Will this do what you want?

use strict;

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

while ($screen =~ /(^|(?<=X))([^X]+)/g) {
    print "Gene $2 found at position ", length($`), "\n";
}
[download]

Update: added $2 gene string.