We model the evolution of our sequences according to the Hein & Støvlbaek [5] model. When looking at a nucleotide in the ancestral sequence, for each reading frame we assign a certain state-dependent 'degeneracy-type' t to it, depending on its context. This will, in a coding region in a particular reading frame, be either of degeneracy 1, 2 or 4 and for non-coding will always be designated as 0. Since we are considering overlapping reading frames, we thus obtain for each nucleotide in the ancestral sequence a certain state-dependent 'degeneracy-type-array' t = [t1, t2, t3] -an array consisting of the degeneracy annotation of a nucleotide for each of the three reading frames. In our example in Figure 5 we can see an overlap between two genes, say genes A and B. This results in an annotation of [2, 1, 0] for our nucleotide C in the overlap, meaning that we have a degeneracy annotation of 2 and 1 with respect to gene A and B respectively.