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 TTCATCCAATGCTGCTGCTTC AGTGGCAACATTTCATTTGAGAT ATCAGGGTATTGAAGTGGCAACATTTCATTTGAGATTGTTAATGAACTTGATTTCATATCAGTTGAAGTTTCATCCAATGCTGCTGCTTCTGACCAAAAA AGTACATCATTTATTGGTATTACAATCAAACTCTAACCTTTTCTCCTAATTAAAGAAAAAATAAAAAAATGTCTAAGACTTGTTGTTTTTCACAATATACATTGAAAATAAAAATCAATGTTTCCCTTGTAATCCCTCTTTACATAGAGATAGATTACATATCATTACCTTGGAGACAATGATCACATCACATATTTTTCTTGTCACATTCAAACTGAAATTACCACGTTGCAATGAAACTCATATCTTCATATCACATAAAGATAAGAATTTGAATCTCGTTGTCAATGTGAGAGAATCTCTTTACTGAATAGCGTACACTATTAGTATATGAGCCGAGACCTGCTCTGATAGACCGTACCCAATTCCAACTTGTCTAAACTTTTAGTTGTCAAAAAAAATTGGAGTTACTATGTTTTTTTGAACTTTCTATTAACTCAAAACTCAGGCAATTCTATTTGATCTCCAGTCCTAATAAATATATCATACCAAAAATCCATGCCATCATCCATGTTAGAATTATAATCTTCATGACTTTCTGGAAGAATTTCATCAGGGTATTGAAGTGGCAACATTTCATTTGAGATTGTTAATGAACTTGATTTCATATCAGTTGAAGTTTCATCCAATGCTGCTGCTTCTGACCAAAAACTCTCATCAATTACAGCCATTGTTTCTTCCATAGACTCAATGTCTTCACTTTTTATATCCTTTCTTTCACCAACTGTGACAGATGAAAAATCACTAGAACTAGTAGTGCATGCAAATGCTGATTCTGATTTGTGGTATGTGCTTTGAA 4 2 3' arm Medicago_truncatula mirnest 100 100 -26.3 .....(((...(((((((((.((((.....(((((((.....(((...((....))..))).....)))))))...)))).)))))))))..)))..... (-26.3)