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
16576	3'	-51.3	NC_004117.1	+	113835	0.66	0.993086
	Target:  5'- --cGCCAggucaugucgUUGGCAaaGUUCACCUGCGg -3' miRNA:   3'- cuuUGGUa---------AGCUGUg-CAGGUGGACGC- -5'
16576	3'	-51.3	NC_004117.1	+	136885	0.66	0.992987
	Target:  5'- aAGACguUUCGGCccuuuuaACGUuuGCCUGCa -3' miRNA:   3'- cUUUGguAAGCUG-------UGCAggUGGACGc -5'
16576	3'	-51.3	NC_004117.1	+	17871	0.66	0.990886
	Target:  5'- -uGGCCGUUaCGACACG-UgAUCUGCa -3' miRNA:   3'- cuUUGGUAA-GCUGUGCaGgUGGACGc -5'
16576	3'	-51.3	NC_004117.1	+	16244	0.67	0.986596
	Target:  5'- ----gUAUUCGGCGCGUgCUACUUGCc -3' miRNA:   3'- cuuugGUAAGCUGUGCA-GGUGGACGc -5'
16576	3'	-51.3	NC_004117.1	+	26411	0.67	0.984865
	Target:  5'- cGAAGCCAaacugUCGAUGaauaguuugucCGUCCACgUUGCGg -3' miRNA:   3'- -CUUUGGUa----AGCUGU-----------GCAGGUG-GACGC- -5'
16576	3'	-51.3	NC_004117.1	+	19524	0.68	0.967656
	Target:  5'- cGGGCCA--CGuACACGaUCCugCUGCGu -3' miRNA:   3'- cUUUGGUaaGC-UGUGC-AGGugGACGC- -5'
16576	3'	-51.3	NC_004117.1	+	155512	0.69	0.960868
	Target:  5'- -cAGCCc-UCGAUACGUUgauagCGCCUGCGa -3' miRNA:   3'- cuUUGGuaAGCUGUGCAG-----GUGGACGC- -5'
16576	3'	-51.3	NC_004117.1	+	97924	1.09	0.009241
	Target:  5'- aGAAACCAUUCGACACGUCCACCUGCGc -3' miRNA:   3'- -CUUUGGUAAGCUGUGCAGGUGGACGC- -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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