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
11304	3'	-47.5	NC_003083.1	+	114221	0.66	0.999069
	Target:  5'- ----cGGCUGGUgaauauccagGGCUGcgGCGCUGCa -3' miRNA:   3'- uagaaCUGAUCAa---------UUGGCa-CGUGACG- -5'
11304	3'	-47.5	NC_003083.1	+	57567	0.66	0.998853
	Target:  5'- cUCUguuACUAGgcuguGCCGUGCuGCUGUu -3' miRNA:   3'- uAGAac-UGAUCaau--UGGCACG-UGACG- -5'
11304	3'	-47.5	NC_003083.1	+	3723	0.66	0.998595
	Target:  5'- uGUCccGGCauGUUGAUCGgugUGCACUGCa -3' miRNA:   3'- -UAGaaCUGauCAAUUGGC---ACGUGACG- -5'
11304	3'	-47.5	NC_003083.1	+	58892	0.66	0.998595
	Target:  5'- uGUCaaGAU--GUUGACUGUGCACUaacGCg -3' miRNA:   3'- -UAGaaCUGauCAAUUGGCACGUGA---CG- -5'
11304	3'	-47.5	NC_003083.1	+	18484	0.66	0.998289
	Target:  5'- uGUCUUG-CUuGUacGCCG-GCGCUGUu -3' miRNA:   3'- -UAGAACuGAuCAauUGGCaCGUGACG- -5'
11304	3'	-47.5	NC_003083.1	+	1800	0.67	0.997369
	Target:  5'- -gCUUGACUcagcGUUGACCaccugccgucgucgGUGCACgccgGCg -3' miRNA:   3'- uaGAACUGAu---CAAUUGG--------------CACGUGa---CG- -5'
11304	3'	-47.5	NC_003083.1	+	36152	1.1	0.011018
	Target:  5'- cAUCUUGACUAGUUAACCGUGCACUGCc -3' miRNA:   3'- -UAGAACUGAUCAAUUGGCACGUGACG- -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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