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
3502	5'	-53.3	NC_001623.1	+	120774	0.66	0.93231
	Target:  5'- -cGCGCAgCCCGCgUgCUACCACc--- -3' miRNA:   3'- auUGCGU-GGGCGgAaGAUGGUGaaga -5'
3502	5'	-53.3	NC_001623.1	+	61517	0.67	0.915317
	Target:  5'- cGGCGcCGCCCGCCga--ACCGCUaacUCa -3' miRNA:   3'- aUUGC-GUGGGCGGaagaUGGUGA---AGa -5'
3502	5'	-53.3	NC_001623.1	+	31034	0.67	0.915317
	Target:  5'- gAACGCGCCCGCCgccgacaUGaacgaCACUUUUu -3' miRNA:   3'- aUUGCGUGGGCGGaag----AUg----GUGAAGA- -5'
3502	5'	-53.3	NC_001623.1	+	113217	0.68	0.896014
	Target:  5'- -uGCGCAUCCGUUUUg-ACCAUUUCg -3' miRNA:   3'- auUGCGUGGGCGGAAgaUGGUGAAGa -5'
3502	5'	-53.3	NC_001623.1	+	58574	0.68	0.881895
	Target:  5'- ---aGCACuuGCCUUCUuCCAUgUCUu -3' miRNA:   3'- auugCGUGggCGGAAGAuGGUGaAGA- -5'
3502	5'	-53.3	NC_001623.1	+	16439	0.69	0.842503
	Target:  5'- -cACGCugCUgcuauuucuGCCUUCggagACCACUUCc -3' miRNA:   3'- auUGCGugGG---------CGGAAGa---UGGUGAAGa -5'
3502	5'	-53.3	NC_001623.1	+	107271	0.72	0.708442
	Target:  5'- gUGugGCGCCUGCUgggcgUUUGCCACU-CUg -3' miRNA:   3'- -AUugCGUGGGCGGa----AGAUGGUGAaGA- -5'
3502	5'	-53.3	NC_001623.1	+	16565	1.07	0.005325
	Target:  5'- gUAACGCACCCGCCUUCUACCACUUCUa -3' miRNA:   3'- -AUUGCGUGGGCGGAAGAUGGUGAAGA- -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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