Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024880.1 Corchorus olitorius cultivar O-4 contig24913, 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: 19912
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2693 original size:23 final size:23
Alignment explanation
Indices: 2667--2714 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2657 AAATATGATA
2667 TACAAAGATGAGTCAAACCAAGT
1 TACAAAGATGAGTCAAACCAAGT
2690 TACAAAGATGAGTCAAACCAAGT
1 TACAAAGATGAGTCAAACCAAGT
2713 TA
1 TA
2715 AAGGGACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (23 bp):
TACAAAGATGAGTCAAACCAAGT
Found at i:6151 original size:56 final size:55
Alignment explanation
Indices: 6040--6147 Score: 121
Period size: 56 Copynumber: 2.0 Consensus size: 55
6030 ATAAGTCAAA
* * *
6040 TCCTCTTCTAGGGGCAAAGTCGTAATTGTACCAATTCTAGGGTAAAATGGTAATT
1 TCCTCTTATAGGGGCAAAATCGTAATTGTACCAATTCTAGGGTAAAATAGTAATT
* * * *
6095 TCCTCATTATAGGGGTAAAATCGTAATTTTATCAA-TC-AGGGGTAATATAGTAA
1 TCCTC-TTATAGGGGCAAAATCGTAATTGTACCAATTCTA-GGGTAAAATAGTAA
6148 ATTTGTCCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
54 1 0.02
55 19 0.43
56 24 0.55
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (55 bp):
TCCTCTTATAGGGGCAAAATCGTAATTGTACCAATTCTAGGGTAAAATAGTAATT
Found at i:11959 original size:13 final size:13
Alignment explanation
Indices: 11943--11981 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11933 TTTATCTTAC
11943 TATTTTGGTTTAT
1 TATTTTGGTTTAT
**
11956 TATTCCGGTTTAT
1 TATTTTGGTTTAT
*
11969 TACTTTGGTTTAT
1 TATTTTGGTTTAT
11982 GACTTTGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TATTTTGGTTTAT
Found at i:15816 original size:7 final size:7
Alignment explanation
Indices: 15806--15830 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15796 AAAAAAACGA
15806 AAAAAGG
1 AAAAAGG
15813 AAAAAGG
1 AAAAAGG
15820 AAAAAGG
1 AAAAAGG
15827 AAAA
1 AAAA
15831 TTTGGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:17082 original size:21 final size:21
Alignment explanation
Indices: 17042--17084 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17032 TGCTCCCCTC
**
17042 GTTTTCTTCCTCTCTTGTCTG
1 GTTTTCTTCCTCTCCCGTCTG
*
17063 GTTTTCTTTCTCTCCCGTCTG
1 GTTTTCTTCCTCTCCCGTCTG
17084 G
1 G
17085 CATTTTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.30, G:0.16, T:0.53
Consensus pattern (21 bp):
GTTTTCTTCCTCTCCCGTCTG
Found at i:18097 original size:30 final size:31
Alignment explanation
Indices: 18061--18131 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
18051 ATTGAATTGT
*
18061 TCAAATCCT-TTGGTTTGAACCTCAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
18091 TCAAAT-CTGTTGGTTTGAACCTAAGCCTTA
1 TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
18121 TCAAAT-CTGTT
1 TCAAATCCTGTT
18132 ACTAGTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 2 0.05
30 37 0.95
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (31 bp):
TCAAATCCTGTTGGTTTGAACCTAAGCCTTA
Done.