Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021861.1 Corchorus olitorius cultivar O-4 contig21894, 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: 12136
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:3004 original size:43 final size:43
Alignment explanation
Indices: 2956--3040 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
2946 GGATTTTTCT
2956 TTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGG
1 TTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGG
2999 TTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTG
1 TTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTG
3041 CAGATAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.07, G:0.34, T:0.40
Consensus pattern (43 bp):
TTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGG
Found at i:3290 original size:304 final size:304
Alignment explanation
Indices: 2741--3314 Score: 1067
Period size: 304 Copynumber: 1.9 Consensus size: 304
2731 TTTCTCGAAT
**
2741 TAAAAGCTTTTGAATCTCCTCCAAATCGAACCCAAAAGCGAGCCTCCCTCACCTCAAATCCAACA
1 TAAAAGCCATTGAATCTCCTCCAAATCGAACCCAAAAGCGAGCCTCCCTCACCTCAAATCCAACA
*
2806 ACTTCACCGTTGTTTCCTCACAAAACTTAAATATGTTATTCACCTTTCCATCCTCTCCTTTTCAA
66 ACTTCACCGTCGTTTCCTCACAAAACTTAAATATGTTATTCACCTTTCCATCCTCTCCTTTTCAA
*
2871 GAACCCTAGTTTTTTACTTTTTGTGTGCAAGAAAGTCGAGAGAAAGAGAGAGTGTTCGGGAGAGA
131 GAACCCTAGTTTTCTACTTTTTGTGTGCAAGAAAGTCGAGAGAAAGAGAGAGTGTTCGGGAGAGA
2936 TTAAGGCTCAGGATTTTTCTTTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGGTT
196 TTAAGGCTCAGGATTTTTCTTTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGGTT
* *
3001 TCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGCAGA
261 GCTGTGTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGCAGA
3045 TAAAAGCCATTGAATCTCCTCCAAATCGAACCCAAAAGCGAGCCTCCCTCACCTCAAATCCAACA
1 TAAAAGCCATTGAATCTCCTCCAAATCGAACCCAAAAGCGAGCCTCCCTCACCTCAAATCCAACA
3110 ACTTCACCGTCGTTTCCTCACAAAACTTAAATATGTTATTCACCTTTCCATCCTCTCCTTTTCAA
66 ACTTCACCGTCGTTTCCTCACAAAACTTAAATATGTTATTCACCTTTCCATCCTCTCCTTTTCAA
3175 GAACCCTAGTTTTCTACTTTTTGTGTGCAAGAAAGTCGAGAGAAAGAGAGAGTGTTCGGGAGAGA
131 GAACCCTAGTTTTCTACTTTTTGTGTGCAAGAAAGTCGAGAGAAAGAGAGAGTGTTCGGGAGAGA
* * *
3240 TTGAGGCTCATGATTTTTCTTTTCTGTTTGAGTGTATACTGGTGAGGGAAGATTGTCTTGTGGTT
196 TTAAGGCTCAGGATTTTTCTTTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGGTT
3305 GCTGTGTGAG
261 GCTGTGTGAG
3315 GGTTTTTTTT
Statistics
Matches: 261, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
304 261 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (304 bp):
TAAAAGCCATTGAATCTCCTCCAAATCGAACCCAAAAGCGAGCCTCCCTCACCTCAAATCCAACA
ACTTCACCGTCGTTTCCTCACAAAACTTAAATATGTTATTCACCTTTCCATCCTCTCCTTTTCAA
GAACCCTAGTTTTCTACTTTTTGTGTGCAAGAAAGTCGAGAGAAAGAGAGAGTGTTCGGGAGAGA
TTAAGGCTCAGGATTTTTCTTTTCTGTTTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGGTT
GCTGTGTGAGTGTATACTGGAGAGGGAAGATTGTCTTGTGCAGA
Found at i:5267 original size:28 final size:28
Alignment explanation
Indices: 5236--5299 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
5226 CGACCACGAT
5236 GCCCCCT-GAACATGCAAATGACCAAAAC
1 GCCCCCTAG-ACATGCAAATGACCAAAAC
* *
5264 G-CCCCTAGACGTGCAAATGACCAAAAT
1 GCCCCCTAGACATGCAAATGACCAAAAC
5291 G-CCCCTAGA
1 GCCCCCTAGA
5300 TAACCCTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.36, C:0.34, G:0.17, T:0.12
Consensus pattern (28 bp):
GCCCCCTAGACATGCAAATGACCAAAAC
Found at i:5278 original size:27 final size:27
Alignment explanation
Indices: 5248--5299 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
5238 CCCCTGAACA
5248 TGCAAATGACCAAAACGCCCCTAGACG
1 TGCAAATGACCAAAACGCCCCTAGACG
*
5275 TGCAAATGACCAAAATGCCCCTAGA
1 TGCAAATGACCAAAACGCCCCTAGA
5300 TAACCCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.17, T:0.13
Consensus pattern (27 bp):
TGCAAATGACCAAAACGCCCCTAGACG
Found at i:9224 original size:21 final size:22
Alignment explanation
Indices: 9182--9280 Score: 69
Period size: 22 Copynumber: 4.5 Consensus size: 22
9172 CTATCGTATT
9182 AAATTTTGATAACCACCCTATG
1 AAATTTTGATAACCACCCTATG
* **
9204 CAATTTTGATAATTA-CCTATG
1 AAATTTTGATAACCACCCTATG
* * *
9225 AAATTGTGATAAACTCCAC-ATG
1 AAATTTTGATAACCACC-CTATG
* * *
9247 AAACTTTGATAGCCTAACC-ATG
1 AAATTTTGATAACC-ACCCTATG
*
9269 AAATTTTAATAA
1 AAATTTTGATAA
9281 ACCTTCATAT
Statistics
Matches: 57, Mismatches: 17, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
21 16 0.28
22 39 0.68
23 2 0.04
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
AAATTTTGATAACCACCCTATG
Done.