Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013120.1 Corchorus olitorius cultivar O-4 contig13153, 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: 4634
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Found at i:3629 original size:8 final size:7
Alignment explanation
Indices: 3609--3661 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
3599 TCCCAATAAT
*
3609 AAAAAAT
1 AAAAAAG
3616 AAAAAAG
1 AAAAAAG
3623 AAGAAAAG
1 AA-AAAAG
3631 AAAAAATG
1 AAAAAA-G
3639 -AAAAAG
1 AAAAAAG
*
3645 AAAAATG
1 AAAAAAG
3652 AAAAAA-
1 AAAAAAG
3658 AAAA
1 AAAA
3662 CACTTGGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 5 0.12
7 27 0.68
8 8 0.20
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (7 bp):
AAAAAAG
Found at i:3637 original size:22 final size:21
Alignment explanation
Indices: 3609--3661 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
3599 TCCCAATAAT
3609 AAAAAATAAAAAAGAAGAAAAG
1 AAAAAATAAAAAAGAA-AAAAG
* *
3631 AAAAAATGAAAAAGAAAAATG
1 AAAAAATAAAAAAGAAAAAAG
3652 AAAAAA-AAAA
1 AAAAAATAAAA
3662 CACTTGGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 10 0.36
22 15 0.54
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (21 bp):
AAAAAATAAAAAAGAAAAAAG
Found at i:3641 original size:13 final size:12
Alignment explanation
Indices: 3616--3661 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
3606 AATAAAAAAT
*
3616 AAAAAAGAA-GA
1 AAAAAAAAATGA
3627 AAAGAAAAAATGA
1 AAA-AAAAAATGA
3640 AAAAGAAAAATGA
1 AAAA-AAAAATGA
3653 AAAAAAAAA
1 AAAAAAAAA
3662 CACTTGGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 11 0.35
13 17 0.55
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:4050 original size:17 final size:17
Alignment explanation
Indices: 4025--4073 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
4015 CCACTCCATC
4025 AAGAAATTCAAAAAAAA
1 AAGAAATTCAAAAAAAA
*
4042 AAGATATTCAAAAAAAA
1 AAGAAATTCAAAAAAAA
*
4059 GAGAAATTCAAAAAA
1 AAGAAATTCAAAAAA
4074 TCAAATCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (17 bp):
AAGAAATTCAAAAAAAA
Found at i:4082 original size:13 final size:13
Alignment explanation
Indices: 4066--4119 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
4056 AAAGAGAAAT
4066 TCAAAAAATCAAA
1 TCAAAAAATCAAA
*
4079 TC--AAAGTC-AA
1 TCAAAAAATCAAA
*
4089 TAAAAAAATCAAAA
1 TCAAAAAATC-AAA
4103 T-AAAAAATCAAA
1 TCAAAAAATCAAA
4115 TCAAA
1 TCAAA
4120 TCAAAATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
10 3 0.09
11 5 0.15
12 9 0.27
13 13 0.39
14 3 0.09
ACGTcount: A:0.69, C:0.13, G:0.02, T:0.17
Consensus pattern (13 bp):
TCAAAAAATCAAA
Found at i:4115 original size:18 final size:19
Alignment explanation
Indices: 4066--4125 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
4056 AAAGAGAAAT
*
4066 TCAAAAAATCAAATCAAAG
1 TCAAAAAATCAAATCAAAA
4085 TCAATAAAA--AAATCAAAA
1 TCAA-AAAATCAAATCAAAA
4103 T-AAAAAATCAAATC-AAA
1 TCAAAAAATCAAATCAAAA
4120 TCAAAA
1 TCAAAA
4126 TCAAAGGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 4 0.11
17 6 0.17
18 18 0.50
19 4 0.11
20 4 0.11
ACGTcount: A:0.68, C:0.13, G:0.02, T:0.17
Consensus pattern (19 bp):
TCAAAAAATCAAATCAAAA
Done.