Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009514.1 Corchorus capsularis cultivar CVL-1 contig09535, 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: 11016
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39 GATTAGATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1383 original size:25 final size:27
Alignment explanation
Indices: 1331--1383 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1321 TTACTCAACT
* **
1331 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAAATCTATTTTTATTTTAATGTAA
1358 AAAAAATCTATTTTTA-TTTAAT-TAA
1 AAAAAATCTATTTTTATTTTAATGTAA
1383 A
1 A
1384 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAAATCTATTTTTATTTTAATGTAA
Found at i:3468 original size:33 final size:32
Alignment explanation
Indices: 3399--3482 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
3389 GAAAAATCAC
3399 CGAAAACGTTTTGCCCTTA--TTTGTAAAGTA
1 CGAAAACGTTTTGCCCTTATTTTTGTAAAGTA
* * *
3429 CAAAAACGTTCTGCCTTTATTTGTTGTAATA-TA
1 CGAAAACGTTTTGCCCTTATTT-TTGTAA-AGTA
*
3462 CGAAAACATTTTGCCCTTATT
1 CGAAAACGTTTTGCCCTTATT
3483 CGCTCATCCC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
30 16 0.37
32 1 0.02
33 25 0.58
34 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (32 bp):
CGAAAACGTTTTGCCCTTATTTTTGTAAAGTA
Found at i:4429 original size:18 final size:18
Alignment explanation
Indices: 4406--4441 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4396 TGCAACACAT
4406 TTCCCATCCAATTAGACG
1 TTCCCATCCAATTAGACG
4424 TTCCCATCCAATTAGACG
1 TTCCCATCCAATTAGACG
4442 GTCTGCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.11, T:0.28
Consensus pattern (18 bp):
TTCCCATCCAATTAGACG
Found at i:7634 original size:32 final size:32
Alignment explanation
Indices: 7593--7655 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
7583 CAATTTAGAA
*
7593 ATATGTTTAAAAAAAACGGGTACAATCGGAAAT
1 ATATGTTTAAAAAAAA-GGATACAATCGGAAAT
7626 ATAT-TTTAAAAAAAAGGATACAATCGGAAA
1 ATATGTTTAAAAAAAAGGATACAATCGGAAA
7656 ACATAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 14 0.48
32 11 0.38
33 4 0.14
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (32 bp):
ATATGTTTAAAAAAAAGGATACAATCGGAAAT
Found at i:9526 original size:15 final size:15
Alignment explanation
Indices: 9500--9542 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
9490 TACAAAGCCC
*
9500 GGCACTCGACCACCT
1 GGCACCCGACCACCT
*
9515 GGCGCCCGACCACCT
1 GGCACCCGACCACCT
*
9530 GGCACTCGACCAC
1 GGCACCCGACCAC
9543 TTATGACCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (15 bp):
GGCACCCGACCACCT
Found at i:9617 original size:26 final size:25
Alignment explanation
Indices: 9588--9702 Score: 106
Period size: 26 Copynumber: 4.4 Consensus size: 25
9578 AAATGGCACT
*
9588 CCACACGTGACCTCCAACGTACGACC
1 CCACACGTGACCTCCAA-GTACAACC
* * *
9614 CCACACGTGATTCTCGAAGTACAACT
1 CCACACGTGA-CCTCCAAGTACAACC
*
9640 CCACACGTGACCTCCAACGGAC-ACC
1 CCACACGTGACCTCCAA-GTACAACC
* *
9665 TTCAACACGTGACCTCCGAAGTACAACT
1 --CCACACGTGACCTCC-AAGTACAACC
9693 CCACACGTGA
1 CCACACGTGA
9703 TCTCGCGCGT
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
25 7 0.10
26 38 0.54
27 22 0.31
28 4 0.06
ACGTcount: A:0.30, C:0.39, G:0.16, T:0.16
Consensus pattern (25 bp):
CCACACGTGACCTCCAAGTACAACC
Found at i:9694 original size:53 final size:52
Alignment explanation
Indices: 9585--9702 Score: 168
Period size: 53 Copynumber: 2.2 Consensus size: 52
9575 GCCAAATGGC
* * *
9585 ACTCCACACGTGACCTCCAACGTACGACCCCACACGTGATTCTCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGACTCTCGAAGTACA
9637 ACTCCACACGTGACCTCCAACGGAC-ACCTTCAACACGTGAC-CTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACGGACGACC--CAACACGTGACTCT-CGAAGTACA
9690 ACTCCACACGTGA
1 ACTCCACACGTGA
9703 TCTCGCGCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
51 3 0.05
52 26 0.43
53 31 0.52
ACGTcount: A:0.30, C:0.39, G:0.15, T:0.16
Consensus pattern (52 bp):
ACTCCACACGTGACCTCCAACGGACGACCCAACACGTGACTCTCGAAGTACA
Done.