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
22535	5'	-52	NC_005083.1	+	2375	0.66	0.993984
	Target:  5'- uCUGCgGUGAuucGCUuccuuCCUGCAAAAGG-Cg -3' miRNA:   3'- -GACGgUAUU---CGGu----GGACGUUUUCCcG- -5'
22535	5'	-52	NC_005083.1	+	175756	0.66	0.993984
	Target:  5'- cCUGCUcauuacaaGUGAGCUGCaCUGCcAAuugugcuaucAGGGCg -3' miRNA:   3'- -GACGG--------UAUUCGGUG-GACGuUU----------UCCCG- -5'
22535	5'	-52	NC_005083.1	+	165849	0.67	0.986686
	Target:  5'- uCUGUaCGUAGccGCCGCCcGCAAuAGGuGCg -3' miRNA:   3'- -GACG-GUAUU--CGGUGGaCGUUuUCC-CG- -5'
22535	5'	-52	NC_005083.1	+	217133	0.68	0.983136
	Target:  5'- gUGCguuUAUAAGaaGCCUGaAGAGGGGCa -3' miRNA:   3'- gACG---GUAUUCggUGGACgUUUUCCCG- -5'
22535	5'	-52	NC_005083.1	+	163893	0.68	0.977508
	Target:  5'- -cGCCGaucuuuugaacguAGCCACCgcccGCAAucGGGGCa -3' miRNA:   3'- gaCGGUau-----------UCGGUGGa---CGUUu-UCCCG- -5'
22535	5'	-52	NC_005083.1	+	243112	0.72	0.874817
	Target:  5'- aUGCCGUGAGCUagaGCCU-CAGuuGGGUc -3' miRNA:   3'- gACGGUAUUCGG---UGGAcGUUuuCCCG- -5'
22535	5'	-52	NC_005083.1	+	203298	1.03	0.023411
	Target:  5'- uCUGCCAauAGCCACCUGCAAAAGGGCg -3' miRNA:   3'- -GACGGUauUCGGUGGACGUUUUCCCG- -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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