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
30475	5'	-56.2	NC_006548.1	+	31951	1.06	0.000689
	Target:  5'- gAGGAAGUCCAUCCGGCACAGACCGAAa -3' miRNA:   3'- -UCCUUCAGGUAGGCCGUGUCUGGCUU- -5'
30475	5'	-56.2	NC_006548.1	+	17270	0.69	0.371116
	Target:  5'- gGGGAAGuUCCAcUCGGUcagccaACGGGCCGGg -3' miRNA:   3'- -UCCUUC-AGGUaGGCCG------UGUCUGGCUu -5'
30475	5'	-56.2	NC_006548.1	+	856	0.68	0.417946
	Target:  5'- -cGAGGUCCAggUCaucgaGGCGCAGcugGCCGAGa -3' miRNA:   3'- ucCUUCAGGU--AGg----CCGUGUC---UGGCUU- -5'
30475	5'	-56.2	NC_006548.1	+	26475	0.66	0.521379
	Target:  5'- cAGGAcugCC-UCCGGCGCuauGAUCGAGa -3' miRNA:   3'- -UCCUucaGGuAGGCCGUGu--CUGGCUU- -5'
30475	5'	-56.2	NC_006548.1	+	8758	0.66	0.521379
	Target:  5'- uGGGgcGcuccuggcuuUCCAUgCCGGCAgccaAGACCGAGa -3' miRNA:   3'- -UCCuuC----------AGGUA-GGCCGUg---UCUGGCUU- -5'
30475	5'	-56.2	NC_006548.1	+	14086	0.66	0.532306
	Target:  5'- aAGGAA--CCAUCCGGCAaguGGuucGCCGAu -3' miRNA:   3'- -UCCUUcaGGUAGGCCGUg--UC---UGGCUu -5'
30475	5'	-56.2	NC_006548.1	+	29805	0.66	0.554395
	Target:  5'- cGGGAAGUCauCAUCCGG-GCGGcgGCCGc- -3' miRNA:   3'- -UCCUUCAG--GUAGGCCgUGUC--UGGCuu -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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