Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016208.1 Corchorus capsularis cultivar CVL-1 contig16229, 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: 6778
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Found at i:30 original size:17 final size:17
Alignment explanation
Indices: 8--40 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1 TTCGGGT
8 TTTTCGGGTTCGGGTTA
1 TTTTCGGGTTCGGGTTA
25 TTTTCGGGTTCGGGTT
1 TTTTCGGGTTCGGGTT
41 CGGGTCCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.36, T:0.48
Consensus pattern (17 bp):
TTTTCGGGTTCGGGTTA
Found at i:36 original size:6 final size:6
Alignment explanation
Indices: 27--64 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
17 TCGGGTTATT
*
27 TTCGGG TTCGGG TTCGGG -TCCGG TTCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
65 ACTTTCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.00, C:0.21, G:0.45, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:40 original size:23 final size:23
Alignment explanation
Indices: 10--64 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1 TTCGGGTTT
* **
10 TTCGGGTTCGGGTTATTTTCGGG
1 TTCGGGTTCGGGTCAGGTTCGGG
*
33 TTCGGGTTCGGGTCCGGTTCGGG
1 TTCGGGTTCGGGTCAGGTTCGGG
56 TTCGGGTTC
1 TTCGGGTTC
65 ACTTTCGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.02, C:0.18, G:0.42, T:0.38
Consensus pattern (23 bp):
TTCGGGTTCGGGTCAGGTTCGGG
Found at i:842 original size:16 final size:16
Alignment explanation
Indices: 809--910 Score: 71
Period size: 16 Copynumber: 6.3 Consensus size: 16
799 TATTTTGATC
*
809 TCGGGCTCGGGTCGGGT
1 TCGGGTTCGGG-CGGGT
826 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
* **
842 TCGGGTTTGGG-TTGT
1 TCGGGTTCGGGCGGGT
****
857 CTCGGGTTCGGGTATTT
1 -TCGGGTTCGGGCGGGT
****
874 TCGGGTTCGGGTAATT
1 TCGGGTTCGGGCGGGT
890 TCGGGTTCGGGCGGGT
1 TCGGGTTCGGGCGGGT
906 TCGGG
1 TCGGG
911 ACGTTGACTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
15 2 0.03
16 57 0.80
17 12 0.17
ACGTcount: A:0.03, C:0.17, G:0.48, T:0.32
Consensus pattern (16 bp):
TCGGGTTCGGGCGGGT
Found at i:862 original size:32 final size:32
Alignment explanation
Indices: 826--910 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 32
816 CGGGTCGGGT
* **
826 TCGGGTTCGGGCGGGTTCGGGTTTGGGTTGTC
1 TCGGGTTCGGGCGGGTTCGGGTTCGGGTAATC
**** *
858 TCGGGTTCGGGTATTTTCGGGTTCGGGTAATT
1 TCGGGTTCGGGCGGGTTCGGGTTCGGGTAATC
890 TCGGGTTCGGGCGGGTTCGGG
1 TCGGGTTCGGGCGGGTTCGGG
911 ACGTTGACTT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.04, C:0.15, G:0.47, T:0.34
Consensus pattern (32 bp):
TCGGGTTCGGGCGGGTTCGGGTTCGGGTAATC
Found at i:885 original size:6 final size:6
Alignment explanation
Indices: 809--854 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
799 TATTTTGATC
* *
809 TCGGGC TCGGG- TCGGGT TCGGGT TCGGG- -CGGGT TCGGGT TTGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
854 T
1 T
855 GTCTCGGGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 27 0.75
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.30
Consensus pattern (6 bp):
TCGGGT
Found at i:3219 original size:46 final size:47
Alignment explanation
Indices: 3152--3243 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
3142 TACTTTTGAA
3152 TCCCATTCCCTCCAAATTAGAAGTCTTTGAAGTGATTT-ATTTAGAT
1 TCCCATTCCCTCCAAATTAGAAGTCTTTGAAGTGATTTAATTTAGAT
3198 TCCCATTCCCTCCAAATTAGAAGTCTTTGAAGTGATTTAATTTAGA
1 TCCCATTCCCTCCAAATTAGAAGTCTTTGAAGTGATTTAATTTAGA
3244 AGCTGTGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 38 0.84
47 7 0.16
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (47 bp):
TCCCATTCCCTCCAAATTAGAAGTCTTTGAAGTGATTTAATTTAGAT
Found at i:3550 original size:33 final size:33
Alignment explanation
Indices: 3512--3627 Score: 142
Period size: 33 Copynumber: 3.5 Consensus size: 33
3502 AGAAGCCGTG
* *
3512 CACCACAGGCCACACGACTCGACCATGCCCGAC
1 CACCACCGGCCACATGACTCGACCATGCCCGAC
* * * *
3545 TACCACCGGCCACATGACTTGGCCATGCCCGGC
1 CACCACCGGCCACATGACTCGACCATGCCCGAC
* * *
3578 CACAACCGGCCACATGACTCGACCATGTCCGGC
1 CACCACCGGCCACATGACTCGACCATGCCCGAC
*
3611 CACAACCGGCCACATGA
1 CACCACCGGCCACATGA
3628 TCCTTTAACT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.25, C:0.44, G:0.21, T:0.10
Consensus pattern (33 bp):
CACCACCGGCCACATGACTCGACCATGCCCGAC
Done.