Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016923.1 Corchorus olitorius cultivar O-4 contig16956, 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: 23160
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4650 original size:54 final size:54
Alignment explanation
Indices: 4568--4676 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
4558 GAAACAGGTG
*
4568 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
*
4622 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
4676 T
1 T
4677 CGTTTCAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (54 bp):
TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAGAGTTGATC
Found at i:4688 original size:35 final size:35
Alignment explanation
Indices: 4641--4959 Score: 399
Period size: 35 Copynumber: 9.0 Consensus size: 35
4631 TCCAGTGCGG
*
4641 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* *
4676 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * **
4711 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
4746 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4781 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* * *
4816 TCCTTTCAA-AGAGTTTTTGTTGATCAGAGTTGATC
1 TCATTTCAAGA-AGTTTTCGATGATCAGAGTTGATC
** *
4851 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATC
1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC
* ** *
4888 TCCTTTCAAGAAGCTTTTTTATTATCAGAGTTGATC
1 TCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
4924 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
4959 T
1 T
4960 TCACATTGAT
Statistics
Matches: 246, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
34 14 0.06
35 158 0.64
36 44 0.18
37 30 0.12
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Found at i:6415 original size:19 final size:19
Alignment explanation
Indices: 6391--6485 Score: 91
Period size: 19 Copynumber: 4.6 Consensus size: 19
6381 TTTTTTAAAT
*
6391 TATTATTTATTAATTTAAC
1 TATTATTTATTAATTTAGC
*
6410 TATTATCTATTTATTTACTATTTATC
1 ---TAT-TATTTA-TTA--ATTTAGC
6436 TATTTATTTATTAATTTAGC
1 TA-TTATTTATTAATTTAGC
6456 TATTATTTATTAATTTAGC
1 TATTATTTATTAATTTAGC
*
6475 TATTATCTATT
1 TATTATTTATT
6486 TTTTTTACCT
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
19 27 0.42
20 8 0.12
22 6 0.09
23 14 0.22
24 4 0.06
26 6 0.09
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTATTTATTAATTTAGC
Found at i:6426 original size:4 final size:4
Alignment explanation
Indices: 6393--6590 Score: 77
Period size: 4 Copynumber: 50.0 Consensus size: 4
6383 TTTTAAATTA
* * * * * *
6393 TTAT TTAT TAAT TTAA CTA- TTAT CTAT TTAT TTA- CTAT TTAT CTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * * * * *
6439 TTAT TTAT TAAT TTAG CTA- TTAT TTAT TAAT TTAG CTA- TTAT CTATT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T
* * * * * * * * * * *
6486 TTTT TTAC CTAC CTAT TTAT CTAA TTAT CTAT ATAC CTAT TTAT CTT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT
*
6534 TTAT TTAT TTA- TTATT CTTAC TTAT TT-T TCTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTA-T -TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT
6583 TTAT TTAT
1 TTAT TTAT
6591 CCATTACTTT
Statistics
Matches: 141, Mismatches: 41, Indels: 24
0.68 0.20 0.12
Matches are distributed among these distances:
3 15 0.11
4 117 0.83
5 6 0.04
6 3 0.02
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.63
Consensus pattern (4 bp):
TTAT
Found at i:6446 original size:46 final size:46
Alignment explanation
Indices: 6393--6486 Score: 145
Period size: 46 Copynumber: 2.0 Consensus size: 46
6383 TTTTAAATTA
*
6393 TTATTTATTAATTTAACTATTATCTATTTATTTA-CTATTTATCTAT
1 TTATTTATTAATTTAACTATTATCTATTAATTTAGCTA-TTATCTAT
* *
6439 TTATTTATTAATTTAGCTATTATTTATTAATTTAGCTATTATCTAT
1 TTATTTATTAATTTAACTATTATCTATTAATTTAGCTATTATCTAT
6485 TT
1 TT
6487 TTTTTACCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 41 0.93
47 3 0.07
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (46 bp):
TTATTTATTAATTTAACTATTATCTATTAATTTAGCTATTATCTAT
Found at i:6613 original size:41 final size:41
Alignment explanation
Indices: 6533--6613 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
6523 TATTTATCTT
* *
6533 TTTATTTATTTATTATTCTTACTTATTTTTCTATTTATTTA
1 TTTATTTATTTATTATCCTTACTTATTTTTCTATATATTTA
*
6574 TTTATTTATTTATTTATCCATTACTT-TTTTTTTA-ATATTT
1 TTTATTTATTTA-TTATCC-TTACTTATTTTTCTATATATTT
6614 TTTTTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 17 0.49
42 12 0.34
43 6 0.17
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (41 bp):
TTTATTTATTTATTATCCTTACTTATTTTTCTATATATTTA
Found at i:22401 original size:25 final size:24
Alignment explanation
Indices: 22373--22434 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
22363 GTGGATTGTA
*
22373 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTGAAGAATTAA-ACATT
* *
22398 AAATAAATTTAAGAATTAAATATT
1 AAATAAATTGAAGAATTAAACATT
*
22422 AAA-AAATTCAAGA
1 AAATAAATTGAAGA
22435 CTGGCCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 9 0.27
24 7 0.21
25 17 0.52
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (24 bp):
AAATAAATTGAAGAATTAAACATT
Done.