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
18230	3'	-52.5	NC_004680.1	+	51415	0.66	0.873056
	Target:  5'- cCCACcaAGGGCcguggGGGUguGGUGUCCGGg -3' miRNA:   3'- -GGUG--UCUCGua---CCUAguCUGCAGGUC- -5'
18230	3'	-52.5	NC_004680.1	+	13915	0.67	0.830412
	Target:  5'- -uGCAGGGCAacUGGAUCAaACuGUCgAGg -3' miRNA:   3'- ggUGUCUCGU--ACCUAGUcUG-CAGgUC- -5'
18230	3'	-52.5	NC_004680.1	+	23113	0.67	0.8118
	Target:  5'- gCCACGGGugGUGGAUaugcgcgggagCAGACGUCguGg -3' miRNA:   3'- -GGUGUCUcgUACCUA-----------GUCUGCAGguC- -5'
18230	3'	-52.5	NC_004680.1	+	31076	0.69	0.719809
	Target:  5'- uUCACAaGGCGUGGAUUaagccaGGACGUgaaCCAGc -3' miRNA:   3'- -GGUGUcUCGUACCUAG------UCUGCA---GGUC- -5'
18230	3'	-52.5	NC_004680.1	+	10066	0.71	0.608368
	Target:  5'- aCCAgAcGGCAuucggacUGGAUCAGGCGUUCAa -3' miRNA:   3'- -GGUgUcUCGU-------ACCUAGUCUGCAGGUc -5'
18230	3'	-52.5	NC_004680.1	+	12499	0.72	0.576298
	Target:  5'- -aGCGGGGC-UGGGUUAGGCGcCCAc -3' miRNA:   3'- ggUGUCUCGuACCUAGUCUGCaGGUc -5'
18230	3'	-52.5	NC_004680.1	+	50711	1.11	0.001691
	Target:  5'- aCCACAGAGCAUGGAUCAGACGUCCAGc -3' miRNA:   3'- -GGUGUCUCGUACCUAGUCUGCAGGUC- -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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