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
29059	3'	-51.6	NC_006146.1	+	15255	0.66	0.995181
	Target:  5'- gCCGGUaa-GCG-GUCCACCaguaaGGGUa -3' miRNA:   3'- -GGCCAaagCGCuCAGGUGGaaa--CUCA- -5'
29059	3'	-51.6	NC_006146.1	+	18333	0.66	0.995181
	Target:  5'- gCCGGUaa-GCG-GUCCACCaguaaGGGUa -3' miRNA:   3'- -GGCCAaagCGCuCAGGUGGaaa--CUCA- -5'
29059	3'	-51.6	NC_006146.1	+	21411	0.66	0.995181
	Target:  5'- gCCGGUaa-GCG-GUCCACCaguaaGGGUa -3' miRNA:   3'- -GGCCAaagCGCuCAGGUGGaaa--CUCA- -5'
29059	3'	-51.6	NC_006146.1	+	24489	0.66	0.995181
	Target:  5'- gCCGGUaa-GCG-GUCCACCaguaaGGGUa -3' miRNA:   3'- -GGCCAaagCGCuCAGGUGGaaa--CUCA- -5'
29059	3'	-51.6	NC_006146.1	+	27567	0.66	0.995181
	Target:  5'- gCCGGUaa-GCG-GUCCACCaguaaGGGUa -3' miRNA:   3'- -GGCCAaagCGCuCAGGUGGaaa--CUCA- -5'
29059	3'	-51.6	NC_006146.1	+	60868	0.67	0.990286
	Target:  5'- cCCGGgggUCaCGAGgCCAUCUUUGAu- -3' miRNA:   3'- -GGCCaa-AGcGCUCaGGUGGAAACUca -5'
29059	3'	-51.6	NC_006146.1	+	83643	0.69	0.955622
	Target:  5'- gCGGgggcUCuGCGGGccagaccUCCACCUUUGGGUu -3' miRNA:   3'- gGCCaa--AG-CGCUC-------AGGUGGAAACUCA- -5'
29059	3'	-51.6	NC_006146.1	+	95893	1.09	0.009379
	Target:  5'- gCCGGUUUCGCGAGUCCACCUUUGAGUc -3' miRNA:   3'- -GGCCAAAGCGCUCAGGUGGAAACUCA- -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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