## Untested
open my $match_in, '<', $match_file or die "1st open failed: $!";
open my $fh_in, '<', $in_file       or die "2nd open failed: $!";
open my $fh_out, '>>', $out_file    or die "3rd open failed: $!";

while (my $lines = <$fh_in>) {
  while (my $matches = <$match_in>) {
    chomp $matches;
    my $matchtmp = qr/$matches.*(?:SUPSOSODEV|AJTSOSO(?:CFD|ISI|CLA))/;
    ## Assuming you want to print $lines
    print $fh_out $lines if $lines =~ m/$matchtmp/;
  }
}

close $fh_out;
close $fh_in;
close $match_in;