Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022851.1 Corchorus olitorius cultivar O-4 contig22884, 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: 3927
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:225 original size:30 final size:31
Alignment explanation
Indices: 146--225 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 31
136 TTTTTTAAGA
* *
146 AAAACGCAAAAACCTTTTTTTTTTTCGACGC
1 AAAACACAAAAACCTTTTTTTTCTTCGACGC
* * **
177 AAAAAACAAACAGATTTTTTTTCTT-GACGC
1 AAAACACAAAAACCTTTTTTTTCTTCGACGC
207 AAAACACAAAAACCTTTTT
1 AAAACACAAAAACCTTTTT
226 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (31 bp):
AAAACACAAAAACCTTTTTTTTCTTCGACGC
Found at i:268 original size:22 final size:21
Alignment explanation
Indices: 226--274 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
216 AAACCTTTTT
226 AAAAAAAAAAAAACGCAACAAA
1 AAAAAAAAAAAAACG-AACAAA
*
248 CAAAAAAATTAAAAACG-ACAAA
1 -AAAAAAA-AAAAAACGAACAAA
270 AAAAA
1 AAAAA
275 TCTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 5 0.21
23 7 0.29
24 7 0.29
ACGTcount: A:0.80, C:0.12, G:0.04, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAAACGAACAAA
Done.