Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012143.1 Corchorus capsularis cultivar CVL-1 contig12164, 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: 18731
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:3021 original size:83 final size:85
Alignment explanation
Indices: 2934--3130 Score: 224
Period size: 83 Copynumber: 2.3 Consensus size: 85
2924 ATCCTACTCC
* *
2934 TTTTTTCTAATTACCATTTTC-TACCTCCT-TCTTTTACTAACTACCCTTTCCTTAC-TCT-TTT
1 TTTTTTCTGATTACCATTTTCTTA-CT-CTGTCTTTTACTAACTACCCTTTACTTACTTCTCTTT
* * *
2995 TATTGATTACCATTTTTTCTCT
64 TACTAAATACCATTTTTTCTCT
* * * * *
3017 TTTTTACTGATTACCCTTTTCTTACTCTGTTTTTTACTAATTACCCTTTACTTACTTTTTCTTTT
1 TTTTTTCTGATTACCATTTTCTTACTCTGTCTTTTACTAACTACCCTTTACTTAC-TTCTCTTTT
3082 ACTAAATACCATTTTTTCTCT
65 ACTAAATACCATTTTTTCTCT
*
3103 TTTTTTACTGAGTACCATTTT-TTACTCT
1 TTTTTT-CTGATTACCATTTTCTTACTCT
3131 TTTCTAATGA
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
82 2 0.02
83 43 0.45
84 2 0.02
85 2 0.02
86 34 0.36
87 12 0.13
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (85 bp):
TTTTTTCTGATTACCATTTTCTTACTCTGTCTTTTACTAACTACCCTTTACTTACTTCTCTTTTA
CTAAATACCATTTTTTCTCT
Found at i:3052 original size:30 final size:28
Alignment explanation
Indices: 2928--3133 Score: 163
Period size: 30 Copynumber: 7.3 Consensus size: 28
2918 TAATCTATCC
* *
2928 TACTCCTTTTTT-CTAATTACCATTTTC
1 TACTCTTTTTTTACTAATTACCATTTTT
* * * *
2955 TACCTCCTTCTTTTACTAACTACCCTTTCCT
1 TA-CT-CTTTTTTTACTAATTACCATTT-TT
* *
2986 TACTC--TTTTTATTGATTACCATTTTT
1 TACTCTTTTTTTACTAATTACCATTTTT
* *
3012 T-CTC-TTTTTTACTGATTACCCTTTTCT
1 TACTCTTTTTTTACTAATTACCATTTT-T
* *
3039 TACTCTGTTTTTTACTAATTACCCTTTACT
1 TACTCT-TTTTTTACTAATTACCATTT-TT
* *
3069 TACTTTTTCTTTTACTAAATACCATTTTT
1 TACTCTTT-TTTTACTAATTACCATTTTT
* *
3098 T-CTCTTTTTTTACTGAGTACCATTTTT
1 TACTCTTTTTTTACTAATTACCATTTTT
3125 TACTCTTTT
1 TACTCTTTT
3134 CTAATGATTA
Statistics
Matches: 144, Mismatches: 23, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.02
26 20 0.14
27 37 0.26
28 17 0.12
29 11 0.08
30 54 0.38
31 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.56
Consensus pattern (28 bp):
TACTCTTTTTTTACTAATTACCATTTTT
Found at i:3128 original size:56 final size:59
Alignment explanation
Indices: 2934--3135 Score: 163
Period size: 57 Copynumber: 3.5 Consensus size: 59
2924 ATCCTACTCC
* * ** * * *
2934 TTTTTT-CTAATTACCATTTTCTACCTCCTTCTTTTACTAACTACCCTTTCCTTACTC--
1 TTTTTTACTGATTACCATTTTTTA-CTTTTTCTTTTACTAAATACCATTTTCTTACTCTG
* * * * *
2991 -TTTTTATTGATTACCATTTTTT-C-TCTT-TTTTACTGATTACCCTTTTCTTACTCTG
1 TTTTTTACTGATTACCATTTTTTACTTTTTCTTTTACTAAATACCATTTTCTTACTCTG
* * *
3046 TTTTTTACTAATTACCCTTTACTTACTTTTTCTTTTACTAAATACCATTTT-TT-CTCT-
1 TTTTTTACTGATTACCATTT-TTTACTTTTTCTTTTACTAAATACCATTTTCTTACTCTG
*
3103 TTTTTTACTGAGTACCATTTTTTACTCTTTTCT
1 TTTTTTACTGATTACCATTTTTTACT-TTTTCT
3136 AATGATTATC
Statistics
Matches: 117, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
53 23 0.20
54 3 0.03
55 1 0.01
56 26 0.22
57 38 0.32
58 5 0.04
59 5 0.04
60 16 0.14
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.57
Consensus pattern (59 bp):
TTTTTTACTGATTACCATTTTTTACTTTTTCTTTTACTAAATACCATTTTCTTACTCTG
Found at i:3148 original size:27 final size:27
Alignment explanation
Indices: 3088--3150 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3078 TTTTACTAAA
* *
3088 TACCATTTTTTCTCTTTTTTTACTGAG
1 TACCATTTTTTCTCTTTTTCTAATGAG
*
3115 TACCATTTTTTACTC-TTTTCTAATGAT
1 TACCATTTTTT-CTCTTTTTCTAATGAG
*
3142 TATCATTTT
1 TACCATTTT
3151 CACATTACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.59
Consensus pattern (27 bp):
TACCATTTTTTCTCTTTTTCTAATGAG
Found at i:3209 original size:7 final size:7
Alignment explanation
Indices: 3199--3317 Score: 57
Period size: 7 Copynumber: 16.6 Consensus size: 7
3189 TTTTTACTGA
3199 TTACTCT
1 TTACTCT
*
3206 TTACTTT
1 TTACTCT
3213 TTAC-CATT
1 TTACTC--T
*
3221 TTACCCT
1 TTACTCT
3228 TTACT-T
1 TTACTCT
3234 ATTACTCT
1 -TTACTCT
*
3242 TTACTTT
1 TTACTCT
* *
3249 TTCCTATT
1 TTACT-CT
3257 TTACTCT
1 TTACTCT
**
3264 TTACTGA
1 TTACTCT
*
3271 TTACCCT
1 TTACTCT
3278 TTA-TGCT
1 TTACT-CT
3285 TTAC-CATT
1 TTACTC--T
3293 TTACTCT
1 TTACTCT
**
3300 TTACTGA
1 TTACTCT
3307 TTACTCT
1 TTACTCT
3314 TTAC
1 TTAC
3318 CATTTTACTA
Statistics
Matches: 84, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
6 2 0.02
7 63 0.75
8 17 0.20
9 2 0.02
ACGTcount: A:0.18, C:0.24, G:0.03, T:0.55
Consensus pattern (7 bp):
TTACTCT
Found at i:3274 original size:29 final size:29
Alignment explanation
Indices: 3199--3332 Score: 76
Period size: 29 Copynumber: 4.4 Consensus size: 29
3189 TTTTTACTGA
** * *
3199 TTACTCTTTACTTTTTACCATTTTACC-CT
1 TTACTCTTTACTGATTACTATTTT-CCATT
**
3228 TTACT-TATTACTCTTTACT-TTTTCCTATT
1 TTACTCT-TTACTGATTACTATTTTCC-ATT
3257 TTACTCTTTACTGATTACCCTTTATGCTTTACCATT
1 TTACTCTTTACTGATTA--C--TAT--TTT-CCATT
* *
3293 TTACTCTTTACTGATTACTCTTTACCATT
1 TTACTCTTTACTGATTACTATTTTCCATT
*
3322 TTACTATTTAC
1 TTACTCTTTAC
3333 CTTAATTACT
Statistics
Matches: 85, Mismatches: 8, Indels: 24
0.73 0.07 0.21
Matches are distributed among these distances:
27 2 0.02
28 5 0.06
29 44 0.52
30 3 0.04
31 1 0.01
32 2 0.02
33 1 0.01
34 2 0.02
36 23 0.27
37 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.02, T:0.54
Consensus pattern (29 bp):
TTACTCTTTACTGATTACTATTTTCCATT
Found at i:3301 original size:15 final size:15
Alignment explanation
Indices: 3283--3333 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
3273 ACCCTTTATG
3283 CTTTACCATTTTACT
1 CTTTACCATTTTACT
*
3298 CTTTA-C-TGATTACT
1 CTTTACCAT-TTTACT
3312 CTTTACCATTTTACT
1 CTTTACCATTTTACT
*
3327 ATTTACC
1 CTTTACC
3334 TTAATTACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
15 17 0.57
16 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.02, T:0.51
Consensus pattern (15 bp):
CTTTACCATTTTACT
Found at i:3332 original size:36 final size:36
Alignment explanation
Indices: 3155--3317 Score: 195
Period size: 36 Copynumber: 4.5 Consensus size: 36
3145 CATTTTCACA
* * * * * *
3155 TTACTAATTACTATTTACTCTTTCCCATTTTATTTTT
1 TTACTGATTACTCTTTACTTTTTACCATTTTA-CTCT
*
3192 TTACTGATTACTCTTTACTTTTTACCATTTTACCCT
1 TTACTGATTACTCTTTACTTTTTACCATTTTACTCT
*
3228 TTACTTATTACTCTTTACTTTTT-CCTATTTTACTCT
1 TTACTGATTACTCTTTACTTTTTACC-ATTTTACTCT
* *
3264 TTACTGATTACCCTTTA-TGCTTTACCATTTTACTCT
1 TTACTGATTACTCTTTACT-TTTTACCATTTTACTCT
3300 TTACTGATTACTCTTTAC
1 TTACTGATTACTCTTTAC
3318 CATTTTACTA
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
35 3 0.03
36 76 0.70
37 30 0.28
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (36 bp):
TTACTGATTACTCTTTACTTTTTACCATTTTACTCT
Found at i:3405 original size:40 final size:40
Alignment explanation
Indices: 3360--3440 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
3350 ATCTTTCGAC
**
3360 CTTAATTACTGATTTACTGACT-ACTTCTTTTACTTTTACT
1 CTTAATTACCAATTTACTG-CTCACTTCTTTTACTTTTACT
*
3400 CTTAATTACCAATTTACTGCTCCCTTCTTTTACTTTTACT
1 CTTAATTACCAATTTACTGCTCACTTCTTTTACTTTTACT
3440 C
1 C
3441 CATTCTACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.21, C:0.25, G:0.04, T:0.51
Consensus pattern (40 bp):
CTTAATTACCAATTTACTGCTCACTTCTTTTACTTTTACT
Found at i:3454 original size:40 final size:40
Alignment explanation
Indices: 3363--3454 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 40
3353 TTTCGACCTT
* *
3363 AATTACTGATTTACTGACTACTTCTTTTACTTTTACTCTT
1 AATTACTAATTTACTGACTACTTCTTTTACTTTTACTCTC
* *
3403 AATTACCAATTTACTG-CTCCCTTCTTTTACTTTTACTC-C
1 AATTACTAATTTACTGACT-ACTTCTTTTACTTTTACTCTC
*
3442 ATTCTACTAATTT
1 AAT-TACTAATTT
3455 CTTCTTTTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
39 4 0.09
40 40 0.91
ACGTcount: A:0.23, C:0.24, G:0.03, T:0.50
Consensus pattern (40 bp):
AATTACTAATTTACTGACTACTTCTTTTACTTTTACTCTC
Found at i:3656 original size:40 final size:39
Alignment explanation
Indices: 3518--3657 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
3508 TGCCATTTTT
* * *
3518 CTGATAACTTCTTCTACTTTCT-CTCTTAATTATCAATTTA
1 CTGATTACTT-TTTTACTTT-TACTCTTAATTACCAATTTA
* * * * *
3558 CTGATTAATTTTTTTAGTTTCACTTTTATTTACCAATTTA
1 CTGATT-ACTTTTTTACTTTTACTCTTAATTACCAATTTA
* ** *
3598 CCGATTACCCCTTTTACTTTTACTCTTAATTACCAAGTTA
1 CTGATTA-CTTTTTTACTTTTACTCTTAATTACCAATTTA
*
3638 CTGCTTACTTTTTGTACTTT
1 CTGATTACTTTTT-TACTTT
3658 CACCCCATTC
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
39 5 0.07
40 67 0.89
41 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (39 bp):
CTGATTACTTTTTTACTTTTACTCTTAATTACCAATTTA
Found at i:3689 original size:32 final size:32
Alignment explanation
Indices: 3636--3871 Score: 239
Period size: 32 Copynumber: 7.4 Consensus size: 32
3626 ATTACCAAGT
* * *
3636 TACTGCTTACTT-TTTGTACTTTCACCCCATTC
1 TACTGATTACTTCTTT-TACTTTTACTCCATTC
* * *
3668 TTCTGATTTCTTCTTTTACTTTTACTCCATTT
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
3700 TACTGATTACTTCTTTTACTCTCACTCCATTC
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
3732 TGCTGATTAC-CCTTTTTACTTTTACTCCATTC
1 TACTGATTACTTC-TTTTACTTTTACTCCATTC
*
3764 TACTGATTA-TTACTTTTAATTTTACTCCATT-
1 TACTGATTACTT-CTTTTACTTTTACTCCATTC
* * *
3795 TACTGATTACCTCTTTTACTTTTACTCTAGT-
1 TACTGATTACTTCTTTTACTTTTACTCCATTC
* *
3826 TACTGATTACTTCCTCTTACTTTTGCTCCATTC
1 TACTGATTACTT-CTTTTACTTTTACTCCATTC
* *
3859 TAATGATCACTTC
1 TACTGATTACTTC
3872 CTCTTTTCCT
Statistics
Matches: 168, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
31 37 0.22
32 117 0.70
33 14 0.08
ACGTcount: A:0.18, C:0.26, G:0.05, T:0.51
Consensus pattern (32 bp):
TACTGATTACTTCTTTTACTTTTACTCCATTC
Found at i:3710 original size:64 final size:63
Alignment explanation
Indices: 3635--3902 Score: 242
Period size: 64 Copynumber: 4.3 Consensus size: 63
3625 AATTACCAAG
* * * *
3635 TTACTGCTTACTT-TTTGTACTTTCACCCCATTCTTCTGATTTCTTCTTTTACTTTTACTCCATT
1 TTACTGATTACTTCTTT-TACTTTCACTCCATTCTACTGATTAC-TCTTTTACTTTTACTCCATT
* * *
3699 TTACTGATTACTTCTTTTACTCTCACTCCATTCTGCTGATTACCCTTTTTACTTTTACTCCATT
1 TTACTGATTACTTCTTTTACTTTCACTCCATTCTACTGATTACTC-TTTTACTTTTACTCCATT
* * * * *
3763 CTACTGATTA-TTACTTTTAATTTTACTCCATT-TACTGATTACCTCTTTTACTTTTACTCTA-G
1 TTACTGATTACTT-CTTTTACTTTCACTCCATTCTACTGATTA-CTCTTTTACTTTTACTCCATT
* ** * * ** * * *
3825 TTACTGATTACTTCCTCTTACTTTTGCTCCATTCTAATGATCACT-TCCT-CTTTTCCTTCTTT
1 TTACTGATTACTT-CTTTTACTTTCACTCCATTCTACTGATTACTCTTTTACTTTTACTCCATT
3887 TTACTGATTACTTCTT
1 TTACTGATTACTTCTT
3903 CTCTTTTTTT
Statistics
Matches: 168, Mismatches: 29, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
61 9 0.05
62 24 0.14
63 46 0.27
64 86 0.51
65 3 0.02
ACGTcount: A:0.17, C:0.26, G:0.05, T:0.52
Consensus pattern (63 bp):
TTACTGATTACTTCTTTTACTTTCACTCCATTCTACTGATTACTCTTTTACTTTTACTCCATT
Found at i:3855 original size:95 final size:96
Alignment explanation
Indices: 3652--3865 Score: 247
Period size: 95 Copynumber: 2.2 Consensus size: 96
3642 TTACTTTTTG
* * * * * *
3652 TACTTTCACCCCATTCTTCTGATTTCTTCTTTTACTTTTACTCCATTTTACTGATTACTTCTTTT
1 TACTTTTACTCCATTCTACTGATTTCTACTTTTAATTTTACTCCATTTTACTGATTACCTCTTTT
* * *
3717 ACTCTCACTCCATTCTGCTGATTACCCTTTT
66 ACTCTCACTCCAGTCTACTGATTACCCTTCT
3748 TACTTTTACTCCATTCTACTGATTAT-TACTTTTAATTTTACTCCA-TTTACTGATTACCTCTTT
1 TACTTTTACTCCATTCTACTGATT-TCTACTTTTAATTTTACTCCATTTTACTGATTACCTCTTT
* * *
3811 TACTTTTACTCTAGT-TACTGATTACTTCC-TCT
65 TACTCTCACTCCAGTCTACTGATTAC--CCTTCT
* *
3843 TACTTTTGCTCCATTCTAATGAT
1 TACTTTTACTCCATTCTACTGAT
3866 CACTTCCTCT
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
94 9 0.09
95 51 0.50
96 40 0.40
97 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.51
Consensus pattern (96 bp):
TACTTTTACTCCATTCTACTGATTTCTACTTTTAATTTTACTCCATTTTACTGATTACCTCTTTT
ACTCTCACTCCAGTCTACTGATTACCCTTCT
Found at i:4059 original size:32 final size:32
Alignment explanation
Indices: 3991--4063 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
3981 CTGATTAATC
* * *
3991 CTTTTACCTTGACTCTTAATTACTGACTTACC
1 CTTTTACTTTGACCCTTAATTACTGACTTACA
*
4023 CTTTTACTTTGACCCTTAATTACTGA-TTGCTA
1 CTTTTACTTTGACCCTTAATTACTGACTTAC-A
4055 CTTTTACTT
1 CTTTTACTT
4064 CCTCTCTTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.48
Consensus pattern (32 bp):
CTTTTACTTTGACCCTTAATTACTGACTTACA
Found at i:4137 original size:38 final size:40
Alignment explanation
Indices: 4052--4137 Score: 113
Period size: 38 Copynumber: 2.2 Consensus size: 40
4042 TTACTGATTG
* * *
4052 CTACTTTTACTTCCTCTCTTAGTTATCAATTTACTAATTA
1 CTACTTTTACTTCCTCTCTTAATTACCAATTGACTAATTA
* *
4092 ATCCTTTTACTT-C-CTCTTAATTACCAATTGACTAATTA
1 CTACTTTTACTTCCTCTCTTAATTACCAATTGACTAATTA
4130 CTACTTTT
1 CTACTTTT
4138 TATATCTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 28 0.72
39 1 0.03
40 10 0.26
ACGTcount: A:0.26, C:0.23, G:0.02, T:0.49
Consensus pattern (40 bp):
CTACTTTTACTTCCTCTCTTAATTACCAATTGACTAATTA
Done.