Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014795.1 Corchorus capsularis cultivar CVL-1 contig14816, 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: 26337
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Found at i:2967 original size:27 final size:27
Alignment explanation
Indices: 2929--3001 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
2919 TACTTTTTTC
* **
2929 TTTTACTAAATACCATTTTTTTGTCTT
1 TTTTACTGAATACCATTTTTTACTCTT
2956 TTTTACTGAATACCATTTTTTACTCTT
1 TTTTACTGAATACCATTTTTTACTCTT
* * *
2983 TTCTGCTGATTACCATTTT
1 TTTTACTGAATACCATTTT
3002 CACTTTACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.56
Consensus pattern (27 bp):
TTTTACTGAATACCATTTTTTACTCTT
Found at i:3015 original size:21 final size:21
Alignment explanation
Indices: 2991--3030 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2981 TTTTCTGCTG
*
2991 ATTACCATTTTCACTTTACTA
1 ATTACCATTTACACTTTACTA
* *
3012 ATTACTATTTACTCTTTAC
1 ATTACCATTTACACTTTAC
3031 CATTTTACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTACCATTTACACTTTACTA
Found at i:3029 original size:7 final size:7
Alignment explanation
Indices: 3013--3313 Score: 98
Period size: 7 Copynumber: 41.7 Consensus size: 7
3003 ACTTTACTAA
*
3013 TTACTAT
1 TTACTCT
3020 TTACTCT
1 TTACTCT
3027 TTAC-CATT
1 TTACTC--T
*
3035 TTACTTT
1 TTACTCT
**
3042 TTACTGA
1 TTACTCT
3049 TTACTCT
1 TTACTCT
3056 TTACT-T
1 TTACTCT
3062 CTTAC-CATT
1 -TTACTC--T
*
3071 TTACCCT
1 TTACTCT
**
3078 TTACTGA
1 TTACTCT
3085 TTACTCT
1 TTACTCT
*
3092 TTACTTT
1 TTACTCT
3099 TTAC-CATT
1 TTACTC--T
*
3107 TTTCTCT
1 TTACTCT
**
3114 TTACTGA
1 TTACTCT
3121 TTACTCT
1 TTACTCT
*
3128 TTACTTT
1 TTACTCT
3135 TTAC-CATT
1 TTACTC--T
3143 TTACTCT
1 TTACTCT
**
3150 TTACTGA
1 TTACTCT
3157 TTACTCT
1 TTACTCT
3164 TTACTCT
1 TTACTCT
3171 TTAC-CATT
1 TTACTC--T
3179 TTACTCT
1 TTACTCT
**
3186 TTACTGA
1 TTACTCT
*
3193 TTACTCC
1 TTACTCT
**
3200 TTGTTCT
1 TTACTCT
3207 TTAC-CATT
1 TTACTC--T
3215 TTACTCT
1 TTACTCT
* **
3222 TTATTGA
1 TTACTCT
3229 TTACTCT
1 TTACTCT
3236 TTAC-CATT
1 TTACTC--T
*
3244 TTACTATT
1 TTACT-CT
3252 TTACTCT
1 TTACTCT
**
3259 TTACTGA
1 TTACTCT
*
3266 TTACTCC
1 TTACTCT
**
3273 TTGTTCT
1 TTACTCT
3280 TTAC-CATT
1 TTACTC--T
*
3288 TTACTAT
1 TTACTCT
**
3295 TTACTGA
1 TTACTCT
3302 TTACTCT
1 TTACTCT
3309 TTACT
1 TTACT
3314 TTCTTACCAT
Statistics
Matches: 211, Mismatches: 56, Indels: 54
0.66 0.17 0.17
Matches are distributed among these distances:
6 6 0.03
7 155 0.73
8 44 0.21
9 6 0.03
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:3052 original size:36 final size:36
Alignment explanation
Indices: 2992--3333 Score: 465
Period size: 36 Copynumber: 9.5 Consensus size: 36
2982 TTTCTGCTGA
* * *
2992 TTACCATTTT-CACTTTACTAATTACTATTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
*
3027 TTACCATTTTACTTTTTACTGATTACTCTTTACT-T
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
* *
3062 CTTACCATTTTACCCTTTACTGATTACTCTTTACTTT
1 -TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
* *
3099 TTACCATTTTTCTCTTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
3135 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
* **
3171 TTACCATTTTACTCTTTACTGATTACTCCTTGTTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
*
3207 TTACCATTTTACTCTTTATTGATTACTCTTTAC-CATT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTC--T
* * **
3244 TTACTATTTTACTCTTTACTGATTACTCCTTGTTCT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
* *
3280 TTACCATTTTACTATTTACTGATTACTCTTTACTTT
1 TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
3316 CTTACCATTTTACTCTTT
1 -TTACCATTTTACTCTTT
3334 TTAACTTAAT
Statistics
Matches: 271, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
35 12 0.04
36 212 0.78
37 46 0.17
38 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (36 bp):
TTACCATTTTACTCTTTACTGATTACTCTTTACTCT
Found at i:3181 original size:29 final size:29
Alignment explanation
Indices: 3149--3263 Score: 70
Period size: 29 Copynumber: 3.7 Consensus size: 29
3139 CATTTTACTC
3149 TTTACTGATTACTCTTTACTCTTTACCATTTTACT
1 TTTACTGATTACTCTTTACTCTTTACC-----A-T
* **
3184 CTTTACTGATTACTCCTTGTTCTTTACCAT
1 -TTTACTGATTACTCTTTACTCTTTACCAT
** * **
3214 TTTACTCTTTATTGATTACTCTTTACCAT
1 TTTACTGATTACTCTTTACTCTTTACCAT
3243 TTTACT-ATTTTACTCTTTACT
1 TTTACTGA--TTACTCTTTACT
3264 GATTACTCCT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
29 28 0.44
30 10 0.16
31 1 0.02
36 24 0.38
ACGTcount: A:0.19, C:0.23, G:0.03, T:0.55
Consensus pattern (29 bp):
TTTACTGATTACTCTTTACTCTTTACCAT
Found at i:3224 original size:15 final size:15
Alignment explanation
Indices: 3204--3248 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3194 TACTCCTTGT
3204 TCTTTACCATTTTAC
1 TCTTTACCATTTTAC
3219 TCTTT---ATTGATTAC
1 TCTTTACCATT--TTAC
3233 TCTTTACCATTTTAC
1 TCTTTACCATTTTAC
3248 T
1 T
3249 ATTTTACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 3 0.12
14 9 0.36
15 10 0.40
17 3 0.12
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (15 bp):
TCTTTACCATTTTAC
Found at i:3262 original size:44 final size:43
Alignment explanation
Indices: 3214--3313 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 43
3204 TCTTTACCAT
* *
3214 TTTACTCTTTATTGATTACTCTTTACCATTTTACTATTTTACTC
1 TTTACTCTTTACTCATTACTCTTTACCATTTTACTA-TTTACTC
** * ** *
3258 TTTACTGATTACTCCTTGTTCTTTACCATTTTACTATTTACTG
1 TTTACTCTTTACTCATTACTCTTTACCATTTTACTATTTACTC
*
3301 ATTACTCTTTACT
1 TTTACTCTTTACT
3314 TTCTTACCAT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 16 0.36
44 29 0.64
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (43 bp):
TTTACTCTTTACTCATTACTCTTTACCATTTTACTATTTACTC
Found at i:3412 original size:40 final size:40
Alignment explanation
Indices: 3357--3445 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
3347 TAAATACCAT
* *
3357 CTTTTGAC-CTTAATTACTGATATACTGACT-ACTTCTTTTG
1 CTTTT-ACTCTTAATTACTAATATACTG-CTCACTTCTTTTA
* *
3397 CTTTTACTCTTAATTACTAATTTACTGCTCCCTTCTTTTA
1 CTTTTACTCTTAATTACTAATATACTGCTCACTTCTTTTA
3437 CTTTTACTC
1 CTTTTACTC
3446 CATTCTACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 4 0.09
40 39 0.91
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.51
Consensus pattern (40 bp):
CTTTTACTCTTAATTACTAATATACTGCTCACTTCTTTTA
Found at i:3529 original size:32 final size:32
Alignment explanation
Indices: 3486--3687 Score: 185
Period size: 32 Copynumber: 6.6 Consensus size: 32
3476 TCTTAATTAA
*
3486 CCATT-TACTGATTACTTCTTTTACTCTTACT
1 CCATTCTACTGATTACTTCTTTTACTTTTACT
*
3517 CCATTCTGCTGATTA---C---T--TTTTA-T
1 CCATTCTACTGATTACTTCTTTTACTTTTACT
* * *
3540 CAATTCTATTGATTACTTATTTTACTTTTACT
1 CCATTCTACTGATTACTTCTTTTACTTTTACT
3572 CCATTCTACTGATTA-TATCTTTTACTTTTACT
1 CCATTCTACTGATTACT-TCTTTTACTTTTACT
* * * * *
3604 CAATTCTATTGATTATTTCGTCTTACTTTTGCT
1 CCATTCTACTGATTACTTC-TTTTACTTTTACT
* *
3637 CCATT-TACTGATTACTTCCTCTTACTTTCACT
1 CCATTCTACTGATTACTT-CTTTTACTTTTACT
3669 CCATTCTACTGATTACTTC
1 CCATTCTACTGATTACTTC
3688 CTCTTTTACT
Statistics
Matches: 138, Mismatches: 18, Indels: 29
0.75 0.10 0.16
Matches are distributed among these distances:
23 13 0.09
24 4 0.03
26 1 0.01
29 2 0.01
31 11 0.08
32 78 0.57
33 29 0.21
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.51
Consensus pattern (32 bp):
CCATTCTACTGATTACTTCTTTTACTTTTACT
Found at i:3597 original size:64 final size:64
Alignment explanation
Indices: 3529--3692 Score: 190
Period size: 65 Copynumber: 2.5 Consensus size: 64
3519 ATTCTGCTGA
*
3529 TTACTTTTTA-TCAATTCTATTGATTACTT-ATTTTACTTTTACTCCATTCTACTGATTATATCT
1 TTAC-TTTTACTCAATTCTATTGATTACTTCATCTTACTTTTACTCCATT-TACTGATTATATCT
3592 T
64 T
* * *
3593 TTACTTTTACTCAATTCTATTGATTATTTCGTCTTACTTTTGCTCCATTTACTGATTACT-TCCT
1 TTACTTTTACTCAATTCTATTGATTACTTCATCTTACTTTTACTCCATTTACTGATTA-TAT-CT
*
3657 C
64 T
* * * *
3658 TTACTTTCACTCCATTCTACTGATTACTTCCTCTT
1 TTACTTTTACTCAATTCTATTGATTACTTCATCTT
3693 TTACTTCTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 5 0.06
64 32 0.37
65 49 0.57
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (64 bp):
TTACTTTTACTCAATTCTATTGATTACTTCATCTTACTTTTACTCCATTTACTGATTATATCTT
Found at i:8576 original size:70 final size:70
Alignment explanation
Indices: 8447--8625 Score: 243
Period size: 70 Copynumber: 2.6 Consensus size: 70
8437 GCTTGGATGG
* * * *
8447 AACTGACTCGTATGGAAACGAGATTGGCTTGTGGAAAATCCCCTAAATGCTTGGATGGAACCAAA
1 AACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCCTGGATGGAACCAAA
8512 GCTTA
66 GCTTA
* * *
8517 AACT-ACCTTGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGAATGCCTGGGTGGAACCAA
1 AACTCA-CTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCCTGGATGGAACCAA
*
8581 AGCTTG
65 AGCTTA
* * *
8587 AACTCACTCATATGGAAATGAGTTTGACTTGTGGAAAAG
1 AACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAG
8626 TCGAAGCATT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
69 1 0.01
70 94 0.98
71 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (70 bp):
AACTCACTCGTATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTAAATGCCTGGATGGAACCAAA
GCTTA
Found at i:16704 original size:31 final size:33
Alignment explanation
Indices: 16669--16731 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 33
16659 GCAATTTGTG
* *
16669 AGAGCAAGGCCGATTGGAGG-AG-AAGTCGACT
1 AGAGCAAAGCCGATTAGAGGAAGCAAGTCGACT
*
16700 AGAGCAAAGTCGATTAGAGGAAGCAAGTCGAC
1 AGAGCAAAGCCGATTAGAGGAAGCAAGTCGAC
16732 AAGGAAGTCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 17 0.63
32 2 0.07
33 8 0.30
ACGTcount: A:0.37, C:0.16, G:0.35, T:0.13
Consensus pattern (33 bp):
AGAGCAAAGCCGATTAGAGGAAGCAAGTCGACT
Found at i:17786 original size:24 final size:23
Alignment explanation
Indices: 17759--17805 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
17749 AGTTATTTAG
17759 TTTATGCTT-TATCTTTAATTTTTC
1 TTTAT-CTTATATCTTT-ATTTTTC
*
17783 TTTATCTTATGTCTTTATTTTTC
1 TTTATCTTATATCTTTATTTTTC
17806 AAGTTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68
Consensus pattern (23 bp):
TTTATCTTATATCTTTATTTTTC
Found at i:21119 original size:7 final size:7
Alignment explanation
Indices: 21103--21153 Score: 61
Period size: 7 Copynumber: 7.3 Consensus size: 7
21093 TTAGGCTGAG
21103 TTTT-TT
1 TTTTCTT
21109 TTTTCTT
1 TTTTCTT
21116 TTTTCTT
1 TTTTCTT
21123 TTTTCTT
1 TTTTCTT
21130 CTTCTT-TT
1 -TT-TTCTT
*
21138 TTTTCCT
1 TTTTCTT
21145 TTTTCTT
1 TTTTCTT
21152 TT
1 TT
21154 CTTTGAGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 6 0.15
7 27 0.69
8 4 0.10
9 2 0.05
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:21142 original size:22 final size:21
Alignment explanation
Indices: 21114--21157 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
21104 TTTTTTTTTC
*
21114 TTTTTTCTTTTTTCTTCTTCTT
1 TTTTTTCCTTTTTCTT-TTCTT
21136 TTTTTTCCTTTTTCTTTTCTT
1 TTTTTTCCTTTTTCTTTTCTT
21157 T
1 T
21158 GAGTTGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTCCTTTTTCTTTTCTT
Found at i:21862 original size:15 final size:14
Alignment explanation
Indices: 21812--21865 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
21802 ACTCAAAAAC
21812 TTTTTTGAAAAC-T
1 TTTTTTGAAAACAT
* *
21825 CATTTTTGAAAACCT
1 -TTTTTTGAAAACAT
*
21840 TTTCTTGAAAACAAT
1 TTTTTTGAAAAC-AT
21855 TTTTTTGAAAA
1 TTTTTTGAAAA
21866 ATGTCTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (14 bp):
TTTTTTGAAAACAT
Done.