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
31540	5'	-45	NC_006820.1	+	136788	0.66	0.999998
	Target:  5'- aUGGAGUUUgugcuauuugUAAAGGAGAagguGAUGGUa -3' miRNA:   3'- gACCUUAGG----------AUUUCCUCUau--CUAUCA- -5'
31540	5'	-45	NC_006820.1	+	7422	0.67	0.999991
	Target:  5'- uCUGGaAAUCCUGuGAGGAGGcAGAcaaAGUa -3' miRNA:   3'- -GACC-UUAGGAU-UUCCUCUaUCUa--UCA- -5'
31540	5'	-45	NC_006820.1	+	137960	0.68	0.999955
	Target:  5'- uUGGggUCCUGAgucucaAGGAGAUAu----- -3' miRNA:   3'- gACCuuAGGAUU------UCCUCUAUcuauca -5'
31540	5'	-45	NC_006820.1	+	181007	0.69	0.99986
	Target:  5'- aCUGGaAGUCgCUGAGGGAGAUAccaugAGUu -3' miRNA:   3'- -GACC-UUAG-GAUUUCCUCUAUcua--UCA- -5'
31540	5'	-45	NC_006820.1	+	64141	0.7	0.999621
	Target:  5'- aCUGGAGaguUCCaGAcGGAGGcAGAUGGUg -3' miRNA:   3'- -GACCUU---AGGaUUuCCUCUaUCUAUCA- -5'
31540	5'	-45	NC_006820.1	+	81554	0.72	0.998621
	Target:  5'- aCUGGAAcUCUUuGAGGGGGUAGAUu-- -3' miRNA:   3'- -GACCUU-AGGAuUUCCUCUAUCUAuca -5'
31540	5'	-45	NC_006820.1	+	116059	0.75	0.981074
	Target:  5'- uUGGuGUCCgaagGGAGGAGAcGGAUGGg -3' miRNA:   3'- gACCuUAGGa---UUUCCUCUaUCUAUCa -5'
31540	5'	-45	NC_006820.1	+	81744	1.08	0.046916
	Target:  5'- uCUGGAAUCCUAAAGGAGAUAGAUAGUu -3' miRNA:   3'- -GACCUUAGGAUUUCCUCUAUCUAUCA- -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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