We compared the baseline to the results achievable from a reduced database. When orthologous sequences are aligned between closely related species, gaps may be introduced, and there are often portions of the sequence that do not align; thus, the overall feasible search space for transcription factor binding sites is reduced. A search of such a reduced database in and of itself will allow the detection of more statistically significant transcription factor binding sites than will a search of a full set of intergenic regions from a single species. Therefore, the scanning results from a database reduced in size, yet containing data from only one species, will provide a measure of the increase in sensitivity to the baseline scan that is due simply to a reduction in search space.