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print join'',unpack 'C*',   
  'AGGCGGAAGCACCCAACAGCAACAG' 
^ 'ACACGCAAAAACCGAAGAGAAAGCG';

0460040062000400400200420

print $_ = grep $_,unpack 'C*', 
  'AGGCGGAAGCACCCAACAGCAACAG' 
^ 'ACACGCAAAAACCGAAGAGAAAGCG';

10

#! perl -slw
use strict;
...
}

close SEQ;