Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018892.1 Corchorus olitorius cultivar O-4 contig18925, 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: 11184
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Found at i:6074 original size:29 final size:29
Alignment explanation
Indices: 6042--6100 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
6032 AAACCTCAAA
6042 TTTCATTTTCCCTT-TACT-TTTCTTTTTCT
1 TTTCATTTTCCCTTCT-CTCTTT-TTTTTCT
* *
6071 TTTCTTTTTTCCTTCTCTCTTTTTTTTCT
1 TTTCATTTTCCCTTCTCTCTTTTTTTTCT
6100 T
1 T
6101 CCTTTTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTCATTTTCCCTTCTCTCTTTTTTTTCT
Found at i:6106 original size:27 final size:26
Alignment explanation
Indices: 6062--6122 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
6052 CCTTTACTTT
*
6062 TCTTTTTCTTTTCTTTTTTCCTTCTC
1 TCTTTTTCTTTTCCTTTTTCCTTCTC
* *
6088 TCTTTTTTTTCTTCCTTTTTCCTTTTC
1 TCTTTTTCTT-TTCCTTTTTCCTTCTC
6115 -CTTTTTCT
1 TCTTTTTCT
6123 CTTTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (26 bp):
TCTTTTTCTTTTCCTTTTTCCTTCTC
Found at i:6115 original size:13 final size:13
Alignment explanation
Indices: 6058--6127 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
6048 TTTCCCTTTA
6058 CTTTT-CTTTTT-
1 CTTTTCCTTTTTC
*
6069 CTTTTCTTTTTTC
1 CTTTTCCTTTTTC
*
6082 CTTCTCTCTTTTT-
1 CTTTTC-CTTTTTC
*
6095 TTTCTTCCTTTTTC
1 CTT-TTCCTTTTTC
6109 CTTTTCCTTTTTC
1 CTTTTCCTTTTTC
6122 TCTTTT
1 -CTTTT
6128 TTCTTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
11 5 0.11
12 5 0.11
13 23 0.49
14 14 0.30
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTCCTTTTTC
Found at i:6133 original size:41 final size:39
Alignment explanation
Indices: 6063--6142 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 39
6053 CTTTACTTTT
* *
6063 CTTTTTCTTTTCTTTTTTCCTTCTCTCTTTTTTTTCTTC
1 CTTTTTCTTTTCCTTTTTCCTTCTCTCTTTTATTTCTTC
* *
6102 CTTTTTCCTTTTCCTTTTTCTCTTTTTTCTTTTATTTCTTC
1 CTTTTT-CTTTTCCTTTTTC-CTTCTCTCTTTTATTTCTTC
6143 AATTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.17
40 12 0.34
41 17 0.49
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (39 bp):
CTTTTTCTTTTCCTTTTTCCTTCTCTCTTTTATTTCTTC
Found at i:6952 original size:2 final size:2
Alignment explanation
Indices: 6940--6975 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6930 CATGAGATTT
*
6940 AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6976 TTTGGGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Done.