Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014637.1 Corchorus capsularis cultivar CVL-1 contig14658, 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: 10585
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--64 Score: 54
Period size: 2 Copynumber: 35.0 Consensus size: 2
1 TA TA TA TA TA TA TA -A TA TA -A TA -A TA -A TA -A TA GTA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA
40 TA TA T- TA TA -A TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65 ATAATAATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
1 8 0.15
2 40 0.77
3 4 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11 original size:6 final size:6
Alignment explanation
Indices: 1--64 Score: 54
Period size: 5 Copynumber: 11.7 Consensus size: 6
1 TATATA TATATA TA-ATA TA-ATA -ATA-A TA-ATA GTACTATA TATAT-
1 TATATA TATATA TATATA TATATA TATATA TATATA -TA-TATA TATATA
45 TATA-A TATATA TATA-A TATA
1 TATATA TATATA TATATA TATA
65 ATAATAATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
4 3 0.06
5 24 0.48
6 18 0.36
7 2 0.04
8 3 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:25 original size:3 final size:3
Alignment explanation
Indices: 12--76 Score: 53
Period size: 3 Copynumber: 21.0 Consensus size: 3
2 ATATATATAT
* * *
12 ATA AT- ATA ATA ATA ATA ATA GTA CTA TATA TATT ATA ATA TATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA -ATA -ATA
60 AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA
77 GTAGTAGTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 37 0.70
4 12 0.23
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:31 original size:14 final size:15
Alignment explanation
Indices: 8--76 Score: 81
Period size: 14 Copynumber: 4.7 Consensus size: 15
1 TATATAT
8 ATATATAATATAATA
1 ATATATAATATAATA
*
23 ATA-ATAATAGTACT-
1 ATATATAATA-TAATA
*
37 ATATATATTATAATA
1 ATATATAATATAATA
52 TATATATAATATAATA
1 -ATATATAATATAATA
68 ATA-ATAATA
1 ATATATAATA
77 GTAGTAGTAG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
14 18 0.39
15 14 0.30
16 14 0.30
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (15 bp):
ATATATAATATAATA
Found at i:98 original size:45 final size:44
Alignment explanation
Indices: 1--101 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 44
*
1 TATATATATATATAATATAATAATAATAATAGTACTATATATAT
1 TATATATATATATAATATAATAATAATAATAGTACTATATATAG
* *
45 TATAATATATATATAATATAATAATAATAATAGTAGTAGTA-GTAG
1 TAT-ATATATATATAATATAATAATAATAATAGTACTA-TATATAG
90 TACTATATATAT
1 TA-TATATATAT
102 TATCCAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
44 3 0.06
45 45 0.88
46 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (44 bp):
TATATATATATATAATATAATAATAATAATAGTACTATATATAG
Found at i:9403 original size:20 final size:20
Alignment explanation
Indices: 9378--9416 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9368 TTTAGGTTTC
*
9378 CTCTTCTTTTCATTCTTCTT
1 CTCTTCTTCTCATTCTTCTT
*
9398 CTCTTCTTCTCCTTCTTCT
1 CTCTTCTTCTCATTCTTCT
9417 CTTCGGCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.36, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTCTTCTCATTCTTCTT
Found at i:9404 original size:8 final size:8
Alignment explanation
Indices: 9391--9420 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
9381 TTCTTTTCAT
9391 TCTTCTTC
1 TCTTCTTC
9399 TCTTCTTC
1 TCTTCTTC
9407 TCCTTCTTC
1 T-CTTCTTC
9416 TCTTC
1 TCTTC
9421 GGCCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (8 bp):
TCTTCTTC
Done.