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
19602	5'	-54.3	NC_004686.1	+	7665	0.66	0.776696
	Target:  5'- aGGGGCGCGagccaucauGGCCGAuucaaAGAAUGUGUg -3' miRNA:   3'- gCUCCGCGUgc-------CUGGCU-----UCUUGUACA- -5'
19602	5'	-54.3	NC_004686.1	+	55396	0.66	0.766583
	Target:  5'- gGAGGCGCACaccuGACCGccgcGGACAa-- -3' miRNA:   3'- gCUCCGCGUGc---CUGGCuu--CUUGUaca -5'
19602	5'	-54.3	NC_004686.1	+	44161	0.67	0.735456
	Target:  5'- aCGcGGUGC-CGGACCGG---GCAUGg -3' miRNA:   3'- -GCuCCGCGuGCCUGGCUucuUGUACa -5'
19602	5'	-54.3	NC_004686.1	+	42979	0.67	0.692547
	Target:  5'- aCGuGGCGUccaACGGGCUGu-GGGCAUGc -3' miRNA:   3'- -GCuCCGCG---UGCCUGGCuuCUUGUACa -5'
19602	5'	-54.3	NC_004686.1	+	55986	0.68	0.681645
	Target:  5'- gCGGGGCG-GCaGGCUGuuGAGCAUGUc -3' miRNA:   3'- -GCUCCGCgUGcCUGGCuuCUUGUACA- -5'
19602	5'	-54.3	NC_004686.1	+	39823	0.75	0.298357
	Target:  5'- gGAGGCGCcgucgucgagcagGCGGGCCGccugggccAGGACAUGUu -3' miRNA:   3'- gCUCCGCG-------------UGCCUGGCu-------UCUUGUACA- -5'
19602	5'	-54.3	NC_004686.1	+	37717	0.77	0.219627
	Target:  5'- cCGAGGUGUAcCGGACCGggGcguCGUGg -3' miRNA:   3'- -GCUCCGCGU-GCCUGGCuuCuu-GUACa -5'
19602	5'	-54.3	NC_004686.1	+	27180	1.07	0.001924
	Target:  5'- uCGAGGCGCACGGACCGAAGAACAUGUu -3' miRNA:   3'- -GCUCCGCGUGCCUGGCUUCUUGUACA- -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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