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
16327	5'	-57.4	NC_004084.1	+	5722	0.66	0.590472
	Target:  5'- uCGCucggGCCGAGguCCUCGAUcGGGAu-- -3' miRNA:   3'- -GCGua--CGGCUC--GGAGCUAaCCCUcga -5'
16327	5'	-57.4	NC_004084.1	+	56840	0.66	0.579672
	Target:  5'- gCGCggGCCucGAGCCUCGGgccaGAGCa -3' miRNA:   3'- -GCGuaCGG--CUCGGAGCUaaccCUCGa -5'
16327	5'	-57.4	NC_004084.1	+	14675	0.67	0.558208
	Target:  5'- aGCGUcccgGCCGGGuCCUCGAUUGGcccaacuaauGGCUc -3' miRNA:   3'- gCGUA----CGGCUC-GGAGCUAACCc---------UCGA- -5'
16327	5'	-57.4	NC_004084.1	+	476	0.67	0.536974
	Target:  5'- cCGCGUGCUGcuGGCaggCGggUGGGuGCa -3' miRNA:   3'- -GCGUACGGC--UCGga-GCuaACCCuCGa -5'
16327	5'	-57.4	NC_004084.1	+	52928	0.68	0.455382
	Target:  5'- gGCAUacGCCGAGCgCgucacgaccggCGGcUGGGAGCUc -3' miRNA:   3'- gCGUA--CGGCUCG-Ga----------GCUaACCCUCGA- -5'
16327	5'	-57.4	NC_004084.1	+	20301	0.68	0.455382
	Target:  5'- -uCAUGCUcuGGGCCUCuuuGcgUGGGAGCa -3' miRNA:   3'- gcGUACGG--CUCGGAG---CuaACCCUCGa -5'
16327	5'	-57.4	NC_004084.1	+	19398	1.09	0.000653
	Target:  5'- aCGCAUGCCGAGCCUCGAUUGGGAGCUg -3' miRNA:   3'- -GCGUACGGCUCGGAGCUAACCCUCGA- -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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