Example of output generated when the competion algorithm analyzes the pbr322.toy.fa sequence.  These results are described in the Bioinformatics citation.

To execute type the following on the command line:
perl master.pl -f pbr322.toy.fa -a A -o pbr322.toy.compete.txt -b -p -r

Input files:
1. pbr322.toy.fa

Output files:
1. one_line.pbr322.toy.fa : sequences file format required by Inverted Repeat Finder (IRF)
2. one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.html: IRF output file 
3. one_line.pbr322.toy.fa.2.10.10.80.10.20.10000.100.1.txt.html: IRF output file
4. pbr322.toy.compete.txt : output file

Figure all.eps represents graphically the output shown in pbr322.toy.compete.txt