Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006404.1 Corchorus capsularis cultivar CVL-1 contig06425, 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: 4578
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Found at i:469 original size:18 final size:18
Alignment explanation
Indices: 446--483 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
436 TTAACGATGA
446 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
464 ACTAAACCGGATTAAACT
1 ACTAAACCGGATTAAACT
482 AC
1 AC
484 CACAAAGCTA
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:0.45, C:0.24, G:0.11, T:0.21
Consensus pattern (18 bp):
ACTAAACCGGATTAAACT
Found at i:700 original size:28 final size:27
Alignment explanation
Indices: 668--742 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
658 AAGTGATCTT
*
668 AAAATGACCAAAATGCTCCCTAAATATG
1 AAAATGACCAAAATGC-CCCTAAATATA
* * *
696 AAAATGACCAAAATG-CCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTAAATATA
722 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
743 GATGACCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.54
27 4 0.10
28 15 0.37
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTAAATATA
Found at i:2147 original size:28 final size:27
Alignment explanation
Indices: 2116--2200 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
2106 ACTTTTGCTA
*
2116 CTTTTATTATTTTTACTCTTTTCTTACT
1 CTTTT-TTATTTTTACTCCTTTCTTACT
***
2144 CTTTTTTACCAATTACTCCTTTCTTACT
1 CTTTTTTA-TTTTTACTCCTTTCTTACT
*
2172 CTCTTTTATTTATTAC-CACTTT-TTACT
1 CTTTTTTATTT-TTACTC-CTTTCTTACT
2199 CT
1 CT
2201 CCCTTTTCTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
27 11 0.24
28 35 0.76
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (27 bp):
CTTTTTTATTTTTACTCCTTTCTTACT
Found at i:2342 original size:15 final size:15
Alignment explanation
Indices: 2310--2373 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
2300 TTTTTACTTC
*
2310 TTACTGATTA-TCTT
1 TTACTGATTACTATT
2324 TTACTGATTACTATT
1 TTACTGATTACTATT
2339 TTACTGATTTACT-TT
1 TTACTGA-TTACTATT
* *
2354 TTACTGGTTACCATT
1 TTACTGATTACTATT
2369 TTACT
1 TTACT
2374 CTTTTTCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
14 14 0.32
15 25 0.57
16 5 0.11
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.55
Consensus pattern (15 bp):
TTACTGATTACTATT
Found at i:2377 original size:53 final size:51
Alignment explanation
Indices: 2320--2436 Score: 139
Period size: 53 Copynumber: 2.3 Consensus size: 51
2310 TTACTGATTA
*
2320 TCTTTTACTGATTACTATTTTACTGAT-TTACTTTTTACTGGTTACCATTTTAC
1 TCTTTTACTGATTACCATTTT-CTGATCTT-CTTTTTACTGGTTA-CATTTTAC
* * * *
2373 TCTTTTTCTGATTACCATTTTCTGCTCCTTTTTTTTACTGGTTACTTTTTAC
1 TCTTTTACTGATTACCATTTTCTGAT-CTTCTTTTTACTGGTTACATTTTAC
2425 T-TTTTACTGATT
1 TCTTTTACTGATT
2437 GTCTTTTGCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
51 10 0.18
52 12 0.21
53 32 0.57
54 2 0.04
ACGTcount: A:0.16, C:0.18, G:0.08, T:0.58
Consensus pattern (51 bp):
TCTTTTACTGATTACCATTTTCTGATCTTCTTTTTACTGGTTACATTTTAC
Found at i:2378 original size:23 final size:22
Alignment explanation
Indices: 2346--2393 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
2336 ATTTTACTGA
*
2346 TTTACTTTTTACTGGTTACCAT
1 TTTACTTTTTACTGATTACCAT
*
2368 TTTACTCTTTTTCTGATTACCAT
1 TTTACT-TTTTACTGATTACCAT
2391 TTT
1 TTT
2394 CTGCTCCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTACTTTTTACTGATTACCAT
Found at i:2428 original size:22 final size:22
Alignment explanation
Indices: 2404--2555 Score: 134
Period size: 21 Copynumber: 7.0 Consensus size: 22
2394 CTGCTCCTTT
*
2404 TTTTTACTGGTTA-CTTTTTAC
1 TTTTTACTGATTACCTTTTTAC
** *
2425 TTTTTACTGATTGTC-TTTTGC
1 TTTTTACTGATTACCTTTTTAC
2446 TTTTTA-TCGATTACCTTTTTAC
1 TTTTTACT-GATTACCTTTTTAC
* *
2468 TTTTTGCTGATTAGCTTTTTAC
1 TTTTTACTGATTACCTTTTTAC
*
2490 TCTTTACTGATTACCTTTTTAC
1 TTTTTACTGATTACCTTTTTAC
* * * *
2512 -TCTTACTAATTTCC-TTTTGC
1 TTTTTACTGATTACCTTTTTAC
* *
2532 TTCTTACTTATTACCCTTTTTAC
1 TTTTTACTGATTA-CCTTTTTAC
2555 T
1 T
2556 CTTAATGATT
Statistics
Matches: 105, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.06
21 47 0.45
22 45 0.43
23 7 0.07
ACGTcount: A:0.15, C:0.19, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTTTACTGATTACCTTTTTAC
Found at i:2558 original size:22 final size:21
Alignment explanation
Indices: 2455--2559 Score: 95
Period size: 22 Copynumber: 4.9 Consensus size: 21
2445 CTTTTTATCG
* * *
2455 ATTACCTTTTTACTTTTTGCTG
1 ATTACCTTTTTAC-TCTTACTA
* *
2477 ATTAGCTTTTTACTCTTTACTG
1 ATTACCTTTTTACTC-TTACTA
2499 ATTACCTTTTTACTCTTACTA
1 ATTACCTTTTTACTCTTACTA
* * *
2520 ATTTCC-TTTTGCTTCTTACTT
1 ATTACCTTTTTAC-TCTTACTA
2541 ATTACCCTTTTTACTCTTA
1 ATTA-CCTTTTTACTCTTA
2560 ATGATTACTA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
20 5 0.07
21 21 0.30
22 38 0.55
23 5 0.07
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTACCTTTTTACTCTTACTA
Found at i:2701 original size:16 final size:16
Alignment explanation
Indices: 2680--2741 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
2670 GGCTCTTTAA
2680 TTACTGATTACTCAAT
1 TTACTGATTACTCAAT
**
2696 TTACTGATTACTATCTTT
1 TTACTGATTAC--TCAAT
*
2714 TTACCTGATTACT-GAT
1 TTA-CTGATTACTCAAT
2730 TTACTGATTACT
1 TTACTGATTACT
2742 ATTACCTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.23
16 15 0.38
17 1 0.03
18 6 0.15
19 8 0.21
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (16 bp):
TTACTGATTACTCAAT
Found at i:2752 original size:15 final size:16
Alignment explanation
Indices: 2713--2753 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2703 TTACTATCTT
2713 TTTACCTGATTACTGA
1 TTTACCTGATTACTGA
2729 TTTA-CTGATTACT-A
1 TTTACCTGATTACTGA
2743 -TTACCTTGATT
1 TTTACC-TGATT
2754 CTTAATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.13
14 2 0.09
15 14 0.61
16 4 0.17
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (16 bp):
TTTACCTGATTACTGA
Found at i:2776 original size:71 final size:72
Alignment explanation
Indices: 2686--2822 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 72
2676 TTAATTACTG
* * * * *
2686 ATTACTCAATTTACTGATTACTATCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTG
1 ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
2751 ATTCTTA
66 ATTCTTA
* * *
2758 ATTA-TCAATTTACCGATTAATCTCTTCTTACTTAACTACTTATTTACTGATTACTATTACCTTG
1 ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
2822 A
66 A
2823 CTCTGATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
71 53 0.93
72 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (72 bp):
ATTACTCAATTTACCGATTAATATCTTCTTACCTAACTACTGATTTACTGATTACTATTACCTTG
ATTCTTA
Found at i:2833 original size:55 final size:55
Alignment explanation
Indices: 2772--2966 Score: 304
Period size: 55 Copynumber: 3.5 Consensus size: 55
2762 TCAATTTACC
* *
2772 GATTAATCTCTTCTTACTTAACTACTTATTTACTGATTACTATTACCTTGACTCT
1 GATTAATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACTTTGACTCT
*
2827 GATTAATCTCTTCTTACTTGACTACTGATTTACTGATTACTATTACTTTGACTCT
1 GATTAATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACTTTGACTCT
* *
2882 GATTAATCTCTT-TTCACTTAATTACTGATTTACTGATTACTATTACTTTGACCCT
1 GATTAATCTCTTCTT-ACTTAACTACTGATTTACTGATTACTATTACTTTGACTCT
*
2937 GATTAATCTCTTTTTACTTAA-TCACTGATT
1 GATTAATCTCTTCTTACTTAACT-ACTGATT
2967 GCCCCCTTTC
Statistics
Matches: 131, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
54 3 0.02
55 126 0.96
56 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.48
Consensus pattern (55 bp):
GATTAATCTCTTCTTACTTAACTACTGATTTACTGATTACTATTACTTTGACTCT
Found at i:3775 original size:50 final size:49
Alignment explanation
Indices: 3712--3926 Score: 213
Period size: 50 Copynumber: 4.3 Consensus size: 49
3702 AATTACTTTT
* * *
3712 TAAAACTTCAATCTTTTATTCAAAGGTTACATCTCTATTTACTAATTAATC
1 TAAAA-TTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATT-ATC
* * *
3763 TAAAAATCAATCTTTTGCTCAAAGGTGACATCTTTACTTACTAATTAT-
1 TAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC
* * *
3811 TAAAAGTTTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTA-C
1 TAAAA--TTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC
* * * * *
3861 TAAGAATTCAATCTTTTACCCAAAGATGACATTTTTATTTA--AGTTATT
1 TAA-AATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC
*
3909 TAAAGCTTCAATCTTTTA
1 TAAA-ATTCAATCTTTTA
3927 TTTACAAGTT
Statistics
Matches: 143, Mismatches: 15, Indels: 15
0.83 0.09 0.09
Matches are distributed among these distances:
47 5 0.03
48 20 0.14
49 37 0.26
50 74 0.52
51 7 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (49 bp):
TAAAATTCAATCTTTTACTCAAAGGTGACATCTTTATTTACTAATTATC
Found at i:3851 original size:100 final size:97
Alignment explanation
Indices: 3711--3926 Score: 249
Period size: 99 Copynumber: 2.2 Consensus size: 97
3701 AAATTACTTT
** * *
3711 TTAAAA-CTTCAATCTTTTATTCAAAGGTTACATCTCTATTTACTAATTAATCTAA-AAATCAAT
1 TTAAAAGCTTCAATCTTTTACCCAAAGATGACATCTCTATTTACTAATT-A-CTAAGAAATCAAT
* * *
3774 CTTTTGCTCAAAGGTGACATCTTTACTTACTAA-TTA
64 CTTTTACCCAAAGATGACATCTTTA-TT--TAAGTTA
* * * *
3810 TTAAAAGTTTCAATCTTTTACCCAAAGATGACATTTTTATTTACTAATTACTAAGAATTCAATCT
1 TTAAAAGCTTCAATCTTTTACCCAAAGATGACATCTCTATTTACTAATTACTAAGAAATCAATCT
*
3875 TTTACCCAAAGATGACATTTTTATTTAAGTTA
66 TTTACCCAAAGATGACATCTTTATTTAAGTTA
*
3907 TTTAAAGCTTCAATCTTTTA
1 TTAAAAGCTTCAATCTTTTA
3927 TTTACAAGTT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
96 3 0.03
97 21 0.21
98 6 0.06
99 35 0.35
100 35 0.35
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (97 bp):
TTAAAAGCTTCAATCTTTTACCCAAAGATGACATCTCTATTTACTAATTACTAAGAAATCAATCT
TTTACCCAAAGATGACATCTTTATTTAAGTTA
Done.