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
12375	3'	-51.7	NC_003324.1	+	23098	0.66	0.862288
	Target:  5'- cGGGCgccaAGGUCCUggcGACGAcugaGAAGGAu -3' miRNA:   3'- -CUCG----UCCGGGAa--CUGCUaaa-CUUCCU- -5'
12375	3'	-51.7	NC_003324.1	+	28608	0.66	0.853713
	Target:  5'- cGGCAGGCCUcagUGGucuCGGUccGAAGGGc -3' miRNA:   3'- cUCGUCCGGGa--ACU---GCUAaaCUUCCU- -5'
12375	3'	-51.7	NC_003324.1	+	55577	0.66	0.853713
	Target:  5'- cGGCAGGCuCCUgcccGGCGuggaagaaaUGGAGGAu -3' miRNA:   3'- cUCGUCCG-GGAa---CUGCuaa------ACUUCCU- -5'
12375	3'	-51.7	NC_003324.1	+	57245	0.68	0.790345
	Target:  5'- cGGCAGGCCCUUGGCuucgcacucagucGggGGc -3' miRNA:   3'- cUCGUCCGGGAACUGcuaaa--------CuuCCu -5'
12375	3'	-51.7	NC_003324.1	+	16438	0.68	0.777026
	Target:  5'- cGAGCAGGUCCUgGACGAcgcGAucGAc -3' miRNA:   3'- -CUCGUCCGGGAaCUGCUaaaCUucCU- -5'
12375	3'	-51.7	NC_003324.1	+	48938	0.68	0.777026
	Target:  5'- uGAGCGcaauGCCCUcugagcUGGCGA--UGAAGGAc -3' miRNA:   3'- -CUCGUc---CGGGA------ACUGCUaaACUUCCU- -5'
12375	3'	-51.7	NC_003324.1	+	34854	1.1	0.001935
	Target:  5'- cGAGCAGGCCCUUGACGAUUUGAAGGAu -3' miRNA:   3'- -CUCGUCCGGGAACUGCUAAACUUCCU- -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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