well I tested it on different files,
but the main idea is:

foreach (<*.in.sep>){
        $name = $` if /.in.sep/;
        open IN, $_ or die $!;
        open OUT, $name.'.out.sep' or die $!;
                %hash = map{ s/E99/99/g; $_ => $hash{$_}++;} <IN>, <OU
+T>;
        close IN, OUT;

        foreach (sort keys %hash){
                print "$_ $hash{$_}\n" if !$hash{$_};
        }
}
[download]

correct if there are mistakes,
or if it might be optimized
ty)