# here is where I messed up for the query. I cannot control this loop.
# it finds the things but fails to print them only once. 

foreach $1 (sort keys %file1){
    foreach my $position1 (@{$file1{$1}}){
        $found =0;
        foreach $contig_id(sort keys %hash_1){
            foreach my $position (@{$hash_1{$contig_id}}){
                $found = 1 if $1 =~ /^$contig_id/ && $contig_id=~ /^$1/ && $position1==$position;
                print RESULTS "$position1\t$1\n" if $found;

                print "not matched\n" if !$found;
            }
        }
    }
}