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
20749	3'	-54.6	NC_004688.1	+	874	0.66	0.916509
	Target:  5'- cGCUgaCGGUUGCacgCCGCguggagcAGGCGGUGugGc -3' miRNA:   3'- -UGA--GUCAGCGa--GGCG-------UCUGCCAUugC- -5'
20749	3'	-54.6	NC_004688.1	+	106782	0.66	0.911079
	Target:  5'- cACUCGGuaUCGCgUCCGUcaucauCGGUGGCGc -3' miRNA:   3'- -UGAGUC--AGCG-AGGCGucu---GCCAUUGC- -5'
20749	3'	-54.6	NC_004688.1	+	37632	0.66	0.904809
	Target:  5'- --aCGGUCGCcgggggCCGCcccucGGCGGUGACc -3' miRNA:   3'- ugaGUCAGCGa-----GGCGu----CUGCCAUUGc -5'
20749	3'	-54.6	NC_004688.1	+	36984	0.67	0.846103
	Target:  5'- -aUCGGuUCGUUCCGCcAGAgGGUGuaaACGu -3' miRNA:   3'- ugAGUC-AGCGAGGCG-UCUgCCAU---UGC- -5'
20749	3'	-54.6	NC_004688.1	+	100432	0.68	0.802581
	Target:  5'- cGCUCcgcaAGaCGCUCCGCAagaaucGACGGgcGCu -3' miRNA:   3'- -UGAG----UCaGCGAGGCGU------CUGCCauUGc -5'
20749	3'	-54.6	NC_004688.1	+	104160	0.69	0.745109
	Target:  5'- -aUgGGUgGCUCaCGCGcGCGGUAGCGg -3' miRNA:   3'- ugAgUCAgCGAG-GCGUcUGCCAUUGC- -5'
20749	3'	-54.6	NC_004688.1	+	6221	0.74	0.478214
	Target:  5'- cGCUCgcccgugcggAGUUGCUCCaGCGcGCGGUAGCGg -3' miRNA:   3'- -UGAG----------UCAGCGAGG-CGUcUGCCAUUGC- -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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