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
21752	5'	-55.8	NC_004813.1	+	43287	0.66	0.690294
	Target:  5'- aGGCACCggCAUCGGGUUCcccuggGCAAucauguuAUCCa -3' miRNA:   3'- -CCGUGG--GUGGUCCGAGa-----CGUU-------UAGGa -5'
21752	5'	-55.8	NC_004813.1	+	38880	0.66	0.669488
	Target:  5'- gGGCugCCGCCAcGGC-CUGCuGAgcaCg -3' miRNA:   3'- -CCGugGGUGGU-CCGaGACGuUUag-Ga -5'
21752	5'	-55.8	NC_004813.1	+	44461	0.66	0.669488
	Target:  5'- aGGCACCagGCCGGGUuauugCUGUAug-CCg -3' miRNA:   3'- -CCGUGGg-UGGUCCGa----GACGUuuaGGa -5'
21752	5'	-55.8	NC_004813.1	+	46023	0.66	0.655175
	Target:  5'- cGCAgauuucCCCACCAGGUugacgCUGCGcacguaaaaccagaAAUCCUu -3' miRNA:   3'- cCGU------GGGUGGUCCGa----GACGU--------------UUAGGA- -5'
21752	5'	-55.8	NC_004813.1	+	32180	0.67	0.614315
	Target:  5'- aGGCGCCgGCaaaGGGCUCaGCcaccgCCUg -3' miRNA:   3'- -CCGUGGgUGg--UCCGAGaCGuuua-GGA- -5'
21752	5'	-55.8	NC_004813.1	+	11698	0.68	0.559516
	Target:  5'- cGGCGgCCACCGGGgauuuuuuCUUUGUGAuUCCa -3' miRNA:   3'- -CCGUgGGUGGUCC--------GAGACGUUuAGGa -5'
21752	5'	-55.8	NC_004813.1	+	41664	1.09	0.000819
	Target:  5'- uGGCACCCACCAGGCUCUGCAAAUCCUc -3' miRNA:   3'- -CCGUGGGUGGUCCGAGACGUUUAGGA- -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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