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
27334	5'	-55.7	NC_005857.1	+	11698	0.66	0.603213
	Target:  5'- --uGCUgauggCAUugCCguguaauacgCCUGCAGUAGCGa -3' miRNA:   3'- cauCGA-----GUAugGGa---------GGACGUCGUCGC- -5'
27334	5'	-55.7	NC_005857.1	+	4810	0.67	0.579776
	Target:  5'- -cAGCUgAcagaguuUGCUggCCUGCAGCAGCa -3' miRNA:   3'- caUCGAgU-------AUGGgaGGACGUCGUCGc -5'
27334	5'	-55.7	NC_005857.1	+	46368	0.67	0.547753
	Target:  5'- --uGC-CGUAuUCCUCCUGCAGCGccguauGCGg -3' miRNA:   3'- cauCGaGUAU-GGGAGGACGUCGU------CGC- -5'
27334	5'	-55.7	NC_005857.1	+	30290	0.67	0.536835
	Target:  5'- --cGCUCAUGCCC-CgCUGCuGCGGa- -3' miRNA:   3'- cauCGAGUAUGGGaG-GACGuCGUCgc -5'
27334	5'	-55.7	NC_005857.1	+	26364	0.68	0.515236
	Target:  5'- -cAGCUgGUggacaauuAUCCUCCUGacuCGGCAGCGc -3' miRNA:   3'- caUCGAgUA--------UGGGAGGAC---GUCGUCGC- -5'
27334	5'	-55.7	NC_005857.1	+	35038	0.68	0.515236
	Target:  5'- cGUGGUUUuuacACCCUcaaaucagcaacCCUGCGGCAGUa -3' miRNA:   3'- -CAUCGAGua--UGGGA------------GGACGUCGUCGc -5'
27334	5'	-55.7	NC_005857.1	+	3230	1.08	0.000826
	Target:  5'- uGUAGCUCAUACCCUCCUGCAGCAGCGc -3' miRNA:   3'- -CAUCGAGUAUGGGAGGACGUCGUCGC- -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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