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
27486	3'	-56.1	NC_005872.1	+	3240	0.67	0.37836
	Target:  5'- -gUUGGGAGuGAaccGCCUcacgaguugccGGGCAC-GCCc -3' miRNA:   3'- agAACCCUCuCU---CGGA-----------UCCGUGuCGG- -5'
27486	3'	-56.1	NC_005872.1	+	23931	0.67	0.37836
	Target:  5'- ---gGGGGGAGAGUUgaaacaaaaaAGGCGC-GCCg -3' miRNA:   3'- agaaCCCUCUCUCGGa---------UCCGUGuCGG- -5'
27486	3'	-56.1	NC_005872.1	+	21101	0.68	0.360045
	Target:  5'- ---aGGGGGAGAGUUgaaacaaaaaAGGCGC-GCCg -3' miRNA:   3'- agaaCCCUCUCUCGGa---------UCCGUGuCGG- -5'
27486	3'	-56.1	NC_005872.1	+	24707	0.68	0.342358
	Target:  5'- --gUGGGGGAGGGUgucauaacuaUUAGGC-CGGUCg -3' miRNA:   3'- agaACCCUCUCUCG----------GAUCCGuGUCGG- -5'
27486	3'	-56.1	NC_005872.1	+	13694	0.68	0.325306
	Target:  5'- --aUGGcu-AGAGCCacguacggAGGCACAGCCg -3' miRNA:   3'- agaACCcucUCUCGGa-------UCCGUGUCGG- -5'
27486	3'	-56.1	NC_005872.1	+	20576	0.69	0.293121
	Target:  5'- cCUaGGGcgcaugguGAGGGCUaAGGCugAGCCu -3' miRNA:   3'- aGAaCCCu-------CUCUCGGaUCCGugUCGG- -5'
27486	3'	-56.1	NC_005872.1	+	8148	1.12	0.00018
	Target:  5'- cUCUUGGGAGAGAGCCUAGGCACAGCCu -3' miRNA:   3'- -AGAACCCUCUCUCGGAUCCGUGUCGG- -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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