Modelling of additional/missing bases in gene predictions. Case A shows the result of the search of a kinesin from Neurospora crassa (query sequence) in Neusrospora discreta (target sequence) using the old and the new Scipio version. The --min_intron_len parameter has been set to 22. Case B shows the result of a search of the dynactin p62 homolog from Phytophthora ramorum (query sequence) in Phytophthora sojae (target sequence). To get the correct gene prediction the following Scipio parameters have been used: --min_identity = 60%, --min_score = 0.3, --max_mismatch = ∞, --gap_to_close = 15, --min_intron_length = 22. The colour coding is explained in the legend and applies to all gene structure figures. For further information see Additional file 2.