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
30547	5'	-56.7	NC_006548.1	+	18716	0.67	0.45699
	Target:  5'- cUGCCGcAGaUCCUCgCCCAgccgcaGGCCGu- -3' miRNA:   3'- -ACGGCaUC-AGGAGaGGGUa-----CCGGUug -5'
30547	5'	-56.7	NC_006548.1	+	18438	0.67	0.45699
	Target:  5'- cGgCGUGGUCUUCUgcagggcgCCC-UGGaCCAACu -3' miRNA:   3'- aCgGCAUCAGGAGA--------GGGuACC-GGUUG- -5'
30547	5'	-56.7	NC_006548.1	+	32704	0.67	0.45699
	Target:  5'- cGCCGUuGcUCgaCUCCCGacgugcUGGUCAGCa -3' miRNA:   3'- aCGGCAuC-AGgaGAGGGU------ACCGGUUG- -5'
30547	5'	-56.7	NC_006548.1	+	17441	0.67	0.436847
	Target:  5'- cGCCGUGG-CCUCggCCUggGUGGaCuCAACu -3' miRNA:   3'- aCGGCAUCaGGAGa-GGG--UACC-G-GUUG- -5'
30547	5'	-56.7	NC_006548.1	+	6086	0.67	0.436847
	Target:  5'- gGCCGUcaGGUCUUCuauguccuUCCCAaGGUCGAg -3' miRNA:   3'- aCGGCA--UCAGGAG--------AGGGUaCCGGUUg -5'
30547	5'	-56.7	NC_006548.1	+	25709	0.68	0.361722
	Target:  5'- aUGCCGcuuugcuUCCUCUCCCccGGCgAAUg -3' miRNA:   3'- -ACGGCauc----AGGAGAGGGuaCCGgUUG- -5'
30547	5'	-56.7	NC_006548.1	+	26850	1.1	0.000317
	Target:  5'- uUGCCGUAGUCCUCUCCCAUGGCCAACa -3' miRNA:   3'- -ACGGCAUCAGGAGAGGGUACCGGUUG- -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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