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 TCATCATCATCATCATCTCCT CAGATGGTGGTGGTGGTTTGA TCTCCTTTACCTATTCATGGCTCATCATCATCATCATCTCCTTCTCCTCCTCCTTTAAGATCTGCCGCCGGTGGTGTTGGTGGTAATGGCGGCGTTGTTGGTAGTGATAATGGTCATTATCGTCATACAAGGAGGGCAGCATCATCAGATGGTGGTGGTGGTTTGAAGAGGAGCAAGTCCACCG GTTTGCATATATCTTCATTCATTGTCCCTTTGATGTGTAGAAGAAAAAAAATCAAAGATTGTAGTACACTTGAAGGTATCATCAATGGTGGAAAAGTTGGGGAAGGTGAAGATATAAGAGACAATAATAATATACAACACTGTATCAATCATCCTTATGGGAAAAACCCAGGTGGGATCTGTGCTTTTTGTCTTCAAGAAAAGCTTGGGAAATTGGTTTCTTCATCGTCTCCTTTACCTATTCATGGCTCATCATCATCATCATCTCCTTCTCCTCCTCCTTTAAGATCTGCCGCCGGTGGTGTTGGTGGTAATGGCGGCGTTGTTGGTAGTGATAATGGTCATTATCGTCATACAAGGAGGGCAGCATCATCAGATGGTGGTGGTGGTTTGAAGAGGAGCAAGTCCACCGTAACACCTAGGGGCGGCCGGTTCGTAGAAGGCGGCGATGAGTTTAGAAAAAGAAGCGGTTTCTGGTCTTTTCTTTATGTTTCTTCAAAGACCCATAGTGCCAAAAAACCAGCTTCCATTGGTATGAAGCTAGCAAAGAAGGGATCATCATCATTATCAATGGATGATGATCATGCATCATCATTTGAAAGGAAGGTTTCAAGGTCCAGATCCGTCGGCTGTGGAAGCCGGAGCTTTTCCGGTGATTTTTTCGAAAGGATCTCAACTGGTTTTGGTGATTGTACTCTTAGAAGAGTAGAATCACAAAGAGAGGGCAAATCAAAACCTACTCATCATCATGGCCATGCCCCATCATCATCATCATCATCTGGAATGAAAGAAAGGGTTAAATGTGGCGGTATATTTAGTGGATTCATGATCATGACATCATCATCATCATCTTCTTCATCATCATCATCTTCATA 5 0 5' arm Gossypium_raimondii mirnest 100 100 -51.7 .........(((.((((......((((((((((((((((........((((((((((.((..((((((((.((.(......).)).))))))))....((((((((((....)))))))))))).)).))))))))..........)))))))))))))))).)))).)))............. (-51.7)