Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022392.1 Corchorus olitorius cultivar O-4 contig22425, 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: 33591
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:4927 original size:15 final size:15
Alignment explanation
Indices: 4907--4936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4897 CATCATTCTT
4907 AAGTAGCTATAATCA
1 AAGTAGCTATAATCA
*
4922 AAGTAGCTCTAATCA
1 AAGTAGCTATAATCA
4937 CTTACCATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.27
Consensus pattern (15 bp):
AAGTAGCTATAATCA
Found at i:7867 original size:11 final size:11
Alignment explanation
Indices: 7851--7876 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7841 CCTTGCCTAA
7851 AAAACTAGAAG
1 AAAACTAGAAG
7862 AAAACTAGAAG
1 AAAACTAGAAG
7873 AAAA
1 AAAA
7877 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:10706 original size:5 final size:6
Alignment explanation
Indices: 10691--10724 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
10681 TTGAAATCCT
**
10691 AAAAAG AAAAAG AAAAAG AAAACT AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
10725 TTAACATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:13891 original size:11 final size:11
Alignment explanation
Indices: 13875--13900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13865 CCTTGCCTAA
13875 AAAACTAGAAG
1 AAAACTAGAAG
13886 AAAACTAGAAG
1 AAAACTAGAAG
13897 AAAA
1 AAAA
13901 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:15653 original size:17 final size:17
Alignment explanation
Indices: 15631--15667 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
15621 GTTAGAAATT
*
15631 AAAAATTAA-AAATTAA
1 AAAAAATAAGAAATTAA
15647 AAAAAATAAGAAATTAA
1 AAAAAATAAGAAATTAA
15664 AAAA
1 AAAA
15668 TATTGGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (17 bp):
AAAAAATAAGAAATTAA
Found at i:29518 original size:12 final size:13
Alignment explanation
Indices: 29495--29523 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
29485 TATCACTCTT
29495 TAAAAATAAATAA
1 TAAAAATAAATAA
29508 TAAAAAT-AATAA
1 TAAAAATAAATAA
29520 TAAA
1 TAAA
29524 TAAGGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAATAA
Found at i:29626 original size:26 final size:25
Alignment explanation
Indices: 29584--29632 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
29574 TGTCCCTCTG
*
29584 AAAAAAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
29609 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
29633 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.16
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Done.