Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005422.1 Corchorus capsularis cultivar CVL-1 contig05440, 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: 3242
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:616 original size:23 final size:23
Alignment explanation
Indices: 590--634 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
580 AATTTGTAAA
*
590 TAGGAAAGCCAATGTGCAATAGT
1 TAGGAAAGCCAATATGCAATAGT
* *
613 TAGGGAAGCCAATATGCGATAG
1 TAGGAAAGCCAATATGCAATAG
635 CTAAGATTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (23 bp):
TAGGAAAGCCAATATGCAATAGT
Found at i:762 original size:10 final size:10
Alignment explanation
Indices: 747--779 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
737 AAAATCTTAC
747 CATTACTAGA
1 CATTACTAGA
757 CATTACTAGA
1 CATTACTAGA
767 CATTACTAGA
1 CATTACTAGA
777 CAT
1 CAT
780 CCATGTCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (10 bp):
CATTACTAGA
Found at i:1490 original size:31 final size:31
Alignment explanation
Indices: 1454--1514 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1444 AAAAGATAAT
*
1454 AATGCCATTTTAGATTATAAATGATGAAGAG
1 AATGCCATTTTAAATTATAAATGATGAAGAG
* *
1485 AATGCCTTTTTAAATTGTAAATGATGAAGA
1 AATGCCATTTTAAATTATAAATGATGAAGA
1515 TAGATGTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (31 bp):
AATGCCATTTTAAATTATAAATGATGAAGAG
Found at i:2360 original size:6 final size:6
Alignment explanation
Indices: 2350--2408 Score: 82
Period size: 6 Copynumber: 9.8 Consensus size: 6
2340 TAACAAATAT
* * *
2350 ATTATT ATTATC ATTATC ATTATC ATTATC ATTATC ATTATT ATCATC
1 ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC ATTATC
*
2398 ATTATT ATTAT
1 ATTATC ATTAT
2409 ATATATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTATC
Found at i:2365 original size:12 final size:12
Alignment explanation
Indices: 2350--2408 Score: 91
Period size: 12 Copynumber: 4.9 Consensus size: 12
2340 TAACAAATAT
2350 ATTATTATTATC
1 ATTATTATTATC
*
2362 ATTATCATTATC
1 ATTATTATTATC
*
2374 ATTATCATTATC
1 ATTATTATTATC
*
2386 ATTATTATCATC
1 ATTATTATTATC
2398 ATTATTATTAT
1 ATTATTATTAT
2409 ATATATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:2371 original size:18 final size:18
Alignment explanation
Indices: 2350--2408 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
2340 TAACAAATAT
2350 ATTATTATTATCATTATC
1 ATTATTATTATCATTATC
*
2368 ATTATCATTATCATTATC
1 ATTATTATTATCATTATC
* *
2386 ATTATTATCATCATTATT
1 ATTATTATTATCATTATC
2404 ATTAT
1 ATTAT
2409 ATATATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTATTATCATTATC
Found at i:3091 original size:33 final size:33
Alignment explanation
Indices: 3013--3230 Score: 305
Period size: 33 Copynumber: 6.6 Consensus size: 33
3003 CCGTGACGAA
* * *
3013 GCCGCCCCACTGGGACGGCTT-ACCGTGACGAA-
1 GCCGCCCCACTGGGGCGGCTTCACCATGA-AAAG
* * **
3045 GCCACCCCACTGGGACGGCTTCACCATGAGCAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
3078 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
*
3111 GCCGCCCTACTGGGGCGGCTTCACCATGAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
* * *
3144 GCCGCCCTACTAGGGCGGCTTGACCATGAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
3177 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
1 GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
*
3210 GCCGCCCCACTGGGGTGGCTT
1 GCCGCCCCACTGGGGCGGCTT
3231 AGCCAGGGTA
Statistics
Matches: 170, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
32 22 0.13
33 148 0.87
ACGTcount: A:0.20, C:0.36, G:0.31, T:0.14
Consensus pattern (33 bp):
GCCGCCCCACTGGGGCGGCTTCACCATGAAAAG
Done.