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
17656	5'	-51.5	NC_004466.2	+	31140	0.66	0.871078
	Target:  5'- cCCAGGGGugGGguCGAuCCGuucGGcCUUGAg -3' miRNA:   3'- -GGUUCUCugCU--GCU-GGCuu-CC-GAACU- -5'
17656	5'	-51.5	NC_004466.2	+	38979	0.66	0.854309
	Target:  5'- -gAGGAGucuuuCGACGGCCucGGGCUUc- -3' miRNA:   3'- ggUUCUCu----GCUGCUGGcuUCCGAAcu -5'
17656	5'	-51.5	NC_004466.2	+	4007	0.68	0.798404
	Target:  5'- uUCAGGAGgucuacgaaGCGACGACCuGAGGUa--- -3' miRNA:   3'- -GGUUCUC---------UGCUGCUGGcUUCCGaacu -5'
17656	5'	-51.5	NC_004466.2	+	33137	0.68	0.778181
	Target:  5'- gCCcuGGGugGACGAauccuucguuCCGAGGGUUcGAc -3' miRNA:   3'- -GGuuCUCugCUGCU----------GGCUUCCGAaCU- -5'
17656	5'	-51.5	NC_004466.2	+	37351	0.69	0.703009
	Target:  5'- aCAGGuugucGAUGACuuccaGGCCGAAaGGCUUGAu -3' miRNA:   3'- gGUUCu----CUGCUG-----CUGGCUU-CCGAACU- -5'
17656	5'	-51.5	NC_004466.2	+	38046	0.75	0.40123
	Target:  5'- aCCugacGGAGACGAUGGCC-AAGGCUuUGGg -3' miRNA:   3'- -GGu---UCUCUGCUGCUGGcUUCCGA-ACU- -5'
17656	5'	-51.5	NC_004466.2	+	35792	1.12	0.00148
	Target:  5'- gCCAAGAGACGACGACCGAAGGCUUGAg -3' miRNA:   3'- -GGUUCUCUGCUGCUGGCUUCCGAACU- -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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