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
13077	5'	-59	NC_003390.1	+	38068	0.67	0.393689
	Target:  5'- cACCUUUAGGuCCCuGGgGGCCagCAUCAc -3' miRNA:   3'- cUGGAAGUCC-GGG-CCaUCGGg-GUAGU- -5'
13077	5'	-59	NC_003390.1	+	36625	0.67	0.393689
	Target:  5'- cGACg-UUGGGCCCGcGaAGCCCCAcCAa -3' miRNA:   3'- -CUGgaAGUCCGGGC-CaUCGGGGUaGU- -5'
13077	5'	-59	NC_003390.1	+	38331	0.67	0.383832
	Target:  5'- gGGCCUUCuGGGCCuUGGgGGCCaacagcaCCGUCAa -3' miRNA:   3'- -CUGGAAG-UCCGG-GCCaUCGG-------GGUAGU- -5'
13077	5'	-59	NC_003390.1	+	43761	0.7	0.247343
	Target:  5'- aGGCCccaCAGGcCCCGGUGGgaggccuuauaUCCCAUCAa -3' miRNA:   3'- -CUGGaa-GUCC-GGGCCAUC-----------GGGGUAGU- -5'
13077	5'	-59	NC_003390.1	+	4542	0.72	0.177364
	Target:  5'- uGACCUcaagaauaaccccauUCuGGCCUGGUcuGGCCCCcUCAu -3' miRNA:   3'- -CUGGA---------------AGuCCGGGCCA--UCGGGGuAGU- -5'
13077	5'	-59	NC_003390.1	+	37807	0.78	0.063902
	Target:  5'- gGGCCUUCAGGaCCaaUGGCCCCAUCAg -3' miRNA:   3'- -CUGGAAGUCCgGGccAUCGGGGUAGU- -5'
13077	5'	-59	NC_003390.1	+	37986	1.08	0.000382
	Target:  5'- gGACCUUCAGGCCCGGUAGCCCCAUCAg -3' miRNA:   3'- -CUGGAAGUCCGGGCCAUCGGGGUAGU- -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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