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
29354	5'	-53.6	NC_006150.1	+	57169	0.66	0.981849
	Target:  5'- -aGGugcuUCGCaCCCuGGUCACC-GAGGCGg -3' miRNA:   3'- gaCCu---AGCG-GGG-CUAGUGGuCUUUGU- -5'
29354	5'	-53.6	NC_006150.1	+	220706	0.68	0.963302
	Target:  5'- aCUGGAUUGUCCUuGUCGCCAccuugguccauGAAAUg -3' miRNA:   3'- -GACCUAGCGGGGcUAGUGGU-----------CUUUGu -5'
29354	5'	-53.6	NC_006150.1	+	77484	0.7	0.900642
	Target:  5'- gUGcAUCGCCCCGcgaggcacaAUCuCCAGAAACGu -3' miRNA:   3'- gACcUAGCGGGGC---------UAGuGGUCUUUGU- -5'
29354	5'	-53.6	NC_006150.1	+	38834	0.7	0.900642
	Target:  5'- uCUGGAUUGCCCCGcaacgaGCaCAGGAGuCAg -3' miRNA:   3'- -GACCUAGCGGGGCuag---UG-GUCUUU-GU- -5'
29354	5'	-53.6	NC_006150.1	+	201633	0.72	0.826637
	Target:  5'- -gGGAUCgGCCuCCGAUCGCCcAGggGu- -3' miRNA:   3'- gaCCUAG-CGG-GGCUAGUGG-UCuuUgu -5'
29354	5'	-53.6	NC_006150.1	+	140908	0.78	0.495434
	Target:  5'- aCUGGAcgucUUGCCggcaccggccgugCCGGUCACCAGAAGCGu -3' miRNA:   3'- -GACCU----AGCGG-------------GGCUAGUGGUCUUUGU- -5'
29354	5'	-53.6	NC_006150.1	+	209817	1.09	0.007411
	Target:  5'- uCUGGAUCGCCCCGAUCACCAGAAACAa -3' miRNA:   3'- -GACCUAGCGGGGCUAGUGGUCUUUGU- -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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