... this is what I have. ...

I'm guessing, but the only thing that occurs to me is that you actually have the line
    perl -wMstrict -l  your_file.pl  GGGGaaaaaaCatttatatat  atatataaatttttATtcccc
as the first non-blank line in your source code file. If so, this line should not be in the source code file. This line is intended as the command line invocation of the source code file. Please see previous examples.

The source code file (which I have named  your_file.pl in these examples) should have everything from the first
    die "Please enter two sequences as arguments on the command line\n"
         unless @ARGV == 2;
statement to the very last  } closing curly brace on the final if-statement.

If this is not the problem, please include exact copies of all warnings or error messages in future posts.