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
14714	5'	-55	NC_003529.1	+	49579	0.66	0.943276
	Target:  5'- cGUucUGUGGCg-GAUCGCGauUUUGGCa -3' miRNA:   3'- aCAu-GCACCGagCUAGCGC--AAGCCGc -5'
14714	5'	-55	NC_003529.1	+	34230	0.66	0.938651
	Target:  5'- uUGUGCGccgcgGGCgccCGAgaccggucuggCGUGUUUGGCGa -3' miRNA:   3'- -ACAUGCa----CCGa--GCUa----------GCGCAAGCCGC- -5'
14714	5'	-55	NC_003529.1	+	101760	0.66	0.938651
	Target:  5'- uUGU-CGUGGC-CGAcggCGCGUUCGauGUGu -3' miRNA:   3'- -ACAuGCACCGaGCUa--GCGCAAGC--CGC- -5'
14714	5'	-55	NC_003529.1	+	70324	0.67	0.917791
	Target:  5'- aUGUugGUGGCgucgUUGAUgGUGaUCuGGCGa -3' miRNA:   3'- -ACAugCACCG----AGCUAgCGCaAG-CCGC- -5'
14714	5'	-55	NC_003529.1	+	45397	0.68	0.879487
	Target:  5'- uUGUGCGUua-UCGAUcCGUGUUCGGuCGa -3' miRNA:   3'- -ACAUGCAccgAGCUA-GCGCAAGCC-GC- -5'
14714	5'	-55	NC_003529.1	+	147567	0.69	0.852689
	Target:  5'- aGUACGUGGCUCGgcacAugcaucacgaucgauUCGUGUUCGuCGu -3' miRNA:   3'- aCAUGCACCGAGC----U---------------AGCGCAAGCcGC- -5'
14714	5'	-55	NC_003529.1	+	20747	1.09	0.00439
	Target:  5'- gUGUACGUGGCUCGAUCGCGUUCGGCGu -3' miRNA:   3'- -ACAUGCACCGAGCUAGCGCAAGCCGC- -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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