Nice work on processing the Output.txt file. However, if I'm understanding the OP correctly, the contents of domain.txt are used to filter the contents of Output.txt, such that expand.com will not appear in the final output when using the OP's shown data sets. Given this, perhaps something like the following additions are needed:
...
open my $fh2, '<', 'domains.txt' or die "could not open domains.txt: $
+!\n";
my %domains = map { chomp; $_ => 1 } <$fh2>;
close $fh2;
open my $fh, "<", "output.txt" or die "could not open output.txt: $!\n
+";
my %data;
while (<$fh>) {
chomp;
$_ =~ m/(.*?)\s++(\d++)/;
next unless $domains{$1};
...