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
27959	5'	-49.5	NC_005886.2	+	1526	0.66	0.949644
	Target:  5'- uGGggCAUCGUGgcgUGCGuGGCGG-GCu -3' miRNA:   3'- cCCaaGUAGUACaa-GCGC-UCGCUaCG- -5'
27959	5'	-49.5	NC_005886.2	+	14317	0.67	0.928459
	Target:  5'- ---cUUAUCGUGUugaUCGCGAuGCuuGAUGCg -3' miRNA:   3'- cccaAGUAGUACA---AGCGCU-CG--CUACG- -5'
27959	5'	-49.5	NC_005886.2	+	21857	0.67	0.902468
	Target:  5'- uGGcUCGUCAacaaagcgUGUUcacagaugccgCGCGAuGCGAUGCg -3' miRNA:   3'- cCCaAGUAGU--------ACAA-----------GCGCU-CGCUACG- -5'
27959	5'	-49.5	NC_005886.2	+	46015	0.68	0.887698
	Target:  5'- aGGUUCGUCAcgGUgCGCaacgucaaGGGCGGUGg -3' miRNA:   3'- cCCAAGUAGUa-CAaGCG--------CUCGCUACg -5'
27959	5'	-49.5	NC_005886.2	+	21190	0.71	0.712315
	Target:  5'- uGGuUUCGUCGaacugcuguuUGUUCGCGAGCaccUGCg -3' miRNA:   3'- cCC-AAGUAGU----------ACAAGCGCUCGcu-ACG- -5'
27959	5'	-49.5	NC_005886.2	+	37633	0.73	0.594655
	Target:  5'- cGGGUUCgAUCGUGUcggUuguuuuccgugccuUGCGAGCGGUGa -3' miRNA:   3'- -CCCAAG-UAGUACA---A--------------GCGCUCGCUACg -5'
27959	5'	-49.5	NC_005886.2	+	6037	1.17	0.001136
	Target:  5'- cGGGUUCAUCAUGUUCGCGAGCGAUGCa -3' miRNA:   3'- -CCCAAGUAGUACAAGCGCUCGCUACG- -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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