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
16277	3'	-50.8	NC_004084.1	+	37409	0.66	0.932319
	Target:  5'- ---cUGGC-CGAUGAugGACGcuugGAUCu -3' miRNA:   3'- agacACCGcGCUACUugCUGUa---CUAG- -5'
16277	3'	-50.8	NC_004084.1	+	34884	0.66	0.920493
	Target:  5'- cCUGUGGCGgGA-GAucuuCGAUcccUGGUCg -3' miRNA:   3'- aGACACCGCgCUaCUu---GCUGu--ACUAG- -5'
16277	3'	-50.8	NC_004084.1	+	29821	0.66	0.907496
	Target:  5'- ----cGGCGCGAgGAACGGgAaGAUCu -3' miRNA:   3'- agacaCCGCGCUaCUUGCUgUaCUAG- -5'
16277	3'	-50.8	NC_004084.1	+	54292	0.67	0.893343
	Target:  5'- uUCUGcUGGC-CGAaGAcgACGuCGUGAUCg -3' miRNA:   3'- -AGAC-ACCGcGCUaCU--UGCuGUACUAG- -5'
16277	3'	-50.8	NC_004084.1	+	51208	0.67	0.885844
	Target:  5'- ---cUGGCGCGGgcuacUGGGCGugGUGcGUCg -3' miRNA:   3'- agacACCGCGCU-----ACUUGCugUAC-UAG- -5'
16277	3'	-50.8	NC_004084.1	+	12925	0.67	0.870024
	Target:  5'- aCUG-GGCGaCGAUGA-CGACGUcuUCg -3' miRNA:   3'- aGACaCCGC-GCUACUuGCUGUAcuAG- -5'
16277	3'	-50.8	NC_004084.1	+	49652	0.85	0.130258
	Target:  5'- gCUGUGG-GCGGUGGuCGACAUGAUCu -3' miRNA:   3'- aGACACCgCGCUACUuGCUGUACUAG- -5'
16277	3'	-50.8	NC_004084.1	+	45078	1.12	0.001919
	Target:  5'- aUCUGUGGCGCGAUGAACGACAUGAUCg -3' miRNA:   3'- -AGACACCGCGCUACUUGCUGUACUAG- -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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