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
12738	5'	-52.5	NC_003356.1	+	42054	0.66	0.765282
	Target:  5'- cGAUGCCGGAacuggaagaacUGGCGgCAGCaauGGcgCAg -3' miRNA:   3'- aCUACGGUUU-----------ACCGC-GUCGg--UCaaGU- -5'
12738	5'	-52.5	NC_003356.1	+	35357	1.09	0.001086
	Target:  5'- gUGAUGCCAAAUGGCGCAGCCAGUUCAc -3' miRNA:   3'- -ACUACGGUUUACCGCGUCGGUCAAGU- -5'
12738	5'	-52.5	NC_003356.1	+	28635	0.73	0.33492
	Target:  5'- cGAUGCCcgcguuuuGAggaucguguugGUGGCGCGGCgCAGUUUAa -3' miRNA:   3'- aCUACGG--------UU-----------UACCGCGUCG-GUCAAGU- -5'
12738	5'	-52.5	NC_003356.1	+	27836	0.66	0.719933
	Target:  5'- uUGAUGUCugggcaaAGGUGGCuCAGCCAGg--- -3' miRNA:   3'- -ACUACGG-------UUUACCGcGUCGGUCaagu -5'
12738	5'	-52.5	NC_003356.1	+	24139	0.66	0.754424
	Target:  5'- uUGuUGCCGg--GGCGCuguGCCuGUUCu -3' miRNA:   3'- -ACuACGGUuuaCCGCGu--CGGuCAAGu -5'
12738	5'	-52.5	NC_003356.1	+	20008	0.66	0.754424
	Target:  5'- gGAUGUC--GUGGCcuacauugGUAGCCAGgugUCAu -3' miRNA:   3'- aCUACGGuuUACCG--------CGUCGGUCa--AGU- -5'
12738	5'	-52.5	NC_003356.1	+	7736	0.66	0.743425
	Target:  5'- cUGAUGCCuguGAUGGagaacaUAGCCAGUaCGg -3' miRNA:   3'- -ACUACGGu--UUACCgc----GUCGGUCAaGU- -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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