Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000092.1 Corchorus olitorius cultivar O-4 contig00092, 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, 652
Length: 1087
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Found at i:216 original size:28 final size:28
Alignment explanation
Indices: 148--222 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
138 TATGGGCATA
* *
148 AAATTACCGTTTTACCCTAAGAATGAAT
1 AAATTACAGTTTTACCCTTAGAATGAAT
**
176 AAATTACCA-TTTTACCCTTAGAA-GGTT
1 AAATTA-CAGTTTTACCCTTAGAATGAAT
*
203 AAATTTACAGTTTTAACCTT
1 AAA-TTACAGTTTTACCCTT
223 GTACTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 7 0.18
28 31 0.79
29 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATTACAGTTTTACCCTTAGAATGAAT
Found at i:339 original size:28 final size:28
Alignment explanation
Indices: 308--366 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
298 ACGATTTTAC
*
308 CCCTATCAT-GAA-AAAAGTTACTGTTTTG
1 CCCT-TCATCGAATAAAA-TTACCGTTTTG
*
336 CCCTTTATCGAATAAAATTACCGTTTTG
1 CCCTTCATCGAATAAAATTACCGTTTTG
364 CCC
1 CCC
367 CTGTAGACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 20 0.74
29 4 0.15
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (28 bp):
CCCTTCATCGAATAAAATTACCGTTTTG
Done.