Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010330.1 Corchorus olitorius cultivar O-4 contig10362, 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: 11339
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:2689 original size:24 final size:28
Alignment explanation
Indices: 2659--2708 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 28
2649 AGATTGGACT
2659 TTATTTTA-AT-TTT-TAA-AGATTAGG
1 TTATTTTAGATATTTATAACAGATTAGG
2683 TTATTTTAGATATTTATAACAGATTA
1 TTATTTTAGATATTTATAACAGATTA
2709 AAGGAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 3 0.14
27 3 0.14
28 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (28 bp):
TTATTTTAGATATTTATAACAGATTAGG
Found at i:3785 original size:26 final size:26
Alignment explanation
Indices: 3756--3833 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 26
3746 ACGGTTTTTT
3756 ATTAATGGGACAAATTAAAATAAAAA
1 ATTAATGGGACAAATTAAAATAAAAA
*
3782 ATT-ATGGGGACAAATTCAAA-AAAAA
1 ATTAAT-GGGACAAATTAAAATAAAAA
*
3807 A-GAA-GGGACTAAATTAGAAAATAAAAA
1 ATTAATGGGAC-AAATT--AAAATAAAAA
3834 TAATAGGGGC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
25 9 0.21
26 19 0.44
27 5 0.12
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.19
Consensus pattern (26 bp):
ATTAATGGGACAAATTAAAATAAAAA
Found at i:5242 original size:20 final size:20
Alignment explanation
Indices: 5217--5256 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5207 ATTACAAAGA
5217 AACTCACATTCCGTGAGAGT
1 AACTCACATTCCGTGAGAGT
5237 AACTCACATTCCGTGAGAGT
1 AACTCACATTCCGTGAGAGT
5257 TGAACCCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (20 bp):
AACTCACATTCCGTGAGAGT
Found at i:6255 original size:15 final size:15
Alignment explanation
Indices: 6235--6280 Score: 92
Period size: 15 Copynumber: 3.1 Consensus size: 15
6225 TGTTTGGAAG
6235 TTTTTATAGAAAGTT
1 TTTTTATAGAAAGTT
6250 TTTTTATAGAAAGTT
1 TTTTTATAGAAAGTT
6265 TTTTTATAGAAAGTT
1 TTTTTATAGAAAGTT
6280 T
1 T
6281 AGGACTAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (15 bp):
TTTTTATAGAAAGTT
Found at i:7458 original size:7 final size:7
Alignment explanation
Indices: 7446--7504 Score: 77
Period size: 7 Copynumber: 8.3 Consensus size: 7
7436 GTCGAGAGGC
7446 AAAAA-A
1 AAAAAGA
7452 AAAAA-A
1 AAAAAGA
7458 AAAAAGA
1 AAAAAGA
7465 AGAAGAAGAA
1 A-AA-AAG-A
7475 AAAAAGA
1 AAAAAGA
7482 AAAAAGA
1 AAAAAGA
7489 AAAAAGA
1 AAAAAGA
7496 AAAAAGA
1 AAAAAGA
7503 AA
1 AA
7505 TGAAATCTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
6 11 0.22
7 26 0.53
8 5 0.10
9 5 0.10
10 2 0.04
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:9759 original size:14 final size:14
Alignment explanation
Indices: 9740--9767 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9730 AGCTAGCTGT
9740 TTGTTTTGTTTATG
1 TTGTTTTGTTTATG
9754 TTGTTTTGTTTATG
1 TTGTTTTGTTTATG
9768 CAGACCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.71
Consensus pattern (14 bp):
TTGTTTTGTTTATG
Found at i:10681 original size:23 final size:23
Alignment explanation
Indices: 10651--10695 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
10641 TTTTTTCCTG
10651 TTTTCTCTTCCCTT-TCCCTTCTA
1 TTTTCTCTTCCCTTCT-CCTTCTA
*
10674 TTTTCTCTTTCCTTCTCCTTCT
1 TTTTCTCTTCCCTTCTCCTTCT
10696 TCCTTCTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTCTCTTCCCTTCTCCTTCTA
Done.