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
27948	5'	-56.4	NC_005886.2	+	8196	0.67	0.563495
	Target:  5'- aGCa---GGCGUCAuGAucaacgcaccCCCAUCGCAGc -3' miRNA:   3'- aCGcaagCCGCAGU-CU----------GGGUAGCGUC- -5'
27948	5'	-56.4	NC_005886.2	+	22704	0.67	0.541897
	Target:  5'- gGCGaUCguaccuaguGGCGUCAGACCagcugcguUAUCGCAc -3' miRNA:   3'- aCGCaAG---------CCGCAGUCUGG--------GUAGCGUc -5'
27948	5'	-56.4	NC_005886.2	+	17363	0.67	0.520581
	Target:  5'- cUGuCGUUaaaCGGuCGUCGGGCCgAUCgGCAGc -3' miRNA:   3'- -AC-GCAA---GCC-GCAGUCUGGgUAG-CGUC- -5'
27948	5'	-56.4	NC_005886.2	+	41578	0.68	0.479003
	Target:  5'- gGCaacgUCGGCGUCAGcGCCggaCGUUGCGGc -3' miRNA:   3'- aCGca--AGCCGCAGUC-UGG---GUAGCGUC- -5'
27948	5'	-56.4	NC_005886.2	+	32719	0.69	0.448918
	Target:  5'- aUGUGguaUCGGaacguaGUaCAGGCCCAUCGuCAGu -3' miRNA:   3'- -ACGCa--AGCCg-----CA-GUCUGGGUAGC-GUC- -5'
27948	5'	-56.4	NC_005886.2	+	34829	0.72	0.271865
	Target:  5'- gGCaauUUCgGGCGguUCGGACCCGUUGCAGu -3' miRNA:   3'- aCGc--AAG-CCGC--AGUCUGGGUAGCGUC- -5'
27948	5'	-56.4	NC_005886.2	+	41543	1.08	0.000784
	Target:  5'- gUGCGUUCGGCGUCAGACCCAUCGCAGc -3' miRNA:   3'- -ACGCAAGCCGCAGUCUGGGUAGCGUC- -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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