I actually used the exact same structure (and even used the exact same error messages!) that you provided in the original post. Did you write that code yourself? Anyway, I also gave a direct example of how to run the script. Assuming you saved the script as 1041523.pl (an odd name, to be sure—feel free to choose a better one), type the following:

perl 1041523.pl GGGGaaaaaaaatttatatat atatataaattttttttcccc

Of course, substitute any two sequences for the two shown here.