTCAATAATA
Found at i:8796 original size:6 final size:6
Alignment explanation
Indices: 8785--8814 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
8775 ATTCTGCTTC
8785 AGATTT AGATTT AGATTT AGATTT AGATTT
1 AGATTT AGATTT AGATTT AGATTT AGATTT
8815 GCTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:16966 original size:19 final size:18
Alignment explanation
Indices: 16942--16978 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
16932 TTGAAGATTT
16942 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
16961 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
16979 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Found at i:20518 original size:21 final size:21
Alignment explanation
Indices: 20480--20520 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20470 GCTTGGCTTA
*
20480 TGATCTTCAAAACTCTTCAAT
1 TGATCTTCAAAACACTTCAAT
**
20501 TGATCTTCAAAGGACTTCAA
1 TGATCTTCAAAACACTTCAA
20521 GCCTTCAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TGATCTTCAAAACACTTCAAT
Found at i:24672 original size:6 final size:6
Alignment explanation
Indices: 24661--24696 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
24651 AAAGCAAAGC
24661 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAATCT
24697 GAAGCAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATCT
Found at i:25556 original size:10 final size:10
Alignment explanation
Indices: 25541--25566 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
25531 GAGGACTCTA
25541 GAATTTTCTG
1 GAATTTTCTG
25551 GAATTTTCTG
1 GAATTTTCTG
25561 GAATTT
1 GAATTT
25567 GGCAGCAACT
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:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:30190 original size:15 final size:16
Alignment explanation
Indices: 30158--30191 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30148 AAAGAAGAAT
*
30158 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
30174 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
30189 TAA
1 TAA
30192 GAGAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:31483 original size:19 final size:18
Alignment explanation
Indices: 31450--31485 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31440 TTGAAATAAT
31450 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
31468 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
31486 GAAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:31687 original size:20 final size:21
Alignment explanation
Indices: 31649--31687 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
31639 TAGAAAATAA
*
31649 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
31670 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
31688 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:34147 original size:33 final size:32
Alignment explanation
Indices: 34105--34166 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
34095 TTTGCTTCCA
*
34105 AAAGTCGACTTGTGTAGTCGAATTGCTCCTTGT
1 AAAGTCGACTTGTATAGTCGAATT-CTCCTTGT
*
34138 AAAGTCGACTTGTATAGTCGACTTCTCCT
1 AAAGTCGACTTGTATAGTCGAATTCTCCT
34167 CCCAATAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (32 bp):
AAAGTCGACTTGTATAGTCGAATTCTCCTTGT
Found at i:34177 original size:33 final size:33
Alignment explanation
Indices: 34105--34181 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
34095 TTTGCTTCCA
* ***
34105 AAAGTCGACTTGTGTAGTCGAATTGCTCCTTGT
1 AAAGTCGACTTGTATAGTCGAATTGCTCCTCCC
*
34138 AAAGTCGACTTGTATAGTCGACTT-CTCCTCCC
1 AAAGTCGACTTGTATAGTCGAATTGCTCCTCCC
34170 AATAGTCGACTT
1 AA-AGTCGACTT
34182 CTCTTCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
32 7 0.18
33 31 0.82
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (33 bp):
AAAGTCGACTTGTATAGTCGAATTGCTCCTCCC
Found at i:40148 original size:15 final size:15
Alignment explanation
Indices: 40119--40151 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
40109 AAAGAAGAAT
40119 TAAAATAAATATAAC
1 TAAAATAAATATAAC
40134 TAAAAGTAAAT-TAAC
1 TAAAA-TAAATATAAC
40149 TAA
1 TAA
40152 GAGAGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (15 bp):
TAAAATAAATATAAC
Found at i:41467 original size:19 final size:18
Alignment explanation
Indices: 41434--41469 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
41424 TTGAAATAAT
41434 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
41452 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
41470 GAAATTTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:41671 original size:20 final size:21
Alignment explanation
Indices: 41633--41671 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
41623 TAGAAAATAA
*
41633 GGTAAAAATGCATATAAAAGT
1 GGTAAAAATGCATAGAAAAGT
*
41654 GGTAAAAA-GTATAGAAAA
1 GGTAAAAATGCATAGAAAA
41672 ATAGCCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.56, C:0.03, G:0.21, T:0.21
Consensus pattern (21 bp):
GGTAAAAATGCATAGAAAAGT
Found at i:51489 original size:431 final size:433
Alignment explanation
Indices: 50851--51666 Score: 1110
Period size: 431 Copynumber: 1.9 Consensus size: 433
50841 TAGTTTTTTC
* * * *
50851 TCCACATGTCCAATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTCT
1 TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATGATCTACGACTTCT
* * * *
50916 ATGAAGGACCCGAAAACTAAATTTGATCTACGAGTTTCGTTAAGGGTTCAAAAGGGAATTTTTAT
66 ATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
* * *
50981 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATTATTGATCAAATGACCCTCATACTT
131 GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTAATACTT
*
51046 TTATACTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATCGCTTT-A-TT-TTTTCTTTAA
196 TTATACTTTATACTACTT--TCCTTTACAAATTCTATCTTAATCGATTTAACTTATTTTCTTTAA
* * * *
51108 -TCTTTGTTCTATTTGTCCGATTAAGCTGATTCATGTGTCTATTAAAAGACAATTTCATAATCTA
259 TTCTTTGTTCTATTTGTCCAATTAAGCTAATTCAGGTATCTATTAAAAGACAATTTCATAATCTA
* *
51172 CATA-TTTCATGAAGGATTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAAT
324 CA-ACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAAT
51236 GTGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGA
388 GTGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGA
* *
51282 TCCACATGTGCAATTAAAGTTATTCAAGTGTCGGTTAAAAAGGTTACTGTAT-AGTCTACGACTT
1 TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTT-AAAAGGTTACTGCATGA-TCTACGACTT
* * * *
51346 -TCATGAAGAACCCG-AAAGTTAATTTGATCTATGAGTTTCATGAAGGGTTCAATAGGAAATTTT
64 CT-ATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTT
* * *
51409 TATGTTTCAGGATCTCCATTAAGAAATATTTTCTTATTTGAATTAGTT-ATCAAATCACCCTAAT
128 TATGTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTA-TTGATCAAATCACCCTAAT
* * * * * *
51473 ACTTTTCTATTTTATACTACTTTCCTTTACAAATTCTATTTTACTTGATTTAACACTTCATTTTT
192 ACTTTTATACTTTATACTACTTTCCTTTACAAATTCTATCTTAATCGATTT-A-ACTT-ATTTTC
* **
51538 TTTAATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAGGTAATTTCA
254 TTTAA--TTCTTTGTTCTATTTGTCCAATTAAGCTAATTCAGGTATCTATTAAAAGACAATTTCA
* * *
51603 TGATCTACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTCAATTCTAAAAAATGCTT
317 TAATCTACAACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTT
51667 TTGAAATTTT
Statistics
Matches: 332, Mismatches: 39, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
429 25 0.08
431 152 0.46
432 36 0.11
433 2 0.01
435 9 0.03
437 1 0.00
438 107 0.32
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (433 bp):
TCCACATGTCCAATTAAAGTTATTCAAGTGTCGGTTAAAAGGTTACTGCATGATCTACGACTTCT
ATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
GTTTCAAGATCTCCATTAACAAACATTTTCTTATTTGAATTATTGATCAAATCACCCTAATACTT
TTATACTTTATACTACTTTCCTTTACAAATTCTATCTTAATCGATTTAACTTATTTTCTTTAATT
CTTTGTTCTATTTGTCCAATTAAGCTAATTCAGGTATCTATTAAAAGACAATTTCATAATCTACA
ACTTTCATGAAAGACTCAAAAGCAAATTTTTATATTTCAATTCAAAAAAATGCTTCCTAAATGTG
GTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGA
Found at i:52698 original size:2 final size:2
Alignment explanation
Indices: 52691--52725 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
52681 CGGGTATTCC
52691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52726 ATAATGTAAT
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:52913 original size:22 final size:22
Alignment explanation
Indices: 52885--52931 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
52875 AGCCACAATA
*
52885 TTGGGTTTTAATTAATTTGAAG
1 TTGGGTTTTAATTAATCTGAAG
52907 TTGGGTTTTAATTAATCTGAAG
1 TTGGGTTTTAATTAATCTGAAG
52929 TTG
1 TTG
52932 AGTTGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.49
Consensus pattern (22 bp):
TTGGGTTTTAATTAATCTGAAG
Found at i:52993 original size:16 final size:18
Alignment explanation
Indices: 52967--53000 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52957 GGGAAGAAGC
52967 TCTCTTAATGCT-TATTT
1 TCTCTTAATGCTATATTT
52984 TCTC-TAATGCTATATTT
1 TCTCTTAATGCTATATTT
53001 GGTAGGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.18, G:0.06, T:0.56
Consensus pattern (18 bp):
TCTCTTAATGCTATATTT
Found at i:53026 original size:16 final size:17
Alignment explanation
Indices: 53005--53036 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52995 ATATTTGGTA
53005 GGAAGGAAA-GAAATAC
1 GGAAGGAAATGAAATAC
53021 GGAAGGAAATGAAATA
1 GGAAGGAAATGAAATA
53037 GGGATGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.03, G:0.31, T:0.09
Consensus pattern (17 bp):
GGAAGGAAATGAAATAC
Found at i:53297 original size:2 final size:2
Alignment explanation
Indices: 53292--53322 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
53282 AAGGGAGAGA
*
53292 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53323 CTAATTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.