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
27552	3'	-58.6	NC_005881.1	+	207090	0.68	0.76413
	Target:  5'- aCuuGAUGACCUCAUGGGGgagGAgUUa -3' miRNA:   3'- -GggCUACUGGGGUACCCCag-CUgGAa -5'
27552	3'	-58.6	NC_005881.1	+	184686	0.68	0.76413
	Target:  5'- aCuuGAUGACCUCAUGGGGgagGAgUUa -3' miRNA:   3'- -GggCUACUGGGGUACCCCag-CUgGAa -5'
27552	3'	-58.6	NC_005881.1	+	74635	0.69	0.698315
	Target:  5'- cCCCGAUGAgCCUAUGGgaugcaucauGGUCGAguuCCa- -3' miRNA:   3'- -GGGCUACUgGGGUACC----------CCAGCU---GGaa -5'
27552	3'	-58.6	NC_005881.1	+	207131	0.7	0.639795
	Target:  5'- --aGGUcGACCCCAUGGGGUcaucggggucaCGGCCg- -3' miRNA:   3'- gggCUA-CUGGGGUACCCCA-----------GCUGGaa -5'
27552	3'	-58.6	NC_005881.1	+	184645	0.7	0.639795
	Target:  5'- --aGGUcGACCCCAUGGGGUcaucggggucaCGGCCg- -3' miRNA:   3'- gggCUA-CUGGGGUACCCCA-----------GCUGGaa -5'
27552	3'	-58.6	NC_005881.1	+	184414	1.06	0.003756
	Target:  5'- cCCCGAUGACCCCAUGGGGUCGACCUUu -3' miRNA:   3'- -GGGCUACUGGGGUACCCCAGCUGGAA- -5'
27552	3'	-58.6	NC_005881.1	+	207363	1.06	0.003756
	Target:  5'- cCCCGAUGACCCCAUGGGGUCGACCUUu -3' miRNA:   3'- -GGGCUACUGGGGUACCCCAGCUGGAA- -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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