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
21352	3'	-58.2	NC_004778.3	+	119477	0.66	0.77024
	Target:  5'- aGCGUCuGAGCUGGAcaGCgaCUC-CGACa -3' miRNA:   3'- cCGCGGuCUCGACCU--UGa-GGGaGCUG- -5'
21352	3'	-58.2	NC_004778.3	+	81789	0.66	0.761752
	Target:  5'- cGGCcuGCCGGGGCggcgucuguaaccaGAACUCCUgCGGCg -3' miRNA:   3'- -CCG--CGGUCUCGac------------CUUGAGGGaGCUG- -5'
21352	3'	-58.2	NC_004778.3	+	121126	0.67	0.741598
	Target:  5'- cGGCGCCGGGGCaGcGGGCgcggCCCgCGcCc -3' miRNA:   3'- -CCGCGGUCUCGaC-CUUGa---GGGaGCuG- -5'
21352	3'	-58.2	NC_004778.3	+	68237	0.67	0.741598
	Target:  5'- uGGCGCUcGGGCUGuucGAACacagCCugCUCGACg -3' miRNA:   3'- -CCGCGGuCUCGAC---CUUGa---GG--GAGCUG- -5'
21352	3'	-58.2	NC_004778.3	+	34311	0.69	0.620904
	Target:  5'- aGUGCCGGcgcguGCUGGAACUggugcagggcgUgCUCGACa -3' miRNA:   3'- cCGCGGUCu----CGACCUUGA-----------GgGAGCUG- -5'
21352	3'	-58.2	NC_004778.3	+	123412	0.7	0.550096
	Target:  5'- aGGaGCUGGAGCUGGAACUgg-UCGACg -3' miRNA:   3'- -CCgCGGUCUCGACCUUGAgggAGCUG- -5'
21352	3'	-58.2	NC_004778.3	+	123451	1.12	0.000968
	Target:  5'- uGGCGCCAGAGCUGGAACUCCCUCGACg -3' miRNA:   3'- -CCGCGGUCUCGACCUUGAGGGAGCUG- -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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