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$a = 'PF01389   6   218 1   255 430.09';
$b = 'PF00691   PF01389';
...
if ( @common ) {
    print "correct\n";
}

$a = 'PF01389   6   218 1   255 430.09';
$b = 'PF00691   PF01389';
...
if ( @in_both ) {
    print "correct\n";
}