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
26071	5'	-52.2	NC_005342.2	+	14739	0.68	0.747141
	Target:  5'- cGGGGAacgacAGCAG-CGUGAAauucgguugGCCUUCCAu -3' miRNA:   3'- -CCUCU-----UCGUUaGCACUUg--------CGGAGGGU- -5'
26071	5'	-52.2	NC_005342.2	+	42985	0.68	0.71448
	Target:  5'- cGGGGgcGCAAg---GGGCGCCgaUCCCGg -3' miRNA:   3'- -CCUCuuCGUUagcaCUUGCGG--AGGGU- -5'
26071	5'	-52.2	NC_005342.2	+	40327	0.69	0.669782
	Target:  5'- --cGAAGCGGUCGUGAacgaagucgucGCGCUgUUCCAg -3' miRNA:   3'- ccuCUUCGUUAGCACU-----------UGCGG-AGGGU- -5'
26071	5'	-52.2	NC_005342.2	+	2568	0.69	0.669782
	Target:  5'- ---cAGGCGGUCGUGAAgGUCgCCCAa -3' miRNA:   3'- ccucUUCGUUAGCACUUgCGGaGGGU- -5'
26071	5'	-52.2	NC_005342.2	+	666	0.7	0.601823
	Target:  5'- cGGuGAGcGCGAUCGUGc-CGCCgCCCGc -3' miRNA:   3'- -CCuCUU-CGUUAGCACuuGCGGaGGGU- -5'
26071	5'	-52.2	NC_005342.2	+	33065	0.71	0.57928
	Target:  5'- cGAGAacGGCGcgccGUCGUgGAACGCCUgcugCCCGa -3' miRNA:   3'- cCUCU--UCGU----UAGCA-CUUGCGGA----GGGU- -5'
26071	5'	-52.2	NC_005342.2	+	25810	1.11	0.001254
	Target:  5'- aGGAGAAGCAAUCGUGAACGCCUCCCAc -3' miRNA:   3'- -CCUCUUCGUUAGCACUUGCGGAGGGU- -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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