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
9792	3'	-47.3	NC_002593.1	+	68260	0.66	0.998099
	Target:  5'- gAGGAggUGGUGGUUGAGGaagacgagccCGAagAGGUg -3' miRNA:   3'- aUCUUuaACUACUAGCUCC----------GCU--UCCA- -5'
9792	3'	-47.3	NC_002593.1	+	37290	0.67	0.996074
	Target:  5'- gUAGGcuguGUUGcggcGUGAUCGGGGUGAAGcGg -3' miRNA:   3'- -AUCUu---UAAC----UACUAGCUCCGCUUC-Ca -5'
9792	3'	-47.3	NC_002593.1	+	57607	0.67	0.996074
	Target:  5'- -uGGAGUcGGUGGUgGAGGaagaGggGGUg -3' miRNA:   3'- auCUUUAaCUACUAgCUCCg---CuuCCA- -5'
9792	3'	-47.3	NC_002593.1	+	57860	0.67	0.995356
	Target:  5'- gAGGAGUUGGUGGaggggUCGGugguggugucGGUGGAGGa -3' miRNA:   3'- aUCUUUAACUACU-----AGCU----------CCGCUUCCa -5'
9792	3'	-47.3	NC_002593.1	+	23908	0.71	0.954419
	Target:  5'- cUGGAGGgugguugUGGUGGUCGAGGCGcAGu- -3' miRNA:   3'- -AUCUUUa------ACUACUAGCUCCGCuUCca -5'
9792	3'	-47.3	NC_002593.1	+	57812	0.73	0.889395
	Target:  5'- gAGGAggUGGUGGUgGAGGUGGuggAGGUg -3' miRNA:   3'- aUCUUuaACUACUAgCUCCGCU---UCCA- -5'
9792	3'	-47.3	NC_002593.1	+	18173	0.96	0.076381
	Target:  5'- cUAGAAA-UGAUGAUCGAGGCGAAGGUu -3' miRNA:   3'- -AUCUUUaACUACUAGCUCCGCUUCCA- -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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