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
2932	3'	-51.3	NC_001493.1	+	36622	0.68	0.953802
	Target:  5'- ----uGGUGGCCgUGGGgcUGUGGgUGUCc -3' miRNA:   3'- aguauCUACCGG-ACCU--ACACCgAUAG- -5'
2932	3'	-51.3	NC_001493.1	+	112693	0.68	0.94493
	Target:  5'- ----cGAUGGCCUGGAggaacgGGCgAUCc -3' miRNA:   3'- aguauCUACCGGACCUaca---CCGaUAG- -5'
2932	3'	-51.3	NC_001493.1	+	89048	0.7	0.891916
	Target:  5'- ---aGGGUGGUCUGGuacGUGUGGUUAc- -3' miRNA:   3'- aguaUCUACCGGACC---UACACCGAUag -5'
2932	3'	-51.3	NC_001493.1	+	117542	0.7	0.884716
	Target:  5'- aCAUu-GUGGCCgucaaGGA-GUGGCUGUCu -3' miRNA:   3'- aGUAucUACCGGa----CCUaCACCGAUAG- -5'
2932	3'	-51.3	NC_001493.1	+	1988	0.7	0.884716
	Target:  5'- aCAUu-GUGGCCgucaaGGA-GUGGCUGUCu -3' miRNA:   3'- aGUAucUACCGGa----CCUaCACCGAUAG- -5'
2932	3'	-51.3	NC_001493.1	+	61265	0.72	0.770962
	Target:  5'- cCAUGGAcccaGGCCgGGAUGUGaCUAUCc -3' miRNA:   3'- aGUAUCUa---CCGGaCCUACACcGAUAG- -5'
2932	3'	-51.3	NC_001493.1	+	98641	0.75	0.612514
	Target:  5'- uUCAcAGGucgUGGCaCUGGAagagGUGGCUAUCg -3' miRNA:   3'- -AGUaUCU---ACCG-GACCUa---CACCGAUAG- -5'
2932	3'	-51.3	NC_001493.1	+	61465	1.12	0.003865
	Target:  5'- aUCAUAGAUGGCCUGGAUGUGGCUAUCg -3' miRNA:   3'- -AGUAUCUACCGGACCUACACCGAUAG- -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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