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
24133	3'	-55	NC_005263.2	+	43846	0.66	0.734505
	Target:  5'- gUCGACCgGgCGcaacaacGUGcgCGGCAUCCUg -3' miRNA:   3'- -AGCUGGgCaGC-------CACuaGCUGUAGGAg -5'
24133	3'	-55	NC_005263.2	+	16888	0.67	0.659953
	Target:  5'- cUCGACgCGUucuacgacgCGGUG-UCGACcgUCUCg -3' miRNA:   3'- -AGCUGgGCA---------GCCACuAGCUGuaGGAG- -5'
24133	3'	-55	NC_005263.2	+	17950	0.69	0.561287
	Target:  5'- aCGACCCG-CGccagccGUGAaCGGCAUCCa- -3' miRNA:   3'- aGCUGGGCaGC------CACUaGCUGUAGGag -5'
24133	3'	-55	NC_005263.2	+	15792	0.69	0.53977
	Target:  5'- gUCG-CCCGUCGucGAUCGACGUgacaCUCg -3' miRNA:   3'- -AGCuGGGCAGCcaCUAGCUGUAg---GAG- -5'
24133	3'	-55	NC_005263.2	+	8928	0.69	0.529115
	Target:  5'- gUCGAg--GUCGGUGAUCGGCAUaCCg- -3' miRNA:   3'- -AGCUgggCAGCCACUAGCUGUA-GGag -5'
24133	3'	-55	NC_005263.2	+	19314	0.72	0.390608
	Target:  5'- gCGGCCCGccggcugugCGGUGGUCGAUGUCgaaguaCUCg -3' miRNA:   3'- aGCUGGGCa--------GCCACUAGCUGUAG------GAG- -5'
24133	3'	-55	NC_005263.2	+	17325	0.76	0.220259
	Target:  5'- uUCGGCCCGgcgcCGGUGGcuUCGACGUUCg- -3' miRNA:   3'- -AGCUGGGCa---GCCACU--AGCUGUAGGag -5'
24133	3'	-55	NC_005263.2	+	39475	1.11	0.000793
	Target:  5'- gUCGACCCGUCGGUGAUCGACAUCCUCg -3' miRNA:   3'- -AGCUGGGCAGCCACUAGCUGUAGGAG- -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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