Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010043.1 Corchorus capsularis cultivar CVL-1 contig10064, 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: 32835
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1029 original size:14 final size:13
Alignment explanation
Indices: 985--1032 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
975 CTAACTTAAG
*
985 AAAATACTGACAT
1 AAAATACTAACAT
* *
998 AAAATACCAAAAT
1 AAAATACTAACAT
1011 GAAAATACTAACAT
1 -AAAATACTAACAT
1025 AAAA-ACTA
1 AAAATACTA
1033 CGGCTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 4 0.14
13 14 0.48
14 11 0.38
ACGTcount: A:0.62, C:0.15, G:0.04, T:0.19
Consensus pattern (13 bp):
AAAATACTAACAT
Found at i:9724 original size:28 final size:27
Alignment explanation
Indices: 9654--9723 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
9644 GCTAAGGGGG
*
9654 CAAAACGTCCCAAAATTGAGTTCAGGGA
1 CAAAACAT-CCAAAATTGAGTTCAGGGA
* **
9682 CACAATGTCCAAAATTGAAGTTCAGGGAA
1 CAAAACATCCAAAATTG-AGTTCAGGG-A
9711 CAAAACATCCAAA
1 CAAAACATCCAAA
9724 TGCTACAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 9 0.26
28 15 0.43
29 11 0.31
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
CAAAACATCCAAAATTGAGTTCAGGGA
Found at i:10585 original size:2 final size:2
Alignment explanation
Indices: 10578--10604 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10568 TTACTCTTAC
10578 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 A
10605 GTTATAATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11738 original size:6 final size:6
Alignment explanation
Indices: 11727--11756 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
11717 TAGCGATCCT
11727 CGTTCC CGTTCC CGTTCC CGTTCC CGTTCC
1 CGTTCC CGTTCC CGTTCC CGTTCC CGTTCC
11757 ACGACCCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
CGTTCC
Found at i:12356 original size:11 final size:11
Alignment explanation
Indices: 12332--12366 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12322 TTGACAGCGC
12332 AACAAAAACAA
1 AACAAAAACAA
* *
12343 AACGAAAACGA
1 AACAAAAACAA
12354 AACAAAAACAA
1 AACAAAAACAA
12365 AA
1 AA
12367 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:25543 original size:21 final size:21
Alignment explanation
Indices: 25513--25554 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
25503 ATTAATTTGA
*
25513 TTAATCAATTACGTATAATTT
1 TTAATAAATTACGTATAATTT
25534 TTAATAAATTACGTATAATTT
1 TTAATAAATTACGTATAATTT
25555 GATGCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (21 bp):
TTAATAAATTACGTATAATTT
Found at i:27155 original size:30 final size:30
Alignment explanation
Indices: 27121--27182 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
27111 ATGGATTAAA
27121 TTCAGTACTTATGAA-ATTCAGTG-TTAAAAT
1 TTCAGTACTTA--AATATTCAGTGCTTAAAAT
* *
27151 TTCAGTGCTTAAATTTTCAGTGCTTAAAAT
1 TTCAGTACTTAAATATTCAGTGCTTAAAAT
27181 TT
1 TT
27183 TTAGTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.07
29 7 0.25
30 19 0.68
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (30 bp):
TTCAGTACTTAAATATTCAGTGCTTAAAAT
Found at i:27156 original size:14 final size:15
Alignment explanation
Indices: 27137--27182 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
27127 ACTTATGAAA
27137 TTCAGTG-TTAAAAT
1 TTCAGTGCTTAAAAT
*
27151 TTCAGTGCTTAAATT
1 TTCAGTGCTTAAAAT
27166 TTCAGTGCTTAAAAT
1 TTCAGTGCTTAAAAT
27181 TT
1 TT
27183 TTAGTTTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (15 bp):
TTCAGTGCTTAAAAT
Found at i:31313 original size:31 final size:31
Alignment explanation
Indices: 31278--31342 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
31268 AACTGAACAA
31278 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
31309 ACTCAAACATCCAAGATCTAAAGATCTGGAG
1 ACTCAAACATCCAAGATCTAAAGATCTGGAG
31340 ACT
1 ACT
31343 GATAACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (31 bp):
ACTCAAACATCCAAGATCTAAAGATCTGGAG
Found at i:32780 original size:2 final size:2
Alignment explanation
Indices: 32773--32830 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
32763 TCCGTAGCAG
32773 TA TA TA TA 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
32815 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
32831 CGTAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.