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
18576	5'	-55.5	NC_004682.1	+	38062	0.66	0.654707
	Target:  5'- uUGGGG-GAGGCCgguUUCGGGGcgUCAg -3' miRNA:   3'- cAUCUCgCUCUGG---AGGCCCCuaAGUg -5'
18576	5'	-55.5	NC_004682.1	+	33106	0.67	0.620305
	Target:  5'- --uGAGCGAaguucucGACCaggCCGGGGAU-CAUc -3' miRNA:   3'- cauCUCGCU-------CUGGa--GGCCCCUAaGUG- -5'
18576	5'	-55.5	NC_004682.1	+	48154	0.67	0.588207
	Target:  5'- cGUAGAaCGucgucgcGACCUUCGGGGAcagCGCg -3' miRNA:   3'- -CAUCUcGCu------CUGGAGGCCCCUaa-GUG- -5'
18576	5'	-55.5	NC_004682.1	+	39348	0.67	0.588207
	Target:  5'- --uGAGUGGGGUCgaacgCCGGGGAUuUCGCu -3' miRNA:   3'- cauCUCGCUCUGGa----GGCCCCUA-AGUG- -5'
18576	5'	-55.5	NC_004682.1	+	19054	0.69	0.512405
	Target:  5'- cGUGGAGaaCGAggauGACCUCUGGGGcUUcCGCg -3' miRNA:   3'- -CAUCUC--GCU----CUGGAGGCCCCuAA-GUG- -5'
18576	5'	-55.5	NC_004682.1	+	46230	0.73	0.279434
	Target:  5'- --cGAGCGuGGCCUCCGGGacgauGAUgccUCGCg -3' miRNA:   3'- cauCUCGCuCUGGAGGCCC-----CUA---AGUG- -5'
18576	5'	-55.5	NC_004682.1	+	31396	1.08	0.000939
	Target:  5'- uGUAGAGCGAGACCUCCGGGGAUUCACc -3' miRNA:   3'- -CAUCUCGCUCUGGAGGCCCCUAAGUG- -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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