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
30743	3'	-59.5	NC_006552.1	+	26205	0.66	0.565201
	Target:  5'- aGGuGCu--UGCcGGUCGGCaugGGCGACa -3' miRNA:   3'- gCCuCGccuAUGaCCAGCCG---CCGCUG- -5'
30743	3'	-59.5	NC_006552.1	+	16187	0.66	0.565201
	Target:  5'- gGGuAGCGGAguuCUGGUCGaccGUGGUccgGACc -3' miRNA:   3'- gCC-UCGCCUau-GACCAGC---CGCCG---CUG- -5'
30743	3'	-59.5	NC_006552.1	+	34514	0.66	0.554863
	Target:  5'- gCGGcGGCGGcagcucgauCUGGUCcauguaGGUGGCGAUg -3' miRNA:   3'- -GCC-UCGCCuau------GACCAG------CCGCCGCUG- -5'
30743	3'	-59.5	NC_006552.1	+	59399	0.67	0.474683
	Target:  5'- aGGGcGCGGcaGCgucaGG-CGGUGGCGGCg -3' miRNA:   3'- gCCU-CGCCuaUGa---CCaGCCGCCGCUG- -5'
30743	3'	-59.5	NC_006552.1	+	61370	0.67	0.474683
	Target:  5'- gGGAGcCGGGccauguuUUGGcgcgcCGGCGGCGGCu -3' miRNA:   3'- gCCUC-GCCUau-----GACCa----GCCGCCGCUG- -5'
30743	3'	-59.5	NC_006552.1	+	8243	0.75	0.151986
	Target:  5'- uCGGcGCGGGccaugguguccaggcUAC-GGUCGGUGGCGGCg -3' miRNA:   3'- -GCCuCGCCU---------------AUGaCCAGCCGCCGCUG- -5'
30743	3'	-59.5	NC_006552.1	+	42985	1.09	0.000564
	Target:  5'- aCGGAGCGGAUACUGGUCGGCGGCGACc -3' miRNA:   3'- -GCCUCGCCUAUGACCAGCCGCCGCUG- -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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