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
18416	5'	-55.3	NC_004681.1	+	12229	0.66	0.81279
	Target:  5'- gGUGGcCCGUucugggcugagUCGGGUGG--CCCGgugcugUGGc -3' miRNA:   3'- -CACC-GGCA-----------AGUCCACCuuGGGCa-----ACC- -5'
18416	5'	-55.3	NC_004681.1	+	75618	0.66	0.794189
	Target:  5'- cGUGGaUCGUUCGGGUuGAGCCUc-UGGc -3' miRNA:   3'- -CACC-GGCAAGUCCAcCUUGGGcaACC- -5'
18416	5'	-55.3	NC_004681.1	+	22983	0.66	0.794189
	Target:  5'- aUGuCCGUgUAGGUGGAGCUC-UUGGu -3' miRNA:   3'- cACcGGCAaGUCCACCUUGGGcAACC- -5'
18416	5'	-55.3	NC_004681.1	+	29241	0.67	0.749112
	Target:  5'- cGUGGCCGUUgAGGUcgccacgccugacgcGGAaACCgUGUUGa -3' miRNA:   3'- -CACCGGCAAgUCCA---------------CCU-UGG-GCAACc -5'
18416	5'	-55.3	NC_004681.1	+	30867	0.7	0.575991
	Target:  5'- -cGGCCGUUggugacCAGGcccuUGGAGCCCGc-GGa -3' miRNA:   3'- caCCGGCAA------GUCC----ACCUUGGGCaaCC- -5'
18416	5'	-55.3	NC_004681.1	+	21657	0.71	0.523755
	Target:  5'- aUGGCCaUUUAGGUGGAAUUCGgUGa -3' miRNA:   3'- cACCGGcAAGUCCACCUUGGGCaACc -5'
18416	5'	-55.3	NC_004681.1	+	22915	1.09	0.001552
	Target:  5'- gGUGGCCGUUCAGGUGGAACCCGUUGGc -3' miRNA:   3'- -CACCGGCAAGUCCACCUUGGGCAACC- -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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