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
18576	3'	-56.2	NC_004682.1	+	13303	0.66	0.653629
	Target:  5'- --cGcCGGCCCGGUGGAgcaaggGCaCCg -3' miRNA:   3'- guaCuGCUGGGCCACCUagaa--CG-GGa -5'
18576	3'	-56.2	NC_004682.1	+	8215	0.66	0.60959
	Target:  5'- uGUGGCGugCCGGgucgaugacgGGAUgUUGuUCCUg -3' miRNA:   3'- gUACUGCugGGCCa---------CCUAgAAC-GGGA- -5'
18576	3'	-56.2	NC_004682.1	+	43108	0.67	0.54428
	Target:  5'- --aGGCGACgggcaCCGG-GGAUCUuggucagguUGCCCUc -3' miRNA:   3'- guaCUGCUG-----GGCCaCCUAGA---------ACGGGA- -5'
18576	3'	-56.2	NC_004682.1	+	22878	0.68	0.522978
	Target:  5'- -cUGACGAauCUCGG-GGA-CUUGCCCc -3' miRNA:   3'- guACUGCU--GGGCCaCCUaGAACGGGa -5'
18576	3'	-56.2	NC_004682.1	+	42858	0.69	0.481407
	Target:  5'- cCGUG-CGAUCCGGUGGAcggUCUcaaCCCUc -3' miRNA:   3'- -GUACuGCUGGGCCACCU---AGAac-GGGA- -5'
18576	3'	-56.2	NC_004682.1	+	36959	0.7	0.399865
	Target:  5'- cCGUGAacCGGCCuCGGUGGAUCggaaccgucucgGCCUUg -3' miRNA:   3'- -GUACU--GCUGG-GCCACCUAGaa----------CGGGA- -5'
18576	3'	-56.2	NC_004682.1	+	31357	1.07	0.00105
	Target:  5'- cCAUGACGACCCGGUGGAUCUUGCCCUu -3' miRNA:   3'- -GUACUGCUGGGCCACCUAGAACGGGA- -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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