Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011145.1 Corchorus capsularis cultivar CVL-1 contig11166, 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: 30183
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:540 original size:23 final size:23
Alignment explanation
Indices: 495--539 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
485 TAGAAAAACT
495 CTCTCACAAAGAAGTTCCAAAAA
1 CTCTCACAAAGAAGTTCCAAAAA
* *
518 CTCTCACTAAGGAG-TCCAAAAA
1 CTCTCACAAAGAAGTTCCAAAAA
540 AAAACAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.18
Consensus pattern (23 bp):
CTCTCACAAAGAAGTTCCAAAAA
Found at i:2552 original size:20 final size:20
Alignment explanation
Indices: 2529--2566 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2519 TAAATATACC
2529 AAAAAGTACCCAAAAGAAAA
1 AAAAAGTACCCAAAAGAAAA
2549 AAAAAGTACCCAAAAGAA
1 AAAAAGTACCCAAAAGAA
2567 TGAGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.16, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAAAGTACCCAAAAGAAAA
Found at i:7051 original size:6 final size:6
Alignment explanation
Indices: 7040--7065 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7030 GAGTGGCACT
7040 AATTAA AATTAA AATTAA AATTAA AA
1 AATTAA AATTAA AATTAA AATTAA AA
7066 ATAAGAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATTAA
Found at i:14003 original size:2 final size:2
Alignment explanation
Indices: 13996--14031 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13986 ATTAGCACAG
13996 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14032 GTGTACTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17358 original size:2 final size:2
Alignment explanation
Indices: 17351--17378 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17341 GCAACAAACC
17351 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
17379 GTGGAAGATA
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:17595 original size:19 final size:19
Alignment explanation
Indices: 17568--17606 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17558 TCCTATCCTA
17568 ATTTCCTTACTACATATAT
1 ATTTCCTTACTACATATAT
* *
17587 ATTTTCTTACTATATATAT
1 ATTTCCTTACTACATATAT
17606 A
1 A
17607 GAAAGGGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTTCCTTACTACATATAT
Found at i:18743 original size:2 final size:2
Alignment explanation
Indices: 18736--18764 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18726 ATATAAGTAC
18736 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
18765 CACACACACA
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:20873 original size:47 final size:47
Alignment explanation
Indices: 20804--20893 Score: 146
Period size: 47 Copynumber: 1.9 Consensus size: 47
20794 TTAAACAGCA
*
20804 AATATCAATGGGACAAGTCTTTCTAAG-TAAAAGATTTTCTTTAAGCT
1 AATATCAACGGGACAAGTCTTTCTAAGTTAAAAG-TTTTCTTTAAGCT
*
20851 AATATCAACGGGACAAGTCTTTCTAAGTTAAATGTTTTCTTTA
1 AATATCAACGGGACAAGTCTTTCTAAGTTAAAAGTTTTCTTTA
20894 GACGGTCAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
47 35 0.88
48 5 0.12
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (47 bp):
AATATCAACGGGACAAGTCTTTCTAAGTTAAAAGTTTTCTTTAAGCT
Found at i:26208 original size:5 final size:6
Alignment explanation
Indices: 26191--26218 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
26181 AGGGATTTAT
26191 ACAAAA ACAAAA ACAAAA ACAAAA ACAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAA
26219 CAAGGAAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Done.