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
2876	5'	-58.5	NC_001493.1	+	34105	0.67	0.710465
	Target:  5'- uCUGCCAUauuuggggaugCUCGggGCucgGGAGUUGGGa -3' miRNA:   3'- -GACGGUGa----------GAGCuaCG---CCUCGACCCa -5'
2876	5'	-58.5	NC_001493.1	+	29865	0.68	0.639507
	Target:  5'- -cGCCAg-CUCGAgagucgcguUGCGGAGCUccaGGGg -3' miRNA:   3'- gaCGGUgaGAGCU---------ACGCCUCGA---CCCa -5'
2876	5'	-58.5	NC_001493.1	+	121506	0.95	0.012539
	Target:  5'- gCUaCCACUCUCGAUGCGGAGCUGGGUc -3' miRNA:   3'- -GAcGGUGAGAGCUACGCCUCGACCCA- -5'
2876	5'	-58.5	NC_001493.1	+	5952	0.95	0.012539
	Target:  5'- gCUaCCACUCUCGAUGCGGAGCUGGGUc -3' miRNA:   3'- -GAcGGUGAGAGCUACGCCUCGACCCA- -5'
2876	5'	-58.5	NC_001493.1	+	121392	0.98	0.007413
	Target:  5'- gCUGCCACUCUCGAUGCGGAGCUGGu- -3' miRNA:   3'- -GACGGUGAGAGCUACGCCUCGACCca -5'
2876	5'	-58.5	NC_001493.1	+	5838	0.98	0.007413
	Target:  5'- gCUGCCACUCUCGAUGCGGAGCUGGu- -3' miRNA:   3'- -GACGGUGAGAGCUACGCCUCGACCca -5'
2876	5'	-58.5	NC_001493.1	+	121591	1.06	0.002012
	Target:  5'- gCUGCCACUCUCGAUGCGGAGCUGGGUc -3' miRNA:   3'- -GACGGUGAGAGCUACGCCUCGACCCA- -5'
2876	5'	-58.5	NC_001493.1	+	6037	1.06	0.002012
	Target:  5'- gCUGCCACUCUCGAUGCGGAGCUGGGUc -3' miRNA:   3'- -GACGGUGAGAGCUACGCCUCGACCCA- -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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