use Bio::SeqIO;

open (LIST1, "list");
    while (<LIST1>){
        ($V1, $V2) = split(/\t/, $_);
    }
close(LIST1);

my $seqIO_object = Bio::SeqIO->new(-file=>"infile.gb");
my $seq_object = $seqio_object ->next_seq;

for my $feat_object ($seq_object->get_SeqFeatures){
    if ($feat_object->primary_tag eq "CDS"){
        if ($feat_object->has_tag('locus_tag')){
            for my $V3 ($feat_object ->get_tag_values('locus_tag')){
                if ($V1 eq $V3){
                    print "locus_tag: ", $V1, " is unique\n";
                }
            } 
         }
     }
}