use strict;

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

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