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 AAGCCAAGAATGACTTGCCTG GGCAGTCTTCTTCGCTTTC AAGAAGAGAGCCTCGCTGGAAAGCCAAGAATGACTTGCCTGCTTCCTCCTTGAGGTTTCAAAATTTCAATGAAACTTTTAAAACCCGCCATTCTGGCTCGCGGGCAGTCTTCTTCGCTTTCTTGACAGGCTATTCTTTTCC 1 2 5' arm Theobroma_cacao mirbase MIR169_5 0.00003 ath-MIR169k 0.0004 -54.8 .((((((((((((..(.(((((((.(((((.((((.((((((.........(((((((((.........)))))))))........(((.....)))..))))))))))))))).))))))).)..))))).))))))).. (-54.80)