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
7111	5'	-52.8	NC_001895.1	+	4773	0.66	0.724183
	Target:  5'- uGGUGAUuguGGGgcgUCAgCUACUGGCGgacaAGUAu -3' miRNA:   3'- -CCACUA---UCCa--AGU-GGUGGCCGU----UCGU- -5'
7111	5'	-52.8	NC_001895.1	+	10897	0.66	0.678546
	Target:  5'- -uUGAUgAGaGUUCACCGCCGGUguGUu -3' miRNA:   3'- ccACUA-UC-CAAGUGGUGGCCGuuCGu -5'
7111	5'	-52.8	NC_001895.1	+	10783	0.72	0.370947
	Target:  5'- gGGUGAcgcGGGUugaugcuuucaccaUgACCACCGGCAccguGGCAg -3' miRNA:   3'- -CCACUa--UCCA--------------AgUGGUGGCCGU----UCGU- -5'
7111	5'	-52.8	NC_001895.1	+	6035	0.72	0.337031
	Target:  5'- cGGUGA-GGGUacgguggUCAUCccgcaACCGGCAGGCGa -3' miRNA:   3'- -CCACUaUCCA-------AGUGG-----UGGCCGUUCGU- -5'
7111	5'	-52.8	NC_001895.1	+	29959	0.73	0.329337
	Target:  5'- aGGUGugggagccGGUaacgaaguaUCACCACCGGUGAGCu -3' miRNA:   3'- -CCACuau-----CCA---------AGUGGUGGCCGUUCGu -5'
7111	5'	-52.8	NC_001895.1	+	3527	0.73	0.32011
	Target:  5'- -cUGGUGGGUcuggccgUCACCGaugacCCGGCAAGCc -3' miRNA:   3'- ccACUAUCCA-------AGUGGU-----GGCCGUUCGu -5'
7111	5'	-52.8	NC_001895.1	+	6835	1.11	0.000691
	Target:  5'- gGGUGAUAGGUUCACCACCGGCAAGCAc -3' miRNA:   3'- -CCACUAUCCAAGUGGUGGCCGUUCGU- -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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