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
22497	3'	-53.5	NC_005069.1	+	19094	0.77	0.202997
	Target:  5'- aCGCuaGCCGCUGaAGUuGCCCGGCAuCAUa -3' miRNA:   3'- -GCG--UGGCGACaUUAuUGGGCCGU-GUG- -5'
22497	3'	-53.5	NC_005069.1	+	44155	0.69	0.556756
	Target:  5'- aCGCGCUGCUGauugcaucuuucuGUuACCCGGCugGa -3' miRNA:   3'- -GCGUGGCGACau-----------UAuUGGGCCGugUg -5'
22497	3'	-53.5	NC_005069.1	+	18376	1.11	0.000853
	Target:  5'- gCGCACCGCUGUAAUAACCCGGCACACg -3' miRNA:   3'- -GCGUGGCGACAUUAUUGGGCCGUGUG- -5'
22497	3'	-53.5	NC_005069.1	+	33289	0.71	0.466297
	Target:  5'- -aCACCGUcGUGAgcUGGCUCGGCAUGCa -3' miRNA:   3'- gcGUGGCGaCAUU--AUUGGGCCGUGUG- -5'
22497	3'	-53.5	NC_005069.1	+	31452	0.68	0.642487
	Target:  5'- uGCACCgGCUGUuacUAGCCCcaaGCuACGCg -3' miRNA:   3'- gCGUGG-CGACAuu-AUUGGGc--CG-UGUG- -5'
22497	3'	-53.5	NC_005069.1	+	12585	0.68	0.642487
	Target:  5'- aCGCuACCGCcaGUcgcucuACCCGGUACAUa -3' miRNA:   3'- -GCG-UGGCGa-CAuuau--UGGGCCGUGUG- -5'
22497	3'	-53.5	NC_005069.1	+	14018	0.66	0.720982
	Target:  5'- uGCAacauauCUGaagaaGUGGUcGCCCGGCGCACg -3' miRNA:   3'- gCGU------GGCga---CAUUAuUGGGCCGUGUG- -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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