Pipeline for the prediction of miRNAs. miRNAs were identified by a series of filters. Black arrows are used to indicate the small RNAs that passed the criteria. The dashed arrow indicates small RNAs that failed to pass the criteria. Numbers of candidate miRNAs and precursors after each filter are indicated. Gray lines indicate where data from two pipelines has been combined. aStrict criteria are ≤4 mismatches + bulges in the miRNA:miRNA* pairing and a bulge size of ≤1 nucleotide. bLess strict criteria are defined as ≤8 mismatches + bulges in the miRNA:miRNA* pairing. cNon-redundant miRNAs from miRBase Release 18. dUp to two nucleotide mismatches from miRBase Release 19 were allowed. eConserved miRNAs include manually identified miR444 precursors and miR2218 precursors. miRNA, microRNA; nt, nucleotide; TP2M, transcripts per 2 million.