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
31644	3'	-61.2	NC_006879.1	+	15158	0.66	0.33435
	Target:  5'- aCGUuccCUCUCCUGGGUCUggccaugcuaGCGAuGGCGg -3' miRNA:   3'- gGCGc--GAGAGGGUCCGGA----------UGCU-CCGC- -5'
31644	3'	-61.2	NC_006879.1	+	17427	0.66	0.310955
	Target:  5'- gCgGCGUUucaggcuuuucaCUCCCAGGCCcACGAuGCu -3' miRNA:   3'- -GgCGCGA------------GAGGGUCCGGaUGCUcCGc -5'
31644	3'	-61.2	NC_006879.1	+	17760	0.66	0.288826
	Target:  5'- aCGCGgUgucCUCCC-GGUCUACG-GGCa -3' miRNA:   3'- gGCGCgA---GAGGGuCCGGAUGCuCCGc -5'
31644	3'	-61.2	NC_006879.1	+	11201	0.67	0.260611
	Target:  5'- uCUGCaGUggcgUCCCAGcgcgcgcGCCUugGAGGCGg -3' miRNA:   3'- -GGCG-CGag--AGGGUC-------CGGAugCUCCGC- -5'
31644	3'	-61.2	NC_006879.1	+	9335	0.67	0.248316
	Target:  5'- -gGCGCUCggccaugcCCCAGGCCUcgcucugacaGCGAcGCa -3' miRNA:   3'- ggCGCGAGa-------GGGUCCGGA----------UGCUcCGc -5'
31644	3'	-61.2	NC_006879.1	+	4287	0.71	0.134644
	Target:  5'- uCUGCa-UCUCCCAGGCCUuaauuucCGAGGgGg -3' miRNA:   3'- -GGCGcgAGAGGGUCCGGAu------GCUCCgC- -5'
31644	3'	-61.2	NC_006879.1	+	22635	1.1	0.000131
	Target:  5'- gCCGCGCUCUCCCAGGCCUACGAGGCGa -3' miRNA:   3'- -GGCGCGAGAGGGUCCGGAUGCUCCGC- -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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