#!/usr/bin/perl-w
use strict;
use Data::Dump qw[ pp ];
my $a="AGAGATATTCAAATT";
my $b="TCGAACGTCGAG";
my (%first,%second,%third);
my @trilet1 = $a =~ /.../g;
my @trilet2 = $b =~ /.../g;
use Data::Dump qw[ pp ];
Code?????

for my $p ( 0 .. length( $seq1 ) - 1 ) {
    my $c1 = substr $seq1, $p, 1;
    my $c2 = substr $seq2, $p, 1;
    next if $c1 eq $c2;
    ++$subs{ $c1 . '2' . $c2 };
}
pp \%first,%second, %third;
exit;

<p>The result should look like:</p>

<code>Counting Results:
{ For 1st position of all 3-letter words:
A2T=> 1,
G2A=> 1,
A2G=> 1,
C2G=> 1,

For 2nd position of all 3-letter words:
G2C=> 1,

For 3rd position of all 3-letter words:
A2G=> 2,
T2C=> 2,
}