Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012033.1 Corchorus capsularis cultivar CVL-1 contig12054, 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: 54712
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2499 original size:23 final size:24
Alignment explanation
Indices: 2472--2519 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2462 TTTTCATTTG
*
2472 TAAATTAT-AATTTTATAATGAAA
1 TAAATTATCAATTTTATAATAAAA
* *
2495 TAAATTGTCAATTTTTTAATAAAA
1 TAAATTATCAATTTTATAATAAAA
2519 T
1 T
2520 TTTTATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
TAAATTATCAATTTTATAATAAAA
Found at i:3603 original size:21 final size:22
Alignment explanation
Indices: 3578--3621 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3568 TGGCGGAGGG
3578 AAGAA-AAAA-AAATTCGGGAAA
1 AAGAAGAAAAGAAATT-GGGAAA
*
3599 AAGAAGAAAAGAAGTTGGGAAA
1 AAGAAGAAAAGAAATTGGGAAA
3621 A
1 A
3622 GAATAGGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.25, T:0.09
Consensus pattern (22 bp):
AAGAAGAAAAGAAATTGGGAAA
Found at i:5185 original size:16 final size:18
Alignment explanation
Indices: 5164--5206 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
5154 CAAAATTAAC
5164 AAAAAACACAAAA-AC-A
1 AAAAAACACAAAATACGA
*
5180 AAAAAAAACAAAATACGA
1 AAAAAACACAAAATACGA
5198 AACAAAACA
1 AA-AAAACA
5207 AAACTAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 2 0.09
18 3 0.14
19 5 0.23
ACGTcount: A:0.79, C:0.16, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAACACAAAATACGA
Found at i:5207 original size:17 final size:16
Alignment explanation
Indices: 5164--5209 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
5154 CAAAATTAAC
*
5164 AAAAAACACAAAAACA
1 AAAAAAAACAAAAACA
*
5180 AAAAAAAACAAAATACG
1 AAAAAAAACAAAA-ACA
*
5197 AAACAAAACAAAA
1 AAAAAAAACAAAA
5210 CTAAAGGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.80, C:0.15, G:0.02, T:0.02
Consensus pattern (16 bp):
AAAAAAAACAAAAACA
Found at i:8176 original size:19 final size:19
Alignment explanation
Indices: 8152--8211 Score: 93
Period size: 19 Copynumber: 3.2 Consensus size: 19
8142 CTCATTACTG
8152 CAATTTCAGAATCAAACCC
1 CAATTTCAGAATCAAACCC
* * *
8171 CAATTTTAGAATCAAATCT
1 CAATTTCAGAATCAAACCC
8190 CAATTTCAGAATCAAACCC
1 CAATTTCAGAATCAAACCC
8209 CAA
1 CAA
8212 CTAAAAACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (19 bp):
CAATTTCAGAATCAAACCC
Found at i:9784 original size:105 final size:108
Alignment explanation
Indices: 9606--9870 Score: 414
Period size: 107 Copynumber: 2.5 Consensus size: 108
9596 AATTTTTCTA
* **
9606 ACCCTTAAAATTAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATATT
1 ACCCTTAAAA-TAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATT
*
9669 ATATTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
65 ATATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
*
9712 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTT-T-TATATTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATTA
*
9775 TATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TATTTCTAAAACCCTATAACAAT-AATTATTAATTATGAAATTT
*
9819 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
9871 AGGATAAACT
Statistics
Matches: 148, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
105 46 0.31
106 26 0.18
107 76 0.51
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (108 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATATTA
TATTTCTAAAACCCTATAACAATAATTATTAATTATGAAATTT
Found at i:12966 original size:16 final size:18
Alignment explanation
Indices: 12945--12989 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
12935 CTGAGCCTGT
*
12945 CTCTGAAGCT-T-TCTCC
1 CTCTGAAGCTCTCTCCCC
12961 CTCTG-AGCCTCTCTCCCC
1 CTCTGAAG-CTCTCTCCCC
12979 CTCTGAAGCTC
1 CTCTGAAGCTC
12990 AGCCTCTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 2 0.08
16 7 0.29
17 1 0.04
18 12 0.50
19 2 0.08
ACGTcount: A:0.11, C:0.44, G:0.13, T:0.31
Consensus pattern (18 bp):
CTCTGAAGCTCTCTCCCC
Found at i:13468 original size:14 final size:14
Alignment explanation
Indices: 13449--13475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13439 AAAACCCTAG
13449 ATCTATTTCTCTAC
1 ATCTATTTCTCTAC
13463 ATCTATTTCTCTA
1 ATCTATTTCTCTA
13476 GATTTATATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.26, G:0.00, T:0.52
Consensus pattern (14 bp):
ATCTATTTCTCTAC
Found at i:20576 original size:12 final size:13
Alignment explanation
Indices: 20535--20579 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
20525 AATTATTGTT
20535 TGCTTTATTAATC
1 TGCTTTATTAATC
*
20548 TGCTTTATTAATT
1 TGCTTTATTAATC
20561 TGCTTTA-TAATC
1 TGCTTTATTAATC
20573 TGCTTTA
1 TGCTTTA
20580 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:20927 original size:22 final size:21
Alignment explanation
Indices: 20902--20953 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
20892 TTGTTTTTCC
20902 GTTTTTTCTAAAAAAAAAAAAA
1 GTTTTTTC-AAAAAAAAAAAAA
** * *
20924 GTTTGAGTCGATAAAAAAAAAA
1 GTTT-TTTCAAAAAAAAAAAAA
20946 GTTTTTTC
1 GTTTTTTC
20954 CGTTTTCCGA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
21 2 0.09
22 19 0.83
23 2 0.09
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
GTTTTTTCAAAAAAAAAAAAA
Found at i:27725 original size:12 final size:13
Alignment explanation
Indices: 27684--27726 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
27674 AATTATTGTT
27684 TGCTTTATTAATC
1 TGCTTTATTAATC
*
27697 TGCTTTATTAATT
1 TGCTTTATTAATC
27710 TGCTTTA-TAATC
1 TGCTTTATTAATC
27722 TGCTT
1 TGCTT
27727 AGATTTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:27736 original size:6 final size:6
Alignment explanation
Indices: 27725--27756 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
27715 TATAATCTGC
27725 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
1 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
27757 TCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (6 bp):
TTAGAT
Found at i:30207 original size:6 final size:6
Alignment explanation
Indices: 30196--30225 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
30186 CATTGCATGC
30196 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
30226 TCTATTTGGA
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:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (6 bp):
ATTTGT
Found at i:35536 original size:19 final size:18
Alignment explanation
Indices: 35503--35538 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35493 TTGAAATAAT
35503 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
35521 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
35539 GAAATCTGTA
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:37168 original size:1 final size:1
Alignment explanation
Indices: 37162--37192 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
37152 TCTCTGTTTT
37162 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
37193 CTCAATCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:39682 original size:21 final size:21
Alignment explanation
Indices: 39642--39684 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39632 CGGAAATCCA
**
39642 CTACTTCCTGTTGTACTTCTT
1 CTACTTCCTGCAGTACTTCTT
*
39663 CTACTTCCTGCAGTATTTCTT
1 CTACTTCCTGCAGTACTTCTT
39684 C
1 C
39685 CCCATTAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.30, G:0.09, T:0.49
Consensus pattern (21 bp):
CTACTTCCTGCAGTACTTCTT
Found at i:47264 original size:4 final size:4
Alignment explanation
Indices: 47250--47285 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
47240 TGCATGCTCC
*
47250 CTAT ATAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
47286 ATAAAAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (4 bp):
CTAT
Found at i:47448 original size:17 final size:18
Alignment explanation
Indices: 47416--47453 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
47406 AATATATCTT
47416 AATCCTTTTACAAAAATA
1 AATCCTTTTACAAAAATA
*
47434 AATCTTTTTACAAAAATA
1 AATCCTTTTACAAAAATA
47452 AA
1 AA
47454 AACGTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (18 bp):
AATCCTTTTACAAAAATA
Found at i:47532 original size:15 final size:15
Alignment explanation
Indices: 47492--47533 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
47482 AACATTAACA
47492 AGTTAAAATTCCAAT
1 AGTTAAAATTCCAAT
47507 AGTGATAAAATTCCAAT
1 AGT--TAAAATTCCAAT
47524 AGTTAAAATT
1 AGTTAAAATT
47534 ACCATATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
17 15 0.60
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
AGTTAAAATTCCAAT
Found at i:49679 original size:20 final size:20
Alignment explanation
Indices: 49654--49692 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
49644 GTAAGGTTAC
49654 GATAAT-ATTATAACATTTTT
1 GATAATCATTATAAC-TTTTT
49674 GATAATCATTATAACTTTT
1 GATAATCATTATAACTTTT
49693 AACTAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (20 bp):
GATAATCATTATAACTTTTT
Found at i:50362 original size:2 final size:2
Alignment explanation
Indices: 50355--50379 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50345 AAGTATAACT
50355 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
50380 TAAAAAACCC
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:52928 original size:94 final size:99
Alignment explanation
Indices: 52820--53019 Score: 248
Period size: 108 Copynumber: 2.0 Consensus size: 99
52810 TTGGATAACA
* * *
52820 ACTACAGTTTTTTAGTTATTTTAGATAAG-ATAATTGGTAA-TTTC-C-AT-TACTTAAGTTGCT
1 ACTACAATTTTTTAGTAATTTTAGATAAGAATAATTGGTAATTTTCACGATCAACTTAAGTTGCT
52880 ATGGATTTAAAGTTACTTAATTTTTGTCGATACC
66 ATGGATTTAAAGTTACTTAATTTTTGTCGATACC
52914 ACTACAATTTTTTAGTAATTTTAGATAAGATATATAATTGGTAATTTTTCATTACTGATGCAACT
1 ACTACAATTTTTTAGTAATTTTAGATAAG--A-ATAATTGGTAA-TTTTC---AC-GAT-CAACT
*
52979 TAAGTTGCTATGGATTTAAAGTTACTTAATTTTTGTTGATA
57 TAAGTTGCTATGGATTTAAAGTTACTTAATTTTTGTCGATA
53020 GCATCATAGT
Statistics
Matches: 88, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
94 27 0.31
98 11 0.12
100 4 0.05
104 1 0.01
106 2 0.02
108 43 0.49
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.46
Consensus pattern (99 bp):
ACTACAATTTTTTAGTAATTTTAGATAAGAATAATTGGTAATTTTCACGATCAACTTAAGTTGCT
ATGGATTTAAAGTTACTTAATTTTTGTCGATACC
Done.