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
8922	5'	-55.2	NC_002484.1	+	4365	0.66	0.719287
	Target:  5'- uGAGUucauuGCGcugGCUUCGCGGCAUuccgcugCGAGCc -3' miRNA:   3'- gCUCGu----CGC---UGAGGUGUCGUA-------GCUCG- -5'
8922	5'	-55.2	NC_002484.1	+	6955	0.66	0.741486
	Target:  5'- -uGGCAGUGGuCUCCGCcugcguAGCGUcCGcAGCg -3' miRNA:   3'- gcUCGUCGCU-GAGGUG------UCGUA-GC-UCG- -5'
8922	5'	-55.2	NC_002484.1	+	48807	0.67	0.644224
	Target:  5'- gCGGGCaauggAGCGGaUUCGCGGCAUCGucaugaccGGCa -3' miRNA:   3'- -GCUCG-----UCGCUgAGGUGUCGUAGC--------UCG- -5'
8922	5'	-55.2	NC_002484.1	+	23853	0.69	0.513033
	Target:  5'- aGAGUAGCGAaucugcuugaUCUuCAGCAugacaguUCGAGCa -3' miRNA:   3'- gCUCGUCGCUg---------AGGuGUCGU-------AGCUCG- -5'
8922	5'	-55.2	NC_002484.1	+	33367	0.69	0.556683
	Target:  5'- uCGGGCAaGCG-CUCgGCGaguGCAUCGaAGCu -3' miRNA:   3'- -GCUCGU-CGCuGAGgUGU---CGUAGC-UCG- -5'
8922	5'	-55.2	NC_002484.1	+	18356	0.7	0.462828
	Target:  5'- aGAGCgcuGGCGAgUUCAgCAGUgaccaGUCGAGCg -3' miRNA:   3'- gCUCG---UCGCUgAGGU-GUCG-----UAGCUCG- -5'
8922	5'	-55.2	NC_002484.1	+	16350	0.71	0.433392
	Target:  5'- aCGGcCAGCGACUUCGCGgaucGCAUcgcCGAGCu -3' miRNA:   3'- -GCUcGUCGCUGAGGUGU----CGUA---GCUCG- -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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