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
18696	5'	-53.7	NC_004682.1	+	17081	0.66	0.769631
	Target:  5'- gCAGGGCgUGGCUCAgg-GCAUGGu--- -3' miRNA:   3'- -GUUCCG-GCCGAGUaagCGUACCuacc -5'
18696	5'	-53.7	NC_004682.1	+	29105	0.66	0.769631
	Target:  5'- gCGGGGUCGGCuUCGagcUUCGCccGGAguucGGc -3' miRNA:   3'- -GUUCCGGCCG-AGU---AAGCGuaCCUa---CC- -5'
18696	5'	-53.7	NC_004682.1	+	48285	0.66	0.769631
	Target:  5'- aCGAGGCCGGCgUCcuggUCGagaCAUGGGa-- -3' miRNA:   3'- -GUUCCGGCCG-AGua--AGC---GUACCUacc -5'
18696	5'	-53.7	NC_004682.1	+	7567	0.66	0.759249
	Target:  5'- cCGAGGCCGGCggg--CGCAUcGA-GGc -3' miRNA:   3'- -GUUCCGGCCGaguaaGCGUAcCUaCC- -5'
18696	5'	-53.7	NC_004682.1	+	37025	0.7	0.560719
	Target:  5'- cCGAGGCCGGUUCAcggUCGac-GGAcgaguuUGGg -3' miRNA:   3'- -GUUCCGGCCGAGUa--AGCguaCCU------ACC- -5'
18696	5'	-53.7	NC_004682.1	+	23396	0.73	0.387325
	Target:  5'- gAAGGCUGGCUCGgcacuggCGCAuucgagguaggUGGcgGGg -3' miRNA:   3'- gUUCCGGCCGAGUaa-----GCGU-----------ACCuaCC- -5'
18696	5'	-53.7	NC_004682.1	+	15984	1.1	0.001171
	Target:  5'- gCAAGGCCGGCUCAUUCGCAUGGAUGGc -3' miRNA:   3'- -GUUCCGGCCGAGUAAGCGUACCUACC- -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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