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
22087	5'	-55.3	NC_004927.1	+	58566	0.66	0.814214
	Target:  5'- gGCCCugAUUGCGUUCGCuguUCAGgcGUCc -3' miRNA:   3'- gUGGG--UGAUGCGAGCGc--AGUCauCGG- -5'
22087	5'	-55.3	NC_004927.1	+	40421	0.66	0.782176
	Target:  5'- cCACCCACUACaaGCUCGaaacCGUCuuccgcuGGUuauggaaauacgagGGCCa -3' miRNA:   3'- -GUGGGUGAUG--CGAGC----GCAG-------UCA--------------UCGG- -5'
22087	5'	-55.3	NC_004927.1	+	27788	0.67	0.725865
	Target:  5'- uCACCgCcCUGCGCUCGgGcCAGUuugaacagcGCCa -3' miRNA:   3'- -GUGG-GuGAUGCGAGCgCaGUCAu--------CGG- -5'
22087	5'	-55.3	NC_004927.1	+	14582	0.68	0.673172
	Target:  5'- -uUCCACgGCGCUCGUggGUCGccAGCCg -3' miRNA:   3'- guGGGUGaUGCGAGCG--CAGUcaUCGG- -5'
22087	5'	-55.3	NC_004927.1	+	65184	0.69	0.641029
	Target:  5'- cCACgC-CUACGgUCGCGUCGGUcguGUCu -3' miRNA:   3'- -GUGgGuGAUGCgAGCGCAGUCAu--CGG- -5'
22087	5'	-55.3	NC_004927.1	+	37409	0.71	0.52433
	Target:  5'- uCGCCCGCguuaUGCGCUCGCG-CG--AGCUa -3' miRNA:   3'- -GUGGGUG----AUGCGAGCGCaGUcaUCGG- -5'
22087	5'	-55.3	NC_004927.1	+	63900	1.13	0.000848
	Target:  5'- aCACCCACUACGCUCGCGUCAGUAGCCg -3' miRNA:   3'- -GUGGGUGAUGCGAGCGCAGUCAUCGG- -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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