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
12282	3'	-49.7	NC_003313.1	+	20101	0.67	0.815342
	Target:  5'- cUCAgaccuUGAUGacguguUAGCCGaaGCCAGCGCCg -3' miRNA:   3'- aAGU-----ACUAC------AUUGGUa-CGGUUGCGGg -5'
12282	3'	-49.7	NC_003313.1	+	914	0.67	0.794471
	Target:  5'- cUUUAUGAUG-AACCGUGgCGACaUCCu -3' miRNA:   3'- -AAGUACUACaUUGGUACgGUUGcGGG- -5'
12282	3'	-49.7	NC_003313.1	+	6479	0.67	0.772789
	Target:  5'- --gGUGGagaGUAGCCAUGCaguACGCCg -3' miRNA:   3'- aagUACUa--CAUUGGUACGgu-UGCGGg -5'
12282	3'	-49.7	NC_003313.1	+	24049	0.67	0.770581
	Target:  5'- ----aGAUGUGGCaggcaugacgGCCAGCGCCg -3' miRNA:   3'- aaguaCUACAUUGgua-------CGGUUGCGGg -5'
12282	3'	-49.7	NC_003313.1	+	20356	0.7	0.608186
	Target:  5'- -cCGUGAaGUcggcguACUGUGCCAACuGCCCg -3' miRNA:   3'- aaGUACUaCAu-----UGGUACGGUUG-CGGG- -5'
12282	3'	-49.7	NC_003313.1	+	26007	0.7	0.59618
	Target:  5'- -gCGUGAcguUGUAuucCCAUGCUuuuagcucuAGCGCCCa -3' miRNA:   3'- aaGUACU---ACAUu--GGUACGG---------UUGCGGG- -5'
12282	3'	-49.7	NC_003313.1	+	10000	1.11	0.001298
	Target:  5'- aUUCAUGAUGUAACCAUGCCAACGCCCu -3' miRNA:   3'- -AAGUACUACAUUGGUACGGUUGCGGG- -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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