Perhaps something like this:

use strict;
use warnings;
use Data::Dumper;

my @genes;
my $screen = "ATCGATCGXXXXXATCGATXXXACTGCTACGGTACXXXAATTATXGCGCGXXT";

my @genes;
while ( $screen =~ /([^X]+)/g ) {
  my $start = pos($screen) - length($1);
  push @genes, [$start, $1];
}

print Dumper \@genes;
[download]

-enlil