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
13363	3'	-47.9	NC_003409.1	+	112119	0.66	0.999595
	Target:  5'- ----aGGACUCAcug-GGGGUCUCGGg -3' miRNA:   3'- caaagUCUGGGUacaaCUCUAGAGCC- -5'
13363	3'	-47.9	NC_003409.1	+	102515	0.66	0.999595
	Target:  5'- ---gCGGGCCaucuucGAGAUCUCGGu -3' miRNA:   3'- caaaGUCUGGguacaaCUCUAGAGCC- -5'
13363	3'	-47.9	NC_003409.1	+	55998	0.67	0.998819
	Target:  5'- --gUCGgcGACCCGUGg-GAGGUCgcgCGGc -3' miRNA:   3'- caaAGU--CUGGGUACaaCUCUAGa--GCC- -5'
13363	3'	-47.9	NC_003409.1	+	13078	0.68	0.996474
	Target:  5'- --gUCAGuACCCuacggGUgGGGAUCUUGGc -3' miRNA:   3'- caaAGUC-UGGGua---CAaCUCUAGAGCC- -5'
13363	3'	-47.9	NC_003409.1	+	12873	1.12	0.010803
	Target:  5'- gGUUUCAGACCCAUGUUGAGAUCUCGGa -3' miRNA:   3'- -CAAAGUCUGGGUACAACUCUAGAGCC- -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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