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 GCGGGGAGACGGTGGAACTTT AAACCGCCTTCAACCCGTGC TCGTCCCCGGATCCCGTCCTGACCCAGAAACCGCCTTCAACCCGTGCGGATACTCCGCAAACATGGTGTCCCCGATCCACGCCGTCACAGTTAGCGGGGAGACGGTGGAACTTTGGGCGGGAACACAGAGAGGGGCCCTCCAG TCGTCCCCGGATCCCGTCCTGACCCAGAAACCGCCTTCAACCCGTGCGGATACTCCGCAAACATGGTGTCCCCGATCCACGCCGTCACAGTTAGCGGGGAGACGGTGGAACTTTGGGCGGGAACACAGAGAGGGGCCCTCCAGCAGCAGAAGTTCCGGGAGGTCAAGTGCACCAGTTCGACCCCTAACCACCAGGGCTGTGAAGGTAAGTGTGTGGAGGAGAGCACGTGGCACAGGGCCGTCGTGATCAAGTCGGGCGACCCGCCCAAGGTTGGCTGGGACATGATCGTTGTCAAGGCTAGCTGCAGCTGTCACGTGATCACACCCAGGAGTCTCTTCACGAAGTTTTCCTCGCTGGGCGAATCAGAGGTGCGTGTCGAGACAGAGTTGGATCGTGATGAAACGAAGAAGACAGAGTTGGAAGGCGAAGAAACAGAGGAGATATCTTAAACACAATAAAGCTACATGAGAAGGCATTGCTATGGTAAGTTTGAAGAGGTAGAGGGCAGGGTTGCAAACCAGGCATTATGTACCATGATGAAAGTACTTTGGTACTTTTTGTATGTATTGCAGATGAAACGGTACCCATTGTTCAGTAAATGTCACGTTTCTGAGGA 5 1 3' arm Branchiostoma_floridae mirnest 100 100 -49.6 ..(.((((...((...(((((.((((((..(((((.((..((((((((((...))))).((((((((((.........)))))))....))).)))))..)).)))))...))))))))))).....))..)))))....... (-49.6)