Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007634.1 Corchorus capsularis cultivar CVL-1 contig07655, 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: 8863
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Found at i:1405 original size:28 final size:27
Alignment explanation
Indices: 1374--1442 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1364 ACTAAAAGTT
*
1374 ACCAAAATGTCCCTGAACGTGCAA-AATG
1 ACCAAAATGCCCCT-AA-GTGCAAGAATG
* *
1402 ACCAAAATGCCCCTTAGTGTAAGAATG
1 ACCAAAATGCCCCTAAGTGCAAGAATG
*
1429 ACCAAAATACCCCT
1 ACCAAAATGCCCCT
1443 GGACGACCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 5 0.14
27 18 0.50
28 13 0.36
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (27 bp):
ACCAAAATGCCCCTAAGTGCAAGAATG
Found at i:3251 original size:105 final size:104
Alignment explanation
Indices: 3159--3354 Score: 242
Period size: 104 Copynumber: 1.9 Consensus size: 104
3149 AATTATTCTA
* * *
3159 CCATGCACATG-T-TAGAAAAAC-TTTTGAACCCAA-TTT-TCTCTAAAACCTTTTGAGAAAAAC
1 CCATGCACATGATCT-GAAAAACTTTTTGAAACCAATTTTATCCCAAAAACC-TTTGAGAAAAA-
* *
3219 CCTTATTCTTTTGCAAAAATAATTTTTA-TTTTTTAAAATAG
63 CATTATTCTTTTGCAAAAACAATTTTTATTTTTTTAAAATAG
* *
3260 GCATGCACTTGCATCTGAAAAACTTTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACA
1 CCATGCACATG-ATCTGAAAAACTTTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACA
*
3325 TTTTTCTTTTGCAAAAACAATTTTTATTTT
65 TTATTCTTTTGCAAAAACAATTTTTATTTT
3355 AGAAACAATT
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
101 9 0.11
103 8 0.10
104 37 0.46
105 17 0.21
106 9 0.11
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (104 bp):
CCATGCACATGATCTGAAAAACTTTTTGAAACCAATTTTATCCCAAAAACCTTTGAGAAAAACAT
TATTCTTTTGCAAAAACAATTTTTATTTTTTTAAAATAG
Found at i:3859 original size:18 final size:18
Alignment explanation
Indices: 3824--3861 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3814 TAGGCCAAGG
*
3824 TTTTTCTTTTCTTCTTCT
1 TTTTTCTTTTCCTCTTCT
3842 TTTTTCTTCTTCCT-TTCT
1 TTTTTCTT-TTCCTCTTCT
3860 TT
1 TT
3862 GAGTTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTCTTTTCCTCTTCT
Found at i:4479 original size:28 final size:28
Alignment explanation
Indices: 4426--4478 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4416 AAAAACTCAT
* *
4426 AAACCTTTTTTTGAAAACTCATTTTTAA
1 AAACCTTTTCTTGAAAACTAATTTTTAA
4454 AAACCTTTTCTTGAAAA-TAATTTTT
1 AAACCTTTTCTTGAAAACTAATTTTT
4479 TGAAAGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (28 bp):
AAACCTTTTCTTGAAAACTAATTTTTAA
Found at i:5668 original size:42 final size:42
Alignment explanation
Indices: 5600--5698 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
5590 TACAAGTGAG
** *
5600 TGCATGATGGATGCATGGGCACATATACCAATGAAA-GGACAA
1 TGCATGATGGATGCATGAACACATATA-CAAAGAAATGGACAA
* *
5642 TGCATGATCGATGCATGAACATATATACAAAGAAATGGACAA
1 TGCATGATGGATGCATGAACACATATACAAAGAAATGGACAA
5684 TGCATGATGGATGCA
1 TGCATGATGGATGCA
5699 CCATATGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.21
Consensus pattern (42 bp):
TGCATGATGGATGCATGAACACATATACAAAGAAATGGACAA
Found at i:7236 original size:21 final size:21
Alignment explanation
Indices: 7212--7278 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
7202 TTTTACTGAA
7212 TTACTGATTACCATTACTATT
1 TTACTGATTACCATTACTATT
* *
7233 TTACTGATTATTCTTTACT-TT
1 TTACTGATTA-CCATTACTATT
* * *
7254 GTACTGATTACTAGTTACCATT
1 TTACTGATTACCA-TTACTATT
7276 TTA
1 TTA
7279 TTCTTTGCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (21 bp):
TTACTGATTACCATTACTATT
Found at i:7428 original size:34 final size:34
Alignment explanation
Indices: 7302--7428 Score: 139
Period size: 34 Copynumber: 3.6 Consensus size: 34
7292 GCCATTACTT
* * *
7302 TTTACTGGTTAATATTTTATTCTTTACCATTTTTTC
1 TTTACTGATTACT-TTTTACTCTTTACCA-TTTTTC
* *
7338 TTTACTGGATTACTTTTTACTCTTCACCATTCTTC
1 TTTACT-GATTACTTTTTACTCTTTACCATTTTTC
** *
7373 TTTACTGACTT-CCCTTCACTCTTTACCATTTTTC
1 TTTACTGA-TTACTTTTTACTCTTTACCATTTTTC
7407 TTTACTGATTACTTTTTACTCT
1 TTTACTGATTACTTTTTACTCT
7429 GCTCTTTACC
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.03
34 36 0.48
35 13 0.17
36 19 0.25
37 5 0.07
ACGTcount: A:0.17, C:0.23, G:0.05, T:0.55
Consensus pattern (34 bp):
TTTACTGATTACTTTTTACTCTTTACCATTTTTC
Found at i:7458 original size:47 final size:47
Alignment explanation
Indices: 7390--7714 Score: 519
Period size: 47 Copynumber: 6.9 Consensus size: 47
7380 ACTTCCCTTC
* * * *
7390 ACTCTTTACCA-TTTTTCTTTACTGATTACT-TTTTACTCTGCTCTTT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCT-CTTTACTCTGT
* *
7436 ACCCCTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
7483 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
*
7530 ACTCTTTATCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
*
7577 ACCCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
7624 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
1 ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
7671 ACTCTTTACCATTTTTTTTCTTTACTGATTAACTCTTCTACTTT
1 ACTCTTTACCA--TTTTTTCTTTACTGATT-ACTCTTCT-CTTT
7715 TTACTGATTA
Statistics
Matches: 261, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
46 9 0.03
47 220 0.84
48 3 0.01
49 17 0.07
50 8 0.03
51 4 0.02
ACGTcount: A:0.15, C:0.26, G:0.04, T:0.55
Consensus pattern (47 bp):
ACTCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGT
Found at i:7487 original size:14 final size:12
Alignment explanation
Indices: 7462--7679 Score: 53
Period size: 12 Copynumber: 18.3 Consensus size: 12
7452 TCTTTACTGA
7462 TTACTCTTCTCT
1 TTACTCTTCTCT
7474 TTACTCTGTACTCT
1 TTACTCT-T-CTCT
7488 TTAC-CATT-T-T
1 TTACTC-TTCTCT
**
7498 TT-CT-TTACTGA
1 TTACTCTT-CTCT
7509 TTACTCTTCTCT
1 TTACTCTTCTCT
7521 TTACTCTGTACTCT
1 TTACTCT-T-CTCT
7535 TTA-TCATT-T-T
1 TTACTC-TTCTCT
**
7545 TT-CT-TTACTGA
1 TTACTCTT-CTCT
7556 TTACTCTTCTCT
1 TTACTCTTCTCT
*
7568 TTACTCTGTACCCT
1 TTACTCT-T-CTCT
7582 TTAC-CATT-T-T
1 TTACTC-TTCTCT
**
7592 TT-CT-TTACTGA
1 TTACTCTT-CTCT
7603 TTACTCTTCTCT
1 TTACTCTTCTCT
7615 TTACTCTGTACTCT
1 TTACTCT-T-CTCT
7629 TTAC-CATT-T-T
1 TTACTC-TTCTCT
**
7639 TT-CT-TTACTGA
1 TTACTCTT-CTCT
7650 TTACTCTTCTCT
1 TTACTCTTCTCT
7662 TTACTCTGTACTCT
1 TTACTCT-T-CTCT
7676 TTAC
1 TTAC
7680 CATTTTTTTT
Statistics
Matches: 154, Mismatches: 14, Indels: 74
0.64 0.06 0.31
Matches are distributed among these distances:
8 8 0.05
9 3 0.02
10 17 0.11
11 11 0.07
12 51 0.33
13 22 0.14
14 42 0.27
ACGTcount: A:0.15, C:0.26, G:0.04, T:0.55
Consensus pattern (12 bp):
TTACTCTTCTCT
Found at i:7746 original size:22 final size:23
Alignment explanation
Indices: 7691--7906 Score: 144
Period size: 22 Copynumber: 9.9 Consensus size: 23
7681 ATTTTTTTTC
*
7691 TTTACTGATTAACTC-TTCTACT-T
1 TTTACTGATT-AC-CATTTTACTCT
7714 TTTACTGATTACCATTTTACTCT
1 TTTACTGATTACCATTTTACTCT
* *
7737 TTT-CTAATTACTATTTTTAC-CT
1 TTTACTGATTACCA-TTTTACTCT
7759 TTTACTGATTACC-TTTGTACT-T
1 TTTACTGATTACCATTT-TACTCT
*
7781 TTTACTGATTACCA--TTGCT-T
1 TTTACTGATTACCATTTTACTCT
* * *
7801 CTTACTGATCA-C-TATTACTC-
1 TTTACTGATTACCATTTTACTCT
* *
7821 TTTACTGACTACTC-TTTTA--AT
1 TTTACTGATTAC-CATTTTACTCT
*
7842 TTTCCATGATTACCATTTTACTC-
1 TTTAC-TGATTACCATTTTACTCT
* *
7865 TTTACTAATTACCATTTTAC-CC
1 TTTACTGATTACCATTTTACTCT
7887 TTTACTGATTACC-TTTTACT
1 TTTACTGATTACCATTTTACT
7907 TTTGACCATT
Statistics
Matches: 154, Mismatches: 20, Indels: 39
0.72 0.09 0.18
Matches are distributed among these distances:
19 1 0.01
20 25 0.16
21 17 0.11
22 80 0.52
23 31 0.20
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.51
Consensus pattern (23 bp):
TTTACTGATTACCATTTTACTCT
Done.