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
12587	5'	-54.3	NC_003345.1	+	63668	0.66	0.860898
	Target:  5'- --aGUGGgGGCGcuCCUGCCGAcguGGGACu -3' miRNA:   3'- cggUAUCaCUGCu-GGAUGGCU---CCCUG- -5'
12587	5'	-54.3	NC_003345.1	+	34379	0.66	0.852745
	Target:  5'- uGCgGUGGauauUGACGuugacGCCgcgAUUGAGGGACa -3' miRNA:   3'- -CGgUAUC----ACUGC-----UGGa--UGGCUCCCUG- -5'
12587	5'	-54.3	NC_003345.1	+	59331	0.66	0.844369
	Target:  5'- gGUCGgu-UGACGGCCcgACCGAgcagaagauguGGGACg -3' miRNA:   3'- -CGGUaucACUGCUGGa-UGGCU-----------CCCUG- -5'
12587	5'	-54.3	NC_003345.1	+	30317	0.66	0.83491
	Target:  5'- cGCuCGUGGggaugGAaaguacgaaagccCGACC-ACCGAGGGAg -3' miRNA:   3'- -CG-GUAUCa----CU-------------GCUGGaUGGCUCCCUg -5'
12587	5'	-54.3	NC_003345.1	+	18923	0.67	0.826986
	Target:  5'- gGUCAUGGUGuACG-CCUGCUGucGGGu -3' miRNA:   3'- -CGGUAUCAC-UGCuGGAUGGCucCCUg -5'
12587	5'	-54.3	NC_003345.1	+	21885	0.67	0.815261
	Target:  5'- cGCCAUgaagucgauaaucuGGUcGGCGGCCUGC---GGGACa -3' miRNA:   3'- -CGGUA--------------UCA-CUGCUGGAUGgcuCCCUG- -5'
12587	5'	-54.3	NC_003345.1	+	3528	1.13	0.001155
	Target:  5'- aGCCAUAGUGACGACCUACCGAGGGACg -3' miRNA:   3'- -CGGUAUCACUGCUGGAUGGCUCCCUG- -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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