$a = 'PF01389   6   218 1   255 430.09';
$b = 'PF00691   PF01389';

my %counts;
foreach ( split /\s+/, $a ) {
    $counts{$_} = 1;
}
foreach ( split /\s+/, $b ) {
    $counts{$_}++ if exists $counts{$_};
}
my @common = grep $counts{$_} > 1, keys %counts;

if ( @common ) {
    print "correct\n";
}