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
3143	5'	-58.4	NC_001498.1	+	2385	0.66	0.236476
	Target:  5'- uCCCCUCCUucugcaguuUCAACaucagaaGCccuGAACCCCAUa -3' miRNA:   3'- -GGGGAGGG---------GGUUG-------CGuu-CUUGGGGUG- -5'
3143	5'	-58.4	NC_001498.1	+	5051	0.66	0.224208
	Target:  5'- gCCC-CCCCCAAaaaAAGGcCCCCAg -3' miRNA:   3'- gGGGaGGGGGUUgcgUUCUuGGGGUg -5'
3143	5'	-58.4	NC_001498.1	+	1143	0.67	0.205941
	Target:  5'- aCUCCUaCUCCCAugGCAu-AGCUCCAg -3' miRNA:   3'- -GGGGA-GGGGGUugCGUucUUGGGGUg -5'
3143	5'	-58.4	NC_001498.1	+	4927	0.68	0.173252
	Target:  5'- cCCCCacCCCCCGAaaaccagaGGGAGCCCC-Ca -3' miRNA:   3'- -GGGGa-GGGGGUUgcg-----UUCUUGGGGuG- -5'
3143	5'	-58.4	NC_001498.1	+	5271	0.68	0.167785
	Target:  5'- aUCCCUgggggaCCCCCAAacCGCAaaAGAcaucaguAUCCCACa -3' miRNA:   3'- -GGGGA------GGGGGUU--GCGU--UCU-------UGGGGUG- -5'
3143	5'	-58.4	NC_001498.1	+	5394	0.7	0.121474
	Target:  5'- uCCCCaCCCCCAaaggagacAC-CGGGAAUCCCAg -3' miRNA:   3'- -GGGGaGGGGGU--------UGcGUUCUUGGGGUg -5'
3143	5'	-58.4	NC_001498.1	+	4753	1.11	5.4e-05
	Target:  5'- cCCCCUCCCCCAACGCAAGAACCCCACa -3' miRNA:   3'- -GGGGAGGGGGUUGCGUUCUUGGGGUG- -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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