We describe the type of problem we are confronted with according to a specific example, shown in Figure 5 . Due to the 3-periodicity of the genetic code, there are three global reading frames in which a sequence may code in the forward direction, henceforth referred to as GRF1, GRF2 and GRF3. In viruses these reading frames tend to encode simultaneously for up to three different overlapping genes on each strand, resulting in multiple coding regions. We will be looking at single stranded RNA viruses, which predominantly code in the forward reading direction only. Amendments to our model would have to be made to include reverse reading frame encoded genes.