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
13143	5'	-56.8	NC_003401.1	+	89743	0.66	0.860967
	Target:  5'- -aUCCAgaCCAGAUCACUccauuUUGGCGGc- -3' miRNA:   3'- gcAGGUa-GGUCUAGUGG-----AGCCGCCua -5'
13143	5'	-56.8	NC_003401.1	+	102977	0.66	0.853197
	Target:  5'- gCGUCCAccuaUCUGGAUCAUCgcCaGCGGAUu -3' miRNA:   3'- -GCAGGU----AGGUCUAGUGGa-GcCGCCUA- -5'
13143	5'	-56.8	NC_003401.1	+	126093	0.66	0.845226
	Target:  5'- aGUCUAUUcaCAGAcccUCACUUCGGUGGc- -3' miRNA:   3'- gCAGGUAG--GUCU---AGUGGAGCCGCCua -5'
13143	5'	-56.8	NC_003401.1	+	63923	0.67	0.775076
	Target:  5'- gGUCaggugauaUAUCUAGAUCACCggcagagGGCGGAUg -3' miRNA:   3'- gCAG--------GUAGGUCUAGUGGag-----CCGCCUA- -5'
13143	5'	-56.8	NC_003401.1	+	21291	0.68	0.73663
	Target:  5'- cCGUacaCCGgccCCAGAUCGCCcucgCGGCGGu- -3' miRNA:   3'- -GCA---GGUa--GGUCUAGUGGa---GCCGCCua -5'
13143	5'	-56.8	NC_003401.1	+	132666	0.73	0.48492
	Target:  5'- gGgggCCGgggcCCGGggCGCCUCGGCGGGg -3' miRNA:   3'- gCa--GGUa---GGUCuaGUGGAGCCGCCUa -5'
13143	5'	-56.8	NC_003401.1	+	101159	1.06	0.003274
	Target:  5'- uCGUCCAUCCAGAUCACCUCGGCGGAUa -3' miRNA:   3'- -GCAGGUAGGUCUAGUGGAGCCGCCUA- -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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