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 GCTGGCGCTATCCATCCTGGG CAGAGGGATAGCGCCCACTG TGATGGAATTACAAAGCTCAGAGGGATAGCGCCCACTGCAAATTTCAAGTGGGGCTGGCGCTATCCATCCTGGGCTTCATAATTTCTTT GTAGGTATTTATAGAGAAAATGACCGGACTGGCTGCATGCCCGGCATACGGCAAAGACAAAGCAATCTGCACACGAATGCAACAGTGTGAAAGAAGATTTGGCGAGGAGGGGTGGGGGAGTCCTCCGGCAGGGGGCCGTGGTGTGGAGTCGTTTTCGACGGTTCAATACCTTTACCGGATCTCAAGGCTTTTTCACGCGAAGAAGTAAAAGCTGCTTTTCTGTACCACTCACGTATTCAATGAGATCTTCCTTCGCGCGGCTTGGAGGACGAAATTGGATATGACGGAGACGAGAGGGGTGAGGTTCGAGTTTCGTTGGGCGACCGGGTTTTTTATGATTGGACATACGGCTGCTTCCAGAGGCCTGAATGGAGGGGATGGTGGACTCCACCATGGCCTGTCTTTTGACCGTTTTTGGAGTCTCGTGCATTCCAGGGGTGGTTGGTTCTTTTTTTTTCTAGTACAACACACACAGCGGCGCAATATCGTTGCGTGATCTCAATGGAGAGAATAGTAGTAACGTGGGGTCGACTGTTCACGGGAGGAATCTCTATCTCATCTCATCTCATCTGTTCTCCTTCCCTCTGACCTTTGCCTGGCTACAGTATGGGGAGCCCCCTCCCCTTCAGGCTTATTATAAGTATTCGGCTGTGGAGCCTTCTTTTTCGTGAGGATTATTTTAGCTTATTGCTGGGCTTCCATGGCGAACCAGCATTGGAACACTGTTTTGCCCAGCATTATGTGAATAAAAAAGGGTTTATGATTTTGTCCTCGTGTTCAGTCACGGGTTCGGTTTCAGATCGGCCAAAAGAAATTTCCTGCGGGGAGCTATTTTTTGCGGCATGATGGAATTACAAAGCTCAGAGGGATAGCGCCCACTGCAAATTTCAAGTGGGGCTGGCGCTATCCATCCTGGGCTTCATAATTTCTTTAT 5 1 3' arm Pinus_taeda mirnest 100 pta-MIR390 6e-39 -34.9 ....(((((((..((((((((..((((((((((..((((.........))))....))))))))))...))))))))..)))))))... (-34.9)