Examination of Arabidopsis PARE libraries using independently validated miRNA targets to establish criteria cut-offs. Comparisons of validated Arabidopsis miRNA targets and total genome-matched sequences in WT and xrn4 are shown. Histograms in (a) and (b) and lines in (c) show the percentages of PARE sequences matching miRNA target cleavage sites or all the PARE sequences from WT and xrn4 PARE libraries. Gray areas in (a), (b) and (c) indicate the selected cut-offs. (a) Distribution of PARE sequences by normalized abundance. (b) Distribution of PARE sequences by abundance rank in an annotated transcript for miRNA targets. (c) Distribution of PARE sequences by the peak percentage in annotated transcripts for miRNA targets or all genes. (d) A flowchart for evaluating miRNA target cleavage sites based on the three prominence criteria. amiRNA targets with PARE sequences at the precise canonical location. (e) Distribution of validated miRNA targets in WT and xrn4 according to level. miRNA, microRNA; PARE, parallel analysis of RNA ends; TP10M, transcripts per 10 million; WT wild type.