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
16712	5'	-55.9	NC_004166.1	+	9972	0.66	0.622024
	Target:  5'- gUGCUCCUgucaACCGuuuuuCUGGCccgccguagaagagGGCGGCGa -3' miRNA:   3'- gAUGGGGA----UGGUuu---GAUCG--------------CCGCCGC- -5'
16712	5'	-55.9	NC_004166.1	+	20350	0.68	0.484068
	Target:  5'- -aGCCCggaUUACUGAAUuagaaaauaaguUAGCGGCGGCa -3' miRNA:   3'- gaUGGG---GAUGGUUUG------------AUCGCCGCCGc -5'
16712	5'	-55.9	NC_004166.1	+	14134	0.69	0.453487
	Target:  5'- -gGCUCUUGC--GGC-GGCGGCGGCGg -3' miRNA:   3'- gaUGGGGAUGguUUGaUCGCCGCCGC- -5'
16712	5'	-55.9	NC_004166.1	+	22371	0.7	0.377475
	Target:  5'- uUAUUCCaUGCaUAGAgUAGCGGCGGCa -3' miRNA:   3'- gAUGGGG-AUG-GUUUgAUCGCCGCCGc -5'
16712	5'	-55.9	NC_004166.1	+	13688	0.72	0.266498
	Target:  5'- -aGCCgCagggAUUAAAUUGGCGGCGGCGa -3' miRNA:   3'- gaUGGgGa---UGGUUUGAUCGCCGCCGC- -5'
16712	5'	-55.9	NC_004166.1	+	23869	0.74	0.201229
	Target:  5'- uUACCCCcucaACCAAucaauaaacaugaauACU-GCGGCGGCGa -3' miRNA:   3'- gAUGGGGa---UGGUU---------------UGAuCGCCGCCGC- -5'
16712	5'	-55.9	NC_004166.1	+	12563	1.1	0.000529
	Target:  5'- aCUACCCCUACCAAACUAGCGGCGGCGg -3' miRNA:   3'- -GAUGGGGAUGGUUUGAUCGCCGCCGC- -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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