Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014062.1 Corchorus capsularis cultivar CVL-1 contig14083, 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: 5739
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42 CT
1 CT
44 TTTTAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:907 original size:25 final size:28
Alignment explanation
Indices: 860--921 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
850 TCTAAATTTG
860 TATTATTTTAATAATGGAATAA-TTAAAA
1 TATTATTTTAATAATGG-ATAATTTAAAA
888 TATT-TTTTAATAATGG-TAATTTAAAA
1 TATTATTTTAATAATGGATAATTTAAAA
914 -ATATATTT
1 TAT-TATTT
922 GAAAAAGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 5 0.16
26 7 0.23
27 15 0.48
28 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (28 bp):
TATTATTTTAATAATGGATAATTTAAAA
Found at i:1440 original size:31 final size:29
Alignment explanation
Indices: 1394--1494 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
1384 GCTTATTGCT
1394 CAAA-AAGACCCCTGAACTTACATAAAACGGC
1 CAAATAAG-CCCCTGAACTT-C-TAAAACGGC
** *
1425 CAAATAAGCCCCTGAAC-TCTAATTGCAGC
1 CAAATAAGCCCCTGAACTTCTAA-AACGGC
* *
1454 CAAATAAGCCCCTGAGCTCTCTAAAAAGGC
1 CAAATAAGCCCCTGAACT-TCTAAAACGGC
1484 CAAATAAGCCC
1 CAAATAAGCCC
1495 TTTTCTGATG
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
28 3 0.05
29 20 0.34
30 14 0.24
31 18 0.31
32 3 0.05
ACGTcount: A:0.40, C:0.31, G:0.14, T:0.16
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTCTAAAACGGC
Found at i:3362 original size:28 final size:26
Alignment explanation
Indices: 3273--3384 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 26
3263 TACCTTCTTC
* *
3273 TTTTACTAATTA-CCTTTCTTACTCT
1 TTTTACTGATTATCTTTTCTTACTCT
*
3298 TTTTACTGATTA-CTAATT-TTACTCT
1 TTTTACTGATTATCT-TTTCTTACTCT
* *
3323 ATTTACTTATTATCATTTTCTTACTCTT
1 TTTTACTGATTATC-TTTTCTTACTC-T
3351 TTTTACTGATTATCCTTTTCTTA--CT
1 TTTTACTGATTAT-CTTTTCTTACTCT
3376 TTTTACTGA
1 TTTTACTGA
3385 ATGCCATTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
25 39 0.53
26 6 0.08
27 7 0.10
28 20 0.27
29 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.58
Consensus pattern (26 bp):
TTTTACTGATTATCTTTTCTTACTCT
Found at i:3394 original size:25 final size:25
Alignment explanation
Indices: 3336--3400 Score: 62
Period size: 25 Copynumber: 2.5 Consensus size: 25
3326 TACTTATTAT
3336 CATTTTCTTACTCTTTTTTACTGATTATC
1 CATTTTCTTA--C-TTTTTACTGA-TATC
3365 C-TTTTCTTACTTTTTACTGA-ATGC
1 CATTTTCTTACTTTTTACTGATAT-C
*
3389 CATTTTTTTACT
1 CATTTTCTTACT
3401 ATTTCCTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 19 0.58
26 1 0.03
28 8 0.24
29 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.58
Consensus pattern (25 bp):
CATTTTCTTACTTTTTACTGATATC
Found at i:3426 original size:7 final size:7
Alignment explanation
Indices: 3410--3500 Score: 51
Period size: 7 Copynumber: 12.4 Consensus size: 7
3400 TATTTCCTAA
*
3410 TTACTAT
1 TTACTCT
3417 TTACTCT
1 TTACTCT
*
3424 TTACCACT
1 TTA-CTCT
*
3432 TTACTTT
1 TTACTCT
3439 TTACTAC-
1 TTACT-CT
3446 TTACTCT
1 TTACTCT
*
3453 TTACTTTT
1 TTAC-TCT
3461 TTAC-CAGT
1 TTACTC--T
3469 TTACTCTT
1 TTACTC-T
* *
3477 TTTCTTT
1 TTACTCT
3484 TTACTCT
1 TTACTCT
*
3491 TGACTCT
1 TTACTCT
3498 TTA
1 TTA
3501 TCATTTTTAC
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
6 1 0.02
7 39 0.62
8 22 0.35
9 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (7 bp):
TTACTCT
Found at i:3427 original size:14 final size:14
Alignment explanation
Indices: 3395--3457 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
3385 ATGCCATTTT
* *
3395 TTTACTATTTCCTA
1 TTTACTATTTACTC
*
3409 ATTACTATTTACTC
1 TTTACTATTTACTC
* *
3423 TTTACCACTTTACTT
1 TTTACTA-TTTACTC
*
3438 TTTACTACTTACTC
1 TTTACTATTTACTC
3452 TTTACT
1 TTTACT
3458 TTTTTACCAG
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 27 0.69
15 12 0.31
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTACTATTTACTC
Found at i:3436 original size:15 final size:15
Alignment explanation
Indices: 3416--3456 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
3406 CTAATTACTA
3416 TTTACTCTTTACCAC
1 TTTACTCTTTACCAC
* *
3431 TTTACTTTTTACTAC
1 TTTACTCTTTACCAC
3446 -TTACTCTTTAC
1 TTTACTCTTTAC
3457 TTTTTTACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTACTCTTTACCAC
Found at i:3441 original size:22 final size:21
Alignment explanation
Indices: 3410--3461 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
3400 TATTTCCTAA
*
3410 TTACTATTTACT-CTTTACCACT
1 TTACTTTTTACTAC-TTA-CACT
*
3432 TTACTTTTTACTACTTACTCT
1 TTACTTTTTACTACTTACACT
3453 TTACTTTTT
1 TTACTTTTT
3462 TACCAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 14 0.52
23 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (21 bp):
TTACTTTTTACTACTTACACT
Found at i:3472 original size:23 final size:21
Alignment explanation
Indices: 3430--3510 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 21
3420 CTCTTTACCA
*
3430 CTTTACTTTTTACTACTTACT
1 CTTTACTTTTTACCACTTACT
*
3451 CTTTACTTTTTTACCAGTTTACT
1 CTTTAC-TTTTTACCA-CTTACT
* *
3474 CTTTTTCTTTTTA-CTCTTGACT
1 C-TTTACTTTTTACCACTT-ACT
3496 CTTTATCATTTTTAC
1 CTTTA-C-TTTTTAC
3511 TTTTTACTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
21 11 0.23
22 14 0.30
23 18 0.38
24 4 0.09
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.59
Consensus pattern (21 bp):
CTTTACTTTTTACCACTTACT
Found at i:3511 original size:23 final size:21
Alignment explanation
Indices: 3416--3511 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 21
3406 CTAATTACTA
*
3416 TTTACTCTTTACCACTTTA-CTT
1 TTTACTC-TTA-CTCTTTATCTT
3438 TTTACTACTTACTCTTTA-CTTT
1 TTTACT-CTTACTCTTTATC-TT
*
3460 TTTAC-CAGTTTACTCTTTTTCTT
1 TTTACTC---TTACTCTTTATCTT
3483 TTTACTCTTGACTCTTTATCATT
1 TTTACTCTT-ACTCTTTATC-TT
3506 TTTACT
1 TTTACT
3512 TTTTACTGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 17
0.76 0.04 0.21
Matches are distributed among these distances:
20 1 0.02
21 9 0.15
22 25 0.40
23 25 0.40
24 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTACTCTTACTCTTTATCTT
Found at i:3514 original size:7 final size:7
Alignment explanation
Indices: 3431--3518 Score: 50
Period size: 7 Copynumber: 11.9 Consensus size: 7
3421 TCTTTACCAC
3431 TTTACTT
1 TTTACTT
*
3438 TTTACTA
1 TTTACTT
* *
3445 CTTACTC
1 TTTACTT
3452 TTTACTTT
1 TTTAC-TT
**
3460 TTTACCAG
1 TTTA-CTT
3468 TTTACTCT
1 TTTACT-T
*
3476 TTTTCTT
1 TTTACTT
*
3483 TTTACTC
1 TTTACTT
* *
3490 TTGACTC
1 TTTACTT
3497 TTTATCATT
1 TTTA-C-TT
3506 TTTACTT
1 TTTACTT
3513 TTTACT
1 TTTACT
3519 GATCACTATT
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
7 39 0.64
8 16 0.26
9 6 0.10
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (7 bp):
TTTACTT
Found at i:3574 original size:14 final size:14
Alignment explanation
Indices: 3555--3591 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3545 AATTACCATT
3555 TTACTCTTTACTTA
1 TTACTCTTTACTTA
* *
3569 TTACTCTTGACTTT
1 TTACTCTTTACTTA
3583 TTACTCTTT
1 TTACTCTTT
3592 TTTTCTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (14 bp):
TTACTCTTTACTTA
Found at i:3601 original size:36 final size:34
Alignment explanation
Indices: 3547--3663 Score: 117
Period size: 36 Copynumber: 3.3 Consensus size: 34
3537 TTGAATTTAA
*
3547 TTACCATTTTACTCTTTACTTATTACTCTTGACTTT
1 TTACCATTTT--TCTTTACTGATTACTCTTGACTTT
* * *
3583 TTACTCTTTTTTTCTTTACTGATTACTCTTGGCTCT
1 TTAC-C-ATTTTTCTTTACTGATTACTCTTGACTTT
* *
3619 TTACCATTTTACTTTTACTGATTACTCTTTACTTT
1 TTACCATTTTTC-TTTACTGATTACTCTTGACTTT
* *
3654 TCATCATTTT
1 TTACCATTTT
3664 ACCTTCTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
34 5 0.07
35 28 0.42
36 29 0.43
37 1 0.01
38 4 0.06
ACGTcount: A:0.17, C:0.21, G:0.04, T:0.57
Consensus pattern (34 bp):
TTACCATTTTTCTTTACTGATTACTCTTGACTTT
Found at i:3805 original size:64 final size:62
Alignment explanation
Indices: 3690--3913 Score: 229
Period size: 64 Copynumber: 3.5 Consensus size: 62
3680 CTCTTACTTG
* ** * * * *
3690 CCATTTTACTAAGCACTCCTTTTACTTTTACTCC-CTTTTACTGATTACTTCTCTTA-ATTA
1 CCATTTTACTGATTACTTCTTTTACTTTTACTCCATTTTTACTGATTACTTCTTTTACTTTA
* * **
3750 CCATTTTTCTGATTACTTCTTTTACTTTTGCTCTTTTACTCTTACTGATTACTTCTTTTACTTTT
1 CCATTTTACTGATTACTTCTTTTACTTTTACTCCATT--T-TTACTGATTACTTCTTTTAC--TT
3815 TA
61 TA
*
3817 CTC-TTTTACTGATTACTTCTTTTACTCTTACTCCATTTTTACTGATTACTTCTTTTACCTTTGC
1 C-CATTTTACTGATTACTTCTTTTACTTTTACTCCATTTTTACTGATTACTTCTTTTA-CTTT--
*
3881 T
62 A
3882 CCATTTTACTGATTACTTCTTTTACTTTTACT
1 CCATTTTACTGATTACTTCTTTTACTTTTACT
3914 GGTTCTCTTA
Statistics
Matches: 135, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
60 27 0.20
61 1 0.01
63 4 0.03
64 38 0.28
65 31 0.23
67 33 0.24
68 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.55
Consensus pattern (62 bp):
CCATTTTACTGATTACTTCTTTTACTTTTACTCCATTTTTACTGATTACTTCTTTTACTTTA
Found at i:3823 original size:15 final size:16
Alignment explanation
Indices: 3791--3907 Score: 116
Period size: 16 Copynumber: 7.3 Consensus size: 16
3781 TCTTTTACTC
3791 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
**
3807 TTACTTTTTAC-TCTT
1 TTACTGATTACTTCTT
3822 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
* *
3838 TTACT-CTTACTCCATTT
1 TTACTGATTACTTC--TT
3855 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
* *
3871 TTACCT--TTGCTCCATT
1 TTA-CTGATTACTTC-TT
3887 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
3903 TTACT
1 TTACT
3908 TTTACTGGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
15 26 0.32
16 35 0.43
17 14 0.17
18 6 0.07
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.56
Consensus pattern (16 bp):
TTACTGATTACTTCTT
Found at i:3829 original size:31 final size:33
Alignment explanation
Indices: 3750--3910 Score: 179
Period size: 33 Copynumber: 4.9 Consensus size: 33
3740 CTCTTAATTA
*
3750 CCATTTTTCTGATTACTTCTTTTACTTTTGCT-CTT
1 CCATTTTACTGATTACTTCTTTTACTTTT--TAC-T
** *
3785 TTACTCTTACTGATTACTTCTTTTACTTTTTACT
1 CCA-TTTTACTGATTACTTCTTTTACTTTTTACT
*
3819 -C-TTTTACTGATTACTTCTTTTAC-TCTTACT
1 CCATTTTACTGATTACTTCTTTTACTTTTTACT
* *
3849 CCATTTTTACTGATTACTTCTTTTAC-CTTTGCT
1 CCA-TTTTACTGATTACTTCTTTTACTTTTTACT
3882 CCATTTTACTGATTACTTCTTTTACTTTT
1 CCATTTTACTGATTACTTCTTTTACTTTT
3911 ACTGGTTCTC
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
30 6 0.06
31 22 0.20
32 22 0.20
33 31 0.28
34 2 0.02
35 2 0.02
36 24 0.22
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (33 bp):
CCATTTTACTGATTACTTCTTTTACTTTTTACT
Found at i:3894 original size:32 final size:32
Alignment explanation
Indices: 3791--3913 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 32
3781 TCTTTTACTC
3791 TTACTGATTACTTCTTTTACTTTTTACT-C-TT
1 TTACTGATTACTTCTTTTAC-TTTTACTCCATT
*
3822 TTACTGATTACTTCTTTTACTCTTACTCCATTT
1 TTACTGATTACTTCTTTTACTTTTACTCCA-TT
* *
3855 TTACTGATTACTTCTTTTACCTTTGCTCCATT
1 TTACTGATTACTTCTTTTACTTTTACTCCATT
3887 TTACTGATTACTTCTTTTACTTTTACT
1 TTACTGATTACTTCTTTTACTTTTACT
3914 GGTTCTCTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
30 6 0.07
31 21 0.25
32 27 0.33
33 29 0.35
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (32 bp):
TTACTGATTACTTCTTTTACTTTTACTCCATT
Done.