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
23362	5'	-60.3	NC_005259.1	+	5072	0.66	0.510118
	Target:  5'- uGGGCCGGGUc--GACGGGC-CGGUg- -3' miRNA:   3'- -CCCGGCUCAuccCUGUCCGcGUCGau -5'
23362	5'	-60.3	NC_005259.1	+	66193	0.66	0.470533
	Target:  5'- -uGCCGgugcAGUAcGGGuCAGGCGCGGUc- -3' miRNA:   3'- ccCGGC----UCAU-CCCuGUCCGCGUCGau -5'
23362	5'	-60.3	NC_005259.1	+	29959	0.66	0.46088
	Target:  5'- cGGCUG-GUGGGG-CGGGCGguGa-- -3' miRNA:   3'- cCCGGCuCAUCCCuGUCCGCguCgau -5'
23362	5'	-60.3	NC_005259.1	+	61598	0.67	0.432571
	Target:  5'- uGGGCCG-GUGGGGuC-GGCGgggaaCAGCa- -3' miRNA:   3'- -CCCGGCuCAUCCCuGuCCGC-----GUCGau -5'
23362	5'	-60.3	NC_005259.1	+	13436	0.67	0.423362
	Target:  5'- gGGGCCGcGcUAGGcGugAccgucGGCGCGGCg- -3' miRNA:   3'- -CCCGGCuC-AUCC-CugU-----CCGCGUCGau -5'
23362	5'	-60.3	NC_005259.1	+	14561	0.68	0.344465
	Target:  5'- aGGCCGAGcGGGGACcGGCGaacaccaucgcGCUGg -3' miRNA:   3'- cCCGGCUCaUCCCUGuCCGCgu---------CGAU- -5'
23362	5'	-60.3	NC_005259.1	+	65701	0.69	0.329545
	Target:  5'- cGGGCCGAGUA-GGACgaggucacgcccaAGGCG-AGUUGg -3' miRNA:   3'- -CCCGGCUCAUcCCUG-------------UCCGCgUCGAU- -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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