Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016776.1 Corchorus olitorius cultivar O-4 contig16809, 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: 13662
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:4497 original size:54 final size:54
Alignment explanation
Indices: 4335--4497 Score: 254
Period size: 54 Copynumber: 3.0 Consensus size: 54
4325 GGAACAGGTG
* * *
4335 TTCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAAAGTTGATC
1 TTCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
* * *
4389 CTGAGATGATACAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
* *
4443 TTCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TTCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
4497 T
1 T
4498 CGTTTCAAGA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 98 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (54 bp):
TTCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
Found at i:4509 original size:35 final size:35
Alignment explanation
Indices: 4462--4782 Score: 403
Period size: 35 Copynumber: 9.0 Consensus size: 35
4452 TCCAGTGCAG
*
4462 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4497 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * **
4532 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
4567 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4602 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4637 TCGTTTCAA-AGAGTTTTCGTTGATCAGAGTTGATC
1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC
** *
4672 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATC
1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC
* **
4709 TCCTTTCAAGAAGTTTTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAG---TTTTCGATGATCAGAGTTGATC
4747 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4782 T
1 T
4783 TCACATTGAT
Statistics
Matches: 251, Mismatches: 28, Indels: 14
0.86 0.10 0.05
Matches are distributed among these distances:
34 14 0.06
35 160 0.64
36 13 0.05
37 30 0.12
38 34 0.14
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:6423 original size:24 final size:24
Alignment explanation
Indices: 6392--6527 Score: 73
Period size: 21 Copynumber: 6.0 Consensus size: 24
6382 ACCAAAAAGA
*
6392 TTTTTTTA-TTATTTATTCACTATT
1 TTTTTTTATTTATTT-TTAACTATT
6416 TTTTTTTATTTATTTTTAACTA--
1 TTTTTTTATTTATTTTTAACTATT
* *
6438 -TTATCTATTTA--TTT-ACTATT
1 TTTTTTTATTTATTTTTAACTATT
*
6458 TATCTTTTTATTTATTTTCAACTA--
1 T-T-TTTTTATTTATTTTTAACTATT
* *
6482 -TTATCTATTTA--TTT-ACTATT
1 TTTTTTTATTTATTTTTAACTATT
*
6502 TATCTATTTATTTATTTTTAACTATT
1 T-T-TTTTTATTTATTTTTAACTATT
6528 ATCTATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 32
0.67 0.08 0.25
Matches are distributed among these distances:
18 8 0.09
19 5 0.06
21 17 0.20
22 3 0.04
23 17 0.20
24 14 0.16
25 11 0.13
26 10 0.12
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTTTATTTATTTTTAACTATT
Found at i:6460 original size:19 final size:19
Alignment explanation
Indices: 6420--6515 Score: 90
Period size: 19 Copynumber: 4.8 Consensus size: 19
6410 ACTATTTTTT
* *
6420 TTTATTTATTT-TTAACTA
1 TTTATCTATTTATTTACTA
6438 -TTATCTATTTATTTACTA
1 TTTATCTATTTATTTACTA
6456 TTTATCTTTTTATTTATTTTCAACTA
1 TTTATC----TATTTA-TTT--ACTA
6482 -TTATCTATTTATTTACTA
1 TTTATCTATTTATTTACTA
6500 TTTATCTATTTATTTA
1 TTTATCTATTTATTTA
6516 TTTTTAACTA
Statistics
Matches: 66, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
17 9 0.14
18 10 0.15
19 20 0.30
20 3 0.05
21 6 0.09
23 6 0.09
24 3 0.05
25 5 0.08
26 4 0.06
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTATCTATTTATTTACTA
Found at i:6481 original size:44 final size:44
Alignment explanation
Indices: 6397--6588 Score: 270
Period size: 44 Copynumber: 4.5 Consensus size: 44
6387 AAAGATTTTT
*
6397 TTAT-TATTTATTCACTATTT-T-TTTTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
*
6438 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTCAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
*
6482 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
*
6526 TTATCTATTT-TTTA--ATTTATCTTTTAATTTATTAATTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATT--TTTAACTA
* *
6569 TTACCTATTTATTTATTATT
1 TTATCTATTTATTTACTATT
6589 ATTATCCTTT
Statistics
Matches: 136, Mismatches: 7, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
41 21 0.15
42 15 0.11
43 22 0.16
44 75 0.55
46 3 0.02
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.65
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTTAACTA
Found at i:6508 original size:8 final size:8
Alignment explanation
Indices: 6422--6647 Score: 63
Period size: 8 Copynumber: 28.1 Consensus size: 8
6412 TATTTTTTTT
6422 TATTTAT-
1 TATTTATC
*
6429 T-TTTAAC
1 TATTTATC
6436 TA-TTATC
1 TATTTATC
6443 TATTTATTTAC
1 TATTTA--T-C
6454 TATTTATC
1 TATTTATC
* *
6462 TTTTTATT
1 TATTTATC
6470 TATTT-TC
1 TATTTATC
*
6477 AACTATTATC
1 TA-T-TTATC
6487 TATTTATTTAC
1 TATTTA--T-C
6498 TATTTATC
1 TATTTATC
*
6506 TATTTATT
1 TATTTATC
*
6514 TATTTTTAAC
1 TA--TTTATC
6524 TA-TTATC
1 TATTTATC
*
6531 TATTT-TT
1 TATTTATC
6538 TAATTTATC
1 T-ATTTATC
6547 T-TTTA--
1 TATTTATC
6552 -ATTTAT-
1 TATTTATC
*
6558 TAATTTAAC
1 T-ATTTATC
*
6567 TA-TTACC
1 TATTTATC
*
6574 TATTTATT
1 TATTTATC
6582 TA-TTAT-
1 TATTTATC
6588 TA-TTATCC
1 TATTTAT-C
6596 T-TTTAGTTACC
1 TATTTA--T--C
6607 TATTTATC
1 TATTTATC
6615 TA-TTATTC
1 TATTTA-TC
* *
6623 TCTATATC
1 TATTTATC
6631 TATTTATC
1 TATTTATC
6639 TATTTATC
1 TATTTATC
6647 T
1 T
6648 CTATACCTAT
Statistics
Matches: 165, Mismatches: 22, Indels: 63
0.66 0.09 0.25
Matches are distributed among these distances:
5 4 0.02
6 10 0.06
7 35 0.21
8 72 0.44
9 10 0.06
10 13 0.08
11 17 0.10
12 4 0.02
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTATC
Found at i:6669 original size:24 final size:24
Alignment explanation
Indices: 6603--6659 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
6593 TCCTTTTAGT
6603 TACCTATTTATCTA-TTATTCTCTA
1 TACCTATTTATCTATTTA-TCTCTA
*
6627 TATCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
6651 TACCTATTT
1 TACCTATTT
6660 TTTTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:8645 original size:30 final size:30
Alignment explanation
Indices: 8594--8654 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
8584 TAAGGCTTAC
*
8594 TATGTTTAATTGTTGCAATTTGGGACTTGT
1 TATGCTTAATTGTTGCAATTTGGGACTTGT
* *
8624 TATGCTTAATT-TCTGCGATTTGGGGCTTGT
1 TATGCTTAATTGT-TGCAATTTGGGACTTGT
8654 T
1 T
8655 TGGGTGTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.16, C:0.10, G:0.25, T:0.49
Consensus pattern (30 bp):
TATGCTTAATTGTTGCAATTTGGGACTTGT
Done.