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
21065	3'	-54.2	NC_004745.1	+	19434	0.66	0.623497
	Target:  5'- cGCCGAggcgGCGGUauugucgccgagcuGGCgCGCCUGUUUGCg -3' miRNA:   3'- -UGGCUga--UGUCA--------------CUG-GUGGGCAAGCG- -5'
21065	3'	-54.2	NC_004745.1	+	3640	0.67	0.5812
	Target:  5'- aACCuGAUUuCAGUGGCaaCGCCCGUUgaGCu -3' miRNA:   3'- -UGG-CUGAuGUCACUG--GUGGGCAAg-CG- -5'
21065	3'	-54.2	NC_004745.1	+	21027	0.69	0.471202
	Target:  5'- cCCGGC-GCAGU-ACCACCCGUcagGCu -3' miRNA:   3'- uGGCUGaUGUCAcUGGUGGGCAag-CG- -5'
21065	3'	-54.2	NC_004745.1	+	10698	0.7	0.410454
	Target:  5'- uACCGGCUGCAcaGGCCagcaucaccGCCCGUgcaGCc -3' miRNA:   3'- -UGGCUGAUGUcaCUGG---------UGGGCAag-CG- -5'
21065	3'	-54.2	NC_004745.1	+	9553	0.73	0.27443
	Target:  5'- gACUGGCUuCAGUGGCUgACCCaucgugccggucGUUCGCg -3' miRNA:   3'- -UGGCUGAuGUCACUGG-UGGG------------CAAGCG- -5'
21065	3'	-54.2	NC_004745.1	+	21752	0.78	0.125368
	Target:  5'- uGCCGACggGCAGgucgGGCUGCCgGUUCGUg -3' miRNA:   3'- -UGGCUGa-UGUCa---CUGGUGGgCAAGCG- -5'
21065	3'	-54.2	NC_004745.1	+	7135	1.12	0.000392
	Target:  5'- cACCGACUACAGUGACCACCCGUUCGCg -3' miRNA:   3'- -UGGCUGAUGUCACUGGUGGGCAAGCG- -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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