Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015587.1 Corchorus capsularis cultivar CVL-1 contig15608, 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: 2932
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Found at i:672 original size:15 final size:15
Alignment explanation
Indices: 654--684 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
644 TTACTTTTGC
*
654 TACTTTTATCATTTT
1 TACTTTTACCATTTT
669 TACTTTTACCATTTT
1 TACTTTTACCATTTT
684 T
1 T
685 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:684 original size:24 final size:24
Alignment explanation
Indices: 639--684 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
629 TACTGATTAC
* *
639 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCACTTTTAT
*
663 CATTTTTACTTTTACCATTTTT
1 CATTTTTACTTTTACCACTTTT
685 CTTACTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (24 bp):
CATTTTTACTTTTACCACTTTTAT
Found at i:801 original size:25 final size:25
Alignment explanation
Indices: 767--842 Score: 134
Period size: 25 Copynumber: 3.0 Consensus size: 25
757 TAACACCATT
* *
767 TTTTAATTAATACCATTCTTTACTC
1 TTTTACTTAATACCATTTTTTACTC
792 TTTTACTTAATACCATTTTTTACTC
1 TTTTACTTAATACCATTTTTTACTC
817 TTTTACTTAATACCATTTTTTACTC
1 TTTTACTTAATACCATTTTTTACTC
842 T
1 T
843 ACACCATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTACTTAATACCATTTTTTACTC
Found at i:873 original size:44 final size:43
Alignment explanation
Indices: 803--908 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 43
793 TTTACTTAAT
* * *
803 ACCATTTTTT-ACTCTT-TTACTTAATACCATTTTTTACTCT-AC
1 ACCATTTTTTGAC-CTTCTTACTCAATACCATATTTCACT-TGAC
*
845 ACCATTTTTTTGACCTTCTTACTCAATACCATATTTCACTTGAT
1 ACCA-TTTTTTGACCTTCTTACTCAATACCATATTTCACTTGAC
889 ACCA-TTTTTGACCTTCTTAC
1 ACCATTTTTTGACCTTCTTAC
909 GGATTATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
42 20 0.36
43 10 0.18
44 26 0.46
ACGTcount: A:0.24, C:0.25, G:0.03, T:0.48
Consensus pattern (43 bp):
ACCATTTTTTGACCTTCTTACTCAATACCATATTTCACTTGAC
Found at i:1384 original size:54 final size:55
Alignment explanation
Indices: 1286--1740 Score: 403
Period size: 54 Copynumber: 8.2 Consensus size: 55
1276 CTTGACTCTT
* * *
1286 AATTACTGATTTACTGACTACTATTACCTTGACTCTGATTAATCTCTTTTTACTG
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
* * * *
1341 ATTTACTGTTTTACCGATTACT-TTACTTTGACTCTGATTAATCTATTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
*
1395 AATTACTGATTTACCGATTTACCGATTTACCGATTACTTTACTTTGACTCTGATTAATCTCTTTT
1 AATTACTGATTTACCGA-TTA-C----T----ATTAC----C-TTGACTCTGATTAATCTATTTT
*
1460 TACTT
51 TACTG
* * * *
1465 AATTACTGATTTACTGATTACTATTACTTTGACTCTTGATTAATCTCTTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTC-TGATTAATCTATTTTTACTG
* * * * * *
1521 AATTACTAATTTACTGATTACTATTACTTTAACTCTGATTAATCT-CTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
* * * *
1575 AATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCT-CTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
* * *
1629 AATTACTGA-TTA-CTATTACT-TT--C---ACTCTGATTAATCT-CTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
** * * *
1675 AATTACTGATTTACTAATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTT
1 AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
1730 AATTACTGATT
1 AATTACTGATT
1741 GCCCCTTTTT
Statistics
Matches: 349, Mismatches: 25, Indels: 52
0.82 0.06 0.12
Matches are distributed among these distances:
46 32 0.09
47 3 0.01
48 6 0.02
49 2 0.01
51 2 0.01
52 6 0.02
53 3 0.01
54 127 0.36
55 57 0.16
56 54 0.15
60 6 0.02
64 1 0.00
65 4 0.01
68 1 0.00
69 3 0.01
70 42 0.12
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (55 bp):
AATTACTGATTTACCGATTACTATTACCTTGACTCTGATTAATCTATTTTTACTG
Found at i:1408 original size:8 final size:8
Alignment explanation
Indices: 1397--1429 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1387 TTTTACTTAA
*
1397 TTACTGAT
1 TTACCGAT
1405 TTACCGAT
1 TTACCGAT
1413 TTACCGAT
1 TTACCGAT
1421 TTACCGAT
1 TTACCGAT
1429 T
1 T
1430 ACTTTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (8 bp):
TTACCGAT
Found at i:1408 original size:70 final size:70
Alignment explanation
Indices: 1334--1483 Score: 264
Period size: 70 Copynumber: 2.1 Consensus size: 70
1324 TTAATCTCTT
* *
1334 TTTACTGATTTACTGTTTTACCGATTACTTTACTTTGACTCTGATTAATCTATTTTTACTTAATT
1 TTTACTGATTTACCGATTTACCGATTACTTTACTTTGACTCTGATTAATCTATTTTTACTTAATT
1399 ACTGA
66 ACTGA
* *
1404 TTTACCGATTTACCGATTTACCGATTACTTTACTTTGACTCTGATTAATCTCTTTTTACTTAATT
1 TTTACTGATTTACCGATTTACCGATTACTTTACTTTGACTCTGATTAATCTATTTTTACTTAATT
1469 ACTGA
66 ACTGA
1474 TTTACTGATT
1 TTTACTGATT
1484 ACTATTACTT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (70 bp):
TTTACTGATTTACCGATTTACCGATTACTTTACTTTGACTCTGATTAATCTATTTTTACTTAATT
ACTGA
Found at i:1612 original size:21 final size:21
Alignment explanation
Indices: 1588--1661 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 21
1578 TACTGATTTA
*
1588 CTGATTACTATTACTTTGACT
1 CTGATTACTATTACTTTAACT
* *
1609 CTGATTAATCTCTTTTAC-TTAATT
1 CTGATT-A---CTATTACTTTAACT
*
1633 ACTGATTACTATTACTTTCACT
1 -CTGATTACTATTACTTTAACT
1655 CTGATTA
1 CTGATTA
1662 ATCTCTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
21 19 0.46
22 5 0.12
24 5 0.12
25 12 0.29
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.49
Consensus pattern (21 bp):
CTGATTACTATTACTTTAACT
Found at i:1639 original size:100 final size:101
Alignment explanation
Indices: 1523--1740 Score: 395
Period size: 100 Copynumber: 2.2 Consensus size: 101
1513 TTTTACTTAA
1523 TTAC-TAATTTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTACTTAATTACTGATTT
1 TTACTTAA-TTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTACTTAATTACTGATTT
*
1587 ACTGATTACTATTACTTTGACTCTGATTAATCTC-TT
65 ACTAATTACTATTACTTTGACTCTGATTAATCTCTTT
*
1623 TTACTTAATTACTGATTACTATTACTTTCACTCTGATTAATCTCTTTTACTTAATTACTGATTTA
1 TTACTTAATTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTACTTAATTACTGATTTA
1688 CTAATTACTATTACTTTGACTCTGATTAATCTCTTT
66 CTAATTACTATTACTTTGACTCTGATTAATCTCTTT
1724 TTACTTAATTACTGATT
1 TTACTTAATTACTGATT
1741 GCCCCTTTTT
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
100 92 0.81
101 22 0.19
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (101 bp):
TTACTTAATTACTGATTACTATTACTTTAACTCTGATTAATCTCTTTTACTTAATTACTGATTTA
CTAATTACTATTACTTTGACTCTGATTAATCTCTTT
Found at i:2435 original size:51 final size:50
Alignment explanation
Indices: 2390--2841 Score: 322
Period size: 51 Copynumber: 8.9 Consensus size: 50
2380 TAAAAGGTTT
* *
2390 AAACTTCTAATTCAAAGGTGACA-TTTTATTTACTAATTACTTAAAAATTC
1 AAACTT-TTATTCAAAGGTGAAAGTTTTATTTACTAATTACTTAAAAATTC
* * * * * *
2440 AATCTTTCATTCAAAGGTTAAAGCTTTATTTACTAATCACTCTAAAGATTC
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACT-TAAAAATTC
* ** * * * * * *
2491 AATCTTTTACCCAAAGATGACATTTTTATTTACCAATTGCTTAAAAATCC
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACTTAAAAATTC
* *
2541 AAATCTTTTATTCAAAGGTTAAA-TCTTTATTTACTAATTACTCTAAAGATTC
1 AAA-CTTTTATTCAAAGGTGAAAGT-TTTATTTACTAATTACT-TAAAAATTC
* ** * * * * *
2593 AATCTTTTACCCAAAGATGACATTTTTATTTACCAATTGCTTAAAAATTC
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACTTAAAAATTC
* * * * *
2643 AATCTTTTATTCAAAGGTTAAA-TCCTTGTTTACTTATTACCTTAAAAATTC
1 AAACTTTTATTCAAAGGTGAAAGT-TTTATTTACTAATTA-CTTAAAAATTC
* * * * * *
2694 AATCTTTTACTCAAAGATGACA-TTTTGTTTACTAATTACTAAAAAAAAATT-
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACT---TAAAAATTC
* * * *
2745 AATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATTACCCTAAAAATTC
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTA-CTTAAAAATTC
* * * * * * *
2796 AATCTTTTACTCAAAGATGATA-TTTTGTTTACCACTTACTTAAAAA
1 AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACTTAAAAA
2842 CAAAATCAAT
Statistics
Matches: 315, Mismatches: 73, Indels: 29
0.76 0.18 0.07
Matches are distributed among these distances:
49 23 0.07
50 98 0.31
51 162 0.51
52 31 0.10
53 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (50 bp):
AAACTTTTATTCAAAGGTGAAAGTTTTATTTACTAATTACTTAAAAATTC
Found at i:2569 original size:102 final size:101
Alignment explanation
Indices: 2402--2875 Score: 589
Period size: 102 Copynumber: 4.7 Consensus size: 101
2392 ACTTCTAATT
* * * * *
2402 CAAAGGTGACATTTTATTTACTAATTACTTAAAAATTC-AATCTTTCATTCAAAGGTTAAAGCTT
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTT
* *
2466 TATTTACTAATCACTCTAAAGATTCAATCTTTTACC
66 TATTTACTAATTACTCTAAAAATTCAATCTTTTACC
*
2502 CAAAGATGACATTTTTATTTACCAATTGCTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCT
1 CAAAGATGACA-TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCT
*
2567 TTATTTACTAATTACTCTAAAGATTCAATCTTTTACC
65 TTATTTACTAATTACTCTAAAAATTCAATCTTTTACC
* * *
2604 CAAAGATGACATTTTTATTTACCAATTGCTTAAAAATTC-AATCTTTTATTCAAAGGTTAAATCC
1 CAAAGATGACA-TTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCT
* * *
2668 TTGTTTACTTATTAC-CTTAAAAATTCAATCTTTTACT
65 TTATTTACTAATTACTC-TAAAAATTCAATCTTTTACC
* * *** *
2705 CAAAGATGACATTTTGTTTACTAATTAC-TAAAAAAAAATTAATCTTTTATTCAAAGGTTAAAGC
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATCCA--AATCTTTTATTCAAAGGTTAAATC
* *
2769 TTTATTTACTAATTACCCTAAAAATTCAATCTTTTACT
64 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTACC
* * * *
2807 CAAAGATGATATTTTGTTTACCACTTACTTAAAAA-CAAAATCAATCTTTTATTCAAAGGTTAAA
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATC--CA--AATCTTTTATTCAAAGGTTAAA
2871 TCTTT
62 TCTTT
2876 TAGCCAAATA
Statistics
Matches: 335, Mismatches: 29, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
99 6 0.02
100 25 0.07
101 90 0.27
102 178 0.53
103 7 0.02
104 29 0.09
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (101 bp):
CAAAGATGACATTTTATTTACCAATTACTTAAAAATCCAAATCTTTTATTCAAAGGTTAAATCTT
TATTTACTAATTACTCTAAAAATTCAATCTTTTACC
Found at i:2712 original size:203 final size:201
Alignment explanation
Indices: 2402--2872 Score: 622
Period size: 203 Copynumber: 2.3 Consensus size: 201
2392 ACTTCTAATT
* * * * *
2402 CAAAGGTGACATTTTATTTACTAATTACTTAAAAATTCAATCTTTCATTCAAAGGTTAAAGCTTT
1 CAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCCTT
* *
2467 ATTTACTAATCACTCTAAAGATTCAATCTTTTACCCAAAGATGACATTTTTATTTACCAATTGCT
66 ATTTACTAATCACTCTAAAAATTCAATCTTTTACCCAAAGATGACA-TTTTATTTACCAATTAC-
*** * * *
2532 TAAAAATCCA-AATCTTTTATTCAAAGGTTAAATCTTTATTTACTAATTACTCTAAAGATTCAAT
129 TAAAAAAAAATAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATTACCCTAAAAATTCAAT
2596 CTTTTACC
194 CTTTTACC
*
2604 CAAAGATGACATTTTTATTTACCAATTGCTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCCT
1 CAAAGATGACA-TTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCCT
* * * * * *
2669 TGTTTACTTATTAC-CTTAAAAATTCAATCTTTTACTCAAAGATGACATTTTGTTTACTAATTAC
65 TATTTACTAATCACTC-TAAAAATTCAATCTTTTACCCAAAGATGACATTTTATTTACCAATTAC
2733 TAAAAAAAAATTAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATTACCCTAAAAATTCAA
129 TAAAAAAAAA-TAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATTACCCTAAAAATTCAA
*
2798 TCTTTTACT
193 TCTTTTACC
* * * *
2807 CAAAGATGATATTTTGTTTACCACTTACTTAAAAACAAAATCAATCTTTTATTCAAAGGTTAAAT
1 CAAAGATGACATTTTATTTACCAATTACTT---AA-AAATTCAATCTTTTATTCAAAGGTTAAAT
2872 C
62 C
2873 TTTTAGCCAA
Statistics
Matches: 235, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
201 7 0.03
202 41 0.17
203 156 0.66
205 2 0.01
206 29 0.12
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (201 bp):
CAAAGATGACATTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCCTT
ATTTACTAATCACTCTAAAAATTCAATCTTTTACCCAAAGATGACATTTTATTTACCAATTACTA
AAAAAAAATAATCTTTTATTCAAAGGTTAAAGCTTTATTTACTAATTACCCTAAAAATTCAATCT
TTTACC
Done.