Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005616.1 Corchorus capsularis cultivar CVL-1 contig05634, 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: 2770
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Found at i:924 original size:6 final size:7
Alignment explanation
Indices: 911--939 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
901 GAGCTTCTTC
911 TTCTTTT
1 TTCTTTT
918 TTCTTTT
1 TTCTTTT
925 TTCTTTT
1 TTCTTTT
932 TTCTTTT
1 TTCTTTT
939 T
1 T
940 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTCTTTT
Found at i:2220 original size:14 final size:13
Alignment explanation
Indices: 2200--2252 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
2190 TCAAAATCTT
2200 TTTTTTGAAAACTC
1 TTTTTTGAAAA-TC
*
2214 ATTTTTGAAAATC
1 TTTTTTGAAAATC
*
2227 TTTTCTTGAAAAATT
1 TTTT-TTG-AAAATC
2242 TTTTTTGAAAA
1 TTTTTTGAAAA
2253 AATGTCTCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 9 0.26
14 16 0.47
15 9 0.26
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (13 bp):
TTTTTTGAAAATC
Found at i:2237 original size:28 final size:29
Alignment explanation
Indices: 2192--2252 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
2182 TTAAAAACTC
* *
2192 AAAATCTTTTTTTTGAAAACTCATTTTTG
1 AAAATCTTTTTCTTGAAAAATCATTTTTG
**
2221 AAAATC-TTTTCTTGAAAAATTTTTTTTG
1 AAAATCTTTTTCTTGAAAAATCATTTTTG
2249 AAAA
1 AAAA
2253 AATGTCTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (29 bp):
AAAATCTTTTTCTTGAAAAATCATTTTTG
Done.