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 TGCCAATGGAGATTTGCCCAG GGGCAAATCTTCACTGGCAGG TTTCAGCTGCAGTTGCATTACAGGGCAAATCTTCACTGGCAGGCAGCCACTTTGGCTTACCATCACCTGTCATGCTTTTTTTTTTTTTTATTGTGCTCTCTGCCAATGGAGATTTGCCCAGCAATTCCACTGCAACATTGG 2 0 3' arm Theobroma_cacao mirbase mir-399 0.0000005 osa-MIR399f 0.00000003 -47.55 .....(.((((((.(.(((.(.(((((((((((((.(((((((.(((.((..((((............))))....................))))).))))))).))))))))))))).).))).).)))))).)..... (-47.55)