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
15389	3'	-46.3	NC_003907.2	+	36421	0.66	0.988612
	Target:  5'- --gAGGUAGGACUcuUUAAGUUCAgUa -3' miRNA:   3'- caaUCCAUCUUGAuuAGUUCGGGUgA- -5'
15389	3'	-46.3	NC_003907.2	+	9018	0.66	0.984871
	Target:  5'- cUUAGGUAGGuacucGCUGuaGUCuuucAGCUCACUc -3' miRNA:   3'- cAAUCCAUCU-----UGAU--UAGu---UCGGGUGA- -5'
15389	3'	-46.3	NC_003907.2	+	2164	0.66	0.982681
	Target:  5'- -aUAGGUAGAcCgucAUCAAuacagcuacGCCCACg -3' miRNA:   3'- caAUCCAUCUuGau-UAGUU---------CGGGUGa -5'
15389	3'	-46.3	NC_003907.2	+	13063	0.67	0.974677
	Target:  5'- ---cGGUGGAGCUGcuauGUCuuGCCCuGCUg -3' miRNA:   3'- caauCCAUCUUGAU----UAGuuCGGG-UGA- -5'
15389	3'	-46.3	NC_003907.2	+	30125	0.71	0.842222
	Target:  5'- --gAGGUagucaagaaguuAGGACUAAUCAAGUCCGa- -3' miRNA:   3'- caaUCCA------------UCUUGAUUAGUUCGGGUga -5'
15389	3'	-46.3	NC_003907.2	+	28618	0.73	0.780591
	Target:  5'- -cUGGGUccaccucaaAGAACUGAgcaagCAAGCCUGCUg -3' miRNA:   3'- caAUCCA---------UCUUGAUUa----GUUCGGGUGA- -5'
15389	3'	-46.3	NC_003907.2	+	1056	1.09	0.005742
	Target:  5'- uGUUAGGUAGAACUAAUCAAGCCCACUa -3' miRNA:   3'- -CAAUCCAUCUUGAUUAGUUCGGGUGA- -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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