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
22839	3'	-45	NC_005135.1	+	151215	0.66	0.999992
	Target:  5'- cGAUAAgccgACUCCGCAaGaGUUaGGUg- -3' miRNA:   3'- aCUAUUaa--UGAGGCGU-C-CAAaCCAau -5'
22839	3'	-45	NC_005135.1	+	94236	0.67	0.999988
	Target:  5'- cGAUAGUUAUUCCGCcuGGgaguugcaucccUUGGUg- -3' miRNA:   3'- aCUAUUAAUGAGGCGu-CCa-----------AACCAau -5'
22839	3'	-45	NC_005135.1	+	10713	0.68	0.999943
	Target:  5'- cGAUGuacACUuuGcCAGGUUUGGUc- -3' miRNA:   3'- aCUAUuaaUGAggC-GUCCAAACCAau -5'
22839	3'	-45	NC_005135.1	+	113489	0.68	0.999898
	Target:  5'- cGcgAAUUACUCCGCA---UUGGUa- -3' miRNA:   3'- aCuaUUAAUGAGGCGUccaAACCAau -5'
22839	3'	-45	NC_005135.1	+	143932	0.69	0.99971
	Target:  5'- cGAUGGUaaaUCCGCAGuagUUGGUUGa -3' miRNA:   3'- aCUAUUAaugAGGCGUCca-AACCAAU- -5'
22839	3'	-45	NC_005135.1	+	109607	0.76	0.966074
	Target:  5'- gUGAU--UUACaaUCuCGCAGGUUUGGUUAu -3' miRNA:   3'- -ACUAuuAAUG--AG-GCGUCCAAACCAAU- -5'
22839	3'	-45	NC_005135.1	+	164960	0.79	0.883276
	Target:  5'- --uUAAUUACUCCGUuuuGGUUUGGUUu -3' miRNA:   3'- acuAUUAAUGAGGCGu--CCAAACCAAu -5'
22839	3'	-45	NC_005135.1	+	109362	1.09	0.034289
	Target:  5'- aUGAUAAUUACUCCGCAGGUUUGGUUAg -3' miRNA:   3'- -ACUAUUAAUGAGGCGUCCAAACCAAU- -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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