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
21146	3'	-54.9	NC_004775.1	+	39304	0.66	0.610414
	Target:  5'- aGCUUG-AGCUgguacuggAUGGGCaggaacuggaaaugCUGGCGCg -3' miRNA:   3'- -CGGACuUCGAaag-----UACCCG--------------GACCGCG- -5'
21146	3'	-54.9	NC_004775.1	+	18016	0.66	0.602453
	Target:  5'- aGCC--AAGCg--CcUGGGCgUUGGCGCg -3' miRNA:   3'- -CGGacUUCGaaaGuACCCG-GACCGCG- -5'
21146	3'	-54.9	NC_004775.1	+	4616	0.67	0.557316
	Target:  5'- aGCCUGucGCagacaguuggaUUUAUcGGGCaaCUGGCGCa -3' miRNA:   3'- -CGGACuuCGa----------AAGUA-CCCG--GACCGCG- -5'
21146	3'	-54.9	NC_004775.1	+	7401	0.67	0.535097
	Target:  5'- aGCCUGGcgauauuguggAGUUUUCcgGGGaggCUGGCa- -3' miRNA:   3'- -CGGACU-----------UCGAAAGuaCCCg--GACCGcg -5'
21146	3'	-54.9	NC_004775.1	+	33802	0.68	0.513197
	Target:  5'- aGCgUGAGGCUcUCGauuUGGGCCUuacuCGCu -3' miRNA:   3'- -CGgACUUCGAaAGU---ACCCGGAcc--GCG- -5'
21146	3'	-54.9	NC_004775.1	+	830	0.68	0.502385
	Target:  5'- aGCCUGccaCUUUC-UGGGCCcGGUGg -3' miRNA:   3'- -CGGACuucGAAAGuACCCGGaCCGCg -5'
21146	3'	-54.9	NC_004775.1	+	6354	1.13	0.000321
	Target:  5'- aGCCUGAAGCUUUCAUGGGCCUGGCGCc -3' miRNA:   3'- -CGGACUUCGAAAGUACCCGGACCGCG- -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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