Table 1.

miRNA categories assigned Ceratobasidium small RNA loci after analysis by ShortStack.

Category	miRNA Prediction
N11	Possible mature miRNA had >5 unpaired bases in predicted precursor secondary structure.
N12	Possible mature miRNA was not contained in a single predicted hairpin
N13	Possible miRNA/miRNA* duplexes had >2 mismatches and/or >3 mismatched nucleotides
N14	Imprecise processing: Reads for possible miRNA, miRNA*, and their 3p variants added up to less than 50% of the total reads at the locus.
N15	Maybe. Passed all tests except that the miRNA* was not sequenced. Insufficient evidence to support a de novo annotation of a new miRNA family.
N5	Locus size is less than maximum allowed for RNA folding per option --foldsize (default is 300 nucleotides).
N6	Locus is not stranded (>20% and <80% of reads aligned to top strand)
N8	Strand of possible mature miRNA is opposite to that of the locus

miRNA* refers to the reverse strand.