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 CAAGATCATCCCCCATGCTGT TGTTCAGGGGGATGAGCTTGGA CAGATGGAGCAAGATTATGACATTGGGTCAACCATTCGAGACAAGATCATCCCCCATGCTGTGTCATGGTTTACCGGGGAGGCTGTTCAGGGGGATGAGCTTGGACTAGATGATGGTGACAATGACGATTATGAAGATATTGA AAAGCAATAGGAACTGAGATCGAATGGTATCCAGGAAAATGCTTGACCCAGAAGCTTCTTAAGAAGAAGCCCAAGAAAGGATCCAAGAATGCCAAGCCAATTACTAAAACTGAAGACTGTGAAAGTTTTTTCAACTTCTTCAGTCCACCACAAGTTCCTGACGATGATGAAGACATAGATGAAGATACTGCTGAGGAATTGCAAAATCAGATGGAGCAAGATTATGACATTGGGTCAACCATTCGAGACAAGATCATCCCCCATGCTGTGTCATGGTTTACCGGGGAGGCTGTTCAGGGGGATGAGCTTGGACTAGATGATGGTGACAATGACGATTATGAAGATATTGATGAGGATGATGACGAGGAGGAAGATGAGGACGATGAAGAAGATGAAGATGAAGAAGATGAGGATGAGGATGAGGATGAAGGCAAGACCAAAAAGAAGTCATCTGCTGGAAACAAGAAAAGTGGAAGAACACAAGTTGGGGATGGTCAGCAGGGTGAGCGGCCTCCAGAATGCAAGCAGCAGTAAAGTTTTCGCCGCAGCGTATTTGTGAAGTCCTTAATGCAATGGTTGGAAGAGGGGGGGGGTATTTGTGGAAGTTCTTAATGCAATGGTTGGAAGAGGGGAGTATTTGTGAAGTTCTTAATGCAATGCTTGGAAGAGGGGAGTATTTGTGAAGTTCTTAATGCAATGCTTGGAAGGGAGATAGGAAGGGGTGTTGAATTTTGGGATGGTTATTCTTTTTTCTCTCTCTCTACATTAGTATGCCATATTCTGAACAGATGATTTGGACTTCTTTTTACCCTGTTGGTTTGGAGGAAATGTGGGTCAAATAGG 4 1 5' arm Populus_trichocarpa mirnest 100 100 -41.1 ..((((...((.((((....(((((.....(((((((.((.((((.(((((((((..((.((.((.(((....)))..)).)).))...))))))))).))))..)).))..)))))..)))))..)))).))....)))).. (-41.1)