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 TCATCTTCATCATCATCCTCC AGGAGAAGAGGAAAATGGAG CTTCATCTCATTCATCTTCATCATCATCCTCCGCTTCATCGTCGTCGTCGGCTTCTTCTTCGTCCAACGGCAGCGACGGCGGAGATAGCAGCAGTGCCAGTGGAAGCGCTAGCAGCGGAGGAGAAGAGGAAAATGGAGAAGAAGTT GCAGAAATTCGCTTTGCTCCTTTTGTTCTGAGAGAGAGAGACCGAAAGACAAAACTAAAAGCATATAATCTCCGATATGGATTTCTCGGAGCAAGATGTGGACCTCTTTGGAGATGACCATAACAAGGACAATCGCGATGATTCCCGTGAATCCTCTTCATCTCATTCATCTTCATCATCATCCTCCGCTTCATCGTCGTCGTCGGCTTCTTCTTCGTCCAACGGCAGCGACGGCGGAGATAGCAGCAGTGCCAGTGGAAGCGCTAGCAGCGGAGGAGAAGAGGAAAATGGAGAAGAAGTTAGCAATGTTAATACCCATAATTATGATTATAATGACAATATTGAAAGGAGTATTTTTGGGTATGAAGAGGAAGAAGAGGAGAAAGATCTCTTTGGGTCTGATAACGAAGATTACTGTAAAACCACTGCCACTAGCCCTTTCCCTATTCCTGTATTGCCCGTTATTCGTAATACTAATAACCCAGGTAGAGGAGGTTTTGGACGGGGTCGTTGGCCCAGTGATAGAGGAGCTGGTATCCTTGGCCGTCCTGGTTATCCTCCTAGGCAAGGTTATGGGTATGGAAACAAATTTGCTAATGGACATCGTGATGAGCGTTTCGTTTCTGAGCTGAAATTTTCCAAGAGTGAAGAGACGTTATCTAGAAAATGCATTGCTTTTCAGGAACCATGTGAACTTGCTTGTTATAGCCGTGTAGAAGGTGGAGATGTCTACTTTG 4 1 5' arm Gossypium_hirsutum mirnest 100 100 -50.8 ((((.((((...(((.(((.((.((.((((((((.((.((((((((((..(((...............))).)))))))))).))..(((((.((.((...))..))))).)).)))))))))).)).))).))))))).)))).. (-50.8)