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
14699	5'	-56.3	NC_003529.1	+	49516	0.66	0.90073
	Target:  5'- --aGUGCCCGUGGaCGUACAGAg---- -3' miRNA:   3'- gccCGCGGGCGCC-GCGUGUUUaauac -5'
14699	5'	-56.3	NC_003529.1	+	78623	0.66	0.887525
	Target:  5'- -cGGCGCCgGCGGCGguUAu------ -3' miRNA:   3'- gcCCGCGGgCGCCGCguGUuuaauac -5'
14699	5'	-56.3	NC_003529.1	+	34239	0.66	0.880583
	Target:  5'- gCGGGCGCCCGagaccggucUGGCGUguuugGCGAu----- -3' miRNA:   3'- -GCCCGCGGGC---------GCCGCG-----UGUUuaauac -5'
14699	5'	-56.3	NC_003529.1	+	25069	0.67	0.863788
	Target:  5'- uGcGCGCCCaGCGGuUGCACGAuaguuuccaccccaAUUAUGg -3' miRNA:   3'- gCcCGCGGG-CGCC-GCGUGUU--------------UAAUAC- -5'
14699	5'	-56.3	NC_003529.1	+	141131	0.67	0.834492
	Target:  5'- -uGGCGCCgGCGGCGaggACGAAg---- -3' miRNA:   3'- gcCCGCGGgCGCCGCg--UGUUUaauac -5'
14699	5'	-56.3	NC_003529.1	+	1964	0.68	0.799114
	Target:  5'- gCGGcGUGUCCGU-GCGCACAAaaacuuuAUUAUGa -3' miRNA:   3'- -GCC-CGCGGGCGcCGCGUGUU-------UAAUAC- -5'
14699	5'	-56.3	NC_003529.1	+	34404	1.09	0.002845
	Target:  5'- uCGGGCGCCCGCGGCGCACAAAUUAUGa -3' miRNA:   3'- -GCCCGCGGGCGCCGCGUGUUUAAUAC- -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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