The genome you specify here will be used as a target of the search. In addition to the genome, you should also specify which region of the genome to be searched. Intergenic means that SCOPE will examine all the sequences upstream of a gene untii the previous gene. You can, instead, choose to examine a fixed length sequence (using the popup menu) for your search. Note that for fixed lengths, SCOPE performs an additional calculation that will likely provide improved results. Note that the fixed length might extend into a previous gene for some locations.