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
16684	3'	-42.9	NC_004156.1	+	59084	0.67	1
	Target:  5'- gGCUGCUGgUaGcACUGgUACUGGUAg -3' miRNA:   3'- aUGAUGAUgAaCuUGACaAUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	171897	0.67	1
	Target:  5'- cACUACUACaaau-UUGUUACUAGUu -3' miRNA:   3'- aUGAUGAUGaacuuGACAAUGAUCAu -5'
16684	3'	-42.9	NC_004156.1	+	124629	0.68	1
	Target:  5'- gUACcagACUGC---AACUGUUACUGGUGc -3' miRNA:   3'- -AUGa--UGAUGaacUUGACAAUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	218662	0.66	1
	Target:  5'- uUACUugUaACUUGuACUGUauaUAUUAGUGu -3' miRNA:   3'- -AUGAugA-UGAACuUGACA---AUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	122792	0.66	1
	Target:  5'- gUACUGgUACUgguACUGgcACUGGUGc -3' miRNA:   3'- -AUGAUgAUGAacuUGACaaUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	39673	0.66	1
	Target:  5'- gUACUACcACUaGuAgUGUUGCUGGUAc -3' miRNA:   3'- -AUGAUGaUGAaCuUgACAAUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	90005	0.7	0.999986
	Target:  5'- -cCUGCUugUcGGcACUGUUACUAGUc -3' miRNA:   3'- auGAUGAugAaCU-UGACAAUGAUCAu -5'
16684	3'	-42.9	NC_004156.1	+	49583	0.71	0.999962
	Target:  5'- aUACUGCUACUaguauUGAuAUUGcUACUAGUAc -3' miRNA:   3'- -AUGAUGAUGA-----ACU-UGACaAUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	135499	0.72	0.999931
	Target:  5'- gUACUACUACU---ACUGguaguagUGCUAGUAg -3' miRNA:   3'- -AUGAUGAUGAacuUGACa------AUGAUCAU- -5'
16684	3'	-42.9	NC_004156.1	+	11332	0.72	0.999905
	Target:  5'- gGCUGCUACUgaUGAugaugauACUGUUGCUAc-- -3' miRNA:   3'- aUGAUGAUGA--ACU-------UGACAAUGAUcau -5'
16684	3'	-42.9	NC_004156.1	+	135209	0.87	0.699795
	Target:  5'- uUACUACUACUaGuACUGUUACUAGUAg -3' miRNA:   3'- -AUGAUGAUGAaCuUGACAAUGAUCAU- -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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