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
27703	3'	-49.9	NC_005882.1	+	27645	0.66	0.881227
	Target:  5'- -----aGCUcGGGGCGGAucgccGGCuGGCGCa -3' miRNA:   3'- gaauagUGAaCCCUGCCU-----UUG-CCGUG- -5'
27703	3'	-49.9	NC_005882.1	+	34263	0.66	0.876302
	Target:  5'- --cGUUGgUUGGGGCuGGGuccgaugcgaucuucAACGGCACu -3' miRNA:   3'- gaaUAGUgAACCCUG-CCU---------------UUGCCGUG- -5'
27703	3'	-49.9	NC_005882.1	+	7756	0.66	0.864409
	Target:  5'- ---uUCACggauGGACGGAuGCGGCcCg -3' miRNA:   3'- gaauAGUGaac-CCUGCCUuUGCCGuG- -5'
27703	3'	-49.9	NC_005882.1	+	55	0.66	0.861789
	Target:  5'- ---------cGGGACGGAAcgggaucacacggaACGGCGCu -3' miRNA:   3'- gaauagugaaCCCUGCCUU--------------UGCCGUG- -5'
27703	3'	-49.9	NC_005882.1	+	26939	0.67	0.817672
	Target:  5'- -----gGCaUGGGGCGGgcGCGGCcgGCa -3' miRNA:   3'- gaauagUGaACCCUGCCuuUGCCG--UG- -5'
27703	3'	-49.9	NC_005882.1	+	15828	0.68	0.797327
	Target:  5'- -cUGUCAUUc-GGACGcuGGAGCGGCGCc -3' miRNA:   3'- gaAUAGUGAacCCUGC--CUUUGCCGUG- -5'
27703	3'	-49.9	NC_005882.1	+	33764	1.12	0.001416
	Target:  5'- cCUUAUCACUUGGGACGGAAACGGCACg -3' miRNA:   3'- -GAAUAGUGAACCCUGCCUUUGCCGUG- -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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