my @officialannotation = (); # An empty list. NOT [] , which is an empty array-ref
my $offgenes;

open(my $infile , "<", "genbankfile.txt") or die "cannot open file genbankfile.txt $!";
while(<$infile>) {
   $offgenes++ if ($_ =~ /\d+/) ;
   my ($start, $stop)  = split;
   push @officialannotation, {start=> $start, stop => $stop};
}
close $infile;
#.. collect the other one in the same way
# Then compare the 2 arrays of hashrefs :

for my $p (@prodigalannotation){
   next unless my ($candidate) = grep {$p->{start} eq $_->{start}} @officialannotation;
   $exactmatching++ if $candidate->{stop}  eq $p->{stop};
}