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
22310	5'	-54.7	NC_005045.1	+	10445	1.11	0.00065
	Target:  5'- aCCCCGUACUUCUUCCAGGUAGCCGCAc -3' miRNA:   3'- -GGGGCAUGAAGAAGGUCCAUCGGCGU- -5'
22310	5'	-54.7	NC_005045.1	+	9608	0.68	0.572007
	Target:  5'- aCCCGcGCUUCgUCCGggacGGUGGCUGgAg -3' miRNA:   3'- gGGGCaUGAAGaAGGU----CCAUCGGCgU- -5'
22310	5'	-54.7	NC_005045.1	+	27543	0.76	0.190179
	Target:  5'- uCCgCCGUGCUgguaccaaacaCCAGGUAGCCGCu -3' miRNA:   3'- -GG-GGCAUGAagaa-------GGUCCAUCGGCGu -5'
22310	5'	-54.7	NC_005045.1	+	29642	0.76	0.198685
	Target:  5'- gCCCCGcUGgUUCaugUCCAGGcUGGCCGCc -3' miRNA:   3'- -GGGGC-AUgAAGa--AGGUCC-AUCGGCGu -5'
22310	5'	-54.7	NC_005045.1	+	24281	0.73	0.303019
	Target:  5'- gCCCagGUGC-UCUUCCAGGUGGaugucaacguCCGCGu -3' miRNA:   3'- -GGGg-CAUGaAGAAGGUCCAUC----------GGCGU- -5'
22310	5'	-54.7	NC_005045.1	+	17753	0.66	0.672738
	Target:  5'- uCCaCCGUcauCUUCUUCCagucgugaggcAGGUAGCCc-- -3' miRNA:   3'- -GG-GGCAu--GAAGAAGG-----------UCCAUCGGcgu -5'
22310	5'	-54.7	NC_005045.1	+	29538	0.66	0.694961
	Target:  5'- -gCCG-GCcUCUUCCAGGcugAGCUGCc -3' miRNA:   3'- ggGGCaUGaAGAAGGUCCa--UCGGCGu -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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