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
16921	5'	-52.6	NC_004313.1	+	6604	0.66	0.750702
	Target:  5'- uGGCCGcucgaAGCCAGGCgaaAACCCCU-CGu -3' miRNA:   3'- gUCGGUa----UUGGUCUGg--UUGGGGAaGU- -5'
16921	5'	-52.6	NC_004313.1	+	10106	0.66	0.750702
	Target:  5'- -cGCCA--GCCcGGCCAuuucuuucugaaAUCCCUUCAg -3' miRNA:   3'- guCGGUauUGGuCUGGU------------UGGGGAAGU- -5'
16921	5'	-52.6	NC_004313.1	+	13807	0.66	0.739718
	Target:  5'- cCGGCCugccgagAACCAG-CCGuCCCCgUUCGu -3' miRNA:   3'- -GUCGGua-----UUGGUCuGGUuGGGG-AAGU- -5'
16921	5'	-52.6	NC_004313.1	+	11834	0.68	0.637033
	Target:  5'- uCAGCCAUGAUguGgguuACUcACCCUUUCGu -3' miRNA:   3'- -GUCGGUAUUGguC----UGGuUGGGGAAGU- -5'
16921	5'	-52.6	NC_004313.1	+	2200	0.68	0.625434
	Target:  5'- -cGCCAUAAUCAGugCAACUgcaCCaUCGa -3' miRNA:   3'- guCGGUAUUGGUCugGUUGG---GGaAGU- -5'
16921	5'	-52.6	NC_004313.1	+	2421	0.71	0.437033
	Target:  5'- cCAGCCAcGACCAGAacaugcaCAgcGCCCCggCAa -3' miRNA:   3'- -GUCGGUaUUGGUCUg------GU--UGGGGaaGU- -5'
16921	5'	-52.6	NC_004313.1	+	11417	1.09	0.001082
	Target:  5'- cCAGCCAUAACCAGACCAACCCCUUCAa -3' miRNA:   3'- -GUCGGUAUUGGUCUGGUUGGGGAAGU- -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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