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
22628	3'	-51.4	NC_005091.1	+	49473	0.66	0.909146
	Target:  5'- cGAGCGCGaCGAGcAGGccaAUUGCGAAc -3' miRNA:   3'- cCUUGCGC-GCUUcUCCaa-UAGCGCUU- -5'
22628	3'	-51.4	NC_005091.1	+	45908	0.66	0.887841
	Target:  5'- uGGAACGCGaCGAAcugcuGGccguUCGCGAGg -3' miRNA:   3'- -CCUUGCGC-GCUUcu---CCaau-AGCGCUU- -5'
22628	3'	-51.4	NC_005091.1	+	24685	0.67	0.879406
	Target:  5'- ---cCGCGCGAAucgaagcGAGGUUGcgcugCGCGAGu -3' miRNA:   3'- ccuuGCGCGCUU-------CUCCAAUa----GCGCUU- -5'
22628	3'	-51.4	NC_005091.1	+	16349	0.67	0.872263
	Target:  5'- uGGAACGUGCucGGcGcGUUcGUCGCGAGc -3' miRNA:   3'- -CCUUGCGCGcuUCuC-CAA-UAGCGCUU- -5'
22628	3'	-51.4	NC_005091.1	+	32836	0.68	0.808991
	Target:  5'- cGGGAgGgGCGGGcagcaucGGGGUaGUCGCGAu -3' miRNA:   3'- -CCUUgCgCGCUU-------CUCCAaUAGCGCUu -5'
22628	3'	-51.4	NC_005091.1	+	38418	0.68	0.800193
	Target:  5'- aGAGCGCGCGuaauggacgccGAGGGGaaacUUGUCgGCGAc -3' miRNA:   3'- cCUUGCGCGC-----------UUCUCC----AAUAG-CGCUu -5'
22628	3'	-51.4	NC_005091.1	+	42174	1	0.01153
	Target:  5'- cGGAACGCGCGAAG-GGUUAUCGCGAAg -3' miRNA:   3'- -CCUUGCGCGCUUCuCCAAUAGCGCUU- -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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