Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008584.1 Corchorus capsularis cultivar CVL-1 contig08605, 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: 7328
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1342 original size:15 final size:15
Alignment explanation
Indices: 1324--1354 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1314 TTTACTTTGC
*
1324 TACTTTTATCATTTT
1 TACTTTTACCATTTT
1339 TACTTTTACCATTTT
1 TACTTTTACCATTTT
1354 T
1 T
1355 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:1388 original size:17 final size:17
Alignment explanation
Indices: 1362--1400 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1352 TTTCTTACTC
*
1362 TTTTACTTAATACCATT
1 TTTTAATTAATACCATT
1379 TTTTAATTAATACCATT
1 TTTTAATTAATACCATT
*
1396 CTTTA
1 TTTTA
1401 CTCTTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAATTAATACCATT
Found at i:1402 original size:42 final size:41
Alignment explanation
Indices: 1356--1557 Score: 203
Period size: 42 Copynumber: 4.7 Consensus size: 41
1346 ACCATTTTTC
* *
1356 TTACTCTTTTACTTAATACCATTTTTTAATTAATACCATTCT
1 TTAC-CTTTTACTTAATACCATTTTTTACTTGATACCATTCT
* *
1398 TTACTCTTTTACTTAATACCATTTTTTTACTCT-ACACCATTTTT
1 TTAC-CTTTTACTTAATACCA-TTTTTTACT-TGATACCA-TTCT
* * *
1442 TTCGACCTTCTTACTCAATACCATATTTCACTTGATACCATTCT
1 TT--ACCTT-TTACTTAATACCATTTTTTACTTGATACCATTCT
* *
1486 TGACCTTCTTACTTAATACCATATTTTACTTGATACCATT-T
1 TTACCTT-TTACTTAATACCATTTTTTACTTGATACCATTCT
1527 TTGACCTTTTTACTTAATACCA-TTTTTACTT
1 TT-ACC-TTTTACTTAATACCATTTTTTACTT
1558 ATTATCTTAC
Statistics
Matches: 138, Mismatches: 13, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
41 10 0.07
42 73 0.53
43 15 0.11
44 11 0.08
45 15 0.11
46 14 0.10
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.50
Consensus pattern (41 bp):
TTACCTTTTACTTAATACCATTTTTTACTTGATACCATTCT
Found at i:1408 original size:25 final size:26
Alignment explanation
Indices: 1379--1430 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1369 TAATACCATT
1379 TTTTAATTAATACCA-TTCTTTACTC
1 TTTTAATTAATACCATTTCTTTACTC
* *
1404 TTTTACTTAATACCATTTTTTTACTC
1 TTTTAATTAATACCATTTCTTTACTC
1430 T
1 T
1431 ACACCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTAATTAATACCATTTCTTTACTC
Found at i:1427 original size:18 final size:18
Alignment explanation
Indices: 1362--1443 Score: 60
Period size: 18 Copynumber: 4.2 Consensus size: 18
1352 TTTCTTACTC
1362 TTTTACTTAATACCA-TT
1 TTTTACTTAATACCATTT
*
1379 TTTTAATTAATACCATTCTTTACT
1 TTTTACTTAATACCA----TT--T
1403 CTTTTACTTAATACCATTT
1 -TTTTACTTAATACCATTT
*
1422 TTTTACTCT-ACACCATTT
1 TTTTACT-TAATACCATTT
1440 TTTT
1 TTTT
1444 CGACCTTCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
17 14 0.26
18 19 0.36
19 2 0.04
21 2 0.04
22 1 0.02
24 1 0.02
25 14 0.26
ACGTcount: A:0.26, C:0.20, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTACTTAATACCATTT
Found at i:1462 original size:88 final size:84
Alignment explanation
Indices: 1364--1553 Score: 231
Period size: 88 Copynumber: 2.2 Consensus size: 84
1354 TCTTACTCTT
* * *
1364 TTACTTAATACCATTTTTTAATTAATACCATTCTTTACTCTT-TTACTTAATACCATTTTTTTAC
1 TTACTTAATACCATTTTTCAATTAATACCATTCTTGAC-CTTCTTACTTAATACCA-TATTTTAC
1428 TCT-ACACCATTTTTTTCGACCTTC
64 T-TGACACCA--TTTTT-GACCTTC
* * * *
1452 TTACTCAATACCATATTTCACTTGATACCATTCTTGACCTTCTTACTTAATACCATATTTTACTT
1 TTACTTAATACCATTTTTCAATTAATACCATTCTTGACCTTCTTACTTAATACCATATTTTACTT
* *
1517 GATACCATTTTTGACCTTT
66 GACACCATTTTTGACCTTC
1536 TTACTTAATACCATTTTT
1 TTACTTAATACCATTTTT
1554 ACTTATTATC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
84 22 0.25
85 5 0.06
86 1 0.01
87 16 0.18
88 45 0.51
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (84 bp):
TTACTTAATACCATTTTTCAATTAATACCATTCTTGACCTTCTTACTTAATACCATATTTTACTT
GACACCATTTTTGACCTTC
Found at i:1505 original size:25 final size:23
Alignment explanation
Indices: 1471--1552 Score: 68
Period size: 25 Copynumber: 3.7 Consensus size: 23
1461 ACCATATTTC
*
1471 ACTTGATACCATTCTTGACCTTCTT
1 ACTTAATACCATT-TTGACCTT-TT
1496 ACTTAATACCA---T-A--TTTT
1 ACTTAATACCATTTTGACCTTTT
*
1513 ACTTGATACCATTTTTGACCTTTTT
1 ACTTAATACCA-TTTTGACC-TTTT
1538 ACTTAATACCATTTT
1 ACTTAATACCATTTT
1553 TACTTATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
17 12 0.26
18 2 0.04
20 1 0.02
21 2 0.04
22 1 0.02
24 4 0.09
25 24 0.52
ACGTcount: A:0.26, C:0.22, G:0.05, T:0.48
Consensus pattern (23 bp):
ACTTAATACCATTTTGACCTTTT
Found at i:1516 original size:17 final size:16
Alignment explanation
Indices: 1494--1558 Score: 54
Period size: 17 Copynumber: 4.4 Consensus size: 16
1484 CTTGACCTTC
1494 TTACTTAATACCATATT
1 TTACTTAATACCAT-TT
*
1511 TTACTTGATACCA--T
1 TTACTTAATACCATTT
*
1525 TT--TT--GACC-TTT
1 TTACTTAATACCATTT
1536 TTACTTAATACCATTT
1 TTACTTAATACCATTT
1552 TTACTTA
1 TTACTTA
1559 TTATCTTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 15
0.68 0.05 0.27
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 2 0.05
13 2 0.05
14 3 0.08
15 3 0.08
16 10 0.26
17 12 0.32
ACGTcount: A:0.28, C:0.18, G:0.03, T:0.51
Consensus pattern (16 bp):
TTACTTAATACCATTT
Found at i:1566 original size:24 final size:25
Alignment explanation
Indices: 1511--1566 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1501 ATACCATATT
* *
1511 TTACTTGATACCATTTTTGACCTTT
1 TTACTTAATACCATTTTTGACCTTA
1536 TTACTTAATACCATTTTT-A-CTTA
1 TTACTTAATACCATTTTTGACCTTA
1559 TTATCTTA
1 TTA-CTTA
1567 CTTGCCATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 5 0.18
25 17 0.61
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.54
Consensus pattern (25 bp):
TTACTTAATACCATTTTTGACCTTA
Found at i:1961 original size:41 final size:39
Alignment explanation
Indices: 1848--2109 Score: 142
Period size: 37 Copynumber: 7.1 Consensus size: 39
1838 AATCACTCAT
* *
1848 CTCTTAATTACTGATTTACTGATT-A-C-CATCACTTTGA
1 CTCTTAATTACTGATTTACTGATTAATCTC-TTACCTTGA
*
1885 CTCTTAATTA-TCGATTTACTGATTACTAT-TTTTACCTTGA
1 CTCTTAATTACT-GATTTACTGATTA--ATCTCTTACCTTGA
1925 CTCTTAAATTACTGACTTTACTGATTAATCTCTTACCTTGA
1 CTCTT-AATTACTGA-TTTACTGATTAATCTCTTACCTTGA
* * * * *
1966 CCCTTAATTA-TCAATTTATTGATTATTATCTT--CTT-A
1 CTCTTAATTACT-GATTTACTGATTAATCTCTTACCTTGA
* *
2002 --CTTAATTACTGATTTACTGATTACTACTTTTA-C-T--
1 CTCTTAATTACTGATTTACTGATTAAT-CTCTTACCTTGA
* *
2036 CCCTTAATTA-TCAATTTACTTGATTAATCT-TT---TT-A
1 CTCTTAATTACT-GATTTAC-TGATTAATCTCTTACCTTGA
*
2071 CT-TT-ATTACTGATTTACTGATT-A-CTATTACCTTGA
1 CTCTTAATTACTGATTTACTGATTAATCTCTTACCTTGA
2106 CTCT
1 CTCT
2110 GATTAATCTC
Statistics
Matches: 180, Mismatches: 18, Indels: 55
0.71 0.07 0.22
Matches are distributed among these distances:
30 2 0.01
31 3 0.02
32 5 0.03
33 10 0.06
34 26 0.14
35 12 0.07
36 20 0.11
37 32 0.18
39 16 0.09
40 21 0.12
41 21 0.12
42 12 0.07
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (39 bp):
CTCTTAATTACTGATTTACTGATTAATCTCTTACCTTGA
Found at i:2081 original size:69 final size:69
Alignment explanation
Indices: 1931--2096 Score: 219
Period size: 69 Copynumber: 2.3 Consensus size: 69
1921 TTGACTCTTA
* *
1931 AATTACTGACTTTACTGATTAAT-CTCTTACCTTGACCCTTAATTATCAATTTATTGATTATTAT
1 AATTACTGA-TTTACTGATTACTACTTTTA-C-T--CCCTTAATTATCAATTTATTGATTA-TAT
1995 CTTCTTACTT
60 CTTCTTACTT
*
2005 AATTACTGATTTACTGATTACTACTTTTACTCCCTTAATTATCAATTTACTTGATTA-ATCTTTT
1 AATTACTGATTTACTGATTACTACTTTTACTCCCTTAATTATCAATTTA-TTGATTATATCTTCT
2069 TACTT
65 TACTT
*
2074 TATTACTGATTTACTGATTACTA
1 AATTACTGATTTACTGATTACTA
2097 TTACCTTGAC
Statistics
Matches: 86, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
69 33 0.38
70 18 0.21
71 7 0.08
72 1 0.01
73 13 0.15
74 14 0.16
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (69 bp):
AATTACTGATTTACTGATTACTACTTTTACTCCCTTAATTATCAATTTATTGATTATATCTTCTT
ACTT
Found at i:2134 original size:55 final size:53
Alignment explanation
Indices: 2056--2164 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 53
2046 TCAATTTACT
*
2056 TGATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTC
2109 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAA--TCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTC
2164 T
1 T
2165 TAATGTATGG
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 7 0.13
55 46 0.87
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (53 bp):
TGATTAATCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTC
Found at i:5559 original size:27 final size:26
Alignment explanation
Indices: 5510--5557 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5500 CACTTGTTTG
5510 AGCTTGGGGAAAGCTCTGTGTTGTCA
1 AGCTTGGGGAAAGCTCTGTGTTGTCA
5536 AGCTTGGGGAAAGCT-TG-GTTGT
1 AGCTTGGGGAAAGCTCTGTGTTGT
5558 TGTAACGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
25 2 0.09
26 15 0.68
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (26 bp):
AGCTTGGGGAAAGCTCTGTGTTGTCA
Found at i:6936 original size:15 final size:15
Alignment explanation
Indices: 6916--6947 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6906 CCATGGACGA
6916 GACAGATACAGAAAT
1 GACAGATACAGAAAT
*
6931 GACAGATTCAGAAAT
1 GACAGATACAGAAAT
6946 GA
1 GA
6948 AGAAGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (15 bp):
GACAGATACAGAAAT
Done.