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
22420	3'	-50.4	NC_005056.1	+	26340	0.66	0.83927
	Target:  5'- ---cGACAGccUCGCGUGGcGCGUUccaUGCa -3' miRNA:   3'- cagaCUGUU--AGCGCGCCcUGUAA---ACG- -5'
22420	3'	-50.4	NC_005056.1	+	12840	0.67	0.77841
	Target:  5'- cUUUGACGG-CGCugGCGGGGC--UUGCu -3' miRNA:   3'- cAGACUGUUaGCG--CGCCCUGuaAACG- -5'
22420	3'	-50.4	NC_005056.1	+	24854	0.68	0.745433
	Target:  5'- -aUUGAUgAAUUGCGUGGGGCAUUc-- -3' miRNA:   3'- caGACUG-UUAGCGCGCCCUGUAAacg -5'
22420	3'	-50.4	NC_005056.1	+	21627	0.68	0.721615
	Target:  5'- --aUGACGGUCGCcgucgcuGCGGGugAUgguaaucUGCg -3' miRNA:   3'- cagACUGUUAGCG-------CGCCCugUAa------ACG- -5'
22420	3'	-50.4	NC_005056.1	+	25150	0.68	0.71126
	Target:  5'- -aCU--UAAUCGUGCGGGGCuucuuUUUGCc -3' miRNA:   3'- caGAcuGUUAGCGCGCCCUGu----AAACG- -5'
22420	3'	-50.4	NC_005056.1	+	9566	0.72	0.468368
	Target:  5'- -gCUGACccAUCGCGCcGGGCGUUcGCg -3' miRNA:   3'- caGACUGu-UAGCGCGcCCUGUAAaCG- -5'
22420	3'	-50.4	NC_005056.1	+	12922	0.77	0.239334
	Target:  5'- -cCUGACAaaaGUCGgGCGGGAUAUUcugGCu -3' miRNA:   3'- caGACUGU---UAGCgCGCCCUGUAAa--CG- -5'
22420	3'	-50.4	NC_005056.1	+	27897	1.12	0.001042
	Target:  5'- aGUCUGACAAUCGCGCGGGACAUUUGCc -3' miRNA:   3'- -CAGACUGUUAGCGCGCCCUGUAAACG- -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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