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
12674	5'	-58.1	NC_003345.1	+	43125	0.68	0.550453
	Target:  5'- -cUUCGUCUUCAUCGAccuccacgGGGaGCGGGACa -3' miRNA:   3'- ucGAGCAGGAGUGGCU--------CUC-CGCUCUG- -5'
12674	5'	-58.1	NC_003345.1	+	19289	0.68	0.509693
	Target:  5'- aAGCUCGUgCCcaaAUCGAGAaggcgcguGGUGAGGCg -3' miRNA:   3'- -UCGAGCA-GGag-UGGCUCU--------CCGCUCUG- -5'
12674	5'	-58.1	NC_003345.1	+	22792	0.69	0.499696
	Target:  5'- cGGUUUGaCCgccgUACCGAGAGcGCGGGAg -3' miRNA:   3'- -UCGAGCaGGa---GUGGCUCUC-CGCUCUg -5'
12674	5'	-58.1	NC_003345.1	+	18580	0.69	0.45112
	Target:  5'- gAGCUaCGUCCccaaaaacCACCGcGAGGCGGuGGCu -3' miRNA:   3'- -UCGA-GCAGGa-------GUGGCuCUCCGCU-CUG- -5'
12674	5'	-58.1	NC_003345.1	+	20771	0.69	0.45112
	Target:  5'- cGCUUGUCCUCACUcuauuAGAcGUGGGACu -3' miRNA:   3'- uCGAGCAGGAGUGGc----UCUcCGCUCUG- -5'
12674	5'	-58.1	NC_003345.1	+	23781	0.74	0.259952
	Target:  5'- cGCUCGgaugaacgagCUUCACCGAGAGGUGcGAa -3' miRNA:   3'- uCGAGCa---------GGAGUGGCUCUCCGCuCUg -5'
12674	5'	-58.1	NC_003345.1	+	70111	1.09	0.000833
	Target:  5'- cAGCUCGUCCUCACCGAGAGGCGAGACu -3' miRNA:   3'- -UCGAGCAGGAGUGGCUCUCCGCUCUG- -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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