Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010699.1 Corchorus capsularis cultivar CVL-1 contig10720, 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: 115850
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:390 original size:2 final size:2
Alignment explanation
Indices: 383--409 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
373 TTAACAATCC
383 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
410 TAATATGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:683 original size:3 final size:3
Alignment explanation
Indices: 670--703 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
660 AAATAAAGTA
670 TAT TA- TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
704 AACAACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:689 original size:14 final size:13
Alignment explanation
Indices: 670--704 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
660 AAATAAAGTA
670 TATTATATTATTAT
1 TATTATATT-TTAT
684 TATTATTATTTTAT
1 TATTA-TATTTTAT
698 TATTATA
1 TATTATA
705 ACAACAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 14 0.70
15 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATATTTTAT
Found at i:692 original size:17 final size:17
Alignment explanation
Indices: 670--703 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
660 AAATAAAGTA
670 TATTATATTATTATTAT
1 TATTATATTATTATTAT
*
687 TATTATTTTATTATTAT
1 TATTATATTATTATTAT
704 AACAACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:3651 original size:3 final size:3
Alignment explanation
Indices: 3638--3668 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
3628 TTAAACCAAC
3638 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3669 GATATTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5432 original size:21 final size:21
Alignment explanation
Indices: 5406--5449 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5396 GGTAGCTGAA
5406 TTGTTAA-ATATCGCCCCATTT
1 TTGTTAATA-ATCGCCCCATTT
*
5427 TTGTTATTAATCGCCCCATTT
1 TTGTTAATAATCGCCCCATTT
5448 TT
1 TT
5450 TACGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (21 bp):
TTGTTAATAATCGCCCCATTT
Found at i:5709 original size:21 final size:19
Alignment explanation
Indices: 5679--5720 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
5669 GGCGGCTCGG
*
5679 TTATTTTTTTTAAATAAATAA
1 TTATTATTTTTAAA-AAA-AA
5700 TTATTATTTTTAAAAAAAA
1 TTATTATTTTTAAAAAAAA
5719 TT
1 TT
5721 TAGTCTAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTATTTTTAAAAAAAA
Found at i:16457 original size:29 final size:29
Alignment explanation
Indices: 16416--16478 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
16406 TTTAATCGAA
16416 TAAAA-ATAGAGTTTTAGTAGAATAATTG
1 TAAAAGATAGAGTTTTAGTAGAATAATTG
16444 TAAAAGATAGAGTTTTAGTAGAATAATTG
1 TAAAAGATAGAGTTTTAGTAGAATAATTG
16473 TAAAAG
1 TAAAAG
16479 TTTATTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (29 bp):
TAAAAGATAGAGTTTTAGTAGAATAATTG
Found at i:16497 original size:25 final size:26
Alignment explanation
Indices: 16468--16517 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
16458 TTAGTAGAAT
**
16468 AATTGTAAAAGTTTAT-TTTTAAAAA
1 AATTGTAAAAGAATATATTTTAAAAA
16493 AATTGTAAAAGAATATATTTTAAAA
1 AATTGTAAAAGAATATATTTTAAAA
16518 GTTCTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
AATTGTAAAAGAATATATTTTAAAAA
Found at i:16981 original size:12 final size:12
Alignment explanation
Indices: 16964--16988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16954 TATAGATATA
16964 TAGCTACTAATT
1 TAGCTACTAATT
16976 TAGCTACTAATT
1 TAGCTACTAATT
16988 T
1 T
16989 TCTAGCTGAG
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:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TAGCTACTAATT
Found at i:21414 original size:15 final size:15
Alignment explanation
Indices: 21394--21424 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
21384 CCCCATGGCT
21394 CATGGCAACCAAGTC
1 CATGGCAACCAAGTC
*
21409 CATGGCAACTAAGTC
1 CATGGCAACCAAGTC
21424 C
1 C
21425 CACATGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.16
Consensus pattern (15 bp):
CATGGCAACCAAGTC
Found at i:21414 original size:22 final size:23
Alignment explanation
Indices: 21369--21414 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
21359 ATATGCCATA
21369 TCATGGCAACCAAGTCCCCATGGC
1 TCATGGCAACCAAGT-CCCATGGC
21393 TCATGGCAACCAAGT-CCATGGC
1 TCATGGCAACCAAGTCCCATGGC
21415 AACTAAGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (23 bp):
TCATGGCAACCAAGTCCCATGGC
Found at i:30094 original size:2 final size:2
Alignment explanation
Indices: 30087--30114 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30077 AATTATAAGT
30087 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
30115 AGGGTTAAAT
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:31037 original size:1 final size:1
Alignment explanation
Indices: 31031--31059 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
31021 ACTCTTCGGC
31031 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31060 CAATCGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:44625 original size:2 final size:2
Alignment explanation
Indices: 44618--44646 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44608 GACGAGGAAC
44618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44647 ATAATTACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45887 original size:66 final size:69
Alignment explanation
Indices: 45807--46035 Score: 268
Period size: 78 Copynumber: 3.2 Consensus size: 69
45797 TTGTTTAGGT
* *
45807 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATAT-A-AT-TTATAATTA
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAATTA
45868 TTTTA
65 TTTTA
45873 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTAT-A--A
45938 TTATATTTTACCA
62 -T-TATTTT---A
* * *
45951 TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAATTA
*
46016 TTATA
65 TTTTA
*
46021 TTTTACAATTTTACT
1 TTTTACTATTTTACT
46036 ATTTTAGTTA
Statistics
Matches: 143, Mismatches: 7, Indels: 22
0.83 0.04 0.13
Matches are distributed among these distances:
66 44 0.31
67 3 0.02
68 2 0.01
70 19 0.13
71 1 0.01
73 6 0.04
74 1 0.01
75 7 0.05
77 1 0.01
78 59 0.41
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (69 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAATTAT
TTTA
Found at i:45956 original size:78 final size:78
Alignment explanation
Indices: 45872--46041 Score: 313
Period size: 78 Copynumber: 2.2 Consensus size: 78
45862 TAATTATTTT
*
45872 ATTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
1 ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
*
45937 ATTATATTTTACC
66 ATTATATTTTACA
*
45950 ATTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
1 ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
46015 ATTATATTTTACA
66 ATTATATTTTACA
46028 ATTTTACTATTTTA
1 ATTTTACTATTTTA
46042 GTTAAAAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.49
Consensus pattern (78 bp):
ATTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
ATTATATTTTACA
Found at i:47710 original size:15 final size:15
Alignment explanation
Indices: 47676--47710 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
47666 TGCTCTTAAT
*
47676 ATTTCTTCTTCTTCT
1 ATTTCTTCTTCTTCC
*
47691 TTTTCTTCTTCTTCC
1 ATTTCTTCTTCTTCC
47706 ATTTC
1 ATTTC
47711 CTTCAACATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTCTTCTTCTTCC
Found at i:56922 original size:8 final size:8
Alignment explanation
Indices: 56909--56934 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
56899 CATTTTCTGG
56909 AATCATGA
1 AATCATGA
56917 AATCATGA
1 AATCATGA
56925 AATCATGA
1 AATCATGA
56933 AA
1 AA
56935 ATAATAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AATCATGA
Found at i:61235 original size:11 final size:10
Alignment explanation
Indices: 61208--61234 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
61198 TTACAAAAAC
61208 AAAAAAACAA
1 AAAAAAACAA
61218 AAAAAAACAA
1 AAAAAAACAA
61228 AAAAAAA
1 AAAAAAA
61235 AGAGGAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:65741 original size:2 final size:2
Alignment explanation
Indices: 65734--65768 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
65724 TATTTTATTT
*
65734 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
65769 GATTCTCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:86116 original size:14 final size:14
Alignment explanation
Indices: 86097--86134 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
86087 ATTTCCCAGC
86097 TTGGTCCCATGACT
1 TTGGTCCCATGACT
86111 TTGGTCCCATGACT
1 TTGGTCCCATGACT
86125 TTGGTCCCAT
1 TTGGTCCCAT
86135 TTCACTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.21, T:0.37
Consensus pattern (14 bp):
TTGGTCCCATGACT
Found at i:86909 original size:26 final size:27
Alignment explanation
Indices: 86855--86911 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
86845 GACCCAAACC
*
86855 TTTAAGTAAAGGGACTAAATTGATCATT
1 TTTAAGTAAAGGGACCAAATTGA-CATT
**
86883 TTTAAGTAGGGGGACCAAATTGA-ATT
1 TTTAAGTAAAGGGACCAAATTGACATT
86909 TTT
1 TTT
86912 CTTGTAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
28 20 0.77
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (27 bp):
TTTAAGTAAAGGGACCAAATTGACATT
Found at i:91643 original size:12 final size:12
Alignment explanation
Indices: 91628--91663 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
91618 CAGATTCAGA
91628 TTCAGACTCACT
1 TTCAGACTCACT
*
91640 TTCAGACTCGCT
1 TTCAGACTCACT
*
91652 TTCTGACTCACT
1 TTCAGACTCACT
91664 ACTTCCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.11, T:0.36
Consensus pattern (12 bp):
TTCAGACTCACT
Found at i:108083 original size:2 final size:2
Alignment explanation
Indices: 108076--108103 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
108066 TATGAGAAAA
108076 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
108104 TAATTGTCAT
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:108664 original size:3 final size:3
Alignment explanation
Indices: 108658--108682 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
108648 GTTTATTATA
108658 AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT A
108683 TATATAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:115627 original size:14 final size:15
Alignment explanation
Indices: 115598--115641 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
115588 TGTCCAACTT
*
115598 TTTACACTTTTGCCC
1 TTTACACTTTTACCC
115613 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
115627 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
115642 ACTGAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:115738 original size:32 final size:33
Alignment explanation
Indices: 115680--115765 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
115670 CCACGGCGGA
115680 GCCTCCCCACTGGGGCGGCTTCACCATGGGCAG
1 GCCTCCCCACTGGGGCGGCTTCACCATGGGCAG
115713 GCCTCCCCACTGGGGC-GCTTCACCATGGGCAG
1 GCCTCCCCACTGGGGCGGCTTCACCATGGGCAG
*
115745 GCC-GCCCACTGGGGCGGCTTC
1 GCCTCCCCACTGGGGCGGCTTC
115766 GCTAAGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 11 0.22
32 24 0.47
33 16 0.31
ACGTcount: A:0.10, C:0.41, G:0.34, T:0.15
Consensus pattern (33 bp):
GCCTCCCCACTGGGGCGGCTTCACCATGGGCAG
Found at i:115756 original size:31 final size:32
Alignment explanation
Indices: 115685--115782 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 32
115675 GCGGAGCCTC
*
115685 CCCACTGGGGCGGCTTCACCATGGGCAGGCCTC
1 CCCACTGGGGCGGCTTCACCATGGGCAGGCC-G
115718 CCCACTGGGGC-GCTTCACCATGGGCAGGCCG
1 CCCACTGGGGCGGCTTCACCATGGGCAGGCCG
* * *
115749 CCCACTGGGGCGGCTTCGCTA-AGGCAGGCCG
1 CCCACTGGGGCGGCTTCACCATGGGCAGGCCG
115780 CCC
1 CCC
115783 TGGTGGGGCG
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
31 23 0.38
32 26 0.43
33 11 0.18
ACGTcount: A:0.12, C:0.40, G:0.35, T:0.13
Consensus pattern (32 bp):
CCCACTGGGGCGGCTTCACCATGGGCAGGCCG
Done.