Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010743.1 Corchorus capsularis cultivar CVL-1 contig10764, 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: 6873
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3242 original size:107 final size:107
Alignment explanation
Indices: 3055--3319 Score: 408
Period size: 107 Copynumber: 2.5 Consensus size: 107
3045 AATTTTTCTA
* **
3055 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
* *
3118 TTTCTAAAACCTTATAACAATAAATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
* * *
3160 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
*
3225 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
** *
3267 AAGCTTAAAATAAAAATAAAATTTCAATTTGGGGCTAAACTTAGTGAAATTAA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
3320 GACTAAACTT
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
105 27 0.19
106 15 0.10
107 103 0.71
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTA
TTTCTAAAACCCTATAACAATAAATTATTAATTATGAAATTT
Found at i:3516 original size:72 final size:68
Alignment explanation
Indices: 3431--3586 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 68
3421 TTATTTAGGT
* * *
3431 TTTTA-TAGTTTTACTTAACTAAAAACTCTATTTTTATTTTTAATTAAATATAATATCTTTATAA
1 TTTTACTA-TTTTACTAAACTAAAAACTCTATTTTTA--TATAATTAAATATAATATCCTTATAA
*
3495 CTATTTTA
63 C--TTATA
* *
3503 TTTTACTATTTTACTAAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATTACTT
1 TTTTACTATTTTACTAAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTT
3568 ATA
66 ATA
*
3571 TTTTACCATTTTACTA
1 TTTTACTATTTTACTA
3587 TTTTAATTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
68 19 0.25
70 23 0.30
72 32 0.42
73 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.52
Consensus pattern (68 bp):
TTTTACTATTTTACTAAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTT
ATA
Found at i:3599 original size:72 final size:72
Alignment explanation
Indices: 3445--3588 Score: 188
Period size: 70 Copynumber: 2.0 Consensus size: 72
3435 ATAGTTTTAC
* * * *
3445 TTAACTAAAAACTCTATTTTTATTTTTAATTAAATATAATATCTTTATAACTATTTTATTTTACT
1 TTAACTAAAAACTCTATTTTTA-TTATAATTAAATATAATATCCTTATAAC-ATTATATTTTACC
3510 ATTTTACTA
64 ATTTTACTA
* *
3519 --AACTAAAAACTCTATTTTTA-TATAATTAAATCTAATATCCTTATTAC-TTATATTTTACCAT
1 TTAACTAAAAACTCTATTTTTATTATAATTAAATATAATATCCTTATAACATTATATTTTACCAT
3580 TTTACTA
66 TTTACTA
3587 TT
1 TT
3589 TTAATTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
68 19 0.31
70 23 0.37
72 20 0.32
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (72 bp):
TTAACTAAAAACTCTATTTTTATTATAATTAAATATAATATCCTTATAACATTATATTTTACCAT
TTTACTA
Found at i:4757 original size:6 final size:6
Alignment explanation
Indices: 4729--4767 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
4719 ACTCATTAAA
*
4729 AAAAAG AAAAA- AAAAGG AGAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAAG AAAAAG AAA
4768 GGAACAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 20 0.69
7 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5454 original size:38 final size:38
Alignment explanation
Indices: 5403--5480 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5393 AATCCCTAAA
5403 AACAAACACCGTGTGGAGACTAAGGCCATTTGAAGCAC
1 AACAAACACCGTGTGGAGACTAAGGCCATTTGAAGCAC
5441 AACAAACACCGTGTGGAGACTAAGGCCATTTGAAGCAC
1 AACAAACACCGTGTGGAGACTAAGGCCATTTGAAGCAC
5479 AA
1 AA
5481 GAGTGGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (38 bp):
AACAAACACCGTGTGGAGACTAAGGCCATTTGAAGCAC
Found at i:6175 original size:20 final size:20
Alignment explanation
Indices: 6146--6195 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
6136 TTTTTTAATA
* *
6146 ATTTATTTAGA-TTATTTGAG
1 ATTTAATTAGACTTAATT-AG
*
6166 ATTTGATTAGACTTAATTAG
1 ATTTAATTAGACTTAATTAG
6186 ATTTAATTAG
1 ATTTAATTAG
6196 GCTCTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (20 bp):
ATTTAATTAGACTTAATTAG
Done.