Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017619.1 Corchorus olitorius cultivar O-4 contig17652, 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: 33481
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5078 original size:13 final size:13
Alignment explanation
Indices: 5060--5084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5050 TTTTTACCAC
5060 CTTAAAATTATTG
1 CTTAAAATTATTG
5073 CTTAAAATTATT
1 CTTAAAATTATT
5085 TTTTGGCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:9583 original size:2 final size:2
Alignment explanation
Indices: 9576--9609 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9566 GTGTAGATTA
9576 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 A
9610 GTAGCAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10230 original size:2 final size:2
Alignment explanation
Indices: 10225--10255 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10215 TCATGCTTCC
10225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10256 GATTTGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13384 original size:6 final size:6
Alignment explanation
Indices: 13373--13403 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
13363 TATATATCAA
13373 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT T
1 TGGGAT TGGGAT TGGGAT TGGGAT TGGGAT T
13404 TCAACTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
TGGGAT
Found at i:24454 original size:42 final size:44
Alignment explanation
Indices: 24403--24497 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
24393 AGTGCATTAC
* * *
24403 CTAA-ATTCTACT-T-CATCTCTGGGTAATTTATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
24444 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
24489 CTAATATTC
1 CTAATATTC
24498 ATTGTTGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:25732 original size:3 final size:3
Alignment explanation
Indices: 25724--25764 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
25714 ATATATTTAT
25724 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25765 TACATTGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27193 original size:15 final size:15
Alignment explanation
Indices: 27173--27203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27163 TATGGTGGTG
*
27173 ATAATAATATATAAT
1 ATAATAATAAATAAT
27188 ATAATAATAAATAAT
1 ATAATAATAAATAAT
27203 A
1 A
27204 GTAAATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATAATAAATAAT
Done.