Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010435.1 Corchorus capsularis cultivar CVL-1 contig10456, 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: 25154
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2460 original size:21 final size:21
Alignment explanation
Indices: 2424--2482 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 21
2414 ATTCAACTCC
*
2424 AAAAAA-GAAAATAAAATAT-
1 AAAAAATGAAAAAAAAATATA
2443 AAAAAATGAAAACAAAAATATA
1 AAAAAATGAAAA-AAAAATATA
2465 AAAAAATGAAAATAAAAA
1 AAAAAATGAAAA-AAAAA
2483 GTAATTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 6 0.17
20 5 0.14
21 7 0.20
22 17 0.49
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.14
Consensus pattern (21 bp):
AAAAAATGAAAAAAAAATATA
Found at i:16236 original size:27 final size:27
Alignment explanation
Indices: 16184--16238 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
16174 AAAAACTCCC
*
16184 TCTGTTCCTTATTACTTATCATCACCA
1 TCTGTTCCTTATTACTTATCACCACCA
* *
16211 TCTGTTCCTT-TCTATTTGTCACCACCA
1 TCTGTTCCTTAT-TACTTATCACCACCA
16238 T
1 T
16239 TTACCAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.18, C:0.31, G:0.05, T:0.45
Consensus pattern (27 bp):
TCTGTTCCTTATTACTTATCACCACCA
Found at i:24107 original size:15 final size:15
Alignment explanation
Indices: 24087--24115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24077 AAAGTACCCT
24087 TATAATTAATTAAAG
1 TATAATTAATTAAAG
24102 TATAATTAATTAAA
1 TATAATTAATTAAA
24116 TACATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TATAATTAATTAAAG
Found at i:24646 original size:13 final size:12
Alignment explanation
Indices: 24610--24656 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
24600 TCAATCTTTA
*
24610 TATATATTGATAA
1 TATATATT-ATAT
*
24623 TA-ATGTTATAT
1 TATATATTATAT
24634 TATATTATTATAT
1 TATA-TATTATAT
24647 TATATATTAT
1 TATATATTAT
24657 CAATAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:24859 original size:16 final size:17
Alignment explanation
Indices: 24840--24912 Score: 82
Period size: 16 Copynumber: 4.5 Consensus size: 17
24830 GAAAATATCT
24840 GAACCC-AATATAACCC
1 GAACCCGAATATAACCC
*
24856 GAACCCGAAAAT-ACCC
1 GAACCCGAATATAACCC
*
24872 GAACCCGACT-TAACCC
1 GAACCCGAATATAACCC
*
24888 GAACCCGAA-AAAACCC
1 GAACCCGAATATAACCC
*
24904 GAACTCGAA
1 GAACCCGAA
24913 CCTACCCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.02
16 43 0.90
17 4 0.08
ACGTcount: A:0.42, C:0.37, G:0.12, T:0.08
Consensus pattern (17 bp):
GAACCCGAATATAACCC
Found at i:24859 original size:32 final size:32
Alignment explanation
Indices: 24823--24912 Score: 110
Period size: 32 Copynumber: 2.8 Consensus size: 32
24813 GAACCCTACT
* * *
24823 CGAACCTGAAAATATCTGAACCC-AATATAACC
1 CGAACCCGAAAATACCCGAACCCGAAT-TAACC
*
24855 CGAACCCGAAAATACCCGAACCCGACTTAACC
1 CGAACCCGAAAATACCCGAACCCGAATTAACC
* *
24887 CGAACCCGAAAAAACCCGAACTCGAA
1 CGAACCCGAAAATACCCGAACCCGAA
24913 CCTACCCAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
32 48 0.96
33 2 0.04
ACGTcount: A:0.42, C:0.34, G:0.12, T:0.11
Consensus pattern (32 bp):
CGAACCCGAAAATACCCGAACCCGAATTAACC
Done.