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
28438	5'	-52.9	NC_005946.1	+	78942	0.66	0.951729
	Target:  5'- aGUAUGUCUcccgucugccuggcgUCGGGCUUGUG-AACGUUg -3' miRNA:   3'- -CGUGUAGG---------------AGUCCGAGCGCuUUGCAG- -5'
28438	5'	-52.9	NC_005946.1	+	37493	0.67	0.924988
	Target:  5'- cCGCAUUCUCAGGCagUUGCauauCGUCc -3' miRNA:   3'- cGUGUAGGAGUCCG--AGCGcuuuGCAG- -5'
28438	5'	-52.9	NC_005946.1	+	102217	0.68	0.871534
	Target:  5'- aGCACAg-CUCGGcCUCGUcgGggGCGUCu -3' miRNA:   3'- -CGUGUagGAGUCcGAGCG--CuuUGCAG- -5'
28438	5'	-52.9	NC_005946.1	+	67718	0.69	0.839035
	Target:  5'- cCACGgugaCCUCGGGCUga-GGGACGUCg -3' miRNA:   3'- cGUGUa---GGAGUCCGAgcgCUUUGCAG- -5'
28438	5'	-52.9	NC_005946.1	+	100677	0.7	0.774602
	Target:  5'- cGCGCAgUCCaCAcGGCUCGCaGuauGCGUCg -3' miRNA:   3'- -CGUGU-AGGaGU-CCGAGCG-Cuu-UGCAG- -5'
28438	5'	-52.9	NC_005946.1	+	77807	0.74	0.56501
	Target:  5'- aGCuGCGUCCUCAGGCUCuuuacccaGCuGGACGUa -3' miRNA:   3'- -CG-UGUAGGAGUCCGAG--------CGcUUUGCAg -5'
28438	5'	-52.9	NC_005946.1	+	89170	1.11	0.002612
	Target:  5'- cGCACAUCCUCAGGCUCGCGAAACGUCc -3' miRNA:   3'- -CGUGUAGGAGUCCGAGCGCUUUGCAG- -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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