Geneious vs Perl script of IN SILICO PCR

Question

[Bio_Crap]

I have tried both methods with the exact same input but the # of results is different. While Geneious can generate more than 400 PCR products, the scripting method only generate 200. Both have the same setting (no mismatches allowed). I am wondering what makes the difference. Algorithm? Or others?

[Istvan Albert]

many things can make a difference - output may be filtered by many other parameters, melting point, distances etc

and of course it could be a flawed implementation of either - especially when you just say "Perl script" ...