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
30273	5'	-51.2	NC_006296.2	+	5347	0.66	0.49222
	Target:  5'- cGGGaCCCA---GUGGCUUGcccuuGGUGCu -3' miRNA:   3'- uUCC-GGGUauaUACCGAAUcu---CCACG- -5'
30273	5'	-51.2	NC_006296.2	+	12663	0.67	0.43462
	Target:  5'- -uGGCCCAcAUGUGGCUUcucAGAGcccuaGCc -3' miRNA:   3'- uuCCGGGUaUAUACCGAA---UCUCca---CG- -5'
30273	5'	-51.2	NC_006296.2	+	4667	0.68	0.391463
	Target:  5'- gGAGGUCCGgaccaGGU--GGGGGUGCa -3' miRNA:   3'- -UUCCGGGUauauaCCGaaUCUCCACG- -5'
30273	5'	-51.2	NC_006296.2	+	5179	0.68	0.381118
	Target:  5'- gGAGuCCCGggggcgGUGGUgggGGGGGUGCg -3' miRNA:   3'- -UUCcGGGUaua---UACCGaa-UCUCCACG- -5'
30273	5'	-51.2	NC_006296.2	+	5216	0.69	0.332197
	Target:  5'- uGGGGCCCucUGUucccaucuggcGUGGUgUGGAGGUGg -3' miRNA:   3'- -UUCCGGGu-AUA-----------UACCGaAUCUCCACg -5'
30273	5'	-51.2	NC_006296.2	+	5088	0.72	0.225156
	Target:  5'- -cGGUCCGgcgucgggGUGGCUcuggguggggggucUGGAGGUGCu -3' miRNA:   3'- uuCCGGGUaua-----UACCGA--------------AUCUCCACG- -5'
30273	5'	-51.2	NC_006296.2	+	12661	1.09	0.000341
	Target:  5'- gAAGGCCCAUAUAUGGCUUAGAGGUGCc -3' miRNA:   3'- -UUCCGGGUAUAUACCGAAUCUCCACG- -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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