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
12166	3'	-52.4	NC_003309.1	+	27482	0.66	0.826683
	Target:  5'- -aGUCGAGCGCGGCGaagaggCGUUCUaucGCa -3' miRNA:   3'- ucUAGCUCGCGUCGUa-----GUAGGAga-UG- -5'
12166	3'	-52.4	NC_003309.1	+	2185	0.66	0.817162
	Target:  5'- uGAUCGGGCGCAccaCGUCGUCa-UUGCc -3' miRNA:   3'- uCUAGCUCGCGUc--GUAGUAGgaGAUG- -5'
12166	3'	-52.4	NC_003309.1	+	5474	0.66	0.807433
	Target:  5'- cGAUCGcaccAGCGCGGC--CAUCUUCUuCg -3' miRNA:   3'- uCUAGC----UCGCGUCGuaGUAGGAGAuG- -5'
12166	3'	-52.4	NC_003309.1	+	11130	0.67	0.756071
	Target:  5'- uGAUCGAGCGguGCcugcaugucgAUCAagCUCgACg -3' miRNA:   3'- uCUAGCUCGCguCG----------UAGUagGAGaUG- -5'
12166	3'	-52.4	NC_003309.1	+	9691	0.71	0.554123
	Target:  5'- cGcgCGAuGCGCAGCA-CGUCgUUCUGCg -3' miRNA:   3'- uCuaGCU-CGCGUCGUaGUAG-GAGAUG- -5'
12166	3'	-52.4	NC_003309.1	+	15709	0.72	0.471777
	Target:  5'- cGAUCGAGCGCGGgaucgcucacgggguUGUCGUCCUUg-- -3' miRNA:   3'- uCUAGCUCGCGUC---------------GUAGUAGGAGaug -5'
12166	3'	-52.4	NC_003309.1	+	39500	1.11	0.001205
	Target:  5'- aAGAUCGAGCGCAGCAUCAUCCUCUACg -3' miRNA:   3'- -UCUAGCUCGCGUCGUAGUAGGAGAUG- -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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