1. TMTOWTDI
2. I love regular expressions

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
[download]

Update: I just noticed, that my first version fails if the real line length is not a multiple of the wanted length. So I had to put in the grep-regex :-(

Update 2: I alos like obfuscation. So here we go:

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

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

print Dumper \%hash;

__DATA__
ABDCX
EFGHX
[download]