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
8822	3'	-52.1	NC_002484.1	+	18971	0.66	0.899214
	Target:  5'- cGAUGCCGggcgcuugacgCUGUAGAuguuguCCCcgcGCUGGa -3' miRNA:   3'- cCUACGGCa----------GGCAUUUu-----GGGa--CGACC- -5'
8822	3'	-52.1	NC_002484.1	+	13190	0.66	0.899214
	Target:  5'- -aAUGCCGUCCccuacagcggaaGUGAGACCguccagcguCUGCgUGGu -3' miRNA:   3'- ccUACGGCAGG------------CAUUUUGG---------GACG-ACC- -5'
8822	3'	-52.1	NC_002484.1	+	49415	0.67	0.84385
	Target:  5'- cGAUGCCgGUCUGU----CCCUGCaugagGGa -3' miRNA:   3'- cCUACGG-CAGGCAuuuuGGGACGa----CC- -5'
8822	3'	-52.1	NC_002484.1	+	39106	0.7	0.681646
	Target:  5'- gGGAaGCUGUcgagCCGaAAGcaauccucGCCCUGCUGGa -3' miRNA:   3'- -CCUaCGGCA----GGCaUUU--------UGGGACGACC- -5'
8822	3'	-52.1	NC_002484.1	+	12919	0.72	0.559868
	Target:  5'- ---aGCUGUuuGUuguAAUCCUGCUGGa -3' miRNA:   3'- ccuaCGGCAggCAuu-UUGGGACGACC- -5'
8822	3'	-52.1	NC_002484.1	+	48691	0.75	0.397011
	Target:  5'- aGGA-GCCGUCCuUGAGAUUCUGCaGGg -3' miRNA:   3'- -CCUaCGGCAGGcAUUUUGGGACGaCC- -5'
8822	3'	-52.1	NC_002484.1	+	17383	1.13	0.001389
	Target:  5'- gGGAUGCCGUCCGUAAAACCCUGCUGGu -3' miRNA:   3'- -CCUACGGCAGGCAUUUUGGGACGACC- -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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