Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011658.1 Corchorus capsularis cultivar CVL-1 contig11679, 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: 22489
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3617 original size:25 final size:27
Alignment explanation
Indices: 3589--3657 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 27
3579 ATATAAATAA
3589 TATAATATAATTAAATAATT-AT-ATT
1 TATAATATAATTAAATAATTAATAATT
* *
3614 TAT-ACATAATATATATAATTGAATAATT
1 TATAATATAAT-TAAATAATT-AATAATT
3642 TATAAGTATATATTAA
1 TATAA-TATA-ATTAA
3658 TTAGAACTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
24 6 0.18
25 11 0.33
27 2 0.06
28 6 0.18
29 1 0.03
30 5 0.15
31 2 0.06
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (27 bp):
TATAATATAATTAAATAATTAATAATT
Found at i:9142 original size:11 final size:10
Alignment explanation
Indices: 9107--9149 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
9097 CAAGCGATCC
9107 CAAAAAAAAA
1 CAAAAAAAAA
*
9117 AAAAAAAAAA
1 CAAAAAAAAA
*
9127 AAAAAAAAAA
1 CAAAAAAAAA
*
9137 CGAAAAATAAA
1 C-AAAAAAAAA
9148 CA
1 CA
9150 CAAAGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.88, C:0.07, G:0.02, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:9143 original size:1 final size:1
Alignment explanation
Indices: 9108--9136 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
9098 AAGCGATCCC
9108 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9137 CGAAAAATAA
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:11581 original size:25 final size:24
Alignment explanation
Indices: 11525--11590 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
11515 TTAAAGTCAC
* *
11525 TTTTAAATAAAGCATGAGTATACT
1 TTTTAAATACAGCATAAGTATACT
** *
11549 AATAAATATACAGCATAAGTATACT
1 TTTTAA-ATACAGCATAAGTATACT
11574 TTTT-AATACAGCATAAG
1 TTTTAAATACAGCATAAG
11591 AAGTTACAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
23 12 0.36
24 4 0.12
25 17 0.52
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (24 bp):
TTTTAAATACAGCATAAGTATACT
Found at i:15099 original size:20 final size:21
Alignment explanation
Indices: 15074--15123 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
15064 GAATCAATCT
*
15074 ACATGATTTG-GGACACGGTA
1 ACATGATTTGCGGACACGGCA
15094 ACATGATTTGCGGACACGGCA
1 ACATGATTTGCGGACACGGCA
15115 ACATGATTT
1 ACATGATTT
15124 TCGGCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
ACATGATTTGCGGACACGGCA
Found at i:15180 original size:30 final size:30
Alignment explanation
Indices: 15140--15196 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
15130 TCAATCTTGG
* *
15140 ATCCTGCTGTAAACAAACTGTTGACTTTGA
1 ATCCTACTGTAAACAAACAGTTGACTTTGA
* *
15170 ATCCTACTGTAAATACACAGTTGACTT
1 ATCCTACTGTAAACAAACAGTTGACTT
15197 ATTTCATCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (30 bp):
ATCCTACTGTAAACAAACAGTTGACTTTGA
Found at i:18850 original size:72 final size:72
Alignment explanation
Indices: 18731--18868 Score: 195
Period size: 72 Copynumber: 1.9 Consensus size: 72
18721 CACTCTGCGG
* * **
18731 GATATCCAATGATCTCATAACATTGATCTTTTGTATGTCCCGTCTTTTGACAATGACCACACCTT
1 GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCACCTTTTGACAATGACCACACCTT
18796 GCAGCAA
66 GCAGCAA
* * * **
18803 GATATCCAATGATCTCATAGCATTGGTCTTTCGTGTGCCCCACCTTTTGACAATGTTCACACCTT
1 GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCACCTTTTGACAATGACCACACCTT
18868 G
66 G
18869 ACTTGTCTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (72 bp):
GATATCCAATGATCTCATAACATTGATCTTTCGTATGCCCCACCTTTTGACAATGACCACACCTT
GCAGCAA
Found at i:19918 original size:21 final size:21
Alignment explanation
Indices: 19876--19923 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
19866 ATCAATCTAT
*
19876 ATGATTTGCGGACACCGTAAC
1 ATGATTTGCGGACACCGCAAC
**
19897 ATGATTTGCGGACATGGCAAC
1 ATGATTTGCGGACACCGCAAC
19918 ATGATT
1 ATGATT
19924 GTCGGCTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (21 bp):
ATGATTTGCGGACACCGCAAC
Found at i:20151 original size:2 final size:2
Alignment explanation
Indices: 20144--20179 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20134 ACATACATAC
20144 AT AT AT AT 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 AT AT AT AT
20180 GGGGAAGGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21823 original size:3 final size:3
Alignment explanation
Indices: 21815--21849 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21805 GTGTTACTTA
21815 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21850 ATGAGATAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:22405 original size:2 final size:2
Alignment explanation
Indices: 22398--22428 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22388 GCAATGTGGG
22398 AT 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 AT A
22429 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22433 original size:2 final size:2
Alignment explanation
Indices: 22428--22482 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
22418 ATATATATAT
22428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22470 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
22483 AGAAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.