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
8567	5'	-60.2	NC_002169.1	+	59685	0.66	0.678776
	Target:  5'- ---aGUCucuaCCGGCGAGCguccgagucGCCGUCGAa- -3' miRNA:   3'- aaugCAG----GGCCGCUCG---------CGGCAGCUca -5'
8567	5'	-60.2	NC_002169.1	+	25911	0.67	0.608612
	Target:  5'- aUugGgaCCGGCGAGCGCCG-CGu-- -3' miRNA:   3'- aAugCagGGCCGCUCGCGGCaGCuca -5'
8567	5'	-60.2	NC_002169.1	+	24362	0.68	0.597597
	Target:  5'- -gGCGUCauggguguacacgUUGGCGAucGCGCCGUCGAu- -3' miRNA:   3'- aaUGCAG-------------GGCCGCU--CGCGGCAGCUca -5'
8567	5'	-60.2	NC_002169.1	+	25845	0.68	0.578646
	Target:  5'- -gACG-CCCGGCGGuUGCCGUCGc-- -3' miRNA:   3'- aaUGCaGGGCCGCUcGCGGCAGCuca -5'
8567	5'	-60.2	NC_002169.1	+	26206	0.68	0.555887
	Target:  5'- -gACGUCgCCGGCGAaggcuuuuacaauuGCGCCGacguaGAGUu -3' miRNA:   3'- aaUGCAG-GGCCGCU--------------CGCGGCag---CUCA- -5'
8567	5'	-60.2	NC_002169.1	+	2975	0.7	0.471819
	Target:  5'- --uCGUCCCgcuaauuuuucgGGCGAGUaauagucgagcguGCCGUCGAGa -3' miRNA:   3'- aauGCAGGG------------CCGCUCG-------------CGGCAGCUCa -5'
8567	5'	-60.2	NC_002169.1	+	100561	1.04	0.002307
	Target:  5'- uUUACGUCCCGGCGAGCGCCGUCGAGUu -3' miRNA:   3'- -AAUGCAGGGCCGCUCGCGGCAGCUCA- -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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