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
31444	5'	-37.3	NC_006645.1	+	5259	0.7	0.999492
	Target:  5'- uAUAGGAAUcAUUCCUAUAcUAUUAUa -3' miRNA:   3'- -UAUCUUUGaUAAGGAUAUaGUAAUAc -5'
31444	5'	-37.3	NC_006645.1	+	5152	0.8	0.829138
	Target:  5'- cGUGGGAACcAUUCCUAUAcUAUUAUGg -3' miRNA:   3'- -UAUCUUUGaUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5220	0.81	0.80596
	Target:  5'- uAUAGGAAUgAUUCCUAUAgCAUUAUGg -3' miRNA:   3'- -UAUCUUUGaUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5289	0.81	0.80596
	Target:  5'- uAUAGGAAUgAUUCCUAUAgCAUUAUGg -3' miRNA:   3'- -UAUCUUUGaUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5303	0.82	0.769116
	Target:  5'- -cAGGAAUUAUUCCUAUAaUAUUAUGg -3' miRNA:   3'- uaUCUUUGAUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5381	0.91	0.347687
	Target:  5'- uAUAGGAAUUAUUCCUGUAgCAUUAUGg -3' miRNA:   3'- -UAUCUUUGAUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5465	0.96	0.183213
	Target:  5'- uAUGGGAACUAUUCCUAUAcCAUUAUGg -3' miRNA:   3'- -UAUCUUUGAUAAGGAUAUaGUAAUAC- -5'
31444	5'	-37.3	NC_006645.1	+	5397	1.1	0.026557
	Target:  5'- uAUAGAAACUAUUCCUAUAUCAUUAUGg -3' miRNA:   3'- -UAUCUUUGAUAAGGAUAUAGUAAUAC- -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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