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
31519	5'	-40.6	NC_006661.1	+	7359	0.67	0.976216
	Target:  5'- aCAGUccAGACuuUUcuaAUGUGGUCUGGGc -3' miRNA:   3'- -GUCA--UUUGuuAAug-UACACUAGACUC- -5'
31519	5'	-40.6	NC_006661.1	+	6772	0.83	0.264835
	Target:  5'- aGGUcAACAA--ACAUGUGGUCUGAGg -3' miRNA:   3'- gUCAuUUGUUaaUGUACACUAGACUC- -5'
31519	5'	-40.6	NC_006661.1	+	11087	0.84	0.232368
	Target:  5'- aGGUuGACAA--ACAUGUGGUCUGAGg -3' miRNA:   3'- gUCAuUUGUUaaUGUACACUAGACUC- -5'
31519	5'	-40.6	NC_006661.1	+	11087	0.85	0.203318
	Target:  5'- uCGGccAACAAUcACAUGUGAUCUGAGa -3' miRNA:   3'- -GUCauUUGUUAaUGUACACUAGACUC- -5'
31519	5'	-40.6	NC_006661.1	+	6771	1.12	0.00381
	Target:  5'- uCAGUAAACAAUUACAUGUGAUCUGAGa -3' miRNA:   3'- -GUCAUUUGUUAAUGUACACUAGACUC- -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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