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
670	3'	-52.5	AC_000018.1	+	7747	0.66	0.740442
	Target:  5'- ---aUUAGCuGCuUGCCAAagGACCCCAu -3' miRNA:   3'- cgcaAAUCG-CG-AUGGUUg-CUGGGGUu -5'
670	3'	-52.5	AC_000018.1	+	24908	0.67	0.636938
	Target:  5'- aGUGUUU-GCGCcGCUuuuucacCGACCCCGAg -3' miRNA:   3'- -CGCAAAuCGCGaUGGuu-----GCUGGGGUU- -5'
670	3'	-52.5	AC_000018.1	+	7638	0.68	0.567099
	Target:  5'- -gGUUUGGggguccUGCcGCCAGCGAUCCCAc -3' miRNA:   3'- cgCAAAUC------GCGaUGGUUGCUGGGGUu -5'
670	3'	-52.5	AC_000018.1	+	13624	0.71	0.435448
	Target:  5'- aCGgcUGGUGCUGCCGcgacCGugCCCGAa -3' miRNA:   3'- cGCaaAUCGCGAUGGUu---GCugGGGUU- -5'
670	3'	-52.5	AC_000018.1	+	8340	0.71	0.415211
	Target:  5'- cCGUgccccuugGGCGCUACCAcCGugCCCu- -3' miRNA:   3'- cGCAaa------UCGCGAUGGUuGCugGGGuu -5'
670	3'	-52.5	AC_000018.1	+	4527	0.72	0.367239
	Target:  5'- cCGUgc--CGCUGCCcACGGCCCCAu -3' miRNA:   3'- cGCAaaucGCGAUGGuUGCUGGGGUu -5'
670	3'	-52.5	AC_000018.1	+	5123	0.73	0.331699
	Target:  5'- gGCGUccAGCGCUGCCAGggucCGAUCCUu- -3' miRNA:   3'- -CGCAaaUCGCGAUGGUU----GCUGGGGuu -5'
670	3'	-52.5	AC_000018.1	+	12758	1.09	0.00099
	Target:  5'- aGCGUUUAGCGCUACCAACGACCCCAAg -3' miRNA:   3'- -CGCAAAUCGCGAUGGUUGCUGGGGUU- -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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