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
4183	5'	-50.6	NC_001664.1	+	1791	0.66	0.993884
	Target:  5'- -cGCUCgGGGGacggagaggaagccGGAGGCCUgAGAGGa -3' miRNA:   3'- caUGAGgCCCC--------------CCUUUGGAgUUUUUa -5'
4183	5'	-50.6	NC_001664.1	+	152873	0.66	0.993884
	Target:  5'- -cGCUCgGGGGacggagaggaagccGGAGGCCUgAGAGGa -3' miRNA:   3'- caUGAGgCCCC--------------CCUUUGGAgUUUUUa -5'
4183	5'	-50.6	NC_001664.1	+	3566	0.67	0.984903
	Target:  5'- uGUGCUCCGGGGaGGggGa-UgGGAGGg -3' miRNA:   3'- -CAUGAGGCCCC-CCuuUggAgUUUUUa -5'
4183	5'	-50.6	NC_001664.1	+	154647	0.67	0.984903
	Target:  5'- uGUGCUCCGGGGaGGggGa-UgGGAGGg -3' miRNA:   3'- -CAUGAGGCCCC-CCuuUggAgUUUUUa -5'
4183	5'	-50.6	NC_001664.1	+	87951	0.68	0.978558
	Target:  5'- gGUGCUCCgaucagGGGGGGAAAaggucaagCGAAGAUa -3' miRNA:   3'- -CAUGAGG------CCCCCCUUUgga-----GUUUUUA- -5'
4183	5'	-50.6	NC_001664.1	+	117919	0.71	0.910281
	Target:  5'- uGUACUCC-GGGGGAGACUUUc----- -3' miRNA:   3'- -CAUGAGGcCCCCCUUUGGAGuuuuua -5'
4183	5'	-50.6	NC_001664.1	+	117765	1.06	0.012663
	Target:  5'- uGUACUCCGGGGGGAAACCUCAAAAAUg -3' miRNA:   3'- -CAUGAGGCCCCCCUUUGGAGUUUUUA- -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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