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
3455	5'	-45.1	NC_001604.1	+	21879	0.66	0.994327
	Target:  5'- aGUGAGUCGUAUUAaaUUCCcg-GCUg- -3' miRNA:   3'- -CACUCAGCAUAAUa-AAGGaugCGAgg -5'
3455	5'	-45.1	NC_001604.1	+	22392	0.66	0.99393
	Target:  5'- -aGAGUUGUccgccgagUCCUACGCUa- -3' miRNA:   3'- caCUCAGCAuaauaa--AGGAUGCGAgg -5'
3455	5'	-45.1	NC_001604.1	+	6437	0.67	0.985692
	Target:  5'- cUGAGUCGUAUUAcUUCCaguC-CUUCa -3' miRNA:   3'- cACUCAGCAUAAUaAAGGau-GcGAGG- -5'
3455	5'	-45.1	NC_001604.1	+	27282	0.68	0.972779
	Target:  5'- aGUGAGUCGUAUUAaUUUCga-GCcaCCa -3' miRNA:   3'- -CACUCAGCAUAAUaAAGGaugCGa-GG- -5'
3455	5'	-45.1	NC_001604.1	+	5878	0.7	0.942937
	Target:  5'- aGUGAGUCGUAUUGaUUUggcgUUACGCgaacgcgaagUCCg -3' miRNA:   3'- -CACUCAGCAUAAUaAAG----GAUGCG----------AGG- -5'
3455	5'	-45.1	NC_001604.1	+	13363	0.7	0.941857
	Target:  5'- aGUGAGUCGUAUUAgaaugggACuCUCCa -3' miRNA:   3'- -CACUCAGCAUAAUaaagga-UGcGAGG- -5'
3455	5'	-45.1	NC_001604.1	+	7806	0.72	0.89725
	Target:  5'- aGUGAGUCGUAUUAccaguuaaCUAUaCUCCa -3' miRNA:   3'- -CACUCAGCAUAAUaaag----GAUGcGAGG- -5'
3455	5'	-45.1	NC_001604.1	+	34567	1.13	0.004574
	Target:  5'- aGUGAGUCGUAUUAUUUCCUACGCUCCc -3' miRNA:   3'- -CACUCAGCAUAAUAAAGGAUGCGAGG- -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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