Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014753.1 Corchorus capsularis cultivar CVL-1 contig14774, 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: 14133
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.33
Found at i:251 original size:13 final size:13
Alignment explanation
Indices: 233--284 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
223 TGAGTTAAGG
233 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
246 AGAGAAAAGAAAAA
1 AGAGAAAA-AAAAA
260 AGA-AAAGAAAAAA
1 AGAGAAA-AAAAAA
*
273 AAAGAAAAAAAA
1 AGAGAAAAAAAA
285 GGATTGTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
13 23 0.66
14 12 0.34
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAGAAAAAAAAA
Found at i:272 original size:7 final size:7
Alignment explanation
Indices: 237--282 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
227 TTAAGGAGAG
237 AAAA-AA
1 AAAAGAA
*
243 AAAAGAG
1 AAAAGAA
250 AAAAGAA
1 AAAAGAA
257 AAAAGAA
1 AAAAGAA
*
264 AAGAAAAA
1 AA-AAGAA
272 AAAAGAA
1 AAAAGAA
279 AAAA
1 AAAA
283 AAGGATTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 4 0.12
7 24 0.71
8 6 0.18
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:5579 original size:16 final size:16
Alignment explanation
Indices: 5546--5578 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5536 ACTAGTAATG
*
5546 AATGAATGAAAATGAA
1 AATGAATGAAAACGAA
5562 AATGAAT-AAAACGAA
1 AATGAATGAAAACGAA
5577 AA
1 AA
5579 AAAGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (16 bp):
AATGAATGAAAACGAA
Found at i:13404 original size:15 final size:15
Alignment explanation
Indices: 13386--13416 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13376 TTACTTTTGC
*
13386 TACTTTTATCATTTT
1 TACTTTTACCATTTT
13401 TACTTTTACCATTTT
1 TACTTTTACCATTTT
13416 T
1 T
13417 CTTACTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:13416 original size:24 final size:24
Alignment explanation
Indices: 13371--13443 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
13361 CTCTTCTTAC
* * *
13371 CATTTTTACTTTTGCTACTTTTAT
1 CATTTTTACTTTTACCATTTTTAT
*
13395 CATTTTTACTTTTACCATTTTTCT
1 CATTTTTACTTTTACCATTTTTAT
* *
13419 TACTCTTTTACTTAATACCATTTTT
1 CA-T-TTTTACTT-TTACCATTTTT
13444 TGACCTTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
24 21 0.52
25 1 0.03
26 8 0.20
27 10 0.25
ACGTcount: A:0.19, C:0.19, G:0.01, T:0.60
Consensus pattern (24 bp):
CATTTTTACTTTTACCATTTTTAT
Found at i:13437 original size:27 final size:25
Alignment explanation
Indices: 13398--13465 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 25
13388 CTTTTATCAT
* *
13398 TTTTACTT-TTACCATTTTTCTTACTC
1 TTTTACTTAATACCATTTTT-TGAC-C
13424 TTTTACTTAATACCATTTTTTGACC
1 TTTTACTTAATACCATTTTTTGACC
13449 TTCTTACTTAATACCAT
1 TT-TTACTTAATACCAT
13466 ACTTTACTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 25 0.66
27 10 0.26
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTTACTTAATACCATTTTTTGACC
Found at i:13474 original size:17 final size:17
Alignment explanation
Indices: 13452--13490 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
13442 TTTGACCTTC
13452 TTACTTAATACCATACT
1 TTACTTAATACCATACT
13469 TTACTTAATACCATACT
1 TTACTTAATACCATACT
13486 TTACT
1 TTACT
13491 CTCTTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (17 bp):
TTACTTAATACCATACT
Found at i:13675 original size:15 final size:15
Alignment explanation
Indices: 13655--13694 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
13645 TCACTACTTC
13655 TTTTACTTTTACCAT
1 TTTTACTTTTACCAT
* *
13670 TTTTACTAATTACCTT
1 TTTTACT-TTTACCAT
13686 TTTTACTTT
1 TTTTACTTT
13695 CTATCTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTACTTTTACCAT
Found at i:14012 original size:37 final size:37
Alignment explanation
Indices: 13957--14097 Score: 133
Period size: 37 Copynumber: 3.7 Consensus size: 37
13947 TAATCACTCA
* * * *
13957 ACTCTTAATTA-CTAATTTACTGATTACCATCACTTTG
1 ACTCTTAATTATC-GATTTACTGATTACTATTACATTG
* *
13994 ACTCTTCATTATCGATTTACTGATTACTATTTTTACCTTG
1 ACTCTTAATTATCGATTTACTGATTACTA---TTACATTG
* *
14034 ACTCTTGATTA-CTGACTTTACTGATCACTATTACATTG
1 ACTCTTAATTATC-GA-TTTACTGATTACTATTACATTG
*
14072 ACTCTTAATTATCAATTTACTGATTA
1 ACTCTTAATTATCGATTTACTGATTA
14098 ATCTCTTTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
37 34 0.40
38 19 0.22
39 2 0.02
40 18 0.21
41 13 0.15
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (37 bp):
ACTCTTAATTATCGATTTACTGATTACTATTACATTG
Done.