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
22246	5'	-53.9	NC_005045.1	+	365	0.71	0.457475
	Target:  5'- cUCCUGUGGuggucuguGGUCCUgucggguggUGGUGCGGGa- -3' miRNA:   3'- -GGGGCACCu-------UCAGGA---------ACUACGCCUag -5'
22246	5'	-53.9	NC_005045.1	+	8962	1.12	0.000605
	Target:  5'- cCCCCGUGGAAGUCCUUGAUGCGGAUCa -3' miRNA:   3'- -GGGGCACCUUCAGGAACUACGCCUAG- -5'
22246	5'	-53.9	NC_005045.1	+	12959	0.7	0.478024
	Target:  5'- aCCCGUGGcacGGUCgaUGAUGCaGGcUCg -3' miRNA:   3'- gGGGCACCu--UCAGgaACUACG-CCuAG- -5'
22246	5'	-53.9	NC_005045.1	+	18866	0.69	0.531244
	Target:  5'- gCCCGcuUGGucuGGUgCUUGGUGCGGcgUa -3' miRNA:   3'- gGGGC--ACCu--UCAgGAACUACGCCuaG- -5'
22246	5'	-53.9	NC_005045.1	+	22457	0.7	0.509668
	Target:  5'- aCCUCGUGGAcgAGgCCaagGGUGCGGuaGUCg -3' miRNA:   3'- -GGGGCACCU--UCaGGaa-CUACGCC--UAG- -5'
22246	5'	-53.9	NC_005045.1	+	23548	0.66	0.73143
	Target:  5'- uCCCCGuUGGGAGUgaaggCCggcgGcgGCGGGa- -3' miRNA:   3'- -GGGGC-ACCUUCA-----GGaa--CuaCGCCUag -5'
22246	5'	-53.9	NC_005045.1	+	42428	0.71	0.457475
	Target:  5'- cUCCUGUGGuggucuguGGUCCUgucggguggUGGUGCGGGa- -3' miRNA:   3'- -GGGGCACCu-------UCAGGA---------ACUACGCCUag -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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