Identification of miRNA regulated genes. The degradome sequences were mapped to EST sequences. A threshold was determined for each EST based on the standard deviation from the average number of matching degradome sequences. Signatures with read numbers above the threshold were considered as degradome peaks and were used to determine Target Sequence Signatures (TSS). Each TSS was obtained from the EST by extracting the 32 nt sequence centred around the 5’end of a peak signature (cleavage site). The TSSs were used to search for miRNAs potentially responsible for the cleavage. The aligned miRNAs were regrouped depending on the offset (indicated in brackets) between their 10th and 11th nucleotide (bold characters) and the cleavage site. The targets were assigned to one of the three categories (Cat-I, II or III) depending on the number and offset distribution of the matching miRNAs.