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
24260	5'	-55	NC_005263.2	+	20126	0.65	0.719436
	Target:  5'- gGGUUacggcaagcGCgACGGuacGGCCGUCGcgCCGg -3' miRNA:   3'- aCCAA---------CGgUGCCua-UCGGCAGUa-GGC- -5'
24260	5'	-55	NC_005263.2	+	39599	0.66	0.708606
	Target:  5'- aGGUcGCCACGuAUGGCgacuacUCGUCCGa -3' miRNA:   3'- aCCAaCGGUGCcUAUCGgc----AGUAGGC- -5'
24260	5'	-55	NC_005263.2	+	14038	0.66	0.708606
	Target:  5'- cGGUucgGCCACGGGc-GCCG-CGUCg- -3' miRNA:   3'- aCCAa--CGGUGCCUauCGGCaGUAGgc -5'
24260	5'	-55	NC_005263.2	+	21045	0.67	0.642411
	Target:  5'- gGGUagcggcuuccUGCCcgACGGGcGGCCGcgCAUCCu -3' miRNA:   3'- aCCA----------ACGG--UGCCUaUCGGCa-GUAGGc -5'
24260	5'	-55	NC_005263.2	+	1899	0.68	0.597938
	Target:  5'- gGGUUGCCGaucaGGAaguaccAGCCGcgCGUCUGc -3' miRNA:   3'- aCCAACGGUg---CCUa-----UCGGCa-GUAGGC- -5'
24260	5'	-55	NC_005263.2	+	5149	0.69	0.532281
	Target:  5'- gUGGUgcaGCC-CGGAcgcacgGGCCGugaucUCGUCCGg -3' miRNA:   3'- -ACCAa--CGGuGCCUa-----UCGGC-----AGUAGGC- -5'
24260	5'	-55	NC_005263.2	+	10333	1.1	0.000767
	Target:  5'- aUGGUUGCCACGGAUAGCCGUCAUCCGg -3' miRNA:   3'- -ACCAACGGUGCCUAUCGGCAGUAGGC- -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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