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
12744	5'	-48.9	NC_003356.1	+	30790	0.77	0.397103
	Target:  5'- cGGCgggaACAGCGuguuCAGuCGGUUCGGGUUAu -3' miRNA:   3'- -CCG----UGUUGUu---GUCuGUCAAGCCCAAU- -5'
12744	5'	-48.9	NC_003356.1	+	21417	1.1	0.002697
	Target:  5'- aGGCACAACAACAGACAGUUCGGGUUAc -3' miRNA:   3'- -CCGUGUUGUUGUCUGUCAAGCCCAAU- -5'
12744	5'	-48.9	NC_003356.1	+	35901	0.71	0.688359
	Target:  5'- gGGCACGACGACuGAauua-CGGGUUGg -3' miRNA:   3'- -CCGUGUUGUUGuCUgucaaGCCCAAU- -5'
12744	5'	-48.9	NC_003356.1	+	39328	0.68	0.866314
	Target:  5'- uGGCGCGuuACAAaguaacCGGGCAGUgaauguuucaggUCGGGUa- -3' miRNA:   3'- -CCGUGU--UGUU------GUCUGUCA------------AGCCCAau -5'
12744	5'	-48.9	NC_003356.1	+	26578	0.67	0.883014
	Target:  5'- cGGCACAACGucCGGAUGGgUgGGGg-- -3' miRNA:   3'- -CCGUGUUGUu-GUCUGUCaAgCCCaau -5'
12744	5'	-48.9	NC_003356.1	+	19160	0.67	0.89628
	Target:  5'- cGGCACGGCuGCGgcgcucggcggggcGACGGUauUCGGGc-- -3' miRNA:   3'- -CCGUGUUGuUGU--------------CUGUCA--AGCCCaau -5'
12744	5'	-48.9	NC_003356.1	+	29616	0.66	0.931873
	Target:  5'- aGGgGCGGCGGC-GACGGUcaGGGUg- -3' miRNA:   3'- -CCgUGUUGUUGuCUGUCAagCCCAau -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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