use Data::Dumper;
my %hash;
my $sub_length = 2;

while (<DATA>) {
    chomp;
    for my $j (0 .. length - $sub_length) {
        push @{$hash{$j}}, substr $_, $j, $sub_length;
    }
}

print Dumper \%hash;

__DATA__
ABDC
EFGH