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
21740	5'	-51.6	NC_004813.1	+	48247	0.66	0.845157
	Target:  5'- cGGAGUCaGCCcggcAGgcgGCAgaaaGUGCAGCCUc -3' miRNA:   3'- uUUUUAG-CGG----UCa--CGUa---CACGUCGGA- -5'
21740	5'	-51.6	NC_004813.1	+	45983	0.66	0.845157
	Target:  5'- cAGAAAUCcuucCCGG-GCuuaAUGUGCGGCCg -3' miRNA:   3'- -UUUUUAGc---GGUCaCG---UACACGUCGGa -5'
21740	5'	-51.6	NC_004813.1	+	31256	0.66	0.826462
	Target:  5'- ------gGaCCAGUGCAUcaGCAGCCg -3' miRNA:   3'- uuuuuagC-GGUCACGUAcaCGUCGGa -5'
21740	5'	-51.6	NC_004813.1	+	32585	0.69	0.675798
	Target:  5'- -----cCGCCGGUGUAUGccgccgggcugGCGGCCa -3' miRNA:   3'- uuuuuaGCGGUCACGUACa----------CGUCGGa -5'
21740	5'	-51.6	NC_004813.1	+	3100	0.69	0.663109
	Target:  5'- ---cGUCGCCAGuUGCcugccauucgauaAUG-GCAGCCUg -3' miRNA:   3'- uuuuUAGCGGUC-ACG-------------UACaCGUCGGA- -5'
21740	5'	-51.6	NC_004813.1	+	38796	0.75	0.345495
	Target:  5'- -----cCGCCAGUGCAacuucauuacGUGCAGCCg -3' miRNA:   3'- uuuuuaGCGGUCACGUa---------CACGUCGGa -5'
21740	5'	-51.6	NC_004813.1	+	28316	1.06	0.002729
	Target:  5'- uAAAAAUCGCCAGUGCAUGUGCAGCCUg -3' miRNA:   3'- -UUUUUAGCGGUCACGUACACGUCGGA- -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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