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
23515	3'	-60	NC_005259.1	+	41642	0.78	0.091241
	Target:  5'- gGUGCcGGUCUGCG-GGCgCUCGGUGAGc -3' miRNA:   3'- -CACGcCCAGACGCaCUG-GAGCCGCUC- -5'
23515	3'	-60	NC_005259.1	+	58784	0.73	0.206892
	Target:  5'- uGUGCGccGGUCgagGCgGUGauuGCCUCGGCGGGc -3' miRNA:   3'- -CACGC--CCAGa--CG-CAC---UGGAGCCGCUC- -5'
23515	3'	-60	NC_005259.1	+	63936	0.71	0.292255
	Target:  5'- -cGUGGGUCUuaccguccggcaGCGaGAUCUCGGCGGu -3' miRNA:   3'- caCGCCCAGA------------CGCaCUGGAGCCGCUc -5'
23515	3'	-60	NC_005259.1	+	65279	0.68	0.394065
	Target:  5'- uGUGUGGGUgCUGcCGUGGauCUUCGGCaAGg -3' miRNA:   3'- -CACGCCCA-GAC-GCACU--GGAGCCGcUC- -5'
23515	3'	-60	NC_005259.1	+	2083	0.68	0.429692
	Target:  5'- -gGCGGGcCUGCucGAUUucaUCGGCGAGg -3' miRNA:   3'- caCGCCCaGACGcaCUGG---AGCCGCUC- -5'
23515	3'	-60	NC_005259.1	+	64791	0.67	0.467144
	Target:  5'- cUGCGacuGG-CUGUGUGccucgGCCUCGGCGGc -3' miRNA:   3'- cACGC---CCaGACGCAC-----UGGAGCCGCUc -5'
23515	3'	-60	NC_005259.1	+	13432	0.67	0.496306
	Target:  5'- -cGcCGGGgccgCgcuagGCGUGACCgUCGGCGcGg -3' miRNA:   3'- caC-GCCCa---Ga----CGCACUGG-AGCCGCuC- -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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