Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015289.1 Corchorus capsularis cultivar CVL-1 contig15310, 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: 72560
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:926 original size:31 final size:29
Alignment explanation
Indices: 888--987 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 29
878 AGAATGCTAA
888 CCCTTATTTGAGCATTTTCGATAACATTAGG
1 CCCTTATTTGAGCATTTT-GA-AACATTAGG
* ** * * **
919 CCCTTATTTGACCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCATTTTGAAACATTAGG
948 CCCTTATTTGAGCATTTTGGCAAACATTAGG
1 CCCTTATTTGAGCATTTT-G-AAACATTAGG
979 CCCTTATTT
1 CCCTTATTT
988 ATTAGCCTAA
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
29 21 0.40
30 1 0.02
31 31 0.58
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACATTAGG
Found at i:2326 original size:29 final size:29
Alignment explanation
Indices: 2293--2354 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2283 CAAACTAAAT
* * *
2293 AATTATGTAACACGTTTATTGGTAGATGG
1 AATTATGTAACACGTATATTCGTAGACGG
*
2322 AATTATGTAGCACGTATATTCGTAGACGG
1 AATTATGTAACACGTATATTCGTAGACGG
2351 AATT
1 AATT
2355 TTAATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (29 bp):
AATTATGTAACACGTATATTCGTAGACGG
Found at i:5368 original size:26 final size:25
Alignment explanation
Indices: 5311--5368 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5301 GACGAAAAGC
5311 TACTAAAATTACAACATATTAAGGT
1 TACTAAAATTACAACATATTAAGGT
* * *
5336 AAATAAAATTACTA-ATGATGTAAGGT
1 TACTAAAATTACAACAT-AT-TAAGGT
5362 TACTAAA
1 TACTAAA
5369 TTTATGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 2 0.08
25 13 0.50
26 11 0.42
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (25 bp):
TACTAAAATTACAACATATTAAGGT
Found at i:6092 original size:52 final size:52
Alignment explanation
Indices: 5973--6072 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
5963 AGATTATATT
*
5973 TTTTTTATG--TTAT-ATTACAAATTATTATGCGATTTATTATATTTATTTA
1 TTTTTTATGATTTATGATTACAAATTAATATGCGATTTATTATATTTATTTA
*
6022 TTTTTTATGATTTATGATTACGAATTAATATGCGATTTATTATATTTATTT
1 TTTTTTATGATTTATGATTACAAATTAATATGCGATTTATTATATTTATTT
6073 GTTTGCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 9 0.20
51 4 0.09
52 33 0.72
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (52 bp):
TTTTTTATGATTTATGATTACAAATTAATATGCGATTTATTATATTTATTTA
Found at i:7754 original size:21 final size:20
Alignment explanation
Indices: 7716--7754 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7706 TTTAGAAGCA
**
7716 ATTAATTAAAACCCTTAAAC
1 ATTAATTAAAACAATTAAAC
7736 ATTAATTAAAAACAATTAA
1 ATTAATT-AAAACAATTAA
7755 GGAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (20 bp):
ATTAATTAAAACAATTAAAC
Found at i:8140 original size:13 final size:13
Alignment explanation
Indices: 8122--8149 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
8112 AATAATGCTA
8122 TTCTAAAGTAGAC
1 TTCTAAAGTAGAC
8135 TTCTAAAGTAGAC
1 TTCTAAAGTAGAC
8148 TT
1 TT
8150 AGGTTTATCT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (13 bp):
TTCTAAAGTAGAC
Found at i:8477 original size:33 final size:33
Alignment explanation
Indices: 8435--8499 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
8425 TTTTTACACT
8435 AGTCTCCCCACTAGGACGGCTCCA-CCATGGCGG
1 AGTCTCCCCACTAGGACGGCT-CAGCCATGGCGG
8468 AGTCTCCCCACTAGGACGGCTCAGCCATGGCG
1 AGTCTCCCCACTAGGACGGCTCAGCCATGGCG
8500 ACAATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.15
Consensus pattern (33 bp):
AGTCTCCCCACTAGGACGGCTCAGCCATGGCGG
Found at i:8630 original size:33 final size:31
Alignment explanation
Indices: 8548--8632 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
8538 AAAATAGCCG
* *
8548 AGCCGCCCCACCGGGGCGGCCTGCCGTGGCGA
1 AGCCGCCCCA-GGGGGCGGCCTGCCATGGCGA
** *
8580 AGCCGCAGCAGGAGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCAGG-GGGCGGCCTG-CCATGGCGA
8613 AGCCGCCCCAGTGGGGCGGC
1 AGCCGCCCCAG-GGGGCGGC
8633 TTGAGCCATG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
31 1 0.02
32 18 0.42
33 23 0.53
34 1 0.02
ACGTcount: A:0.13, C:0.38, G:0.42, T:0.07
Consensus pattern (31 bp):
AGCCGCCCCAGGGGGCGGCCTGCCATGGCGA
Found at i:8747 original size:42 final size:42
Alignment explanation
Indices: 8700--8783 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
8690 TCAAAAATTG
* *
8700 CATTTTTCTTAAATCGTCATGAAAATACAGCACGTTATCGTT
1 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAACGTT
8742 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAACGTT
1 CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAACGTT
8784 ATTCCACGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (42 bp):
CATTTTTCTTAAATCGTCATCAAAATACAGCACGTTAACGTT
Found at i:9251 original size:81 final size:81
Alignment explanation
Indices: 9092--9253 Score: 279
Period size: 81 Copynumber: 2.0 Consensus size: 81
9082 ATGTATTTGC
*
9092 ACATTCTCTAGCTAAGATTGAGCTGGATAATCGTGTGGTGCGGGACTATTCCTCCCGGCTCTCCC
1 ACATTCTCTAGCTAAGATTGAGCTGGATAATCGTGTGGTGCGGGACTATTCCTCACGGCTCTCCC
*
9157 GACGTTTGCAATCTCT
66 GACCTTTGCAATCTCT
*
9173 ACATTCTCTAGCTAAGATTGAGCTGGATAATCGTGTGGTGCGGGACTATTCCTCACGGCTCTCCT
1 ACATTCTCTAGCTAAGATTGAGCTGGATAATCGTGTGGTGCGGGACTATTCCTCACGGCTCTCCC
* *
9238 GGCCTTTGTAATCTCT
66 GACCTTTGCAATCTCT
9254 GATTATTGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (81 bp):
ACATTCTCTAGCTAAGATTGAGCTGGATAATCGTGTGGTGCGGGACTATTCCTCACGGCTCTCCC
GACCTTTGCAATCTCT
Found at i:10233 original size:149 final size:150
Alignment explanation
Indices: 9981--10263 Score: 417
Period size: 149 Copynumber: 1.9 Consensus size: 150
9971 CAGGGGCTTG
* * * *
9981 AAAAGATTGAAAGCGCGGAGCTTCGTTGTTGATTTTTCTCTGAGAAGAGTTGTTTTAGACCTAGA
1 AAAAGATTGAAAACACGGAGCTTCGATGTTGATTTTTCTCTGAAAAGAGTTGTTTTAGACCTAGA
* *
10046 GTCCGAGTTTTTTCCCTGGAGGAGATGAATGGCTGTTGTGTTGAAGAGTTGCTGTCCTTAAAGAG
66 GTCCGAGTTTGTTCCCTGGAGGAGATGAATGGCTGTTGTGTTGAAGAGTTGCTGTCCTTAAAGAC
10111 GTTGAAAGTGCAGGGCTAGA
131 GTTGAAAGTGCAGGGCTAGA
* ** *
10131 AAAAGATTGAAAACACGGAGCTTGGATGTTGA-TTTTCTCTGAAAAGAGTTGTTTTTTACCTTGA
1 AAAAGATTGAAAACACGGAGCTTCGATGTTGATTTTTCTCTGAAAAGAGTTGTTTTAGACCTAGA
* ** *
10195 GTCTGAGTTCTGTT-GTTGGAGGAGATGAGTGGCTGTTGTGTTGAAGAGTTGCTGTCCTTAAAGA
66 GTCCGAGTT-TGTTCCCTGGAGGAGATGAATGGCTGTTGTGTTGAAGAGTTGCTGTCCTTAAAGA
10259 CGTTG
130 CGTTG
10264 GAGGCTTCCT
Statistics
Matches: 118, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
149 87 0.74
150 31 0.26
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (150 bp):
AAAAGATTGAAAACACGGAGCTTCGATGTTGATTTTTCTCTGAAAAGAGTTGTTTTAGACCTAGA
GTCCGAGTTTGTTCCCTGGAGGAGATGAATGGCTGTTGTGTTGAAGAGTTGCTGTCCTTAAAGAC
GTTGAAAGTGCAGGGCTAGA
Found at i:17509 original size:3 final size:3
Alignment explanation
Indices: 17503--17527 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17493 TTTTTTTAAT
17503 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
17528 AAATATGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18413 original size:12 final size:12
Alignment explanation
Indices: 18396--18421 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18386 AGATTTATAC
18396 ATCTATTACTAA
1 ATCTATTACTAA
18408 ATCTATTACTAA
1 ATCTATTACTAA
18420 AT
1 AT
18422 TCAATGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
ATCTATTACTAA
Found at i:29284 original size:39 final size:40
Alignment explanation
Indices: 29241--29319 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
29231 TTTTGCCTTA
*
29241 ATTGGTTTT-CTTCTCATACGTT-TCTCCTCTTTGTTTGAG
1 ATTGGTTTTCCTTCTCATAC-TTGTCTCCTCTTTGCTTGAG
* *
29280 ATTGGTTTTCCTTTTGATACTTGTCTCCTCTTTGCTTGAG
1 ATTGGTTTTCCTTCTCATACTTGTCTCCTCTTTGCTTGAG
29320 CCTGTTTATC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 11 0.31
40 24 0.69
ACGTcount: A:0.10, C:0.20, G:0.16, T:0.53
Consensus pattern (40 bp):
ATTGGTTTTCCTTCTCATACTTGTCTCCTCTTTGCTTGAG
Found at i:36799 original size:18 final size:18
Alignment explanation
Indices: 36776--36813 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
36766 AATCGATTGC
36776 TGTTGTTAGACATCTCAA
1 TGTTGTTAGACATCTCAA
36794 TGTTGTTAGACATCTCAA
1 TGTTGTTAGACATCTCAA
36812 TG
1 TG
36814 GTTCATAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (18 bp):
TGTTGTTAGACATCTCAA
Found at i:56926 original size:4 final size:4
Alignment explanation
Indices: 56919--56959 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
56909 CCACCCACCA
* * *
56919 TCTT TCTT TCTT TCTT TCTT TCTT TGTT TTTT TGTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
56960 TTTGAGGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (4 bp):
TCTT
Found at i:59209 original size:2 final size:2
Alignment explanation
Indices: 59202--59252 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
59192 CTCTTAAAAG
* * * *
59202 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT AG AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59244 AT AT AT AT A
1 AT AT AT AT A
59253 GATAATTAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (2 bp):
AT
Found at i:59213 original size:6 final size:6
Alignment explanation
Indices: 59200--59256 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
59190 AGCTCTTAAA
* * *
59200 AGATAT ATATAT ATATAT ATATAT AGATAT AGATAT AGATAT AGATAT
1 AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT AGATAT
59248 --ATAT AGATA
1 AGATAT AGATA
59257 ATTAGTGTCA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
4 4 0.09
6 43 0.91
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.39
Consensus pattern (6 bp):
AGATAT
Found at i:61688 original size:2 final size:2
Alignment explanation
Indices: 61681--61708 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61671 AAACCAAAGT
61681 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
61709 ATTTCCAGGG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:67525 original size:50 final size:50
Alignment explanation
Indices: 67467--67575 Score: 211
Period size: 50 Copynumber: 2.2 Consensus size: 50
67457 TCCATATGCA
67467 TTAAAATTTAACAGATTACAAACAGCACCTAAACTATCAAATATAATAAC
1 TTAAAATTTAACAGATTACAAACAGCACCTAAACTATCAAATATAATAAC
67517 TTAAAATTTAACAGATTACAAACAGCACCTAAACTATCAAATATAATAAC
1 TTAAAATTTAACAGATTACAAACAGCACCTAAACTATCAAATATAATAAC
67567 TT-AAATTTA
1 TTAAAATTTA
67576 TTCATTAAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 7 0.12
50 52 0.88
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.28
Consensus pattern (50 bp):
TTAAAATTTAACAGATTACAAACAGCACCTAAACTATCAAATATAATAAC
Found at i:68982 original size:2 final size:2
Alignment explanation
Indices: 68975--69003 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
68965 AAAACCATAA
68975 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
69004 AATAATTTCA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.