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
30729	5'	-59	NC_006552.1	+	2042	0.66	0.601325
	Target:  5'- -cGCCUGGGACagGCGcuuGAG-CGcgCCGg -3' miRNA:   3'- ucCGGACCCUGg-CGC---UUCaGCuaGGC- -5'
30729	5'	-59	NC_006552.1	+	16293	0.66	0.580356
	Target:  5'- aAGGCCUGGGGuacUCuCGAAGguggCG-UCCGc -3' miRNA:   3'- -UCCGGACCCU---GGcGCUUCa---GCuAGGC- -5'
30729	5'	-59	NC_006552.1	+	55268	0.66	0.549215
	Target:  5'- aAGGCCUGGGGCUucuuccaggGCGA-----GUCCGg -3' miRNA:   3'- -UCCGGACCCUGG---------CGCUucagcUAGGC- -5'
30729	5'	-59	NC_006552.1	+	14094	0.66	0.549215
	Target:  5'- cGGCCggccGGGCCGCGcuucauGUCGcgcgcAUCCGg -3' miRNA:   3'- uCCGGac--CCUGGCGCuu----CAGC-----UAGGC- -5'
30729	5'	-59	NC_006552.1	+	42707	0.68	0.459638
	Target:  5'- uAGGCCUGGGcggaucgaACUGCGGugccGGUaCGAacacUCCGc -3' miRNA:   3'- -UCCGGACCC--------UGGCGCU----UCA-GCU----AGGC- -5'
30729	5'	-59	NC_006552.1	+	2656	0.7	0.370013
	Target:  5'- uGGGCUaGGGACCGCGcGGcgcCGAUCa- -3' miRNA:   3'- -UCCGGaCCCUGGCGCuUCa--GCUAGgc -5'
30729	5'	-59	NC_006552.1	+	49615	1.07	0.000771
	Target:  5'- cAGGCCUGGGACCGCGAAGUCGAUCCGc -3' miRNA:   3'- -UCCGGACCCUGGCGCUUCAGCUAGGC- -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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