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
16281	3'	-55.9	NC_004084.1	+	58103	0.66	0.701898
	Target:  5'- -gGCGGCcucaugCAGGAUcggggcuacaCCCUUCGCGa -3' miRNA:   3'- agCGCCGuca---GUCCUAa---------GGGAAGCGU- -5'
16281	3'	-55.9	NC_004084.1	+	27369	0.66	0.691114
	Target:  5'- cCGaCGGCuGgcgCGGGAUUCgC-UCGCAg -3' miRNA:   3'- aGC-GCCGuCa--GUCCUAAGgGaAGCGU- -5'
16281	3'	-55.9	NC_004084.1	+	5423	0.66	0.691114
	Target:  5'- cUCGUGGCcGUCcGGAUUCCaccaugacaCGCGg -3' miRNA:   3'- -AGCGCCGuCAGuCCUAAGGgaa------GCGU- -5'
16281	3'	-55.9	NC_004084.1	+	20961	0.68	0.571056
	Target:  5'- aCGuCGG-GGUCGGGAUgcggaCUCUUCGCGa -3' miRNA:   3'- aGC-GCCgUCAGUCCUAa----GGGAAGCGU- -5'
16281	3'	-55.9	NC_004084.1	+	56547	0.69	0.496947
	Target:  5'- gCGUGGCAGUcCAGGAggcgacgucgUCCg-UCGCGc -3' miRNA:   3'- aGCGCCGUCA-GUCCUa---------AGGgaAGCGU- -5'
16281	3'	-55.9	NC_004084.1	+	29765	0.72	0.330899
	Target:  5'- cUGCGGCGG-UAGGucgUCCCcUCGCGg -3' miRNA:   3'- aGCGCCGUCaGUCCua-AGGGaAGCGU- -5'
16281	3'	-55.9	NC_004084.1	+	41916	1.09	0.000947
	Target:  5'- gUCGCGGCAGUCAGGAUUCCCUUCGCAc -3' miRNA:   3'- -AGCGCCGUCAGUCCUAAGGGAAGCGU- -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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