my %ref    = ... ; ## Data::Dump::dd(%ref)    output here
    my @probes = ... ; ## Data::Dump::dd(@probes) output here
##
    foreach my $key ( sort keys %ref ) {

        #intended function
        print OUT $ref{$key} . "\t" . $probes[$key];

        #testing
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) {
                print $key. "\t" . $ref{$key} . "\t" . $probes[$key];
            }
        }
    }
##
    foreach my $key ( sort keys %ref ) {
        print OUT $ref{$key} . "\t" . $probes[$key];
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) { print $key. "\t" . $ref{$key} . "\n"; }
        }
    }