Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022061.1 Corchorus olitorius cultivar O-4 contig22094, 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: 17575
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4199 original size:39 final size:39
Alignment explanation
Indices: 4114--4200 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
4104 ATTGTTAAAT
*
4114 TTAATTAAG-GTTAATTAGTGTTAATTAACTAATTTGTTA
1 TTAATT-AGTGTTAATTACTGTTAATTAACTAATTTGTTA
4153 TTAATTAGTGTTAATTACTGTTAATTAACTAATTTGTTA
1 TTAATTAGTGTTAATTACTGTTAATTAACTAATTTGTTA
4192 TTAATTAGT
1 TTAATTAGT
4201 CAGAGACCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 2 0.04
39 44 0.96
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (39 bp):
TTAATTAGTGTTAATTACTGTTAATTAACTAATTTGTTA
Found at i:4607 original size:18 final size:19
Alignment explanation
Indices: 4575--4610 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4565 TAACTAGTAA
*
4575 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
4594 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
4611 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:4753 original size:33 final size:33
Alignment explanation
Indices: 4700--4778 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
4690 AAAATTGTCT
* *
4700 AGGCGTCGCCAGCGGACGCCTGACCATATGGCG
1 AGGCGTCCCCAGGGGACGCCTGACCATATGGCG
* * *
4733 AGGCGTCCCCAGGGGGCGCCTGACCGTATGGTG
1 AGGCGTCCCCAGGGGACGCCTGACCATATGGCG
4766 AGGCGTCCCCAGG
1 AGGCGTCCCCAGG
4779 TCGTGCCCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.33, G:0.39, T:0.13
Consensus pattern (33 bp):
AGGCGTCCCCAGGGGACGCCTGACCATATGGCG
Found at i:5519 original size:6 final size:6
Alignment explanation
Indices: 5508--5539 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
5498 TCTTTATCCA
*
5508 TCTGGG TCTGGG TCTGGG TTTGGG TCTGGG TC
1 TCTGGG TCTGGG TCTGGG TCTGGG TCTGGG TC
5540 GGACTCGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.16, G:0.47, T:0.38
Consensus pattern (6 bp):
TCTGGG
Found at i:9434 original size:20 final size:20
Alignment explanation
Indices: 9406--9443 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9396 TAAAAATAAC
9406 AATTAAAAAGA-AAAGCAATT
1 AATTAAAAA-ACAAAGCAATT
*
9426 AATTTAAAAACAAAGCAA
1 AATTAAAAAACAAAGCAA
9444 AGTAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.18
Consensus pattern (20 bp):
AATTAAAAAACAAAGCAATT
Found at i:9453 original size:21 final size:21
Alignment explanation
Indices: 9406--9454 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
9396 TAAAAATAAC
*
9406 AATTAAAAAGAAAAGCAATTA
1 AATTAAAAAGAAAAGCAAGTA
* *
9427 ATTTAAAAA-CAAAGCAAAGTA
1 AATTAAAAAGAAAAGC-AAGTA
9448 AATTAAA
1 AATTAAA
9455 TCTAAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.20
Consensus pattern (21 bp):
AATTAAAAAGAAAAGCAAGTA
Found at i:15818 original size:11 final size:11
Alignment explanation
Indices: 15802--15826 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15792 GGGGAATAAT
15802 CAATCCAAAAA
1 CAATCCAAAAA
15813 CAATCCAAAAA
1 CAATCCAAAAA
15824 CAA
1 CAA
15827 ACAATTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Found at i:16824 original size:18 final size:18
Alignment explanation
Indices: 16798--16864 Score: 125
Period size: 18 Copynumber: 3.7 Consensus size: 18
16788 CTATGCAGCA
*
16798 GCGGCAGCAAGCTGCCTC
1 GCGGAAGCAAGCTGCCTC
16816 GCGGAAGCAAGCTGCCTC
1 GCGGAAGCAAGCTGCCTC
16834 GCGGAAGCAAGCTGCCTC
1 GCGGAAGCAAGCTGCCTC
16852 GCGGAAGCAAGCT
1 GCGGAAGCAAGCT
16865 TGTTGCGTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.22, C:0.33, G:0.34, T:0.10
Consensus pattern (18 bp):
GCGGAAGCAAGCTGCCTC
Done.