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 TCATCATCATCATCATCATCA ATGAAGAAGATGGAGAGGATA CTCCTTGCTTTGAATGAAGACGATGAAGAAGATGGAGAGGATAAAGAAACGCCATCAATATCATCATCATCATCATCATCATCATCATCAAATGATAAAC CGGGGGGGAGGGAACAGGGTCGGATCTCGGGTCTCCGGAGCTATCTTCGGAGAGTTCGTCTTCGATCGGAGCTCCGGGAGACAGCGATGATGAAGAGGAAGAGGGCGTCGTTTCATCTGGGGGAAGTGGTGGGTTGGCTTCTTTGGTTTCTATAGAGGACTCTCTTCCCATCAAGAGGGGATTGTCGAATCATTATGCAGGGAAATCAAAGTCATTTGCTAATCTCTCAGATATAAGCTCAGTGGAAGATCTGCTGAAGCCAGAGAATCCTTTCAACAAAAGGAGGAGGGTGTTACTTGCAAACAAGTGGTCCAGGAAGTCATCTTTCTACTCTTGGCGGAACCCCAACTCCATGCCCCTCCTTGCTTTGAATGAAGACGATGAAGAAGATGGAGAGGATAAAGAAACGCCATCAATATCATCATCATCATCATCATCATCATCATCAAATGATAAACTATCAGTAGCAGCACAAAAACCAAAATTGCAGCAAAGCAAGCTGAAGGCCACTTTTAAGTCGCAGAGTTGTTTTTCTCTAACAGATCTGCAAGTAGAACATCAATGACGCCCTTTGCTTTCAGCATGAAAAATGCTTTAGGATTTAGATTAGACCCCCCTTTTTTTGGGTTTTTATTTTTATTTTTTACTTGTCCTGCCTTTTCTTCTCTATTTACTCAGAAGAAAAACAAAATTTTTAGCAAGTACAAGTATATATAAAAATAAATATGTTTACAACAGGAAAAAAAAAAAAAAA 5 0 3' arm Theobroma_cacao mirnest 100 100 -23.5 ........(((((.(((.((.(((((.((.(((((.((.((((..((.......))..)))).)).))))).)).))))).)).))))))))........ (-23.5)