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
8831	5'	-56.6	NC_002484.1	+	6183	0.66	0.643923
	Target:  5'- gCCUgAGUUCCUGuagugcUCGAUGcgcGCCGUCUUg -3' miRNA:   3'- -GGG-UCGAGGACu-----AGCUAC---UGGCGGAG- -5'
8831	5'	-56.6	NC_002484.1	+	24984	0.67	0.611312
	Target:  5'- aCCAGCgacgCCUGAccggagUCGAgaucGACgGCaCUCa -3' miRNA:   3'- gGGUCGa---GGACU------AGCUa---CUGgCG-GAG- -5'
8831	5'	-56.6	NC_002484.1	+	25832	0.67	0.568113
	Target:  5'- aCCAGgUCCUGGUUagccggGGUGaaGCCGCCcuUCa -3' miRNA:   3'- gGGUCgAGGACUAG------CUAC--UGGCGG--AG- -5'
8831	5'	-56.6	NC_002484.1	+	15778	0.67	0.568113
	Target:  5'- aCCAGCaggCCuacgUGAUCGAgcaGCCGcCCUCu -3' miRNA:   3'- gGGUCGa--GG----ACUAGCUac-UGGC-GGAG- -5'
8831	5'	-56.6	NC_002484.1	+	55933	0.68	0.525721
	Target:  5'- uUCCGGauaCCUGAUUGcaGGCCGCCUg -3' miRNA:   3'- -GGGUCga-GGACUAGCuaCUGGCGGAg -5'
8831	5'	-56.6	NC_002484.1	+	37743	0.69	0.454757
	Target:  5'- cCUCGGCgcCCUGG-CcAUGACCGCCUUc -3' miRNA:   3'- -GGGUCGa-GGACUaGcUACUGGCGGAG- -5'
8831	5'	-56.6	NC_002484.1	+	26375	1.12	0.00046
	Target:  5'- aCCCAGCUCCUGAUCGAUGACCGCCUCg -3' miRNA:   3'- -GGGUCGAGGACUAGCUACUGGCGGAG- -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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