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
8919	5'	-59.5	NC_002484.1	+	48766	0.66	0.475002
	Target:  5'- cGUCGCUCAcggcgaucuuGGCGUCGCGG-AGCUUCa -3' miRNA:   3'- -CAGCGAGU----------CUGCGGCGUUgUCGGGGa -5'
8919	5'	-59.5	NC_002484.1	+	15213	0.66	0.495049
	Target:  5'- cUCGCUCcacgauuGAUGCUGCGGCAgaugacaacGCCUCa -3' miRNA:   3'- cAGCGAGu------CUGCGGCGUUGU---------CGGGGa -5'
8919	5'	-59.5	NC_002484.1	+	43040	0.68	0.339652
	Target:  5'- aUCGCagCAGGCuaCGCAGCagaAGCCCUUg -3' miRNA:   3'- cAGCGa-GUCUGcgGCGUUG---UCGGGGA- -5'
8919	5'	-59.5	NC_002484.1	+	25962	0.68	0.34776
	Target:  5'- -aUGCUCAcGCugGCCGUAAcCAGCCCCc -3' miRNA:   3'- caGCGAGUcUG--CGGCGUU-GUCGGGGa -5'
8919	5'	-59.5	NC_002484.1	+	3351	0.7	0.272906
	Target:  5'- -cCGCUCGGGCGCaguUAGCAGCCgCUu -3' miRNA:   3'- caGCGAGUCUGCGgc-GUUGUCGGgGA- -5'
8919	5'	-59.5	NC_002484.1	+	18561	0.71	0.222784
	Target:  5'- cGUCGCgcgaaCGGACGCCGCggUAuuGCCgCUg -3' miRNA:   3'- -CAGCGa----GUCUGCGGCGuuGU--CGGgGA- -5'
8919	5'	-59.5	NC_002484.1	+	35929	0.72	0.190519
	Target:  5'- --aGCUCAGGCGCaGCAACugaaAGCCCUUc -3' miRNA:   3'- cagCGAGUCUGCGgCGUUG----UCGGGGA- -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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