By taking a 600 nucleotide sequence chunk out of a double coding region of the Hepatitis B NC00397 sequence, we construct a long double coding region, flanked by 300 nucleotides on either side of background sequence. We let this evolve according to the TKF91 model [21] into a descendent sequence, where the Match-Match state emits a descendant according to the Hein & Støvlbaek [5] model with specified evolutionary parameters. We use a gap opening probability of 0.02 and a gap extension probability of 0.4 -these being values similar to the ones encountered in the real sequences we wish to analyse. We also only allow gaps of length 3 within coding regions, so as not to cause a frame shift in coding. We fix all selection parameters to 0.5 and test a variety of evolutionary distances, with transition rate a ranging from 0.2 to 0.7 and transversion rate b = a/2.