I'm not sure how long the C sourcecode is, but the entire .exe is about 400-500 kb. Besides, it has additional features, like GUI, together with severeal other character comparison options...
And, yes, i've looked at bioperl, but couldn't find what i needed, so i started from scratch. I plan to do some Monte Carlo simulations, and most of the things i need for the job are ready (like PRNG with **BIG** period), and i've almost ready to start working on Random and Markov chain string generator - (come to think of it, i haven't looked if these two already exist...:-)). I do hope that I didn't overlook the existence of the scripts i need....:-)