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 ATTTCTTCATCTTCATCGTCA GAGATAGAGATGGGGAATCA TGGATGAAAAAGGAGATAGAGATGGGGAATCATAACAGGTACAACATGTGTCATGAATTGCTTTCGTCCTGGTTTTGTCAAGTTTGGAGCAAAATACACAATATCTCCCGCGGAATTCTCCATATTTGTCCTTGATTTCTTCATCTTCATCGTCATTTTCCGTG TTTTTTTTTTTTTGTTTACTCAATACCCGAAATTATATGTTCATTTCTCATCACCCCCTCTTTCCAGGGTTGATTCTTTCTGTGTCTATATACAAAAGAGGAAACAACAGGAAGAAAAGAAAATTAAAGGGTTTAAGGAGAAAATGAAAAAAAAGTGGATGAAAAAGGAGATAGAGATGGGGAATCATAACAGGTACAACATGTGTCATGAATTGCTTTCGTCCTGGTTTTGTCAAGTTTGGAGCAAAATACACAATATCTCCCGCGGAATTCTCCATATTTGTCCTTGATTTCTTCATCTTCATCGTCATTTTCCGTGTTGTCTGCCTTAACCTCTGCGTCATCAGGAGGTGTGTAAACTAAACCCACCTTTGGAAGGATTATCCCAAGGATTTTATCAACAGTGTTGTCGACCCACTTGTTTGCTCTCTTCCAAAAAATGAATGGTGCAACGGCTGCCGCTGCTCCTACACCAAACCCCGCCCCAATGAATATGAACTCCCAATCAAATTCATCATTCTGATTCTTTTCTGCTGCATCGGATTGTGAATTGTGGCCATTGTTGGCATTTTTGCAACTTTTTGTCAAAGGATACCCACATAGTCCCTTATTCCCTTCATAGGACTCATTTTCGAATGTTGAAAATTGCTTTCCTGCTGGGATAGGTCCCTCCAGTTGGTTGTGTG 3 1 3' arm Theobroma_cacao mirnest 100 100 -33.5 .....(((((.((.(((.((((((((((((((....(((.((((.(((((....((((....(((((...(((.((((....((((...))))....)))).)))....)))))))))..))))))))))))))).))))))))))).))).)).))))).... (-33.5)