Welcome to the Monastery! It seems you're doing DNA stuff? You better take a look at CPAN since there are various BIO modules around to ease your live. A few suggestions: Bio::Matrix::PSM::SiteMatrix to work with position scoring/weight matrices, Bio::Align::DNAStatistics calculate some statistics for a DNA alignment, Bio::Tools::DNAGen generating DNA sequences. There are many more. Even if a module does not exactly what you want it can be a useful starting point, i.e. look at how somebody else did it and learn from it;)

HTH
dHarry