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

while (<DATA>) {
    chomp; # remove the chomp. It's unnecessary
    $hash{$.-1}=[ grep /$sub_length/o, split /($sub_length)/o ];
}

print Dumper \%hash;

__DATA__
ABDC
EFGH

##</code><code>##

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

$hash{$.-1}=[ grep /$sub_length/o, split /($sub_length)/o ] while <DATA>;

print Dumper \%hash;

__DATA__
ABDCX
EFGHX