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
25992	5'	-47.4	NC_005340.1	+	22440	0.66	0.938684
	Target:  5'- aCAGCAGUAuuuaGAGGCCGUuuUCAAUgagcuaaaGCGg -3' miRNA:   3'- -GUUGUCAU----UUCUGGCAugGGUUG--------UGC- -5'
25992	5'	-47.4	NC_005340.1	+	28293	0.67	0.926752
	Target:  5'- -cACGGU--AGACCGU-CaCCGGCGCa -3' miRNA:   3'- guUGUCAuuUCUGGCAuG-GGUUGUGc -5'
25992	5'	-47.4	NC_005340.1	+	9378	0.67	0.920285
	Target:  5'- cCAGuCGGUGcgaaguaagaAAGGCCGUAUCaGGCGCGa -3' miRNA:   3'- -GUU-GUCAU----------UUCUGGCAUGGgUUGUGC- -5'
25992	5'	-47.4	NC_005340.1	+	8229	0.7	0.807756
	Target:  5'- aGACAGUGaccagcuuuucGAGACUGUGCUC-GCGCu -3' miRNA:   3'- gUUGUCAU-----------UUCUGGCAUGGGuUGUGc -5'
25992	5'	-47.4	NC_005340.1	+	6267	0.7	0.7644
	Target:  5'- --uCAGUGguGAGGCCGUAUUgCAGCGCGu -3' miRNA:   3'- guuGUCAU--UUCUGGCAUGG-GUUGUGC- -5'
25992	5'	-47.4	NC_005340.1	+	16650	0.72	0.687582
	Target:  5'- cCAGCAGUGcuGACCGgucagggaauuacaGCCCGauuGCGCGg -3' miRNA:   3'- -GUUGUCAUuuCUGGCa-------------UGGGU---UGUGC- -5'
25992	5'	-47.4	NC_005340.1	+	18912	1.09	0.0035
	Target:  5'- gCAACAGUAAAGACCGUACCCAACACGc -3' miRNA:   3'- -GUUGUCAUUUCUGGCAUGGGUUGUGC- -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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