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
19646	3'	-60.4	NC_004686.1	+	19052	0.66	0.445113
	Target:  5'- cGAGG-CUCGUGGACUucuUCCUCaGCCUc -3' miRNA:   3'- -UUCCuGGGCACCUGA---AGGGGcUGGGu -5'
19646	3'	-60.4	NC_004686.1	+	20501	0.66	0.426378
	Target:  5'- -cGGAUCCGUuGuuUUCCCCGAgUCCAa -3' miRNA:   3'- uuCCUGGGCAcCugAAGGGGCU-GGGU- -5'
19646	3'	-60.4	NC_004686.1	+	3978	0.66	0.420849
	Target:  5'- gGAGGAUCCGcaggccgcggauacaUGcGGCgcaCCCGGCCCGg -3' miRNA:   3'- -UUCCUGGGC---------------AC-CUGaagGGGCUGGGU- -5'
19646	3'	-60.4	NC_004686.1	+	43356	0.66	0.419932
	Target:  5'- aGAGGuguucaucguucuGCCCGUGGAUggagauaucgcggaUCCCCGGCUg- -3' miRNA:   3'- -UUCC-------------UGGGCACCUGa-------------AGGGGCUGGgu -5'
19646	3'	-60.4	NC_004686.1	+	25529	0.67	0.408119
	Target:  5'- --uGACCCuGUGGAgUUUCCgGAUCCGa -3' miRNA:   3'- uucCUGGG-CACCUgAAGGGgCUGGGU- -5'
19646	3'	-60.4	NC_004686.1	+	32236	0.69	0.302086
	Target:  5'- cAGGuACCCGgccGAC-UCCCCGAgCCCGa -3' miRNA:   3'- uUCC-UGGGCac-CUGaAGGGGCU-GGGU- -5'
19646	3'	-60.4	NC_004686.1	+	7533	1.06	0.000541
	Target:  5'- cAAGGACCCGUGGACUUCCCCGACCCAg -3' miRNA:   3'- -UUCCUGGGCACCUGAAGGGGCUGGGU- -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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