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
28349	3'	-55.7	NC_005946.1	+	100876	0.66	0.810489
	Target:  5'- cGGCUGCCAUCgaGAcGGUCgauagacuccggacaGCGUUUg -3' miRNA:   3'- -CUGACGGUAGgaCUaCCGGa--------------CGCAAG- -5'
28349	3'	-55.7	NC_005946.1	+	36689	0.66	0.800321
	Target:  5'- uGACgugaGCCucucUCCUGAcgGGCCUGgGcUCg -3' miRNA:   3'- -CUGa---CGGu---AGGACUa-CCGGACgCaAG- -5'
28349	3'	-55.7	NC_005946.1	+	57908	0.66	0.800321
	Target:  5'- uGGCUGCCAgggcCCUGuUGGCCgGgGg-- -3' miRNA:   3'- -CUGACGGUa---GGACuACCGGaCgCaag -5'
28349	3'	-55.7	NC_005946.1	+	97869	0.68	0.700378
	Target:  5'- uGGCU-CCGUCCUGGccugUGGCCgggGCGg-- -3' miRNA:   3'- -CUGAcGGUAGGACU----ACCGGa--CGCaag -5'
28349	3'	-55.7	NC_005946.1	+	102019	0.68	0.700378
	Target:  5'- cGGCUGCCAgCUcGggGGCCUGCu--- -3' miRNA:   3'- -CUGACGGUaGGaCuaCCGGACGcaag -5'
28349	3'	-55.7	NC_005946.1	+	66952	0.7	0.572926
	Target:  5'- cGACcagGCCGUgucgaCCUGcAUGGCCUG-GUUCa -3' miRNA:   3'- -CUGa--CGGUA-----GGAC-UACCGGACgCAAG- -5'
28349	3'	-55.7	NC_005946.1	+	12519	1.1	0.001315
	Target:  5'- cGACUGCCAUCCUGAUGGCCUGCGUUCa -3' miRNA:   3'- -CUGACGGUAGGACUACCGGACGCAAG- -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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