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
8475	5'	-50.3	NC_002167.1	+	36536	0.66	0.880847
	Target:  5'- -aCGUaAGGCguUccUCGAUAUgCUGGCGUg -3' miRNA:   3'- ccGCA-UCCGguA--AGUUAUA-GACCGCG- -5'
8475	5'	-50.3	NC_002167.1	+	38823	0.66	0.855449
	Target:  5'- uGCagAGGCCAUUCAAUGagUGGUc- -3' miRNA:   3'- cCGcaUCCGGUAAGUUAUagACCGcg -5'
8475	5'	-50.3	NC_002167.1	+	15550	0.67	0.817957
	Target:  5'- aGCGaGGGCCAUUUAAgacgCaGGCGa -3' miRNA:   3'- cCGCaUCCGGUAAGUUaua-GaCCGCg -5'
8475	5'	-50.3	NC_002167.1	+	32833	0.68	0.797848
	Target:  5'- cGGCGUuuGCCAgcagUCcuugucGUGUgCUGGCGUa -3' miRNA:   3'- -CCGCAucCGGUa---AGu-----UAUA-GACCGCG- -5'
8475	5'	-50.3	NC_002167.1	+	20821	0.68	0.787495
	Target:  5'- cGGCaGUucAGGCCAgaUGAcAUCcGGCGCg -3' miRNA:   3'- -CCG-CA--UCCGGUaaGUUaUAGaCCGCG- -5'
8475	5'	-50.3	NC_002167.1	+	27120	0.68	0.776959
	Target:  5'- gGGCGauGGCCGUuggcuugacuUUAGUuacugugauucuGUCUGGCGUg -3' miRNA:   3'- -CCGCauCCGGUA----------AGUUA------------UAGACCGCG- -5'
8475	5'	-50.3	NC_002167.1	+	20785	1.16	0.000692
	Target:  5'- aGGCGUAGGCCAUUCAAUAUCUGGCGCa -3' miRNA:   3'- -CCGCAUCCGGUAAGUUAUAGACCGCG- -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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