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
16335	5'	-55	NC_004084.1	+	43886	0.66	0.735081
	Target:  5'- uUCGAUCGAu-----CUGGCCGGGAc -3' miRNA:   3'- gAGUUGGCUcuguauGACCGGCCCUu -5'
16335	5'	-55	NC_004084.1	+	23490	0.66	0.702814
	Target:  5'- -aCGcCCGuGACGagaUGGCCGGGGAg -3' miRNA:   3'- gaGUuGGCuCUGUaugACCGGCCCUU- -5'
16335	5'	-55	NC_004084.1	+	31171	0.67	0.669917
	Target:  5'- -aCAuCCGGGuacuCAU-CUGGCUGGGGAa -3' miRNA:   3'- gaGUuGGCUCu---GUAuGACCGGCCCUU- -5'
16335	5'	-55	NC_004084.1	+	36493	0.68	0.581363
	Target:  5'- uUCAACCGGGAC-UACUggGGCCGaucGAAa -3' miRNA:   3'- gAGUUGGCUCUGuAUGA--CCGGCc--CUU- -5'
16335	5'	-55	NC_004084.1	+	49070	0.7	0.495429
	Target:  5'- --uGACCGucGACGUGCgacGGUCGGGAGa -3' miRNA:   3'- gagUUGGCu-CUGUAUGa--CCGGCCCUU- -5'
16335	5'	-55	NC_004084.1	+	4929	0.7	0.474811
	Target:  5'- aCUUcGCCGucGACGUACUGgaugacguccGCCGGGAGa -3' miRNA:   3'- -GAGuUGGCu-CUGUAUGAC----------CGGCCCUU- -5'
16335	5'	-55	NC_004084.1	+	41387	0.72	0.370067
	Target:  5'- uCUCGAUCGAGGUAgaggGCgaggaGGCCGGGAAg -3' miRNA:   3'- -GAGUUGGCUCUGUa---UGa----CCGGCCCUU- -5'
16335	5'	-55	NC_004084.1	+	14228	1.06	0.001689
	Target:  5'- cCUCAACCGAGACAUACUGGCCGGGAAc -3' miRNA:   3'- -GAGUUGGCUCUGUAUGACCGGCCCUU- -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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