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
11685	3'	-50.2	NC_003102.1	+	21515	0.67	0.984242
	Target:  5'- --cGCCGGCCGGAucgUGuaauUGAUCAAUa- -3' miRNA:   3'- uucUGGCUGGCCU---ACu---ACUAGUUAgc -5'
11685	3'	-50.2	NC_003102.1	+	101676	0.67	0.987717
	Target:  5'- -cGAUCGACCuGGUGAUGAaCGAUg- -3' miRNA:   3'- uuCUGGCUGGcCUACUACUaGUUAgc -5'
11685	3'	-50.2	NC_003102.1	+	74386	0.68	0.980962
	Target:  5'- uGGAUCGACCGGAcGGUuucauacuuagcggcGAUCAGUUc -3' miRNA:   3'- uUCUGGCUGGCCUaCUA---------------CUAGUUAGc -5'
11685	3'	-50.2	NC_003102.1	+	27517	0.69	0.954999
	Target:  5'- -uGGCCGAUCGGuugGAcgcGAUCGAUCa -3' miRNA:   3'- uuCUGGCUGGCCua-CUa--CUAGUUAGc -5'
11685	3'	-50.2	NC_003102.1	+	4308	0.74	0.795312
	Target:  5'- aGAGAuuauauCCGAuCCGGAUG-UGAUCGAUCa -3' miRNA:   3'- -UUCU------GGCU-GGCCUACuACUAGUUAGc -5'
11685	3'	-50.2	NC_003102.1	+	15022	0.76	0.71531
	Target:  5'- -uGACCGACCuaAUGAcGAUCAAUCGg -3' miRNA:   3'- uuCUGGCUGGccUACUaCUAGUUAGC- -5'
11685	3'	-50.2	NC_003102.1	+	14945	0.79	0.534882
	Target:  5'- -cGACCGAUCGaAUGAUGAUCAAUCn -3' miRNA:   3'- uuCUGGCUGGCcUACUACUAGUUAGc -5'
11685	3'	-50.2	NC_003102.1	+	14969	1.09	0.009619
	Target:  5'- aGAGACCGACCGGAUGAUGAUCAAUCGg -3' miRNA:   3'- -UUCUGGCUGGCCUACUACUAGUUAGC- -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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