Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011243.1 Corchorus capsularis cultivar CVL-1 contig11264, 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: 9969
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1459 original size:27 final size:28
Alignment explanation
Indices: 1398--1467 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
1388 TCTAATAATT
* *
1398 AATAATGGAATAATTTTTCTTAGAAAAA
1 AATAATGGAATAATTTATCGTAGAAAAA
*
1426 AATAATGGAATAATTTATGGTA-AAAAA
1 AATAATGGAATAATTTATCGTAGAAAAA
1453 AATAATGGAATAATT
1 AATAATGGAATAATT
1468 AAAATATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 20 0.51
28 19 0.49
ACGTcount: A:0.53, C:0.01, G:0.13, T:0.33
Consensus pattern (28 bp):
AATAATGGAATAATTTATCGTAGAAAAA
Found at i:2265 original size:11 final size:10
Alignment explanation
Indices: 2247--2282 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2237 CATCTCTCTC
2247 TCTTTTTTTT
1 TCTTTTTTTT
2257 TCTTTTTTTT
1 TCTTTTTTTT
*
2267 TCCTTTTCTTT
1 T-CTTTTTTTT
2278 TCTTT
1 TCTTT
2283 CTTGTTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:2536 original size:14 final size:15
Alignment explanation
Indices: 2517--2545 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2507 TTGTTTGACT
2517 TGATTGA-TTTTGAA
1 TGATTGAGTTTTGAA
2531 TGATTGAGTTTTGAA
1 TGATTGAGTTTTGAA
2546 AGTTTGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (15 bp):
TGATTGAGTTTTGAA
Found at i:5386 original size:37 final size:36
Alignment explanation
Indices: 5344--5413 Score: 113
Period size: 37 Copynumber: 1.9 Consensus size: 36
5334 ACATGATTAT
* *
5344 TCATAAAGTTATGTCTATTTGGAAAGACATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGAC-TGTATTGA
5381 TCATAAAGTTATGTCTATATGAAAAGACTGTAT
1 TCATAAAGTTATGTCTATATGAAAAGACTGTAT
5414 GTTGATCAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (36 bp):
TCATAAAGTTATGTCTATATGAAAAGACTGTATTGA
Found at i:8927 original size:34 final size:34
Alignment explanation
Indices: 8889--8960 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
8879 AAAAAACTTG
* *
8889 AAATCTCAAAAACTCTTCTCTCTCTTTTTTCTTC
1 AAATCGCAAAAACCCTTCTCTCTCTTTTTTCTTC
* * *
8923 AAATCGCTATAACCCTTTTCTCTCTTTTTTCTTC
1 AAATCGCAAAAACCCTTCTCTCTCTTTTTTCTTC
8957 AAAT
1 AAAT
8961 GCATAACAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.28, G:0.01, T:0.47
Consensus pattern (34 bp):
AAATCGCAAAAACCCTTCTCTCTCTTTTTTCTTC
Found at i:9881 original size:2 final size:2
Alignment explanation
Indices: 9874--9969 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
9864 ATCTAACTTG
9874 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9916 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
9958 CA CA CA CA CA CA
1 CA CA CA CA CA CA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.