ParaHox example application. SynBlast was used to determine the four pairs of paralogous regions generated by the fish-specific genome duplication from the four gnathostome ParaHox regions. We show alignment dot-plots for the high-ranking hits (according to the gene order alignment score and logRatioSum score (in brackets)) of the four query regions against the zebrafish genome (Zv7, Ensembl release 46, Aug 2007). Parameters for the synteny filtering step were N = 1, L = 2. See text for more details.