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
8428	3'	-62.9	NC_002166.1	+	805	0.66	0.248868
	Target:  5'- gGCCC-CACCAGGUgAGCcaGCagaauuCCGGCAa -3' miRNA:   3'- gUGGGcGUGGUCCA-UCG--CG------GGCCGUa -5'
8428	3'	-62.9	NC_002166.1	+	29436	0.68	0.181959
	Target:  5'- gGCCCgGUAUacGGUcgGGUGCCCGGCGUg -3' miRNA:   3'- gUGGG-CGUGguCCA--UCGCGGGCCGUA- -5'
8428	3'	-62.9	NC_002166.1	+	3227	0.69	0.154862
	Target:  5'- -uCCCGCcauuGCCGGGUGGCGaUgUGGCAa -3' miRNA:   3'- guGGGCG----UGGUCCAUCGC-GgGCCGUa -5'
8428	3'	-62.9	NC_002166.1	+	19080	0.69	0.14273
	Target:  5'- gCACCCGCcaGCCAGGUucGCG-CUGGCc- -3' miRNA:   3'- -GUGGGCG--UGGUCCAu-CGCgGGCCGua -5'
8428	3'	-62.9	NC_002166.1	+	19108	0.7	0.121039
	Target:  5'- uGCCCGUGCC-GGUGGCGCUguuuccguuaaUGGCGa -3' miRNA:   3'- gUGGGCGUGGuCCAUCGCGG-----------GCCGUa -5'
8428	3'	-62.9	NC_002166.1	+	37802	0.73	0.078861
	Target:  5'- gCAUCC-CACCAacgggaaagaagcuGGUAGCGUCCGGCGg -3' miRNA:   3'- -GUGGGcGUGGU--------------CCAUCGCGGGCCGUa -5'
8428	3'	-62.9	NC_002166.1	+	16240	1.05	0.000201
	Target:  5'- gCACCCGCACCAGGUAGCGCCCGGCAUa -3' miRNA:   3'- -GUGGGCGUGGUCCAUCGCGGGCCGUA- -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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