<p>Identification of <i>MIRNA</i> foldbacks with similarity to protein-coding genes. (A) Flowchart for identification of <i>MIRNA</i> foldbacks with similarity, extending beyond the miRNA target site, to protein-coding genes. (B) <i>Arabidopsis</i> gene or transcript hits in FASTA searches using foldback sequences for all conserved and non-conserved <i>MIRNA</i> loci (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000219#pone-0000219-t001" target="_blank">Tables 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000219#pone-0000219-t002" target="_blank">2</a>). The top four hits based on E-values are shown. (C) Z-scores for the Needleman-Wunche alignment values from <i>MIRNA</i> foldback arms with top four gene or transcript FASTA hits. Alignments were done with intact foldback arms (I), and with foldback arms in which miRNA or miRNA-complementary sequences were deleted (D). Z-scores were derived from standard deviation values for alignments of randomized sequences. In (B) and (C), a red symbol represents an experimentally validated target, a pink symbol indicates a gene from a validated target family, and an open symbol indicates a gene that is distinct from either the validated or predicted target family.</p
