The presence of divergently transcribed genes, that is, the circumstance in which an intergenic region is upstream of, and contains the promoters for, both of a given pair of neighboring genes, is quite common in prokaryotes, and also occurs in eukaryotes, albeit much less frequently. Divergently transcribed genes occur frequently in the E. coli genome (644 pairs of divergently transcribed genes), and their presence has raised the question of which orthologous data should be used when we combine p-values. In the present implementation of PhyloScan, the choice was made randomly. Thus, in such cases, we were as likely to make a "correct" choice as to make an "incorrect" choice, if only one of the E. coli genes flanking an intergenic region containing candidate transcription factor binding sites is regulated by the transcription factor of interest. However, in cases where gene synteny is conserved across several species, this choice becomes irrelevant. That is, when synteny is conserved, the same intergenic regions from each species will be examined regardless of the gene chosen; inspection of the output and, ultimately, experimental validation become necessary in order to evaluate whether a predicted site is associated with the chosen gene, with the divergently transcribed gene, or with both. Implementation of a systematic or informed choice in these situations will be a topic for the future development of PhyloScan.