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
1182	3'	-51.4	NC_001132.2	+	13804	0.66	0.993134
	Target:  5'- --aCGGAAUACuaaaaugGUACCGAGGGa-- -3' miRNA:   3'- gcaGCCUUAUGca-----CAUGGCUCCUgua -5'
1182	3'	-51.4	NC_001132.2	+	150535	0.66	0.993134
	Target:  5'- gCGUCGGAGUccuccacgACGgau-UCGGGGACGUc -3' miRNA:   3'- -GCAGCCUUA--------UGCacauGGCUCCUGUA- -5'
1182	3'	-51.4	NC_001132.2	+	8662	0.66	0.992105
	Target:  5'- aGUCuGGAAccgACGUGUGCCGuGGcuCGg -3' miRNA:   3'- gCAG-CCUUa--UGCACAUGGCuCCu-GUa -5'
1182	3'	-51.4	NC_001132.2	+	9481	0.66	0.990957
	Target:  5'- --cCGG-AUACGaccgaugGUACCGAGGACc- -3' miRNA:   3'- gcaGCCuUAUGCa------CAUGGCUCCUGua -5'
1182	3'	-51.4	NC_001132.2	+	2054	0.68	0.967986
	Target:  5'- gCGUCGaGGgagacgccGUGCGUacuaUACCGAGGACGa -3' miRNA:   3'- -GCAGC-CU--------UAUGCAc---AUGGCUCCUGUa -5'
1182	3'	-51.4	NC_001132.2	+	161382	0.69	0.953648
	Target:  5'- aCGUaGGAAUAgGUGUACCGucguacccucuGGACGa -3' miRNA:   3'- -GCAgCCUUAUgCACAUGGCu----------CCUGUa -5'
1182	3'	-51.4	NC_001132.2	+	159600	1.06	0.014523
	Target:  5'- gCGUCGGAAUACGUGUACCGAGGACAUu -3' miRNA:   3'- -GCAGCCUUAUGCACAUGGCUCCUGUA- -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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