Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010183.1 Corchorus capsularis cultivar CVL-1 contig10204, 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: 6760
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Found at i:3190 original size:18 final size:19
Alignment explanation
Indices: 3153--3192 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3143 TAATTGAATT
*
3153 TTTCATTAACCATAAAATC
1 TTTCAATAACCATAAAATC
*
3172 TTTCAATAACC-TCAAATC
1 TTTCAATAACCATAAAATC
3190 TTT
1 TTT
3193 TATTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTCAATAACCATAAAATC
Found at i:3620 original size:21 final size:20
Alignment explanation
Indices: 3592--3642 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
3582 TTTAAAAGCT
*
3592 TTTCAATACCCTTATTAAAA
1 TTTCAATAACCTTATTAAAA
*
3612 TTTCTAATAACCTTATTAAGCA
1 TTTC-AATAACCTTATTAA-AA
3634 TTTCAATAA
1 TTTCAATAA
3643 TATTATACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 4 0.15
21 18 0.67
22 5 0.19
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (20 bp):
TTTCAATAACCTTATTAAAA
Found at i:4034 original size:26 final size:26
Alignment explanation
Indices: 3958--4044 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
3948 TTTTGGTAAC
*
3958 TTTATTAAGACACTAACCTTGTTAAG
1 TTTATTAAGACACTAACCATGTTAAG
* *** *
3984 TTTCTGGCCGA-AATAAACCATGTTAAG
1 TTTAT-TAAGACACT-AACCATGTTAAG
4011 TTTATTAAGACACTAACCATGTTAAG
1 TTTATTAAGACACTAACCATGTTAAG
*
4037 TTTTTTAA
1 TTTATTAA
4045 TAGCAATATA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
26 27 0.59
27 19 0.41
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (26 bp):
TTTATTAAGACACTAACCATGTTAAG
Found at i:4074 original size:20 final size:19
Alignment explanation
Indices: 4051--4101 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
4041 TTAATAGCAA
4051 TATAAGCTTTTTAATAACCT
1 TATAAGCTTTTTAATAA-CT
* * *
4071 TATAAACATTTTCATAACT
1 TATAAGCTTTTTAATAACT
*
4090 TA-AAGTTTTTTA
1 TATAAGCTTTTTA
4102 CCTTATGAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 14 0.58
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (19 bp):
TATAAGCTTTTTAATAACT
Found at i:4633 original size:13 final size:13
Alignment explanation
Indices: 4615--4647 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4605 AAGTGTAATT
4615 AGTGTTTGGAGAA
1 AGTGTTTGGAGAA
4628 AGTGTTTGGAGAA
1 AGTGTTTGGAGAA
4641 AGTGTTT
1 AGTGTTT
4648 TTATAAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (13 bp):
AGTGTTTGGAGAA
Found at i:5270 original size:15 final size:17
Alignment explanation
Indices: 5234--5286 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
5224 CCATGAAAAA
5234 TTATTAATTTAGAGAGG
1 TTATTAATTTAGAGAGG
5251 TTATTAATTTAGAGA-G
1 TTATTAATTTAGAGAGG
5267 -TATTAATTTA-AGCAGG
1 TTATTAATTTAGAG-AGG
5283 TTAT
1 TTAT
5287 ACTGTACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 2 0.06
17 18 0.55
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (17 bp):
TTATTAATTTAGAGAGG
Done.