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
25026	5'	-50.6	NC_005336.1	+	110955	0.66	0.991829
	Target:  5'- aCCCCUGCUUcgCgGGCUCggUGUGc -3' miRNA:   3'- cGGGGGUGGAuaGgUUGAGaaACAUu -5'
25026	5'	-50.6	NC_005336.1	+	127387	0.66	0.984221
	Target:  5'- uGCacaUCUACCUGUCCGGCUuCUUcGUGu -3' miRNA:   3'- -CGg--GGGUGGAUAGGUUGA-GAAaCAUu -5'
25026	5'	-50.6	NC_005336.1	+	70053	0.68	0.969107
	Target:  5'- cGCCgCCACCagagUGUCCAGCguggUGUAc -3' miRNA:   3'- -CGGgGGUGG----AUAGGUUGagaaACAUu -5'
25026	5'	-50.6	NC_005336.1	+	55771	0.68	0.962311
	Target:  5'- gGCUCCUGCgUGUCCGGCUCcugccGUGAc -3' miRNA:   3'- -CGGGGGUGgAUAGGUUGAGaaa--CAUU- -5'
25026	5'	-50.6	NC_005336.1	+	19629	0.68	0.95454
	Target:  5'- -gCCCCGCCgUAUCCAACUgCUUg---- -3' miRNA:   3'- cgGGGGUGG-AUAGGUUGA-GAAacauu -5'
25026	5'	-50.6	NC_005336.1	+	55750	0.72	0.854816
	Target:  5'- gGCUCCCGCgUGUCCGGCUCc------ -3' miRNA:   3'- -CGGGGGUGgAUAGGUUGAGaaacauu -5'
25026	5'	-50.6	NC_005336.1	+	139023	1.09	0.006946
	Target:  5'- cGCCCCCACCUAUCCAACUCUUUGUAAa -3' miRNA:   3'- -CGGGGGUGGAUAGGUUGAGAAACAUU- -5'
25026	5'	-50.6	NC_005336.1	+	139023	1.09	0.006946
	Target:  5'- cGCCCCCACCUAUCCAACUCUUUGUAAa -3' miRNA:   3'- -CGGGGGUGGAUAGGUUGAGAAACAUU- -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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