Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_05997
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, 200
Length: 306
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Found at i:112 original size:69 final size:69
Alignment explanation
Indices: 1--131 Score: 262
Period size: 69 Copynumber: 1.9 Consensus size: 69
1 ATGAGTGATCCCAAGTATGCTTATCCTTACCCTGCTCAAGGTCATTATGAAGGTCCTCCAGTTCC
1 ATGAGTGATCCCAAGTATGCTTATCCTTACCCTGCTCAAGGTCATTATGAAGGTCCTCCAGTTCC
66 AAAA
66 AAAA
70 ATGAGTGATCCCAAGTATGCTTATCCTTACCCTGCTCAAGGTCATTATGAAGGTCCTCCAGT
1 ATGAGTGATCCCAAGTATGCTTATCCTTACCCTGCTCAAGGTCATTATGAAGGTCCTCCAGT
132 CATGGCTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (69 bp):
ATGAGTGATCCCAAGTATGCTTATCCTTACCCTGCTCAAGGTCATTATGAAGGTCCTCCAGTTCC
AAAA
Found at i:201 original size:24 final size:21
Alignment explanation
Indices: 136--210 Score: 132
Period size: 21 Copynumber: 3.6 Consensus size: 21
126 TCCAGTCATG
136 GCTCCACCTCCACAATATGCT
1 GCTCCACCTCCACAATATGCT
157 GCTCCACCTCCACAATATGCT
1 GCTCCACCTCCACAATATGCT
* *
178 GCTCCACCTCCGCAGTATGCT
1 GCTCCACCTCCACAATATGCT
199 GCTCCACCTCCA
1 GCTCCACCTCCA
211 AGACCTGGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.20, C:0.45, G:0.12, T:0.23
Consensus pattern (21 bp):
GCTCCACCTCCACAATATGCT
Done.