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
16955	3'	-52.4	NC_004313.1	+	21431	0.66	0.781849
	Target:  5'- -aGGC-GCGAAAGGCUGCGggggaUGaUCuGGg -3' miRNA:   3'- gaCUGcCGCUUUCCGACGU-----ACaAG-CC- -5'
16955	3'	-52.4	NC_004313.1	+	2563	0.7	0.585408
	Target:  5'- aCUGACGGCGGuuuuuuccugcgucaGAGuGCUgGCAgagUCGGu -3' miRNA:   3'- -GACUGCCGCU---------------UUC-CGA-CGUacaAGCC- -5'
16955	3'	-52.4	NC_004313.1	+	10244	0.71	0.503094
	Target:  5'- aUGGCGGCGGAGGGaauUGCAgagaucGUggcggCGGg -3' miRNA:   3'- gACUGCCGCUUUCCg--ACGUa-----CAa----GCC- -5'
16955	3'	-52.4	NC_004313.1	+	9664	0.71	0.481676
	Target:  5'- gUGACGGCGGcguccGGCUGgAcaGUUCGGu -3' miRNA:   3'- gACUGCCGCUuu---CCGACgUa-CAAGCC- -5'
16955	3'	-52.4	NC_004313.1	+	17149	0.72	0.430194
	Target:  5'- aUGGCGGCGuGAaGCUGCGuaUGUUCGc -3' miRNA:   3'- gACUGCCGCuUUcCGACGU--ACAAGCc -5'
16955	3'	-52.4	NC_004313.1	+	33168	0.75	0.312926
	Target:  5'- --uGCGGCGGGAGGUUGCAUGa--GGc -3' miRNA:   3'- gacUGCCGCUUUCCGACGUACaagCC- -5'
16955	3'	-52.4	NC_004313.1	+	34323	1.1	0.001149
	Target:  5'- gCUGACGGCGAAAGGCUGCAUGUUCGGc -3' miRNA:   3'- -GACUGCCGCUUUCCGACGUACAAGCC- -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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