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
27047	5'	-47	NC_005832.1	+	19619	0.66	0.998921
	Target:  5'- -cAGgagGGAGACCCG-UUGAAGGUg -3' miRNA:   3'- gaUCagaUCUCUGGGCaGAUUUUCAa -5'
27047	5'	-47	NC_005832.1	+	9579	0.67	0.997623
	Target:  5'- aUGGUCUccacgGGAGACaCCGUC-AGGAGc- -3' miRNA:   3'- gAUCAGA-----UCUCUG-GGCAGaUUUUCaa -5'
27047	5'	-47	NC_005832.1	+	6067	0.67	0.997147
	Target:  5'- cCUGGcCUGGGGACCCugcgGGAGGUa -3' miRNA:   3'- -GAUCaGAUCUCUGGGcagaUUUUCAa -5'
27047	5'	-47	NC_005832.1	+	101648	0.67	0.997147
	Target:  5'- uUAGUCUgAGAGAgaUUGUCUAAGAGa- -3' miRNA:   3'- gAUCAGA-UCUCUg-GGCAGAUUUUCaa -5'
27047	5'	-47	NC_005832.1	+	65951	0.68	0.992355
	Target:  5'- gCUGG-CUAGGGACCUGUCccuGGGa- -3' miRNA:   3'- -GAUCaGAUCUCUGGGCAGauuUUCaa -5'
27047	5'	-47	NC_005832.1	+	98083	0.7	0.975207
	Target:  5'- -gGGUCUccaAGAGGCCCGUgCUGGAGc-- -3' miRNA:   3'- gaUCAGA---UCUCUGGGCA-GAUUUUcaa -5'
27047	5'	-47	NC_005832.1	+	21426	0.73	0.914382
	Target:  5'- aCUAGUCUGGAGACUgugauggaauaaauCuUCUGAAAGUa -3' miRNA:   3'- -GAUCAGAUCUCUGG--------------GcAGAUUUUCAa -5'
27047	5'	-47	NC_005832.1	+	21526	0.96	0.086158
	Target:  5'- gCUAGUCUAGAGACCCGUCUAAAAu-- -3' miRNA:   3'- -GAUCAGAUCUCUGGGCAGAUUUUcaa -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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