Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01006579.1 Corchorus olitorius cultivar O-4 contig06604, 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: 4138
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2356 original size:29 final size:30
Alignment explanation
Indices: 2302--2375 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
2292 TACCCAGAAA
*
2302 AATCCCTTATGTTTTGCTTTTGGGACAAAAT
1 AATCCCTTATGTTTT-CTTTCGGGACAAAAT
*
2333 AATCCCTTATGTTTT-TTTCGGGACAAATT
1 AATCCCTTATGTTTTCTTTCGGGACAAAAT
*
2362 AATCCCTTACGTTT
1 AATCCCTTATGTTT
2376 CAAAAATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (30 bp):
AATCCCTTATGTTTTCTTTCGGGACAAAAT
Found at i:2569 original size:31 final size:31
Alignment explanation
Indices: 2519--2612 Score: 136
Period size: 31 Copynumber: 3.1 Consensus size: 31
2509 AAGGGACTAA
*
2519 TTTGTCTCAAAA-AAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
2549 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* * * *
2580 TTCGTTCCAAAAGAAAAAAATTAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
2611 TT
1 TT
2613 AGTATTTAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 11 0.19
31 47 0.81
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:2667 original size:7 final size:7
Alignment explanation
Indices: 2657--2699 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
2647 AAATTAATTT
2657 TTTTTTC
1 TTTTTTC
2664 TTTTTTC
1 TTTTTTC
2671 TTTTTTTC
1 -TTTTTTC
2679 TTTTTTC
1 TTTTTTC
*
2686 TCTTTTC
1 TTTTTTC
2693 TTTTTTC
1 TTTTTTC
2700 CTTCTCCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:2669 original size:8 final size:8
Alignment explanation
Indices: 2656--2691 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2646 AAAATTAATT
2656 TTTTTTTC
1 TTTTTTTC
2664 -TTTTTTC
1 TTTTTTTC
2671 TTTTTTTC
1 TTTTTTTC
2679 TTTTTTCTC
1 TTTTTT-TC
2688 TTTT
1 TTTT
2692 CTTTTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.27
8 13 0.50
9 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2676 original size:15 final size:15
Alignment explanation
Indices: 2656--2699 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
2646 AAAATTAATT
2656 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
2671 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
*
2686 -TCTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
2700 CTTCTCCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:2685 original size:22 final size:22
Alignment explanation
Indices: 2657--2698 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2647 AAATTAATTT
*
2657 TTTTTTCTTTTTTCTTTTTTTC
1 TTTTTTCTCTTTTCTTTTTTTC
2679 TTTTTTCTCTTTTCTTTTTT
1 TTTTTTCTCTTTTCTTTTTT
2699 CCTTCTCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTTTTCTCTTTTCTTTTTTTC
Found at i:2932 original size:125 final size:125
Alignment explanation
Indices: 2787--3024 Score: 327
Period size: 125 Copynumber: 1.9 Consensus size: 125
2777 AATTCCTAAA
*
2787 AAAATGGTAAAGATAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTT-
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAG-ATTTAATTAAATAAAAATAGAATTTTTA
* * *
2850 GGTAAAAAAAACTGTAAAAGTTTAAATAATGCCATTTAAGAAATATATTTAATTAAAATAGT
65 AGTAAAAAAAACTGTAAAAGTATAAA-AATGCCATTTAAAAAATATATTTAATTAAAATAGT
* * *
2912 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAA
1 AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
* * ** * *
2977 TTGAGTAAAATTGTAAAAGTATAAAAATGTCATTTAAAAAATATATTT
66 GTAAAAAAAACTGTAAAAGTATAAAAATGCCATTTAAAAAATATATTT
3025 GAAAAATAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
125 78 0.80
126 20 0.20
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (125 bp):
AAAATGGTAAAAATAAAATAGTTATAAAAATATTAGATTTAATTAAATAAAAATAGAATTTTTAA
GTAAAAAAAACTGTAAAAGTATAAAAATGCCATTTAAAAAATATATTTAATTAAAATAGT
Found at i:3725 original size:31 final size:31
Alignment explanation
Indices: 3649--3714 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3639 ACTAAATACT
*
3649 AAAAAAATTCTCTTATATTTTTCTTTTGGGAC
1 AAAAAAA-TCCCTTATATTTTTCTTTTGGGAC
* *
3681 AAAAAAATCCCTTATGTTTTTCTTTTTGGAC
1 AAAAAAATCCCTTATATTTTTCTTTTGGGAC
3712 AAA
1 AAA
3715 TCAGTCCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 24 0.77
32 7 0.23
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (31 bp):
AAAAAAATCCCTTATATTTTTCTTTTGGGAC
Found at i:3852 original size:29 final size:31
Alignment explanation
Indices: 3810--3877 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
3800 CTCATTTTTG
* * *
3810 AAACGTAAGGGATTAATTTGTC-CTAAAA-A
1 AAACATAAGAGATTAATTTGTCTCAAAAACA
*
3839 AAACATAAGAGATTATTTTGTCTCAAAAACA
1 AAACATAAGAGATTAATTTGTCTCAAAAACA
3870 AAACATAA
1 AAACATAA
3878 AGGATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.58
30 5 0.15
31 9 0.27
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (31 bp):
AAACATAAGAGATTAATTTGTCTCAAAAACA
Done.