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";
    }
}