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
8891	3'	-62.9	NC_002484.1	+	4206	0.67	0.35488
	Target:  5'- cGCCGAUCCaGGUCuCGGCGUccauCUGu -3' miRNA:   3'- cCGGCUAGGgCCAGcGCCGCGc---GACc -5'
8891	3'	-62.9	NC_002484.1	+	53719	0.67	0.31693
	Target:  5'- aGG-CGAUCCCGGaguauuaggUCGCGGUaGgGCcGGg -3' miRNA:   3'- -CCgGCUAGGGCC---------AGCGCCG-CgCGaCC- -5'
8891	3'	-62.9	NC_002484.1	+	46718	0.68	0.295667
	Target:  5'- cGGCCaGGaCCCGGUCcaGUaGCGCGUUGa -3' miRNA:   3'- -CCGG-CUaGGGCCAG--CGcCGCGCGACc -5'
8891	3'	-62.9	NC_002484.1	+	10329	0.69	0.256505
	Target:  5'- cGCCuGUCCCGGcgugCGCaGGCcGCGCaGGu -3' miRNA:   3'- cCGGcUAGGGCCa---GCG-CCG-CGCGaCC- -5'
8891	3'	-62.9	NC_002484.1	+	41779	0.7	0.226648
	Target:  5'- uGGCuCGAUUCCGcaauucagaguucGUCGaCGaccGCGCGCUGGc -3' miRNA:   3'- -CCG-GCUAGGGC-------------CAGC-GC---CGCGCGACC- -5'
8891	3'	-62.9	NC_002484.1	+	47153	0.71	0.19099
	Target:  5'- uGGCUGAUCgCCuuugacaccacGUCGCGGCGCauGUUGGu -3' miRNA:   3'- -CCGGCUAG-GGc----------CAGCGCCGCG--CGACC- -5'
8891	3'	-62.9	NC_002484.1	+	19086	0.72	0.151946
	Target:  5'- aGCCGAucaUCCCGG-CGCca-GCGCUGGu -3' miRNA:   3'- cCGGCU---AGGGCCaGCGccgCGCGACC- -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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