Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015391.1 Corchorus capsularis cultivar CVL-1 contig15412, 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: 65120
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:65 original size:26 final size:27
Alignment explanation
Indices: 12--65 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
2 TTACTCAACT
**
12 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
39 AAAAAGCTCTATTTTTA-TTTAAT-TAA
1 AAAAA-CTCTATTTTTATTTTAATGTAA
65 A
1 A
66 TATAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:5927 original size:114 final size:109
Alignment explanation
Indices: 5695--5969 Score: 419
Period size: 109 Copynumber: 2.5 Consensus size: 109
5685 ACTATTATAG
* *
5695 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
* *
5760 TATTTTTACCAAAAAATTTGGATATACTAAAAGTTTTTCTAATATACAA
61 TACTTTTACCAAAAAAATTGGATATACTAAAAGTTTTTCTAATATACAA
5809 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTACTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTACTT
* *
5874 TTACCAAAAAAATTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAAATTGGATATACTAAAAGTTTTTCTAATATACAA
*
5918 TTTTATTTTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATAT-TTTATA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTTTATA
5970 TGATTTTTTT
Statistics
Matches: 153, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
108 7 0.05
109 120 0.78
110 3 0.02
111 2 0.01
114 21 0.14
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTACTT
TTACCAAAAAAATTGGATATACTAAAAGTTTTTCTAATATACAA
Found at i:7233 original size:9 final size:9
Alignment explanation
Indices: 7219--7244 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
7209 AGATCTGAAA
7219 AAAAAAAAT
1 AAAAAAAAT
7228 AAAAAAAAT
1 AAAAAAAAT
7237 AAAAAAAA
1 AAAAAAAA
7245 AAGAAAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:10538 original size:3 final size:3
Alignment explanation
Indices: 10532--10573 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
10522 AAATTAAAAA
*
10532 AAT AAT AAT AAT AA- AAT ATT AAAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
10574 TATTACAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.12
3 28 0.82
4 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10609 original size:22 final size:21
Alignment explanation
Indices: 10582--10638 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
10572 TATATTACAG
*
10582 TATTTATTTATAAAAAACATTT
1 TATTTATTTATAAAAAA-ATTC
10604 TATTTATTTATATTAAAAAATTC
1 TATTTATTTATA--AAAAAATTC
10627 T-TTTATTTATAA
1 TATTTATTTATAA
10639 TTTTCTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.03
22 22 0.69
23 4 0.12
24 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTATTTATAAAAAAATTC
Found at i:10611 original size:26 final size:26
Alignment explanation
Indices: 10582--10636 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
10572 TATATTACAG
10582 TATTTAT-TTATAAAAA-ACATTTTATT
1 TATTTATATTA-AAAAATAC-TTTTATT
*
10608 TATTTATATTAAAAAATTCTTTTATT
1 TATTTATATTAAAAAATACTTTTATT
10634 TAT
1 TAT
10637 AATTTTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTTATATTAAAAAATACTTTTATT
Found at i:11033 original size:29 final size:31
Alignment explanation
Indices: 10990--11049 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
10980 AAATTAATTA
10990 TTTTTATG--AATATATTTATTCCATATGTT
1 TTTTTATGAAAATATATTTATTCCATATGTT
*
11019 TTTTTTTGAAAATATATTTATTCCATATGTT
1 TTTTTATGAAAATATATTTATTCCATATGTT
11050 AATTAAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
31 21 0.75
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.58
Consensus pattern (31 bp):
TTTTTATGAAAATATATTTATTCCATATGTT
Found at i:12984 original size:18 final size:19
Alignment explanation
Indices: 12937--12984 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
12927 AGATTAAACA
*
12937 TGATTTC-CCACATGTATT
1 TGATTTCACCACATGTACT
12955 TGATGGTTCACCACATG-ACT
1 TGAT--TTCACCACATGTACT
12975 TGATTTCACC
1 TGATTTCACC
12985 TTGATGAGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.38
20 9 0.35
21 7 0.27
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (19 bp):
TGATTTCACCACATGTACT
Found at i:13592 original size:12 final size:12
Alignment explanation
Indices: 13575--13599 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13565 AGAGCCTCTG
13575 TAATTGTGTTAA
1 TAATTGTGTTAA
13587 TAATTGTGTTAA
1 TAATTGTGTTAA
13599 T
1 T
13600 CTATTCGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TAATTGTGTTAA
Found at i:13819 original size:2 final size:2
Alignment explanation
Indices: 13812--13839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13802 AATACGTGTG
13812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13840 GTTTGGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14702 original size:29 final size:30
Alignment explanation
Indices: 14666--14746 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
14656 TCTCGTTTTT
14666 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
*
14695 AAAAGTTAAGGGGTCAATTTGTCCCAAAATG
1 AAAAGTTAAGGGGCCAATTTGTCCCAAAA-G
* * *
14726 GATAGTTAAGGGGCTAATTTG
1 AAAAGTTAAGGGGCCAATTTG
14747 GGTATTAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
29 28 0.62
31 17 0.38
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (30 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAAAG
Found at i:23222 original size:31 final size:32
Alignment explanation
Indices: 23157--23222 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
23147 AAATGTGATA
*
23157 TCCAAAAGCATACCTGCCAACCCCTAAACCTAT
1 TCCAAAAGCATACCTGCCAA-CCCTAAACATAT
23190 TCCAAAAGCATACCTGCCAA-CCTAAACATAT
1 TCCAAAAGCATACCTGCCAACCCTAAACATAT
23221 TC
1 TC
23223 ACTTCATCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 12 0.38
33 20 0.62
ACGTcount: A:0.38, C:0.36, G:0.06, T:0.20
Consensus pattern (32 bp):
TCCAAAAGCATACCTGCCAACCCTAAACATAT
Found at i:33371 original size:31 final size:31
Alignment explanation
Indices: 33335--33500 Score: 157
Period size: 31 Copynumber: 5.5 Consensus size: 31
33325 CTTGGCTAAT
*
33335 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
* * **
33366 TGCTCAAATAAGGGCCTGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
33395 TGGC-CAAATAAGGGCCTAA-CGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATC-TTTGCCAAAA
* ** **
33426 TACTCAAATAAGGGCCCCATCTTTG--AATT
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
*
33455 TGAC-CAAATAAGGGCCTAATATTTGCCAAAA
1 TG-CTCAAATAAGGGCCTAATCTTTGCCAAAA
33486 TGCTCAAATAAGGGC
1 TGCTCAAATAAGGGC
33501 ATGTCTCATG
Statistics
Matches: 105, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.01
29 41 0.39
30 5 0.05
31 57 0.54
32 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
Found at i:33406 original size:60 final size:60
Alignment explanation
Indices: 33339--33500 Score: 261
Period size: 60 Copynumber: 2.7 Consensus size: 60
33329 GCTAATTGCT
** * *
33339 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
* *
33399 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGCCCCATCTTTGAATTTGAC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
*
33459 CAAATAAGGGCCTAATATTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGC
33501 ATGTCTCATG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTGAATTTGAC
Found at i:33574 original size:31 final size:31
Alignment explanation
Indices: 33533--33699 Score: 173
Period size: 31 Copynumber: 5.5 Consensus size: 31
33523 TAACACCAGA
*
33533 CCCTTATTTGAACATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
* *
33564 TCTTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
*
33595 CCCTTATTTGAGCATTTTAGATAACGTTAGG
1 CCCTTATTTGAGCATTTTCGATAACGTTAGG
** * *
33626 CCCTTATTTG-GCCAAATT--A-AAAGATCAGG
1 CCCTTATTTGAG-CATTTTCGATAACG-TTAGG
* * *
33655 TCCTTATTTGAGCATTTT-GACAAACATTAGG
1 CCCTTATTTGAGCATTTTCGA-TAACGTTAGG
33686 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
33700 ATTAGCCTTA
Statistics
Matches: 113, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.03
29 18 0.16
30 3 0.03
31 87 0.77
32 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (31 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGG
Found at i:37627 original size:110 final size:105
Alignment explanation
Indices: 37432--37800 Score: 525
Period size: 110 Copynumber: 3.5 Consensus size: 105
37422 AATTTTTCTA
* ** * * *
37432 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
*
37495 TTTCTAAAACCTTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
* *
37535 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTAAAATTAGTTTTGTGTAGTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAG--TT-T-T-GTA
37600 TTTTATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
61 TTTTATTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
37645 ACCCTTAAAAT-AAAA-AAAA--TTAATTTGGGGCTAAACTTTAGTGAAATTAGTTTTGTATTTT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAAC-TTAGTGAAATTAGTTTTGTATTTT
* *
37706 ATTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 ATTTCTAAAACCCTATAACAAT--ATTATTAATTATGGAATTT
37749 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
37801 AGGCTAAACT
Statistics
Matches: 239, Mismatches: 13, Indels: 24
0.87 0.05 0.09
Matches are distributed among these distances:
102 29 0.12
103 28 0.12
104 42 0.18
105 11 0.05
106 20 0.08
107 26 0.11
108 21 0.09
109 5 0.02
110 57 0.24
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
Found at i:39952 original size:36 final size:36
Alignment explanation
Indices: 39912--39985 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
39902 TTTTATTCAC
39912 CTTAATTCAATGTTGTTAAAAGACATTATTATTATG
1 CTTAATTCAATGTTGTTAAAAGACATTATTATTATG
39948 CTTAATTCAATGTTGTTAAAAGACATTATTATTATG
1 CTTAATTCAATGTTGTTAAAAGACATTATTATTATG
39984 CT
1 CT
39986 AAGTAGGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (36 bp):
CTTAATTCAATGTTGTTAAAAGACATTATTATTATG
Found at i:40023 original size:47 final size:45
Alignment explanation
Indices: 39953--40047 Score: 138
Period size: 47 Copynumber: 2.1 Consensus size: 45
39943 TTATGCTTAA
*
39953 TTCAATGTTGTTAAAAGACATTATTAT-TATGCTAAGTAGGAACCTGG
1 TTCAATGTTGTTAAAAGACATTATTATGT-T--AAAGTAGGAACCTGG
*
40000 TTCAATGTTGTTAAAAGATATTATTATGTTAAAGTAGGAACCTGG
1 TTCAATGTTGTTAAAAGACATTATTATGTTAAAGTAGGAACCTGG
40045 TTC
1 TTC
40048 TTTTCTAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 17 0.38
47 27 0.60
48 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (45 bp):
TTCAATGTTGTTAAAAGACATTATTATGTTAAAGTAGGAACCTGG
Found at i:40786 original size:31 final size:31
Alignment explanation
Indices: 40730--40808 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
40720 TTGCCGCCAT
* *
40730 GATCAATTTGGGATA-AACGTTTCAGAAAAC
1 GATCATTTTAGGATATAACGTTTCAGAAAAC
* *
40760 GATCATTTTAGGATATAATGTTTCAGACAAC
1 GATCATTTTAGGATATAACGTTTCAGAAAAC
*
40791 GATCATTTCAGGATATAA
1 GATCATTTTAGGATATAA
40809 AGATATGCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 13 0.30
31 30 0.70
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (31 bp):
GATCATTTTAGGATATAACGTTTCAGAAAAC
Found at i:48536 original size:2 final size:2
Alignment explanation
Indices: 48531--48558 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48521 TGTGTGTGTG
48531 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
48559 ATAAAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51689 original size:2 final size:2
Alignment explanation
Indices: 51676--51722 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
51666 TCATTTTGTT
*
51676 TA TA TA TG TA TA 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 TA TA TA
51718 TA TA T
1 TA TA T
51723 TACAATTTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Done.