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
11392	5'	-54.2	NC_003084.1	+	97722	0.67	0.820658
	Target:  5'- --aCGGUgGAGCUGCacugcuugaucgaguGGUGCCUaCGUGa -3' miRNA:   3'- uuaGCCGgCUUGACG---------------UCAUGGA-GCAU- -5'
11392	5'	-54.2	NC_003084.1	+	1120	0.69	0.749254
	Target:  5'- cAGUCGGCCGAGgUGUccaGGUAgCUUGg- -3' miRNA:   3'- -UUAGCCGGCUUgACG---UCAUgGAGCau -5'
11392	5'	-54.2	NC_003084.1	+	105650	0.69	0.749254
	Target:  5'- cAGUCGGCCGAGgUGUccaGGUAgCUUGg- -3' miRNA:   3'- -UUAGCCGGCUUgACG---UCAUgGAGCau -5'
11392	5'	-54.2	NC_003084.1	+	39974	0.69	0.719328
	Target:  5'- uAUCGGgCGAGCUGguGgagcugcaaaacucgACCUCGUc -3' miRNA:   3'- uUAGCCgGCUUGACguCa--------------UGGAGCAu -5'
11392	5'	-54.2	NC_003084.1	+	85597	0.73	0.526397
	Target:  5'- aAGUCGGCCGAACUGCccGGUcCgCUgGUGg -3' miRNA:   3'- -UUAGCCGGCUUGACG--UCAuG-GAgCAU- -5'
11392	5'	-54.2	NC_003084.1	+	42888	0.73	0.47559
	Target:  5'- --cCGGCUGAaaaGCUGCGGUACCcgCGUu -3' miRNA:   3'- uuaGCCGGCU---UGACGUCAUGGa-GCAu -5'
11392	5'	-54.2	NC_003084.1	+	79994	1.05	0.004541
	Target:  5'- aAAUCGGCCGAACUGCAGUACCUCGUAa -3' miRNA:   3'- -UUAGCCGGCUUGACGUCAUGGAGCAU- -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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