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
16288	3'	-48.5	NC_004084.1	+	25280	0.66	0.980603
	Target:  5'- uCUGGUaggUCc-GGUUGGccuggcgccggcAGUAGCCGCa -3' miRNA:   3'- -GACCAa--AGcuCCAACUu-----------UCAUCGGCG- -5'
16288	3'	-48.5	NC_004084.1	+	29620	0.67	0.965342
	Target:  5'- -cGGUUUcccgcucgccugcgCGGGGUUGAAcGUGacGCUGCu -3' miRNA:   3'- gaCCAAA--------------GCUCCAACUUuCAU--CGGCG- -5'
16288	3'	-48.5	NC_004084.1	+	25462	0.7	0.861579
	Target:  5'- gUGGcUUCGAGGUUcgcgggcggcgucaGAAGGUGcgcGCCGUc -3' miRNA:   3'- gACCaAAGCUCCAA--------------CUUUCAU---CGGCG- -5'
16288	3'	-48.5	NC_004084.1	+	36127	0.72	0.787757
	Target:  5'- gCUGGUauggugugcaacgUUCGAGcGUUGcuGAGUGacGCCGCa -3' miRNA:   3'- -GACCA-------------AAGCUC-CAACu-UUCAU--CGGCG- -5'
16288	3'	-48.5	NC_004084.1	+	5015	0.72	0.757278
	Target:  5'- -aGGUccUCGAGGa-GuuGGUAGCCGCc -3' miRNA:   3'- gaCCAa-AGCUCCaaCuuUCAUCGGCG- -5'
16288	3'	-48.5	NC_004084.1	+	8209	0.76	0.587848
	Target:  5'- aUGGcgUCGAGGUUGAAccAGUAG-UGCg -3' miRNA:   3'- gACCaaAGCUCCAACUU--UCAUCgGCG- -5'
16288	3'	-48.5	NC_004084.1	+	39494	1.14	0.002499
	Target:  5'- cCUGGUUUCGAGGUUGAAAGUAGCCGCg -3' miRNA:   3'- -GACCAAAGCUCCAACUUUCAUCGGCG- -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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