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
18560	3'	-53.7	NC_004682.1	+	21573	0.66	0.779865
	Target:  5'- aGAGCGaGGcc--GAUGC-CGACUUCAu -3' miRNA:   3'- aCUCGC-CCaacuCUGCGuGCUGAAGU- -5'
18560	3'	-53.7	NC_004682.1	+	26321	0.66	0.748733
	Target:  5'- cGAGCauuGGGUUGGcGGUGUACGuCUUCGa -3' miRNA:   3'- aCUCG---CCCAACU-CUGCGUGCuGAAGU- -5'
18560	3'	-53.7	NC_004682.1	+	28856	0.68	0.661189
	Target:  5'- cGGGUGGGUuuccUGAGACccauuGCGCGggaccagguucGCUUCGg -3' miRNA:   3'- aCUCGCCCA----ACUCUG-----CGUGC-----------UGAAGU- -5'
18560	3'	-53.7	NC_004682.1	+	5427	0.68	0.649997
	Target:  5'- cGAGCGGaGgUGAGGCGCgaaacagcaACGGCgaCAa -3' miRNA:   3'- aCUCGCC-CaACUCUGCG---------UGCUGaaGU- -5'
18560	3'	-53.7	NC_004682.1	+	20969	0.68	0.627575
	Target:  5'- gGAGCGGGUgGAGAaGCACcccgagGGCcUCAa -3' miRNA:   3'- aCUCGCCCAaCUCUgCGUG------CUGaAGU- -5'
18560	3'	-53.7	NC_004682.1	+	4503	0.69	0.593997
	Target:  5'- -cGGCGGGcucgGGGcCGCACGcGCUUCGa -3' miRNA:   3'- acUCGCCCaa--CUCuGCGUGC-UGAAGU- -5'
18560	3'	-53.7	NC_004682.1	+	38923	1.09	0.001244
	Target:  5'- uUGAGCGGGUUGAGACGCACGACUUCAg -3' miRNA:   3'- -ACUCGCCCAACUCUGCGUGCUGAAGU- -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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