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
8799	5'	-57.9	NC_002484.1	+	29595	0.66	0.534194
	Target:  5'- aGGCGGAgaacgagGUGCUgcgcaGGUUCGCcgGCgaGGCa -3' miRNA:   3'- -CCGCCU-------UACGGa----CCGAGCGa-CGa-CUG- -5'
8799	5'	-57.9	NC_002484.1	+	5321	0.67	0.483438
	Target:  5'- aGGCGG-AUGC--GGUcgauUCGCUGCUcGGCg -3' miRNA:   3'- -CCGCCuUACGgaCCG----AGCGACGA-CUG- -5'
8799	5'	-57.9	NC_002484.1	+	34597	0.68	0.443784
	Target:  5'- cGGCGGAccauUGCCUGGagaaaGUcaugagGCUGACc -3' miRNA:   3'- -CCGCCUu---ACGGACCgag--CGa-----CGACUG- -5'
8799	5'	-57.9	NC_002484.1	+	32723	0.7	0.318655
	Target:  5'- uGGUGGGAgcaCCUGGaugagcugcgcgaugCGCUGCUGGCc -3' miRNA:   3'- -CCGCCUUac-GGACCga-------------GCGACGACUG- -5'
8799	5'	-57.9	NC_002484.1	+	3576	0.74	0.187418
	Target:  5'- cGCGGAcgGCCUGGCUC-UUGUuagauUGACc -3' miRNA:   3'- cCGCCUuaCGGACCGAGcGACG-----ACUG- -5'
8799	5'	-57.9	NC_002484.1	+	45891	0.75	0.150974
	Target:  5'- uGGgGuGAGUGCguuaUGGCUUGCUGCUGGg -3' miRNA:   3'- -CCgC-CUUACGg---ACCGAGCGACGACUg -5'
8799	5'	-57.9	NC_002484.1	+	6633	1.11	0.000341
	Target:  5'- aGGCGGAAUGCCUGGCUCGCUGCUGACu -3' miRNA:   3'- -CCGCCUUACGGACCGAGCGACGACUG- -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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