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
3311	3'	-59.6	NC_001545.1	+	8991	0.66	0.115985
	Target:  5'- aGAGCGccccCGGCugCGCCUG-GUCgAc -3' miRNA:   3'- aCUCGCa---GCCGugGCGGACgUAGgUa -5'
3311	3'	-59.6	NC_001545.1	+	2284	0.67	0.095829
	Target:  5'- gGGGCGga-GUGCCGCgaGCGUCCGa -3' miRNA:   3'- aCUCGCagcCGUGGCGgaCGUAGGUa -5'
3311	3'	-59.6	NC_001545.1	+	3425	0.69	0.062966
	Target:  5'- gUGAGCGUUGgaggggguGCACCGCacCUGCGgcaugCCAUg -3' miRNA:   3'- -ACUCGCAGC--------CGUGGCG--GACGUa----GGUA- -5'
3311	3'	-59.6	NC_001545.1	+	6056	0.69	0.057095
	Target:  5'- cGGGCacGUCGGCACCGCggccgGCcucuUCCAUg -3' miRNA:   3'- aCUCG--CAGCCGUGGCGga---CGu---AGGUA- -5'
3311	3'	-59.6	NC_001545.1	+	4231	0.7	0.049595
	Target:  5'- cGAGCGcCGGCugacgaaaccgcucGCCGCCUaccgccGCAUCUAc -3' miRNA:   3'- aCUCGCaGCCG--------------UGGCGGA------CGUAGGUa -5'
3311	3'	-59.6	NC_001545.1	+	4507	0.72	0.032629
	Target:  5'- cGAGCGcacCGGCACCuucGCCUGCAaCCu- -3' miRNA:   3'- aCUCGCa--GCCGUGG---CGGACGUaGGua -5'
3311	3'	-59.6	NC_001545.1	+	4643	1.06	3.7e-05
	Target:  5'- aUGAGCGUCGGCACCGCCUGCAUCCAUg -3' miRNA:   3'- -ACUCGCAGCCGUGGCGGACGUAGGUA- -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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