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
20317	5'	-49.7	NC_004687.1	+	94650	0.66	0.998066
	Target:  5'- gGUCgacgUACUGCUugUUGGcgacgUGCUCaUUGGc -3' miRNA:   3'- -CAG----AUGACGAugAGCU-----ACGAGcAACC- -5'
20317	5'	-49.7	NC_004687.1	+	155103	0.67	0.992949
	Target:  5'- cGUCUGCUGCaggacgcGCUgGAugcUGCUCGUg-- -3' miRNA:   3'- -CAGAUGACGa------UGAgCU---ACGAGCAacc -5'
20317	5'	-49.7	NC_004687.1	+	15472	0.68	0.98787
	Target:  5'- gGUCUGCUGCca---GAUGCU-GUUGGc -3' miRNA:   3'- -CAGAUGACGaugagCUACGAgCAACC- -5'
20317	5'	-49.7	NC_004687.1	+	77733	0.7	0.963178
	Target:  5'- gGUC-GCUGCUGCggCGucUGCUCGUcgaggUGGg -3' miRNA:   3'- -CAGaUGACGAUGa-GCu-ACGAGCA-----ACC- -5'
20317	5'	-49.7	NC_004687.1	+	80438	0.76	0.759306
	Target:  5'- -cCUGCUGCUGCgCGGccUGCUCGgcGGu -3' miRNA:   3'- caGAUGACGAUGaGCU--ACGAGCaaCC- -5'
20317	5'	-49.7	NC_004687.1	+	146386	0.78	0.634223
	Target:  5'- cGUCggaggACUGCUGCUCGuccUGCUCGgggucgUGGc -3' miRNA:   3'- -CAGa----UGACGAUGAGCu--ACGAGCa-----ACC- -5'
20317	5'	-49.7	NC_004687.1	+	127123	1.11	0.009402
	Target:  5'- gGUCUACUGCUACUCGAUGCUCGUUGGu -3' miRNA:   3'- -CAGAUGACGAUGAGCUACGAGCAACC- -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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