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
21349	5'	-51.3	NC_004778.3	+	50221	0.66	0.990265
	Target:  5'- cGCGcGACGGUcaccaCGCGccguUUCGUAGGG-Cg -3' miRNA:   3'- -CGCaUUGCCGa----GCGC----AAGCAUUCCaG- -5'
21349	5'	-51.3	NC_004778.3	+	46750	0.66	0.983886
	Target:  5'- aGCGggcAGCGGCcagCGCGUaCGUGccauGGuGUCg -3' miRNA:   3'- -CGCa--UUGCCGa--GCGCAaGCAU----UC-CAG- -5'
21349	5'	-51.3	NC_004778.3	+	48785	0.67	0.971971
	Target:  5'- cGCGgcAACGGCcggUCGCG-UCGcUAuGGUCg -3' miRNA:   3'- -CGCa-UUGCCG---AGCGCaAGC-AUuCCAG- -5'
21349	5'	-51.3	NC_004778.3	+	48578	0.69	0.950575
	Target:  5'- uCGUcAAUGGuCUCGCGaaCGgUGGGGUCg -3' miRNA:   3'- cGCA-UUGCC-GAGCGCaaGC-AUUCCAG- -5'
21349	5'	-51.3	NC_004778.3	+	32790	0.7	0.895106
	Target:  5'- -gGUGACGcGCaCGgGUUUGUGAGGUUc -3' miRNA:   3'- cgCAUUGC-CGaGCgCAAGCAUUCCAG- -5'
21349	5'	-51.3	NC_004778.3	+	100937	0.72	0.841683
	Target:  5'- uGCGgaaaAACGGCgCGUGUUUGUGGacucGGUCa -3' miRNA:   3'- -CGCa---UUGCCGaGCGCAAGCAUU----CCAG- -5'
21349	5'	-51.3	NC_004778.3	+	112524	1.14	0.003875
	Target:  5'- cGCGUAACGGCUCGCGUUCGUAAGGUCg -3' miRNA:   3'- -CGCAUUGCCGAGCGCAAGCAUUCCAG- -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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