Schematic illustration of the candidate target site generation pipeline. A) MicroRNA - mRNA duplexes sharing the same anchor position on the mRNA are grouped. Duplexes with the lowest free energy in each group are shown in green color, all others in blue. B) Zoom-in at one group. The anchor of each hybrid (red vertical line) is the first nucleotide of the target site base-pairing with the 5' end of the microRNA. Only the energetically most favorable hybrid, shown in green, is retained for further analysis. C) Smoothed attraction graph of all the retained hybrids. A candidate zone is defined as the stretch of the target sequence (shown in purple) where the smoothed hybrid free energy falls below a certain energy threshold. D) For each candidate zone the energetically most favorable hybrid that shows base pairing within the first two nucleotides counting from the microRNA 5' end is selected as its representative.