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
23024	3'	-50.3	NC_005178.1	+	5808	0.66	0.886246
	Target:  5'- cGGUCGUgcccgagGCcgccaccgaugCGGCGAUCUGCUc- -3' miRNA:   3'- -CCAGCAaca----UGa----------GCCGUUAGACGAca -5'
23024	3'	-50.3	NC_005178.1	+	3923	0.66	0.87822
	Target:  5'- gGGUCaacgaUGCgCGGCAAgCUGCUGUg -3' miRNA:   3'- -CCAGcaac-AUGaGCCGUUaGACGACA- -5'
23024	3'	-50.3	NC_005178.1	+	32075	0.66	0.86821
	Target:  5'- aGGUCGUcGgcgugGgUCGGCAcccauagcggcuUCUGCUGg -3' miRNA:   3'- -CCAGCAaCa----UgAGCCGUu-----------AGACGACa -5'
23024	3'	-50.3	NC_005178.1	+	20813	0.66	0.861313
	Target:  5'- --cCGagGUACgccCGGCGcUCUGCUGUu -3' miRNA:   3'- ccaGCaaCAUGa--GCCGUuAGACGACA- -5'
23024	3'	-50.3	NC_005178.1	+	25654	0.67	0.833943
	Target:  5'- -cUCGU--UGCUCGGCugcaaCUGCUGUu -3' miRNA:   3'- ccAGCAacAUGAGCCGuua--GACGACA- -5'
23024	3'	-50.3	NC_005178.1	+	27545	0.67	0.794138
	Target:  5'- uGUUGUuccUGgcCUCGGCGAUCUuCUGg -3' miRNA:   3'- cCAGCA---ACauGAGCCGUUAGAcGACa -5'
23024	3'	-50.3	NC_005178.1	+	22701	0.81	0.170455
	Target:  5'- cGGagCGUUGUGCUCGGCGuUCUGCg-- -3' miRNA:   3'- -CCa-GCAACAUGAGCCGUuAGACGaca -5'
23024	3'	-50.3	NC_005178.1	+	3890	1.1	0.001671
	Target:  5'- cGGUCGUUGUACUCGGCAAUCUGCUGUu -3' miRNA:   3'- -CCAGCAACAUGAGCCGUUAGACGACA- -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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