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
21054	3'	-52.6	NC_004745.1	+	4974	0.67	0.640075
	Target:  5'- uCGUGAUgaGCAUCGcauccGCCGGGAaguACGGGa -3' miRNA:   3'- -GCACUA--CGUAGUc----CGGCCUU---UGCUCg -5'
21054	3'	-52.6	NC_004745.1	+	21992	0.67	0.62841
	Target:  5'- gCGUGGUGuCAugccaggagccuUCAcGGCgGGAAuUGAGCg -3' miRNA:   3'- -GCACUAC-GU------------AGU-CCGgCCUUuGCUCG- -5'
21054	3'	-52.6	NC_004745.1	+	8119	0.68	0.570365
	Target:  5'- gGUGGcacUGCGUCAGGaaCUGGAAaacgccGCGaAGCg -3' miRNA:   3'- gCACU---ACGUAGUCC--GGCCUU------UGC-UCG- -5'
21054	3'	-52.6	NC_004745.1	+	21117	0.7	0.480835
	Target:  5'- cCGUcAUGCAUCAuGCUGGc-ACGGGCg -3' miRNA:   3'- -GCAcUACGUAGUcCGGCCuuUGCUCG- -5'
21054	3'	-52.6	NC_004745.1	+	6175	0.71	0.408471
	Target:  5'- gCGUGAgGCcaucaaGUCAGGCauggCGGAGACGAauGCg -3' miRNA:   3'- -GCACUaCG------UAGUCCG----GCCUUUGCU--CG- -5'
21054	3'	-52.6	NC_004745.1	+	10947	0.74	0.263803
	Target:  5'- -aUGGUGacgCAGGCCGGAGACGGa- -3' miRNA:   3'- gcACUACguaGUCCGGCCUUUGCUcg -5'
21054	3'	-52.6	NC_004745.1	+	26753	0.99	0.005275
	Target:  5'- uCGUGAUGCAUCAGGCC-GAAACGAGCu -3' miRNA:   3'- -GCACUACGUAGUCCGGcCUUUGCUCG- -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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