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
20999	3'	-60.2	NC_004735.1	+	120626	0.66	0.717699
	Target:  5'- uACCACCacaauGgACGGCaUGCuGGUGGUCa -3' miRNA:   3'- cUGGUGGc----UgUGCCG-AUGcCCGCCAG- -5'
20999	3'	-60.2	NC_004735.1	+	38595	0.68	0.582256
	Target:  5'- -uCCGCCGGCGgGGCUuuaagguacgggucgACGGGCGc-- -3' miRNA:   3'- cuGGUGGCUGUgCCGA---------------UGCCCGCcag -5'
20999	3'	-60.2	NC_004735.1	+	101361	0.68	0.568372
	Target:  5'- cGCUAUUGcCGUGGUgGCGGGCGGUCu -3' miRNA:   3'- cUGGUGGCuGUGCCGaUGCCCGCCAG- -5'
20999	3'	-60.2	NC_004735.1	+	35568	0.7	0.436489
	Target:  5'- gGAgCGCCG-CACGG-UGCGGGUGGcUCu -3' miRNA:   3'- -CUgGUGGCuGUGCCgAUGCCCGCC-AG- -5'
20999	3'	-60.2	NC_004735.1	+	129893	0.73	0.30288
	Target:  5'- uACCACCG-UACGGCUGgcgguccgucggUGGGaCGGUCa -3' miRNA:   3'- cUGGUGGCuGUGCCGAU------------GCCC-GCCAG- -5'
20999	3'	-60.2	NC_004735.1	+	66819	0.75	0.245938
	Target:  5'- -gUCACCGAUACGGCgACGGcugggaGCGGUCc -3' miRNA:   3'- cuGGUGGCUGUGCCGaUGCC------CGCCAG- -5'
20999	3'	-60.2	NC_004735.1	+	126812	1.08	0.001175
	Target:  5'- uGACCACCGACACGGCUACGGGCGGUCu -3' miRNA:   3'- -CUGGUGGCUGUGCCGAUGCCCGCCAG- -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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