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
1491	3'	-57.4	NC_001335.1	+	17330	0.66	0.575635
	Target:  5'- gGCUCuGGUCAgcguugcuggcGCGGUGaUUCAGGUGg -3' miRNA:   3'- aCGAG-CCAGU-----------UGCCGCaGGGUCCAUa -5'
1491	3'	-57.4	NC_001335.1	+	13609	0.66	0.532631
	Target:  5'- cGCUC-GUCucgGACGGCGUCCCucGUc- -3' miRNA:   3'- aCGAGcCAG---UUGCCGCAGGGucCAua -5'
1491	3'	-57.4	NC_001335.1	+	18548	0.67	0.522053
	Target:  5'- gGCUCGGUgggacaagUAGCGaGCG-CCgGGGUAg -3' miRNA:   3'- aCGAGCCA--------GUUGC-CGCaGGgUCCAUa -5'
1491	3'	-57.4	NC_001335.1	+	1372	0.67	0.511556
	Target:  5'- aGCUCGGUgGGgGGCa-CCgGGGUGUu -3' miRNA:   3'- aCGAGCCAgUUgCCGcaGGgUCCAUA- -5'
1491	3'	-57.4	NC_001335.1	+	11783	0.68	0.457533
	Target:  5'- cGCgaaggCGGUCGcgaccuugguccgcAUGGUG-CCCAGGUAg -3' miRNA:   3'- aCGa----GCCAGU--------------UGCCGCaGGGUCCAUa -5'
1491	3'	-57.4	NC_001335.1	+	24083	0.7	0.358739
	Target:  5'- aUGCUCcuGG-CGGCGGCGgggcuggugCCCAGGUc- -3' miRNA:   3'- -ACGAG--CCaGUUGCCGCa--------GGGUCCAua -5'
1491	3'	-57.4	NC_001335.1	+	28012	1.06	0.000839
	Target:  5'- gUGCUCGGUCAACGGCGUCCCAGGUAUg -3' miRNA:   3'- -ACGAGCCAGUUGCCGCAGGGUCCAUA- -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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