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
30766	3'	-60.5	NC_006552.1	+	35627	0.66	0.508266
	Target:  5'- gUCGGCGUCCGGGUggGCCUcguagaUCGCa--- -3' miRNA:   3'- -GGCCGCGGGCCUA--CGGAc-----AGCGcaug -5'
30766	3'	-60.5	NC_006552.1	+	30460	0.67	0.469366
	Target:  5'- aCCGGCuaacuCCUGcGAUcGCCUGUgaguagUGCGUACu -3' miRNA:   3'- -GGCCGc----GGGC-CUA-CGGACA------GCGCAUG- -5'
30766	3'	-60.5	NC_006552.1	+	26533	0.68	0.414048
	Target:  5'- gCGGCGCCgGGGUGUCca--GCGUcagGCg -3' miRNA:   3'- gGCCGCGGgCCUACGGacagCGCA---UG- -5'
30766	3'	-60.5	NC_006552.1	+	52948	0.68	0.387934
	Target:  5'- gCCGGCGCCCGcc-GCCgGUgcggcaucCGgGUGCg -3' miRNA:   3'- -GGCCGCGGGCcuaCGGaCA--------GCgCAUG- -5'
30766	3'	-60.5	NC_006552.1	+	36405	0.69	0.362926
	Target:  5'- gCCGGCGCUCGGAgacgccuugGCUUGg-GCG-GCa -3' miRNA:   3'- -GGCCGCGGGCCUa--------CGGACagCGCaUG- -5'
30766	3'	-60.5	NC_006552.1	+	26704	0.7	0.309042
	Target:  5'- aCUGGuCGCCCaGGgcGCCgaaggcGUCGcCGUGCa -3' miRNA:   3'- -GGCC-GCGGG-CCuaCGGa-----CAGC-GCAUG- -5'
30766	3'	-60.5	NC_006552.1	+	27919	1.06	0.000741
	Target:  5'- uCCGGCGCCCGGAUGCCUGUCGCGUAa -3' miRNA:   3'- -GGCCGCGGGCCUACGGACAGCGCAUg -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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