Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004914.1 Corchorus capsularis cultivar CVL-1 contig04932, 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: 10580
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1269 original size:3 final size:3
Alignment explanation
Indices: 1263--1300 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1253 CCACCACCAC
*
1263 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1301 CCTTCTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:1989 original size:2 final size:2
Alignment explanation
Indices: 1982--2014 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1972 AATTTTTGGG
1982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2015 GTCACAAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2276 original size:17 final size:17
Alignment explanation
Indices: 2256--2306 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
2246 TTTGAATCGA
2256 GTTCGAGTTGAATTTGG
1 GTTCGAGTTGAATTTGG
*
2273 GTTC-AGTT-AATTCGG
1 GTTCGAGTTGAATTTGG
*
2288 GTTCGGGTTGAATTTGG
1 GTTCGAGTTGAATTTGG
2305 GT
1 GT
2307 CAGGTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 10 0.34
16 7 0.24
17 12 0.41
ACGTcount: A:0.16, C:0.08, G:0.35, T:0.41
Consensus pattern (17 bp):
GTTCGAGTTGAATTTGG
Found at i:2298 original size:32 final size:32
Alignment explanation
Indices: 2256--2328 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
2246 TTTGAATCGA
*
2256 GTTCGAGTTGAATTTGGGTTCA-GTTAATTCGG
1 GTTCGGGTTGAATTTGGG-TCAGGTTAATTCGG
2288 GTTCGGGTTGAATTTGGGTCAGGTTAATTCGG
1 GTTCGGGTTGAATTTGGGTCAGGTTAATTCGG
2320 GTTCGGGTT
1 GTTCGGGTT
2329 CGGTTTGGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 3 0.08
32 36 0.92
ACGTcount: A:0.15, C:0.10, G:0.36, T:0.40
Consensus pattern (32 bp):
GTTCGGGTTGAATTTGGGTCAGGTTAATTCGG
Found at i:2328 original size:16 final size:17
Alignment explanation
Indices: 2237--2328 Score: 86
Period size: 16 Copynumber: 5.6 Consensus size: 17
2227 TCGGGTCATT
2237 GGGTTCGGGTTTGAA-TC
1 GGGTTCGGG-TTGAATTC
* * *
2254 GAGTTCGAGTTGAATTT
1 GGGTTCGGGTTGAATTC
*
2271 GGGTTC-AGTT-AATTC
1 GGGTTCGGGTTGAATTC
*
2286 GGGTTCGGGTTGAATTT
1 GGGTTCGGGTTGAATTC
*
2303 GGG-TCAGGTT-AATTC
1 GGGTTCGGGTTGAATTC
2318 GGGTTCGGGTT
1 GGGTTCGGGTT
2329 CGGTTTGGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
15 17 0.28
16 24 0.39
17 20 0.33
ACGTcount: A:0.15, C:0.10, G:0.37, T:0.38
Consensus pattern (17 bp):
GGGTTCGGGTTGAATTC
Found at i:2498 original size:16 final size:16
Alignment explanation
Indices: 2477--2566 Score: 108
Period size: 16 Copynumber: 5.6 Consensus size: 16
2467 TTTTCATAAA
* *
2477 TTTTCGGATTCGGGTT
1 TTTTCGGGTTTGGGTT
* *
2493 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTTGGGTT
2509 TTTTCGGGTTTGGGTT
1 TTTTCGGGTTTGGGTT
**
2525 TTTTCGGGTTTGAATT
1 TTTTCGGGTTTGGGTT
* *
2541 TTTTCGGGTTCGGATT
1 TTTTCGGGTTTGGGTT
2557 TTTTCGGGTT
1 TTTTCGGGTT
2567 CAGATTCAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.06, C:0.10, G:0.31, T:0.53
Consensus pattern (16 bp):
TTTTCGGGTTTGGGTT
Found at i:2524 original size:32 final size:32
Alignment explanation
Indices: 2477--2566 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
2467 TTTTCATAAA
* *
2477 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAACT
* *
2509 TTTTCGGGTTTGGGTTTTTTCGGGTTTGAATT
1 TTTTCGGGTTCGGGTTTTTTCGGGTTTGAACT
*
2541 TTTTCGGGTTCGGATTTTTTCGGGTT
1 TTTTCGGGTTCGGGTTTTTTCGGGTT
2567 CAGATTCAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.06, C:0.10, G:0.31, T:0.53
Consensus pattern (32 bp):
TTTTCGGGTTCGGGTTTTTTCGGGTTTGAACT
Found at i:2874 original size:2 final size:2
Alignment explanation
Indices: 2863--2898 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2853 TAAGAGTGTG
*
2863 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2899 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8964 original size:13 final size:13
Alignment explanation
Indices: 8919--8965 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
8909 ATCATTTTTA
8919 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
8932 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
8945 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
8959 CTCTTTT
1 CTCTTTT
8966 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:8980 original size:29 final size:27
Alignment explanation
Indices: 8916--8981 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
8906 TTTATCATTT
*
8916 TTACTCTTTTCTTACTCTTTTTACTAA
1 TTACACTTTTCTTACTCTTTTTACTAA
* * *
8943 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACACTTTTCTTACTCT-TTTTACTAA
8971 TTACCACTTTT
1 TTA-CACTTTT
8982 TACTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 18 0.53
28 10 0.29
29 6 0.18
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.61
Consensus pattern (27 bp):
TTACACTTTTCTTACTCTTTTTACTAA
Found at i:9106 original size:21 final size:22
Alignment explanation
Indices: 9034--9139 Score: 103
Period size: 21 Copynumber: 5.0 Consensus size: 22
9024 ACTGATCACC
*
9034 TTTTACTCTTTATTGATTACTA
1 TTTTACTCTTTACTGATTACTA
* *
9056 TTTTACTC-TTACTAATTACCA
1 TTTTACTCTTTACTGATTACTA
* * * *
9077 CTTTGCTC-TTACTGGTTACTG
1 TTTTACTCTTTACTGATTACTA
9098 TTTTACTCTTTACTGATTAC--
1 TTTTACTCTTTACTGATTACTA
*
9118 TTTTACCTTTTTACTGATTACT
1 TTTTA-CTCTTTACTGATTACT
9140 CTTAGCTTAC
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.07
21 45 0.66
22 18 0.26
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.54
Consensus pattern (22 bp):
TTTTACTCTTTACTGATTACTA
Found at i:9402 original size:51 final size:54
Alignment explanation
Indices: 9346--9556 Score: 199
Period size: 54 Copynumber: 4.0 Consensus size: 54
9336 ACCAATTTTA
*
9346 CTGATTAATC-C-CTT-CTTAATTATTGATTTACTGACTACTATTACCTTGACT
1 CTGATTAATCTCTCTTACTTAATTACTGATTTACTGACTACTATTACCTTGACT
* *
9397 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTA-C----CT
1 CTGATTAATCTC-TCTTACTTAATTACTGATTTACTGACTACTATTACCTTGACT
* * * * * *
9447 -TGATTAATCTCTTTTTACTGATTTACTGATTTACCGATTACT-TTACTTTGACT
1 CTGATTAATCTC-TCTTACTTAATTACTGATTTACTGACTACTATTACCTTGACT
* * ** *
9500 TTGATTAATCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTACTTTGACT
1 CTGATTAATCTC-TCTTACTTAATTACTGATTTACTGACTACTATTACCTTGACT
9555 CT
1 CT
9557 CTTTTTACTT
Statistics
Matches: 137, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
48 3 0.02
49 39 0.28
50 2 0.01
51 10 0.07
52 1 0.01
53 2 0.01
54 41 0.30
55 39 0.28
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (54 bp):
CTGATTAATCTCTCTTACTTAATTACTGATTTACTGACTACTATTACCTTGACT
Found at i:9419 original size:55 final size:55
Alignment explanation
Indices: 9360--9556 Score: 264
Period size: 49 Copynumber: 3.7 Consensus size: 55
9350 TTAATCCCTT
* *
9360 CTTAATTATTGATTTACTGACTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
9415 CTTAATTACTGATTTACTGATTACTATTA-C----CT-TGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * * * *
9464 CTGATTTACTGATTTACCGATTACT-TTACTTTGACTTTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
9518 CTTAATTACTGATTTACTGGTTACTATTACTTTGACTCT
1 CTTAATTACTGATTTACTGATTACTATTACCTTGACTCT
9557 CTTTTTACTT
Statistics
Matches: 124, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
48 3 0.02
49 39 0.31
50 2 0.02
53 2 0.02
54 39 0.31
55 39 0.31
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.50
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:9451 original size:49 final size:49
Alignment explanation
Indices: 9398--9598 Score: 237
Period size: 54 Copynumber: 4.1 Consensus size: 49
9388 ACCTTGACTC
9398 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT
* * * *
9447 TGATTAATCTCTTTTTACTGATTTACTGATTTACCGATTACTTTACTTTGACTT
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTAC--TA--TT-ACCT
*
9501 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTA-CT
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT
* * * ** *
9549 T--TGACTCTCTTTTTACTTAATTACTGATTTTCTTTTTACTATTATCT
1 TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT
9596 TGA
1 TGA
9599 CTCTTGATCA
Statistics
Matches: 130, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
46 38 0.29
47 3 0.02
48 2 0.02
49 39 0.30
50 2 0.02
51 2 0.02
52 2 0.02
53 2 0.02
54 40 0.31
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.53
Consensus pattern (49 bp):
TGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCT
Found at i:9499 original size:103 final size:101
Alignment explanation
Indices: 9363--9578 Score: 308
Period size: 103 Copynumber: 2.1 Consensus size: 101
9353 ATCCCTTCTT
* *
9363 AATTATTGATTTACTGACTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGAT
1 AATTACTGATTTACCGACTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGAT
*
9428 TTACTGATTACTATTACCTTGATTAATCTCTTTTTACTG
66 TTACTGATTACTATTA-CTT--TGAATCTCTTTTTACTG
* * * *
9467 ATTTACTGATTTACCGATTACT-TTACTTTGACTTTGATTAATCTCTTTTTACTTAATTACTGAT
1 AATTACTGATTTACCGACTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGAT
* * *
9531 TTACTGGTTACTATTACTTTGACTCTCTTTTTACTT
66 TTACTGATTACTATTACTTTGAATCTCTTTTTACTG
9567 AATTACTGATTT
1 AATTACTGATTT
9579 TCTTTTTACT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
100 25 0.25
102 3 0.03
103 55 0.54
104 18 0.18
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.51
Consensus pattern (101 bp):
AATTACTGATTTACCGACTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTAATTACTGAT
TTACTGATTACTATTACTTTGAATCTCTTTTTACTG
Found at i:9559 original size:46 final size:46
Alignment explanation
Indices: 9508--9602 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
9498 CTTTGATTAA
9508 TCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTA-CTTTGAC
1 TCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTATC-TTGAC
* **
9554 TCTCTTTTTACTTAATTACTGATTTTCTTTTTACTATTATCTTGAC
1 TCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTATCTTGAC
9600 TCT
1 TCT
9603 TGATCATCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (46 bp):
TCTCTTTTTACTTAATTACTGATTTACTGGTTACTATTATCTTGAC
Found at i:9564 original size:23 final size:23
Alignment explanation
Indices: 9538--9602 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 23
9528 GATTTACTGG
9538 TTACTATTACTTTGACTCTCTTT
1 TTACTATTACTTTGACTCTCTTT
* *
9561 TTACTTAATTAC--TGATTTTCTTT
1 TTAC-T-ATTACTTTGACTCTCTTT
9584 TTACTATTA-TCTTGACTCT
1 TTACTATTACT-TTGACTCT
9603 TGATCATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
21 4 0.12
22 1 0.03
23 22 0.67
24 1 0.03
25 5 0.15
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.57
Consensus pattern (23 bp):
TTACTATTACTTTGACTCTCTTT
Found at i:9640 original size:71 final size:71
Alignment explanation
Indices: 9555--9701 Score: 222
Period size: 71 Copynumber: 2.1 Consensus size: 71
9545 TACTTTGACT
* * ** *
9555 CTCTTTTTACTTAATTACTGATTTTCTTTTTACTATTATCTTGACTCTTGATCATCAATTTACTG
1 CTCTTTTTAATTAATTACTGATTTACTGATTACTATTATCTTGACTCTTGATCATCAAGTTACTG
*
9620 GTTAAG
66 ATTAAG
*
9626 CTCTTTTTAATTAATTACTGATTTACTGATTACTATTATCTTGACTCTTGATCATTAAGTTACTG
1 CTCTTTTTAATTAATTACTGATTTACTGATTACTATTATCTTGACTCTTGATCATCAAGTTACTG
*
9691 ATTAAT
66 ATTAAG
9697 CTCTT
1 CTCTT
9702 GCTGATTTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (71 bp):
CTCTTTTTAATTAATTACTGATTTACTGATTACTATTATCTTGACTCTTGATCATCAAGTTACTG
ATTAAG
Found at i:10461 original size:51 final size:52
Alignment explanation
Indices: 10401--10500 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 52
10391 CTAATGGTCT
* *
10401 AAAAGTTCAAACTTTAATTC-AAAGGTGACAT-TTTATTTACCAATTACTAAA
1 AAAAATTCAAACTTTAATTCAAAAGGT-ACATCCTTATTTACCAATTACTAAA
* * * *
10452 AAAAATTCAATCTTTTATTCAAAAGGTATATCCTTATTTACTAATTACT
1 AAAAATTCAAACTTTAATTCAAAAGGTACATCCTTATTTACCAATTACT
10501 TTTTTTTCGG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 20 0.49
52 21 0.51
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (52 bp):
AAAAATTCAAACTTTAATTCAAAAGGTACATCCTTATTTACCAATTACTAAA
Done.