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
6222	3'	-52.7	NC_001844.1	+	93185	0.66	0.977521
	Target:  5'- -cCAGCGCUCGCUguuUUGGUggcuagcucuacgcuGgCAGUGGc -3' miRNA:   3'- ucGUCGUGAGCGA---AGCUA---------------UgGUCACC- -5'
6222	3'	-52.7	NC_001844.1	+	84014	0.66	0.971091
	Target:  5'- uGCuGCaACUCGCgUCGAggGCCAGg-- -3' miRNA:   3'- uCGuCG-UGAGCGaAGCUa-UGGUCacc -5'
6222	3'	-52.7	NC_001844.1	+	74498	0.67	0.960598
	Target:  5'- gGGCGGCACagucagccugUCGCaugcugggaagCGGcuUGCCGGUGGc -3' miRNA:   3'- -UCGUCGUG----------AGCGaa---------GCU--AUGGUCACC- -5'
6222	3'	-52.7	NC_001844.1	+	85473	0.67	0.95761
	Target:  5'- cGCAGCACgCGUUUCGGgugGCaaauuucuagGGUGGu -3' miRNA:   3'- uCGUCGUGaGCGAAGCUa--UGg---------UCACC- -5'
6222	3'	-52.7	NC_001844.1	+	144401	0.69	0.907003
	Target:  5'- uGGCGGUACUCcCUa-GGUGgCAGUGGa -3' miRNA:   3'- -UCGUCGUGAGcGAagCUAUgGUCACC- -5'
6222	3'	-52.7	NC_001844.1	+	135975	0.7	0.879805
	Target:  5'- aGGCGGguUcCGCgaCGGUAUCGGUGGc -3' miRNA:   3'- -UCGUCguGaGCGaaGCUAUGGUCACC- -5'
6222	3'	-52.7	NC_001844.1	+	97196	1.12	0.003716
	Target:  5'- uAGCAGCACUCGCUUCGAUACCAGUGGg -3' miRNA:   3'- -UCGUCGUGAGCGAAGCUAUGGUCACC- -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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