#!usr/bin/perl-w
use strict;
my $seq1="AAAGATCGTG";
my $seq2="AGTACTTTCC";
my ($A2G,$G2A,$C2T,$T2C,$A2T,$A2C,$G2T,$G2C)
for (0..length($seq1)-1){
   if (substr($seq1, ???) eq substr($seq2, ??))
   {$A2G++;$G2A++;$C2T++;$T2C++;$A2T++;$A2C++;$G2T++;$G2C++;} 
   else { ?????}
   }
print"\n No. of Substitutions:\n
  A2G=$A2G; G2A=$G2A; C2T=$C2T; T2C=$T2C; A2T=$A2T; A2C=$A2C; G2T=$G2T; G2C=$G2C.\n";
exit;