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
18790	5'	-58	NC_004683.1	+	4533	0.66	0.554211
	Target:  5'- --gGUGGAuCGCUGCGCgucgucggacucggCC-GGGUGUu -3' miRNA:   3'- cuaUACCU-GCGGCGCGa-------------GGuCCCACA- -5'
18790	5'	-58	NC_004683.1	+	24046	0.66	0.549961
	Target:  5'- cGAg--GGGCacguaGCCGUGCUcgacgagcuuggCCAGGGUGa -3' miRNA:   3'- -CUauaCCUG-----CGGCGCGA------------GGUCCCACa -5'
18790	5'	-58	NC_004683.1	+	4966	0.66	0.543604
	Target:  5'- ----cGGACGCgggccaguucggcggCGCGCUCCAGGcggcucauGUGg -3' miRNA:   3'- cuauaCCUGCG---------------GCGCGAGGUCC--------CACa -5'
18790	5'	-58	NC_004683.1	+	3511	0.67	0.508083
	Target:  5'- --gGUGGugGCCGCGgUgaaCUcGGGUGa -3' miRNA:   3'- cuaUACCugCGGCGCgA---GGuCCCACa -5'
18790	5'	-58	NC_004683.1	+	23393	0.7	0.332853
	Target:  5'- -cUcgGGAUGCCGCGCUgCAGcGGg-- -3' miRNA:   3'- cuAuaCCUGCGGCGCGAgGUC-CCaca -5'
18790	5'	-58	NC_004683.1	+	39609	0.79	0.083432
	Target:  5'- ---cUGGGCGCC-CGUUCCGGGGUGg -3' miRNA:   3'- cuauACCUGCGGcGCGAGGUCCCACa -5'
18790	5'	-58	NC_004683.1	+	21729	1.07	0.000706
	Target:  5'- gGAUAUGGACGCCGCGCUCCAGGGUGUa -3' miRNA:   3'- -CUAUACCUGCGGCGCGAGGUCCCACA- -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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