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
25931	5'	-60.4	NC_005337.1	+	17933	0.66	0.618858
	Target:  5'- -gGGUCAUGGCCCGGcgcUGcGCC-Cg- -3' miRNA:   3'- uaCCGGUACCGGGCCu--ACuCGGaGaa -5'
25931	5'	-60.4	NC_005337.1	+	51276	0.66	0.608565
	Target:  5'- -cGGCCAUGGCggacaCCGGcGUGAGCgUg-- -3' miRNA:   3'- uaCCGGUACCG-----GGCC-UACUCGgAgaa -5'
25931	5'	-60.4	NC_005337.1	+	3862	0.66	0.59829
	Target:  5'- gAUGGUC-UGGCaCCGGccgcgcAUGAGCgUCUUg -3' miRNA:   3'- -UACCGGuACCG-GGCC------UACUCGgAGAA- -5'
25931	5'	-60.4	NC_005337.1	+	29576	0.69	0.441529
	Target:  5'- -cGGCCcucguUGGCcugCCGGAUGAGCUuggUCUUg -3' miRNA:   3'- uaCCGGu----ACCG---GGCCUACUCGG---AGAA- -5'
25931	5'	-60.4	NC_005337.1	+	45189	0.71	0.355309
	Target:  5'- cUGGCCGU-GCCCGGGgcgcugucgcucaUGAGUCUCg- -3' miRNA:   3'- uACCGGUAcCGGGCCU-------------ACUCGGAGaa -5'
25931	5'	-60.4	NC_005337.1	+	117766	0.71	0.34047
	Target:  5'- uUGGUCuUGGCCCGGGUgaaGAGgCUCUc -3' miRNA:   3'- uACCGGuACCGGGCCUA---CUCgGAGAa -5'
25931	5'	-60.4	NC_005337.1	+	110743	1.03	0.001918
	Target:  5'- gAUGGCCAUGGCCCGGAUGAGCCUCUUc -3' miRNA:   3'- -UACCGGUACCGGGCCUACUCGGAGAA- -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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