Figure 1: Example of a reformatted pre-miRNA structure and predicted localization of a miRNA/miRNA* complex in the pre-miRNA structure. (a) Secondary structure of the pre-miRNA of ath-mir156a in standard representation. The mature miRNA is shown in larger italic characters. (b) Section of the pre-miRNA in an alignment-like format. First and fourth line show the sequence except the sequence region of the hairpin loop; lines 2 and 3 describe the state of the opposing nucleotides: a base pair is marked by “”, nucleotides of an internal loop by “” in both lines, and nucleotides that are part of an asymmetrical internal or a bulge loop by “”. In the fifth line a base pair is marked by “M”, a non-pair by “N”, a deletion in the top strand by “D”, and an insertion in the top strand by “I”. (c) Positions predicted as miRNA/miRNA* complexes are marked by “x” and their relative positions in the sequence.