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 CGTGAGGTACCGATACCTCAA GAAGTACCGGTACCTCACGGT ATATAAACCAGATATTTGCTCCAGTCTAGCAAAAAAATATCTCGAAGTACCGGTACCTCACGGTACCAAATCATCTCTGATCACTAGATATAGCTCGGTAGGATAGGTATCGTCAAATCCAACAATTAGAAAAGATTTAGTACCGTGAGGTACCGATACCTCAAGATATTTTTTATTTGATCGGAGCAAATCTCTATAAACCAT GGACCGATATCGCCGGCAGCAGCGGCGTGGCGCTGGAGCCGGGGGCGGCGCGGGCGATGGAGGAGAGGGAGGCGGCGCGGGTCGTCATGGGCCGCATCGGCGAGCCCGAGGAGGTGGCGTCGCTCGTCGCGTTCCTCTGCATGCCGGCGGCGCCGTACATCACCGGGCAGGTCATCTGCGTCGACGGTGGCCGCACCATCACCGCCTAGGCAGCTAGGCTAATGAATCCAGAATTCCTAAAACATATTTTGCTTTGCTCTCGTTACCGATCATATAAACCAGATATTTGCTCCAGTCTAGCAAAAAAATATCTCGAAGTACCGGTACCTCACGGTACCAAATCATCTCTGATCACTAGATATAGCTCGGTAGGATAGGTATCGTCAAATCCAACAATTAGAAAAGATTTAGTACCGTGAGGTACCGATACCTCAAGATATTTTTTATTTGATCGGAGCAAATCTCTATAAACCATTATCAATCTACCGCCCTACATATAATTTAGTCCCTCAAAACTTCATTCTGAGGTATATTTGTTGAAAAAAAAA 3 0 3' arm Oryza_sativa mirnest 100 100 -69.6 .........(((.(((((((((.(((.....(((((((((((.((.(((.((((((((((((((((.(((((...((((((.....(((......(((((.......)))))....))).....))))))...))))).)))))))))))))))).))).)).)))))))))))....))).))))))))).)))......... (-69.6)