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
27530	5'	-51.4	NC_005879.1	+	8054	0.66	0.785246
	Target:  5'- gGGUAGaacgGAAGCAACCCUGAcggACAGa -3' miRNA:   3'- -UCGUCg---CUUCGUUGGGGUUuagUGUC- -5'
27530	5'	-51.4	NC_005879.1	+	16047	0.67	0.741761
	Target:  5'- cGCAGCGuauccauCAACCCUAA--CACAGg -3' miRNA:   3'- uCGUCGCuuc----GUUGGGGUUuaGUGUC- -5'
27530	5'	-51.4	NC_005879.1	+	35121	0.67	0.718067
	Target:  5'- gAGCGGCGGcagcaagAGCAAUCUUuuucauGUCGCGGa -3' miRNA:   3'- -UCGUCGCU-------UCGUUGGGGuu----UAGUGUC- -5'
27530	5'	-51.4	NC_005879.1	+	11432	0.68	0.66134
	Target:  5'- cGGCGGCGGcucuGGCGgaACCUCGAuUCugGGc -3' miRNA:   3'- -UCGUCGCU----UCGU--UGGGGUUuAGugUC- -5'
27530	5'	-51.4	NC_005879.1	+	21281	0.69	0.636711
	Target:  5'- aGGCAGCGcagaccAAGUGGCuCCCAAAucguugcUCACGGc -3' miRNA:   3'- -UCGUCGC------UUCGUUG-GGGUUU-------AGUGUC- -5'
27530	5'	-51.4	NC_005879.1	+	20747	0.71	0.499695
	Target:  5'- uGGUcacgAGCGAAGUAGCCUC-GGUUACAGu -3' miRNA:   3'- -UCG----UCGCUUCGUUGGGGuUUAGUGUC- -5'
27530	5'	-51.4	NC_005879.1	+	20519	1.08	0.001557
	Target:  5'- uAGCAGCGAAGCAACCCCAAAUCACAGc -3' miRNA:   3'- -UCGUCGCUUCGUUGGGGUUUAGUGUC- -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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