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
27349	3'	-54.2	NC_005857.1	+	45763	0.66	0.79262
	Target:  5'- gGCGGGuCGGUAAUGAUgG-CGUcaAUGCu -3' miRNA:   3'- gCGCCU-GCCAUUGCUGgCgGCA--UAUG- -5'
27349	3'	-54.2	NC_005857.1	+	15196	0.67	0.731401
	Target:  5'- gGCGGAuUGGUGGCGcgauuauuuCCGCCGg---- -3' miRNA:   3'- gCGCCU-GCCAUUGCu--------GGCGGCauaug -5'
27349	3'	-54.2	NC_005857.1	+	20831	0.7	0.567842
	Target:  5'- aCGCGGugcgACGGgcaGCGGCaCGCCGggcUACg -3' miRNA:   3'- -GCGCC----UGCCau-UGCUG-GCGGCau-AUG- -5'
27349	3'	-54.2	NC_005857.1	+	19737	0.7	0.534482
	Target:  5'- gCGCGGACaGGUcaauacuGAUgaGAUCGCgGUAUGCg -3' miRNA:   3'- -GCGCCUG-CCA-------UUG--CUGGCGgCAUAUG- -5'
27349	3'	-54.2	NC_005857.1	+	23364	0.71	0.518586
	Target:  5'- gCGCGGACaGGUuaauacugaugaGAUCGCgGUAUGCg -3' miRNA:   3'- -GCGCCUG-CCAuug---------CUGGCGgCAUAUG- -5'
27349	3'	-54.2	NC_005857.1	+	12196	0.76	0.248395
	Target:  5'- aCGCGuGcCGGUGACGGCuCGCUGgggGUACg -3' miRNA:   3'- -GCGC-CuGCCAUUGCUG-GCGGCa--UAUG- -5'
27349	3'	-54.2	NC_005857.1	+	25457	1.11	0.000996
	Target:  5'- aCGCGGACGGUAACGACCGCCGUAUACg -3' miRNA:   3'- -GCGCCUGCCAUUGCUGGCGGCAUAUG- -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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