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
20779	3'	-51.1	NC_004689.1	+	61013	0.67	0.882179
	Target:  5'- uCAUCAUCGcGUCCAcGCCAa-GGUUu -3' miRNA:   3'- -GUAGUAGCaCAGGUaCGGUggUCAAu -5'
20779	3'	-51.1	NC_004689.1	+	42365	0.68	0.866166
	Target:  5'- aGUC-UCGccGUCUcgGCCACCAGggGa -3' miRNA:   3'- gUAGuAGCa-CAGGuaCGGUGGUCaaU- -5'
20779	3'	-51.1	NC_004689.1	+	10897	0.68	0.857771
	Target:  5'- gCGUCGUUGgcgUCGUGCCACUGGUa- -3' miRNA:   3'- -GUAGUAGCacaGGUACGGUGGUCAau -5'
20779	3'	-51.1	NC_004689.1	+	28360	0.68	0.849127
	Target:  5'- cCGUCAUCGaacuUGaUCGUGCCGCUGGUg- -3' miRNA:   3'- -GUAGUAGC----ACaGGUACGGUGGUCAau -5'
20779	3'	-51.1	NC_004689.1	+	12028	0.68	0.831128
	Target:  5'- aCAgagCGUUGagGUCCGUGCCAUCGGc-- -3' miRNA:   3'- -GUa--GUAGCa-CAGGUACGGUGGUCaau -5'
20779	3'	-51.1	NC_004689.1	+	60661	0.7	0.761762
	Target:  5'- gAUCAUCGUGUCguagGUgACCAGUg- -3' miRNA:   3'- gUAGUAGCACAGgua-CGgUGGUCAau -5'
20779	3'	-51.1	NC_004689.1	+	46887	0.71	0.681078
	Target:  5'- aCAUCAUCGgcugcGUCCAaagucagugacagGCCACCAGa-- -3' miRNA:   3'- -GUAGUAGCa----CAGGUa------------CGGUGGUCaau -5'
20779	3'	-51.1	NC_004689.1	+	20552	1.07	0.004178
	Target:  5'- cCAUCAUCGUGUCCAUGCCACCAGUUAu -3' miRNA:   3'- -GUAGUAGCACAGGUACGGUGGUCAAU- -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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