Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014512.1 Corchorus capsularis cultivar CVL-1 contig14533, 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: 12826
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3885 original size:22 final size:22
Alignment explanation
Indices: 3860--3904 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3850 TAAAGGATTA
3860 AATAGGATACTCCTATTTGCCC
1 AATAGGATACTCCTATTTGCCC
3882 AATAGGATACTCCTATTTGCCC
1 AATAGGATACTCCTATTTGCCC
3904 A
1 A
3905 CTAGCAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (22 bp):
AATAGGATACTCCTATTTGCCC
Found at i:3920 original size:21 final size:22
Alignment explanation
Indices: 3860--3920 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
3850 TAAAGGATTA
*
3860 AATAGGATACTCCTATTTGCCC
1 AATAGCATACTCCTATTTGCCC
*
3882 AATAGGATACTCCTATTTGCCC
1 AATAGCATACTCCTATTTGCCC
* *
3904 ACTAGCA-ACTCCAATTT
1 AATAGCATACTCCTATTT
3921 CATTATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 9 0.25
22 27 0.75
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (22 bp):
AATAGCATACTCCTATTTGCCC
Found at i:3959 original size:14 final size:14
Alignment explanation
Indices: 3922--3959 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3912 CTCCAATTTC
* *
3922 ATTATTATTTTGTT
1 ATTATTAATTTATT
3936 ATTATT-ATTTATT
1 ATTATTAATTTATT
3949 ATTATTAATTT
1 ATTATTAATTT
3960 CTTGAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
ATTATTAATTTATT
Found at i:4004 original size:3 final size:3
Alignment explanation
Indices: 3996--4056 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
3986 CCTTCTCCTC
*
3996 TAT TAT TAT TAT TAT T-T ATAC TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
4042 TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT
4057 ATACTCATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 1 0.02
3 48 0.94
4 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5507 original size:2 final size:2
Alignment explanation
Indices: 5500--5541 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
5490 CAAAAGGGCA
* *
5500 AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5541 A
1 A
5542 GTTGAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9471 original size:2 final size:2
Alignment explanation
Indices: 9464--9491 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9454 CTCCATGAGA
9464 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
9492 GTGTATGTAT
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:11972 original size:2 final size:2
Alignment explanation
Indices: 11967--12017 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
11957 TTTTTTTCTT
11967 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12009 TC TC TC TC T
1 TC TC TC TC T
12018 TTTCGTAGGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.