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
22694	5'	-53.5	NC_005091.1	+	54082	0.66	0.823275
	Target:  5'- -aGCGAGACGCCGGccGcUGG-AUCAUGg -3' miRNA:   3'- gcCGCUCUGCGGCU--CaACUaUGGUAC- -5'
22694	5'	-53.5	NC_005091.1	+	57178	0.68	0.74406
	Target:  5'- gCGGCGaAGACGCUGuucaacGUUcg-GCCAUGg -3' miRNA:   3'- -GCCGC-UCUGCGGCu-----CAAcuaUGGUAC- -5'
22694	5'	-53.5	NC_005091.1	+	27253	0.68	0.690468
	Target:  5'- uGGCGucGCGCCGcAGUccgaGAUACCAc- -3' miRNA:   3'- gCCGCucUGCGGC-UCAa---CUAUGGUac -5'
22694	5'	-53.5	NC_005091.1	+	49149	0.71	0.514654
	Target:  5'- cCGuGUGuGACGCCagccuuuuagggcGAGUUGAUACCAg- -3' miRNA:   3'- -GC-CGCuCUGCGG-------------CUCAACUAUGGUac -5'
22694	5'	-53.5	NC_005091.1	+	51316	0.72	0.505202
	Target:  5'- cCGGCGuuACGC--GGUUGAUACCGUa -3' miRNA:   3'- -GCCGCucUGCGgcUCAACUAUGGUAc -5'
22694	5'	-53.5	NC_005091.1	+	32816	0.73	0.448234
	Target:  5'- uGGCGuAGGCgGCCGAGUagcaguucgagucgaUGAcgGCCAUGa -3' miRNA:   3'- gCCGC-UCUG-CGGCUCA---------------ACUa-UGGUAC- -5'
22694	5'	-53.5	NC_005091.1	+	28206	1.08	0.002129
	Target:  5'- uCGGCGAGACGCCGAGUUGAUACCAUGc -3' miRNA:   3'- -GCCGCUCUGCGGCUCAACUAUGGUAC- -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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