mature_miRNA miRNA* pre-miRNA EST_contig mismatches bulges arm species source_database RFAM_best_hit RFAM_lowest_evalue miRBase_best_hit miRBase_lowest_evalue folding_energy secondary_structure ATGCACTGCCTCTTCCCTGG GCTCAAGGTGAAACCAACCGCTCTGCTCTCCGGCTCCAGTGGAGCCAAACTAGCTAGCAACAGAATCCATGCACTGCCTCTTCCCTGGGGATCGATCATCAAAAGAGGGCGAGCTTGACAAGGACGGCGGCGG 9 58 3' arm Brachypodium_distachyon pmrd MIR408 0.0005 aqc-MIR408 0.000006 -39.1 ......((.....))..(((((..(((.(((((((((...))))))...(.((((.((..(((..........)))((((((((....)))............))))))).)))).)....))).)))))))) (-39.10)