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
1406	3'	-58.3	NC_001335.1	+	13681	0.66	0.507739
	Target:  5'- -cGAUCCUCAAcGCgcccaacGCGuUGGCGCuuGa -3' miRNA:   3'- uuCUAGGAGUU-CGa------CGC-GCCGUGggC- -5'
1406	3'	-58.3	NC_001335.1	+	24839	0.66	0.487058
	Target:  5'- uGAGAUCUUCGAGCacuaccggauCGCGGCAuacauCCUGg -3' miRNA:   3'- -UUCUAGGAGUUCGac--------GCGCCGU-----GGGC- -5'
1406	3'	-58.3	NC_001335.1	+	31781	0.66	0.487058
	Target:  5'- ----gCCUCGcgGGCcugcuUGCGCGGCAagcCCCGg -3' miRNA:   3'- uucuaGGAGU--UCG-----ACGCGCCGU---GGGC- -5'
1406	3'	-58.3	NC_001335.1	+	35514	0.67	0.437218
	Target:  5'- cGAGAaCCcCGAGCUGCGCgauGGCuACCUc -3' miRNA:   3'- -UUCUaGGaGUUCGACGCG---CCG-UGGGc -5'
1406	3'	-58.3	NC_001335.1	+	15507	0.67	0.418115
	Target:  5'- cGGAUCCUCGucgcggaacaGGUcGCGCaGGUcuACCCGg -3' miRNA:   3'- uUCUAGGAGU----------UCGaCGCG-CCG--UGGGC- -5'
1406	3'	-58.3	NC_001335.1	+	38080	0.67	0.418115
	Target:  5'- -cGAUCaccgcCGAGCUGUGUGGgCugCCGa -3' miRNA:   3'- uuCUAGga---GUUCGACGCGCC-GugGGC- -5'
1406	3'	-58.3	NC_001335.1	+	42479	1.07	0.000525
	Target:  5'- gAAGAUCCUCAAGCUGCGCGGCACCCGg -3' miRNA:   3'- -UUCUAGGAGUUCGACGCGCCGUGGGC- -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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