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
21225	5'	-51.8	NC_004778.3	+	63228	0.66	0.965512
	Target:  5'- uUCGuAGCCAGUggaUGUGgagacgUGCGCAAa -3' miRNA:   3'- uAGUuUCGGUCG---ACACaaa---GCGCGUU- -5'
21225	5'	-51.8	NC_004778.3	+	111403	0.66	0.965512
	Target:  5'- uAUCAAAGCCAGUUccGUGg--UGgGCAu -3' miRNA:   3'- -UAGUUUCGGUCGA--CACaaaGCgCGUu -5'
21225	5'	-51.8	NC_004778.3	+	65663	0.66	0.95806
	Target:  5'- uUCGGAGCCAGCguuUGaccuUUUCGCaGCAc -3' miRNA:   3'- uAGUUUCGGUCGac-AC----AAAGCG-CGUu -5'
21225	5'	-51.8	NC_004778.3	+	65364	0.66	0.95806
	Target:  5'- gAUUAAGGCCGaCgGUGUUuacaUCGCGCGc -3' miRNA:   3'- -UAGUUUCGGUcGaCACAA----AGCGCGUu -5'
21225	5'	-51.8	NC_004778.3	+	17092	0.66	0.953949
	Target:  5'- -aCAAGGCCGuguuGCUGUG---CGCGCGg -3' miRNA:   3'- uaGUUUCGGU----CGACACaaaGCGCGUu -5'
21225	5'	-51.8	NC_004778.3	+	74301	0.68	0.883435
	Target:  5'- -aCGAGGCCGGuCUGcGgcUCGCGCu- -3' miRNA:   3'- uaGUUUCGGUC-GACaCaaAGCGCGuu -5'
21225	5'	-51.8	NC_004778.3	+	57551	0.72	0.714676
	Target:  5'- cAUCAGccGCCAGCUGgcaaaGUggCGCGCAAa -3' miRNA:   3'- -UAGUUu-CGGUCGACa----CAaaGCGCGUU- -5'
21225	5'	-51.8	NC_004778.3	+	57440	1.05	0.007944
	Target:  5'- aAUCAAAGCCAGCUGUGUUUCGCGCAAg -3' miRNA:   3'- -UAGUUUCGGUCGACACAAAGCGCGUU- -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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