Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009716.1 Corchorus olitorius cultivar O-4 contig09748, 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: 5849
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Found at i:4258 original size:15 final size:17
Alignment explanation
Indices: 4238--4277 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
4228 CAAGCAGGTA
4238 ATTTTGTT-TTA-CATT
1 ATTTTGTTATTACCATT
4253 ATTTTGTTATTACCATT
1 ATTTTGTTATTACCATT
4270 ACTTTTGT
1 A-TTTTGT
4278 GAGTACTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 5 0.23
18 6 0.27
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.62
Consensus pattern (17 bp):
ATTTTGTTATTACCATT
Found at i:5240 original size:53 final size:53
Alignment explanation
Indices: 5171--5273 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
5161 TGAGGTTAGG
*
5171 TTTTTTTTTTGGTACCTTCGGTTAGTCAATTTAATCGATATTGTTGTGAGGTT
1 TTTTTTTTTTGATACCTTCGGTTAGTCAATTTAATCGATATTGTTGTGAGGTT
* * * *
5224 TTTTTTTTTTTATACCTTCGGTTTGTTAATTTCATCGATATTGTTGTGAG
1 TTTTTTTTTTGATACCTTCGGTTAGTCAATTTAATCGATATTGTTGTGAG
5274 TAGTCCACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.17, C:0.10, G:0.18, T:0.55
Consensus pattern (53 bp):
TTTTTTTTTTGATACCTTCGGTTAGTCAATTTAATCGATATTGTTGTGAGGTT
Done.