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
28943	3'	-49.3	NC_006146.1	+	86799	0.66	0.997298
	Target:  5'- gACUGUucaagUGGUGAAUGaGCGgGUGCAg- -3' miRNA:   3'- -UGACA-----ACCGUUUACgUGUgCACGUaa -5'
28943	3'	-49.3	NC_006146.1	+	128279	0.66	0.996199
	Target:  5'- cGCUGgcgUGGCAcGUcaGCACGUGCu-- -3' miRNA:   3'- -UGACa--ACCGUuUAcgUGUGCACGuaa -5'
28943	3'	-49.3	NC_006146.1	+	11141	0.66	0.996199
	Target:  5'- cCUGggGGCGguGGUGguCACGgagGCAUUc -3' miRNA:   3'- uGACaaCCGU--UUACguGUGCa--CGUAA- -5'
28943	3'	-49.3	NC_006146.1	+	167799	0.67	0.990555
	Target:  5'- aGCUGggcgUGGCGg--GCGCGCGUGg--- -3' miRNA:   3'- -UGACa---ACCGUuuaCGUGUGCACguaa -5'
28943	3'	-49.3	NC_006146.1	+	168731	0.67	0.990555
	Target:  5'- aGCUGggcgUGGCGg--GCGCGCGUGg--- -3' miRNA:   3'- -UGACa---ACCGUuuaCGUGUGCACguaa -5'
28943	3'	-49.3	NC_006146.1	+	169663	0.67	0.990555
	Target:  5'- aGCUGggcgUGGCGg--GCGCGCGUGg--- -3' miRNA:   3'- -UGACa---ACCGUuuaCGUGUGCACguaa -5'
28943	3'	-49.3	NC_006146.1	+	54705	0.67	0.990555
	Target:  5'- gACUGUccUGGUGAAUGgGCugGUGgGa- -3' miRNA:   3'- -UGACA--ACCGUUUACgUGugCACgUaa -5'
28943	3'	-49.3	NC_006146.1	+	9598	1.05	0.018903
	Target:  5'- cACUGUUGGCAAAUGCACACGUGCAUUu -3' miRNA:   3'- -UGACAACCGUUUACGUGUGCACGUAA- -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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