Sorry, wrong paste:

open IN2, $first_tmp;
while(<IN2>)
{
    if($_=~/^(chr.*?)REC:(.*)/)    
    {
        $respective_chrom=$1;
        $all_entries=$2; 

        @split_entries=();
        @split_entries = split(/\#/, $all_entries);    

        @split_sep_entries=();
        %collapsed_loci_HoA=();

        print ">".$respective_chrom."\n";
        foreach $sep_entry(@split_entries)    
        {
            @split_sep_entries = split(/\t/, $sep_entry);
            $locus_to_use = $split_sep_entries[1];
            $rest_entry=$split_sep_entries[0]."\t".$split_sep_entries[
+2]."\t".
                        $split_sep_entries[3]."\t".$split_sep_entries[
+4]."\t".
                        $split_sep_entries[5]."\t".$split_sep_entries[
+6]."\t".
                        $split_sep_entries[7];
            #print $locus_to_use."##".$rest_entry;
            push @{ $collapsed_loci_HoA{$locus_to_use} }, $rest_entry;
        }
        
        $count_arr=0;
        @array_of_loci = keys %collapsed_loci_HoA;
        for $b(sort { $b <=> $a } @array_of_loci) 
        {
            print  "$b"."\n";
        }
        print "//\n";


    }
}
close IN2;
[download]

Now it is printing the numbers sorted.