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
27227	3'	-49.5	NC_005832.1	+	29931	0.66	0.989014
	Target:  5'- uGUCUUCUgAAgacACAGaggccuGGUCUGGGgcgGCg -3' miRNA:   3'- -UAGAAGAgUU---UGUC------CCAGACCCau-UG- -5'
27227	3'	-49.5	NC_005832.1	+	9084	0.66	0.98743
	Target:  5'- cUCaUCUCccuCAGGGUCgcgugGGGUAu- -3' miRNA:   3'- uAGaAGAGuuuGUCCCAGa----CCCAUug -5'
27227	3'	-49.5	NC_005832.1	+	87365	0.66	0.985676
	Target:  5'- ----cCUCAGGCucuccAGGGUgaGGGUGGCc -3' miRNA:   3'- uagaaGAGUUUG-----UCCCAgaCCCAUUG- -5'
27227	3'	-49.5	NC_005832.1	+	23093	0.67	0.970985
	Target:  5'- -gCUUCUCA---GGGGUCUGGaGgcuGCg -3' miRNA:   3'- uaGAAGAGUuugUCCCAGACC-Cau-UG- -5'
27227	3'	-49.5	NC_005832.1	+	72837	0.68	0.952271
	Target:  5'- -----gUC-AACAGGGUCUGGGgccugAGCg -3' miRNA:   3'- uagaagAGuUUGUCCCAGACCCa----UUG- -5'
27227	3'	-49.5	NC_005832.1	+	23510	0.71	0.871474
	Target:  5'- cUCUgcaagacCUCAAGCAGGGUCcggugaaccUGGGUGu- -3' miRNA:   3'- uAGAa------GAGUUUGUCCCAG---------ACCCAUug -5'
27227	3'	-49.5	NC_005832.1	+	90004	1.09	0.006656
	Target:  5'- cAUCUUCUCAAACAGGGUCUGGGUAACg -3' miRNA:   3'- -UAGAAGAGUUUGUCCCAGACCCAUUG- -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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