Hi Chris, I tried to use your code, first one that reads file1 and make the hash. Does not work very well. I think it does not make hash with multiple values. Because changing the -8 +8 does not change any thing for the $lo or $hi in the second part. Probably a hash of array would work.

my %file1=();
while(<INPUT1>){
         chomp;
         (my $id, my $number) = split("\t", $_);

          if ($id=~ m/(^CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]
++)$/i) {
             #for (my $i=$3-8; $i<=$5+8; $i++){
             #   print join ("\t", $1, $i), "\n";
                # push (@{$file1{$1}}, $i);
              $file1{$1} = [$3-8, $5+8];
       }
   }
#}

        foreach (my($k, $v) = (sort keys %file1)){
        print "$k\t$v\n";
}
[download]

Results

CLS_S3_Contig1000       CLS_S3_Contig10000
CLS_S3_Contig1000       CLS_S3_Contig10000
[download]

I should have use DATA::DUMPER Got it