miRNA display CGI

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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
	Predicted miRNA align pattern
31732	5'	-55.1	NC_006938.1	+	25830	0.66	0.766207
	Target:  5'- -uGGGCCUcggGGaUGACCUUCUUGucCAc -3' miRNA:   3'- cuCCUGGAa--CC-ACUGGAGGAACcuGU- -5'
31732	5'	-55.1	NC_006938.1	+	39587	0.67	0.681559
	Target:  5'- cAGGcACCguccgggaUGGUGcCCUCCUUGGuCGc -3' miRNA:   3'- cUCC-UGGa-------ACCACuGGAGGAACCuGU- -5'
31732	5'	-55.1	NC_006938.1	+	29567	0.67	0.669555
	Target:  5'- cGAGGGCCUgugccagucgauaUGGcagaUGugCUCCgaccUGGACu -3' miRNA:   3'- -CUCCUGGA-------------ACC----ACugGAGGa---ACCUGu -5'
31732	5'	-55.1	NC_006938.1	+	12895	0.69	0.539744
	Target:  5'- cGGGGCCUcucccGCCUCCUUGGGCu -3' miRNA:   3'- cUCCUGGAaccacUGGAGGAACCUGu -5'
31732	5'	-55.1	NC_006938.1	+	18254	0.7	0.497698
	Target:  5'- cGAGGGCCacugcgaGGUGACCgccgCCcUGGGCc -3' miRNA:   3'- -CUCCUGGaa-----CCACUGGa---GGaACCUGu -5'
31732	5'	-55.1	NC_006938.1	+	22750	0.72	0.381883
	Target:  5'- -cGGGCgugcuuCUUGGcacgGGCCUCCUUGGACc -3' miRNA:   3'- cuCCUG------GAACCa---CUGGAGGAACCUGu -5'
31732	5'	-55.1	NC_006938.1	+	46431	1.09	0.00115
	Target:  5'- cGAGGACCUUGGUGACCUCCUUGGACAg -3' miRNA:   3'- -CUCCUGGAACCACUGGAGGAACCUGU- -5'

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Note:
      When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.

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