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
27213	3'	-50.1	NC_005832.1	+	66342	0.66	0.985188
	Target:  5'- cCGUCUUcgcccaUGCCCGuCCUGC-CCAGGu -3' miRNA:   3'- -GUAGAAag----AUGGGU-GGAUGaGGUCUu -5'
27213	3'	-50.1	NC_005832.1	+	97358	0.66	0.984614
	Target:  5'- -uUCUUUUUGCCaguaggCaggacacggccgagGCCUGCUCCAGGAg -3' miRNA:   3'- guAGAAAGAUGG------G--------------UGGAUGAGGUCUU- -5'
27213	3'	-50.1	NC_005832.1	+	35557	0.66	0.981041
	Target:  5'- gAUCU-UCUgGCCCACCUAgaCgCAGAGg -3' miRNA:   3'- gUAGAaAGA-UGGGUGGAUgaG-GUCUU- -5'
27213	3'	-50.1	NC_005832.1	+	77363	0.66	0.981041
	Target:  5'- gGUCUUUCggugUACgCCGCCUugUCCucGGGc -3' miRNA:   3'- gUAGAAAG----AUG-GGUGGAugAGG--UCUu -5'
27213	3'	-50.1	NC_005832.1	+	87467	0.66	0.976082
	Target:  5'- -----gUCU-CCCACCUcguCUCCAGGAu -3' miRNA:   3'- guagaaAGAuGGGUGGAu--GAGGUCUU- -5'
27213	3'	-50.1	NC_005832.1	+	39628	0.67	0.973273
	Target:  5'- --cCUgucCUGCCCACa-GCUCCAGGGu -3' miRNA:   3'- guaGAaa-GAUGGGUGgaUGAGGUCUU- -5'
27213	3'	-50.1	NC_005832.1	+	79389	1.07	0.007863
	Target:  5'- aCAUCUUUCUACCCACCUACUCCAGAAa -3' miRNA:   3'- -GUAGAAAGAUGGGUGGAUGAGGUCUU- -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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