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
22322	3'	-49.7	NC_005045.1	+	27063	0.67	0.870049
	Target:  5'- -aGGAGGAcgaggcgacccuggAAGGUCGUCAUgCCGGUg -3' miRNA:   3'- uaCUUCCUa-------------UUCCGGUAGUA-GGCUAg -5'
22322	3'	-49.7	NC_005045.1	+	24344	0.67	0.857798
	Target:  5'- -cGAGGccaAGGGCCGUCGUgCCGGUg -3' miRNA:   3'- uaCUUCcuaUUCCGGUAGUA-GGCUAg -5'
22322	3'	-49.7	NC_005045.1	+	15792	0.68	0.809865
	Target:  5'- --cGAGGAcGAGGCCAUCGacaUGAUCc -3' miRNA:   3'- uacUUCCUaUUCCGGUAGUag-GCUAG- -5'
22322	3'	-49.7	NC_005045.1	+	24522	0.69	0.745374
	Target:  5'- -cGAAGGAUuGGGuCCAcUCGUCCugguGGUCg -3' miRNA:   3'- uaCUUCCUAuUCC-GGU-AGUAGG----CUAG- -5'
22322	3'	-49.7	NC_005045.1	+	15822	0.7	0.711137
	Target:  5'- gGUGGAGGAUGucgaAGGCCGUCuucaugCCGc-- -3' miRNA:   3'- -UACUUCCUAU----UCCGGUAGua----GGCuag -5'
22322	3'	-49.7	NC_005045.1	+	16125	0.7	0.676087
	Target:  5'- cGUGAAGGGcGAGGCCGUgA-UgGAUCa -3' miRNA:   3'- -UACUUCCUaUUCCGGUAgUaGgCUAG- -5'
22322	3'	-49.7	NC_005045.1	+	33113	0.7	0.67491
	Target:  5'- cGUGGAGGGUAuccgcagccugcuGGGCC-UCcgGUCCGAUg -3' miRNA:   3'- -UACUUCCUAU-------------UCCGGuAG--UAGGCUAg -5'
22322	3'	-49.7	NC_005045.1	+	15501	1.07	0.002885
	Target:  5'- cAUGAAGGAUAAGGCCAUCAUCCGAUCc -3' miRNA:   3'- -UACUUCCUAUUCCGGUAGUAGGCUAG- -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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