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
18957	3'	-58.6	NC_004683.1	+	37040	0.67	0.469987
	Target:  5'- gGCUGCCCcuugggguACCCcggcGGGGCGGuucGGGCg -3' miRNA:   3'- -UGACGGGcu------UGGGa---CUCUGCCu--CCUG- -5'
18957	3'	-58.6	NC_004683.1	+	39862	0.67	0.450492
	Target:  5'- uGCUGCUgaCGAuuCCC-GAGACGGcGGAUg -3' miRNA:   3'- -UGACGG--GCUu-GGGaCUCUGCCuCCUG- -5'
18957	3'	-58.6	NC_004683.1	+	52056	0.68	0.431449
	Target:  5'- -gUGCCCGAcgcGCCCUGGcugaucgucGACGcGGGaGGCg -3' miRNA:   3'- ugACGGGCU---UGGGACU---------CUGC-CUC-CUG- -5'
18957	3'	-58.6	NC_004683.1	+	50723	0.68	0.422106
	Target:  5'- uGCUGUUCGugUCgUG-GugGGAGGACg -3' miRNA:   3'- -UGACGGGCuuGGgACuCugCCUCCUG- -5'
18957	3'	-58.6	NC_004683.1	+	18296	0.68	0.403791
	Target:  5'- uGCUGCaguCGGGCCCgGAGACGGGcgcaucGGCa -3' miRNA:   3'- -UGACGg--GCUUGGGaCUCUGCCUc-----CUG- -5'
18957	3'	-58.6	NC_004683.1	+	30018	0.68	0.403791
	Target:  5'- gGCUGCCCgccGAGCCC-GAGA-GGuauGGGCc -3' miRNA:   3'- -UGACGGG---CUUGGGaCUCUgCCu--CCUG- -5'
18957	3'	-58.6	NC_004683.1	+	50426	1.09	0.000515
	Target:  5'- gACUGCCCGAACCCUGAGACGGAGGACu -3' miRNA:   3'- -UGACGGGCUUGGGACUCUGCCUCCUG- -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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