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
24899	5'	-56.1	NC_005284.1	+	22864	0.66	0.682287
	Target:  5'- aGGCGGCgggaaGGGCgUCGAGCgCCGc-- -3' miRNA:   3'- cCUGUCGag---CCCG-AGCUCGaGGUaac -5'
24899	5'	-56.1	NC_005284.1	+	27318	0.66	0.671399
	Target:  5'- aGAUAGUcCGGGUaaaucUCGGGCUCCc--- -3' miRNA:   3'- cCUGUCGaGCCCG-----AGCUCGAGGuaac -5'
24899	5'	-56.1	NC_005284.1	+	17798	0.67	0.583821
	Target:  5'- gGGACGGUgucguuucaggUCGGGCUCGAcgggacGCUUUGUg- -3' miRNA:   3'- -CCUGUCG-----------AGCCCGAGCU------CGAGGUAac -5'
24899	5'	-56.1	NC_005284.1	+	18059	0.67	0.583821
	Target:  5'- gGGACggcaAGCUCccccaguacauGGGCUCGAGCagCGUc- -3' miRNA:   3'- -CCUG----UCGAG-----------CCCGAGCUCGagGUAac -5'
24899	5'	-56.1	NC_005284.1	+	36662	0.68	0.509063
	Target:  5'- gGGAgAGC-CGGGCgCGGGCUCa---- -3' miRNA:   3'- -CCUgUCGaGCCCGaGCUCGAGguaac -5'
24899	5'	-56.1	NC_005284.1	+	46680	0.81	0.08934
	Target:  5'- cGACAGgUCGGGCUCGAGUcggaaacgcgCCAUUGg -3' miRNA:   3'- cCUGUCgAGCCCGAGCUCGa---------GGUAAC- -5'
24899	5'	-56.1	NC_005284.1	+	3479	1.1	0.000702
	Target:  5'- cGGACAGCUCGGGCUCGAGCUCCAUUGc -3' miRNA:   3'- -CCUGUCGAGCCCGAGCUCGAGGUAAC- -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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