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
22140	3'	-54.1	NC_004927.1	+	32624	0.66	0.848098
	Target:  5'- gCUCGUCCGGCUCGAAGuuGaGcuUGCu -3' miRNA:   3'- gGGGUAGGUCGAGUUUCucC-CcuACG- -5'
22140	3'	-54.1	NC_004927.1	+	71325	0.66	0.829907
	Target:  5'- aCCCC-UCCGGUUCAGguggaacAGAcGGaGGA-GCg -3' miRNA:   3'- -GGGGuAGGUCGAGUU-------UCU-CC-CCUaCG- -5'
22140	3'	-54.1	NC_004927.1	+	41852	0.69	0.669987
	Target:  5'- gUCCCAuUCCGGUUUcuuGAGGGcaGAUGCu -3' miRNA:   3'- -GGGGU-AGGUCGAGuuuCUCCC--CUACG- -5'
22140	3'	-54.1	NC_004927.1	+	13049	0.7	0.648364
	Target:  5'- aUCCAUCCAGUaggUCGggAAG-GGGGAgucgGCa -3' miRNA:   3'- gGGGUAGGUCG---AGU--UUCuCCCCUa---CG- -5'
22140	3'	-54.1	NC_004927.1	+	46344	0.7	0.626683
	Target:  5'- uCCCCAUCCccgagauuaccgAGCgCGucGGuGGGAUGCg -3' miRNA:   3'- -GGGGUAGG------------UCGaGUuuCUcCCCUACG- -5'
22140	3'	-54.1	NC_004927.1	+	43995	0.72	0.540835
	Target:  5'- uUUCGUCCAGCUCGGAcuGGGGGUa- -3' miRNA:   3'- gGGGUAGGUCGAGUUUcuCCCCUAcg -5'
22140	3'	-54.1	NC_004927.1	+	61676	0.74	0.430393
	Target:  5'- aCCUGUCCggucuuAGCUCGAAcGAGGGGAgucucGCu -3' miRNA:   3'- gGGGUAGG------UCGAGUUU-CUCCCCUa----CG- -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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