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
4306	5'	-59.8	NC_001716.2	+	10169	0.66	0.675639
	Target:  5'- -aCUGaGuGCUGCGCGCGGCucgCAGa -3' miRNA:   3'- aaGACgCuCGGCGCGCGUCGugaGUC- -5'
4306	5'	-59.8	NC_001716.2	+	153072	0.66	0.675639
	Target:  5'- -aCUGaGuGCUGCGCGCGGCucgCAGa -3' miRNA:   3'- aaGACgCuCGGCGCGCGUCGugaGUC- -5'
4306	5'	-59.8	NC_001716.2	+	5448	0.69	0.528502
	Target:  5'- ---aGCGAGuauaacgcguccagaCCGUGCGUGGCACUCAc -3' miRNA:   3'- aagaCGCUC---------------GGCGCGCGUCGUGAGUc -5'
4306	5'	-59.8	NC_001716.2	+	148351	0.69	0.528502
	Target:  5'- ---aGCGAGuauaacgcguccagaCCGUGCGUGGCACUCAc -3' miRNA:   3'- aagaCGCUC---------------GGCGCGCGUCGUGAGUc -5'
4306	5'	-59.8	NC_001716.2	+	10305	0.7	0.486082
	Target:  5'- cUCUGUGcGCCGCGCuGCAGUuuucuACUCu- -3' miRNA:   3'- aAGACGCuCGGCGCG-CGUCG-----UGAGuc -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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