Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009729.1 Corchorus olitorius cultivar O-4 contig09761, 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: 8742
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--30 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31 ATATATGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2742 original size:39 final size:36
Alignment explanation
Indices: 2693--2839 Score: 120
Period size: 39 Copynumber: 4.0 Consensus size: 36
2683 AAGCAGTAGA
* *
2693 GAAAGGGAGAAGGAAAGGGACAGAGAAAGGAGAGATAGG
1 GAAA-GGAGAAAGAAAGGGAGAGAGAAAGGAGAGA-A-G
* * *
2732 GATAAGGAGAAAGAAAGGGAAAGGGATAGG-GAG-AG
1 GA-AAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAAG
* ** *
2767 GAGA-GAGAGGGAAAAGGAGAGAGAAAGGAGGGAGAAG
1 GAAAGGAGAAAGAAAGGGAGAGAGAAAGGA--GAGAAG
*
2804 GAGAAGGAGAAAGAAAGGGAGAGAGAAAGAAGAGAA
1 GA-AAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAA
2840 CGAAGCAGCA
Statistics
Matches: 85, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
33 18 0.21
34 1 0.01
35 3 0.04
36 4 0.05
37 9 0.11
38 4 0.05
39 44 0.52
40 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.46, T:0.02
Consensus pattern (36 bp):
GAAAGGAGAAAGAAAGGGAGAGAGAAAGGAGAGAAG
Found at i:2746 original size:27 final size:27
Alignment explanation
Indices: 2716--2829 Score: 102
Period size: 27 Copynumber: 4.5 Consensus size: 27
2706 AAAGGGACAG
*
2716 AGAAAGGAGAGATAGGGATAAGGAGAA
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
2743 AGAAAGG-GA-A-AGGGAT-AGG-G--
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
* *
2763 AG--AGGAGAGAGAGGGAAAAGGAGAG
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
* * *
2788 AGAAAGGAGGGAGAAGGAGAAGGAGAA
1 AGAAAGGAGAGAGAGGGATAAGGAGAA
2815 AGAAAGGGAGAGAGA
1 AGAAA-GGAGAGAGA
2830 AAGAAGAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
18 3 0.04
19 2 0.03
20 3 0.04
21 5 0.07
22 4 0.06
23 4 0.06
24 6 0.08
25 3 0.04
26 2 0.03
27 31 0.44
28 8 0.11
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (27 bp):
AGAAAGGAGAGAGAGGGATAAGGAGAA
Found at i:2769 original size:45 final size:45
Alignment explanation
Indices: 2704--2794 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
2694 AAAGGGAGAA
* *
2704 GGAAAGGGACAGAGAAAGGAGAGATAGGGATAAGGAGAAAGAAAG
1 GGAAAGGGACAGAGAAAGGAGAGAGAGGGAAAAGGAGAAAGAAAG
* * * *
2749 GGAAAGGGATAGGGAGAGGAGAGAGAGGGAAAAGGAGAGAGAAAG
1 GGAAAGGGACAGAGAAAGGAGAGAGAGGGAAAAGGAGAAAGAAAG
2794 G
1 G
2795 AGGGAGAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.48, C:0.01, G:0.47, T:0.03
Consensus pattern (45 bp):
GGAAAGGGACAGAGAAAGGAGAGAGAGGGAAAAGGAGAAAGAAAG
Found at i:2785 original size:21 final size:22
Alignment explanation
Indices: 2761--2816 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
2751 AAAGGGATAG
*
2761 GGAGAGGAGAGA-GAGGGAAAA
1 GGAGAGGAGAAAGGAGGGAAAA
*
2782 GGAGA-GAGAAAGGAGGGAGAA
1 GGAGAGGAGAAAGGAGGGAAAA
2803 GGAGAAGGAGAAAG
1 GGAG-AGGAGAAAG
2817 AAAGGGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 17 0.57
22 1 0.03
23 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (22 bp):
GGAGAGGAGAAAGGAGGGAAAA
Found at i:5612 original size:3 final size:3
Alignment explanation
Indices: 5604--5634 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5594 TTATTCAGTT
5604 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5635 GTTTGTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.