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
32268	3'	-54.2	NC_007022.1	+	155794	0.66	0.950056
	Target:  5'- cAAGCCGAgcgcgaucgaaaguuUGAGauGGCUgCGCAAGAa -3' miRNA:   3'- -UUCGGCU---------------AUUCggCUGAgGCGUUCUc -5'
32268	3'	-54.2	NC_007022.1	+	17952	0.66	0.948343
	Target:  5'- -uGCCGGUcuGCaauaGuCUgCCGCAAGAGa -3' miRNA:   3'- uuCGGCUAuuCGg---CuGA-GGCGUUCUC- -5'
32268	3'	-54.2	NC_007022.1	+	109437	0.67	0.929068
	Target:  5'- cAGCCGGUuuAAGgUGACUCCgGCuaccGGAGa -3' miRNA:   3'- uUCGGCUA--UUCgGCUGAGG-CGu---UCUC- -5'
32268	3'	-54.2	NC_007022.1	+	163528	0.68	0.90585
	Target:  5'- aGAGCCcAUAcGCCGACUUCaaGCGGGAu -3' miRNA:   3'- -UUCGGcUAUuCGGCUGAGG--CGUUCUc -5'
32268	3'	-54.2	NC_007022.1	+	162168	0.68	0.885887
	Target:  5'- cAAGCCGAUuGGCuaugauCGACcucCCGCGAGAa -3' miRNA:   3'- -UUCGGCUAuUCG------GCUGa--GGCGUUCUc -5'
32268	3'	-54.2	NC_007022.1	+	168270	0.72	0.698245
	Target:  5'- aGAGCCGGcgAAGCCGGCUCaaaaGCAGa-- -3' miRNA:   3'- -UUCGGCUa-UUCGGCUGAGg---CGUUcuc -5'
32268	3'	-54.2	NC_007022.1	+	150976	1.06	0.006363
	Target:  5'- gAAGCCGAUAAGCCGACUCCGCAAGAGu -3' miRNA:   3'- -UUCGGCUAUUCGGCUGAGGCGUUCUC- -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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