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
8542	3'	-52.3	NC_002169.1	+	97096	0.66	0.977434
	Target:  5'- cGACGGUguugaCGGCGAUgCGGUCgACGcuGCCg- -3' miRNA:   3'- -CUGUCA-----GCCGCUA-GCUAG-UGU--UGGac -5'
8542	3'	-52.3	NC_002169.1	+	77088	0.67	0.958884
	Target:  5'- aACGGUCGGCGG-CGAUU--GACaCUGg -3' miRNA:   3'- cUGUCAGCCGCUaGCUAGugUUG-GAC- -5'
8542	3'	-52.3	NC_002169.1	+	117576	0.67	0.958884
	Target:  5'- aGGCGG-CGGCGA-CGAcgACGACCUc -3' miRNA:   3'- -CUGUCaGCCGCUaGCUagUGUUGGAc -5'
8542	3'	-52.3	NC_002169.1	+	38734	0.68	0.941873
	Target:  5'- cAUAGUCGGCGAaguuaUCGA-UACAACUUu -3' miRNA:   3'- cUGUCAGCCGCU-----AGCUaGUGUUGGAc -5'
8542	3'	-52.3	NC_002169.1	+	84546	0.68	0.926489
	Target:  5'- aGAgGGuUUGGCGAcaucgUUGGUCGCAACCg- -3' miRNA:   3'- -CUgUC-AGCCGCU-----AGCUAGUGUUGGac -5'
8542	3'	-52.3	NC_002169.1	+	15987	0.73	0.720124
	Target:  5'- cGGCAgcGUCGGCGG-CGGUCACGACg-- -3' miRNA:   3'- -CUGU--CAGCCGCUaGCUAGUGUUGgac -5'
8542	3'	-52.3	NC_002169.1	+	26066	0.77	0.532098
	Target:  5'- uGAuCGG-CGGCGAUgGAUCGCAACUUGu -3' miRNA:   3'- -CU-GUCaGCCGCUAgCUAGUGUUGGAC- -5'
8542	3'	-52.3	NC_002169.1	+	15904	1.08	0.006446
	Target:  5'- aGACAGUCGGCGAUCGAUCACAACCUGu -3' miRNA:   3'- -CUGUCAGCCGCUAGCUAGUGUUGGAC- -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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