The cluster A phages have numerous 13bp sequence repeats found throughout the genome, most frequently within intergenic regions (only rarely are they located within genes). These sequences are binding sites for the immunity repressor, and they help prevent transcription elongation during lysogeny. Locating these sequences can help you choose the correct gene start, as the stoperators are mostly not within the genes. Stoperators are also heavily clustered at the right end of the genome, so don't feel you need to add protein encoding genes in all that "empty" space.