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
12610	3'	-51.4	NC_003345.1	+	24640	0.66	0.951735
	Target:  5'- gGAACAggucgcGGGCCGCUGGUcaauucgagguaUUUgUCUgGUg -3' miRNA:   3'- -CUUGU------UCUGGCGACCA------------AGAgAGAgCG- -5'
12610	3'	-51.4	NC_003345.1	+	19710	0.67	0.914223
	Target:  5'- aGAACGAGcCUGCUacucGUUCUUcaUCUCGUa -3' miRNA:   3'- -CUUGUUCuGGCGAc---CAAGAG--AGAGCG- -5'
12610	3'	-51.4	NC_003345.1	+	51588	0.67	0.907753
	Target:  5'- cGGGCAAGACacgacgaccuCGCc-GUaCUCUCUCGCu -3' miRNA:   3'- -CUUGUUCUG----------GCGacCAaGAGAGAGCG- -5'
12610	3'	-51.4	NC_003345.1	+	40888	0.67	0.901009
	Target:  5'- aGGACGAGACCGggGGUUCaaaucccccCUCagGCu -3' miRNA:   3'- -CUUGUUCUGGCgaCCAAGa--------GAGagCG- -5'
12610	3'	-51.4	NC_003345.1	+	62829	0.7	0.780946
	Target:  5'- uGACGAG--CGCgUGGUUC-CUCUCGCu -3' miRNA:   3'- cUUGUUCugGCG-ACCAAGaGAGAGCG- -5'
12610	3'	-51.4	NC_003345.1	+	70203	0.71	0.739837
	Target:  5'- cGGugAGGACgaGCUGGcaaacUUCUCuaUCUCGCg -3' miRNA:   3'- -CUugUUCUGg-CGACC-----AAGAG--AGAGCG- -5'
12610	3'	-51.4	NC_003345.1	+	25341	1.13	0.002039
	Target:  5'- uGAACAAGACCGCUGGUUCUCUCUCGCg -3' miRNA:   3'- -CUUGUUCUGGCGACCAAGAGAGAGCG- -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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