open my $IN, '<', 'domain.txt' or die $!;
while (<$IN>) {
    my ($id, $from, $to) = split /[;\s]+/;
    print "$id; $from $to\n";
    for my $pos (0 .. length($hash1{$id})) {
        print join ' ',
              $pos,
              substr($hash1{$id}, $pos, 1),
              substr($hash2{$id}, $pos * 3, 3),
              $from <= $pos && $pos <= $to ? 'YES' : 'NOT',
              "\n";
    }
}
[download]

Update: The output is now almost the same as yours. The problem was caused by wrong formatting of the post - please use code tags for data, too.

Update 2: This is how I populated the hashes. Again, no BioPerl.

#!/usr/bin/perl
use warnings;
use strict;

sub load_fasta {
    my ($file) = @_;
    open my $IN, '<', $file or die $!;
    my ($seq, $id, %hash) = q();

    my $store = sub {
        $hash{$id} = $seq if $id;
        ($id) = shift =~ /\|(.*)/;
        $seq = q();
    };

    while (<$IN>) {
        chomp;
        if (/^>/) {
            $store->($_);
        } else {
            $seq .= $_;
        }
    }
    $store->(q());
    return %hash
}


my %hash1 = load_fasta('acids.txt');
my %hash2 = load_fasta('nucleotides.txt');
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]