Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g01139.N3
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, 672
Length: 1120
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Found at i:316 original size:40 final size:40
Alignment explanation
Indices: 267--342 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
257 TCTTTCTGCA
267 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
*
307 AATCTCATTCCTCTCTTTCTCTCTTTCTCAGGCAAA
1 AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAA
343 TCTCATTCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.18, C:0.36, G:0.08, T:0.38
Consensus pattern (40 bp):
AATCTCATTCCTCCCTTTCTCTCTTTCTCAGGCAAAGGCC
Found at i:345 original size:34 final size:34
Alignment explanation
Indices: 246--354 Score: 125
Period size: 40 Copynumber: 3.1 Consensus size: 34
236 CATCTTCTTT
*
246 CTCTCTCTCTCTCTTTCT---GCAAATCTCATTC
1 CTCTCTTTCTCTCTTTCTCAGGCAAATCTCATTC
*
277 CTCCCTTTCTCTCTTTCTCAGGCAAAGGCCAATCTCATTC
1 CTCTCTTTCTCTCTTTCTCAGGC--A----AATCTCATTC
317 CTCTCTTTCTCTCTTTCTCAGGCAAATCTCATTC
1 CTCTCTTTCTCTCTTTCTCAGGCAAATCTCATTC
351 CTCT
1 CTCT
355 TCGCAAGGTC
Statistics
Matches: 66, Mismatches: 3, Indels: 15
0.79 0.04 0.18
Matches are distributed among these distances:
31 16 0.24
34 16 0.24
36 1 0.02
38 1 0.02
40 32 0.48
ACGTcount: A:0.15, C:0.38, G:0.06, T:0.41
Consensus pattern (34 bp):
CTCTCTTTCTCTCTTTCTCAGGCAAATCTCATTC
Done.