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
22001	5'	-51.3	NC_004914.1	+	35895	0.66	0.909651
	Target:  5'- aGCAGCAAAGagauGCAGGAgagcaaaacgaUGAaaaaCCGUAa -3' miRNA:   3'- gCGUCGUUUCg---CGUCUU-----------ACU----GGCAUa -5'
22001	5'	-51.3	NC_004914.1	+	27135	0.66	0.902766
	Target:  5'- gCGCAGUAucaCGCAGAGcugaagagucUGACCGg-- -3' miRNA:   3'- -GCGUCGUuucGCGUCUU----------ACUGGCaua -5'
22001	5'	-51.3	NC_004914.1	+	18165	0.66	0.888129
	Target:  5'- uGCAGCGAAa-GCGGGucaGGCCGUGa -3' miRNA:   3'- gCGUCGUUUcgCGUCUua-CUGGCAUa -5'
22001	5'	-51.3	NC_004914.1	+	53923	0.66	0.888129
	Target:  5'- cCGUuacuGCAAAGUGCucaguugacaGGAAUGACUGUc- -3' miRNA:   3'- -GCGu---CGUUUCGCG----------UCUUACUGGCAua -5'
22001	5'	-51.3	NC_004914.1	+	17209	0.67	0.872371
	Target:  5'- gCGCAGau-GGCGCAGGAUaACCa--- -3' miRNA:   3'- -GCGUCguuUCGCGUCUUAcUGGcaua -5'
22001	5'	-51.3	NC_004914.1	+	18624	0.72	0.578349
	Target:  5'- aGCGGCGGAcGCGaucaAGAAUGGCgGUAa -3' miRNA:   3'- gCGUCGUUU-CGCg---UCUUACUGgCAUa -5'
22001	5'	-51.3	NC_004914.1	+	47947	1.07	0.00334
	Target:  5'- gCGCAGCAAAGCGCAGAAUGACCGUAUg -3' miRNA:   3'- -GCGUCGUUUCGCGUCUUACUGGCAUA- -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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