Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010594.1 Corchorus capsularis cultivar CVL-1 contig10615, 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: 7895
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1991 original size:22 final size:22
Alignment explanation
Indices: 1963--2006 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1953 TTCGGATCGA
1963 TTCTATAAAAATATATTAAGAT
1 TTCTATAAAAATATATTAAGAT
*
1985 TTCTATAAGAATATATTAAGAT
1 TTCTATAAAAATATATTAAGAT
2007 AGGTATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (22 bp):
TTCTATAAAAATATATTAAGAT
Found at i:2253 original size:2 final size:2
Alignment explanation
Indices: 2228--2283 Score: 64
Period size: 2 Copynumber: 28.5 Consensus size: 2
2218 ATTATTAGAT
*
2228 TA TA CTA TA TA AA TA -A TA -A T- TA TA TA TA TA TA TA TA CTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
2269 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2284 CGTAAAAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
1 3 0.06
2 40 0.85
3 4 0.09
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2275 original size:17 final size:17
Alignment explanation
Indices: 2228--2280 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
2218 ATTATTAGAT
*
2228 TATACTATATAAATA-A
1 TATACTATATATATATA
*
2244 TA-ATTATATATATATA
1 TATACTATATATATATA
2260 TATACTATATATATATA
1 TATACTATATATATATA
2277 TATA
1 TATA
2281 TATCGTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 10 0.31
16 5 0.16
17 17 0.53
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
TATACTATATATATATA
Found at i:2915 original size:4 final size:4
Alignment explanation
Indices: 2908--2942 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
2898 CTCTCTCTCT
* *
2908 CTCC CTCC CTCG CTCC CTCC CTCG CTCC CTCC CTC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTC
2943 TTTTTTCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.69, G:0.06, T:0.26
Consensus pattern (4 bp):
CTCC
Found at i:2923 original size:12 final size:12
Alignment explanation
Indices: 2908--2942 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2898 CTCTCTCTCT
2908 CTCCCTCCCTCG
1 CTCCCTCCCTCG
2920 CTCCCTCCCTCG
1 CTCCCTCCCTCG
2932 CTCCCTCCCTC
1 CTCCCTCCCTC
2943 TTTTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.06, T:0.26
Consensus pattern (12 bp):
CTCCCTCCCTCG
Found at i:3604 original size:21 final size:22
Alignment explanation
Indices: 3565--3614 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
3555 AAAATTCGGG
*
3565 AAAAAAAGAAATTCCTT-AA-T
1 AAAAAAAGAAATTCATTAAATT
*
3585 AAAAAAATAAATTTCATTAAATT
1 AAAAAAAGAAA-TTCATTAAATT
3608 AAAAAAA
1 AAAAAAA
3615 AAAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 5 0.20
22 2 0.08
23 8 0.32
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAAAGAAATTCATTAAATT
Found at i:4174 original size:37 final size:37
Alignment explanation
Indices: 4131--4201 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
4121 CTTGATCAAC
* *
4131 ATACATGTCTTTTCACATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
4168 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
4202 ATAATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:5436 original size:31 final size:32
Alignment explanation
Indices: 5388--5449 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
5378 CATCATAGTG
5388 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
* *
5420 ATATATCTC-TTTGTTTCTTTAAGAAACCAA
1 ATATAACTCTTTTGTTTCTCTAAGAAACCAA
5450 GACACCCCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATAACTCTTTTGTTTCTCTAAGAAACCAAC
Found at i:6618 original size:37 final size:37
Alignment explanation
Indices: 6574--6644 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
6564 CTTGATCAAC
* *
6574 ATACATGTCTTTTCACATAGACATAACTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
6611 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
6645 ATAATCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Done.