Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019293.1 Corchorus olitorius cultivar O-4 contig19326, 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: 12094
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4337 original size:44 final size:44
Alignment explanation
Indices: 4269--4355 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
4259 TGTCCTATGA
* *
4269 TTCTGAGTAAACTAGGGCTCGTTAGAGAGAACCCTACGATCTCC
1 TTCTAAGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTCC
* *
4313 TTCTAAGTAAACTTGGGCTTGTTAGAGAGAACCCAACGATCTC
1 TTCTAAGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTC
4356 TTAGAGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (44 bp):
TTCTAAGTAAACTAGGGCTCGTTAGAGAGAACCCAACGATCTCC
Found at i:4509 original size:22 final size:22
Alignment explanation
Indices: 4481--4525 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
4471 CAGCAACTAA
*
4481 ACTACCCTCCTAGAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
4503 ACTACCCTCCTAAAACACAGCC
1 ACTACCCTCCTAAAACACAGCC
4525 A
1 A
4526 TAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.44, G:0.07, T:0.13
Consensus pattern (22 bp):
ACTACCCTCCTAAAACACAGCC
Found at i:5874 original size:44 final size:44
Alignment explanation
Indices: 5805--5893 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
5795 TGTCCTATGA
* *
5805 TTCTGAGTAAACTAGGGCTCATTAGAGAGAACCCTACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
* *
5849 TTCTAAGTAAACTTGGGCTCGTTAGAGAGAACCCAACGATCTCC
1 TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
5893 T
1 T
5894 AGAGTTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (44 bp):
TTCTAAGTAAACTAGGGCTCATTAGAGAGAACCCAACGATCTCC
Found at i:9234 original size:16 final size:16
Alignment explanation
Indices: 9211--9315 Score: 106
Period size: 16 Copynumber: 6.6 Consensus size: 16
9201 CGGGCTCGGG
*
9211 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTT
*
9227 CGGATTCGGGTATTTT
1 CGGGTTCGGGTATTTT
**
9243 CGGGTTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
*
9259 CGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTT
* *
9275 CGGATTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
9291 CGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTT
9307 CGGGTTCGG
1 CGGGTTCGG
9316 TCTCGGGTAG
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.03
16 67 0.94
17 2 0.03
ACGTcount: A:0.10, C:0.13, G:0.37, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:9251 original size:32 final size:32
Alignment explanation
Indices: 9211--9315 Score: 156
Period size: 32 Copynumber: 3.3 Consensus size: 32
9201 CGGGCTCGGG
* * * *
9211 CGGGTTCGGGTTTTTTCGGATTCGGGTATTTT
1 CGGGTTCGGGTTATGTCGGGTTCGGATATTTT
*
9243 CGGGTTCGGGTTAAGTCGGGTTCGGATATTTT
1 CGGGTTCGGGTTATGTCGGGTTCGGATATTTT
*
9275 CGGATTCGGGTTATGTCGGGTTCGGATATTTT
1 CGGGTTCGGGTTATGTCGGGTTCGGATATTTT
9307 CGGGTTCGG
1 CGGGTTCGG
9316 TCTCGGGTAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.10, C:0.13, G:0.37, T:0.40
Consensus pattern (32 bp):
CGGGTTCGGGTTATGTCGGGTTCGGATATTTT
Found at i:9360 original size:23 final size:23
Alignment explanation
Indices: 9305--9352 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
9295 TTCGGATATT
* *
9305 TTCGGGTTCGGTCTCGGGTAGGG
1 TTCGGATTCGGGCTCGGGTAGGG
*
9328 TTCGGATTCGGGCTCGGGTCGGG
1 TTCGGATTCGGGCTCGGGTAGGG
9351 TT
1 TT
9353 TGATTTCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.04, C:0.19, G:0.46, T:0.31
Consensus pattern (23 bp):
TTCGGATTCGGGCTCGGGTAGGG
Found at i:9811 original size:31 final size:31
Alignment explanation
Indices: 9776--9847 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
9766 TAAATTATTG
*
9776 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
9807 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
9838 CAAATTAAAA
1 CAAATTAAAA
9848 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Done.