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
20882	5'	-55.3	NC_004689.1	+	796	0.66	0.792988
	Target:  5'- aACCGcuuAUcCGCAGGGUguaGAGCGCCa-- -3' miRNA:   3'- cUGGC---UAaGCGUCCCG---UUUGCGGcag -5'
20882	5'	-55.3	NC_004689.1	+	10490	0.66	0.763414
	Target:  5'- cGGCC-AUgccCGUAGGGCAGcCGCCuUCg -3' miRNA:   3'- -CUGGcUAa--GCGUCCCGUUuGCGGcAG- -5'
20882	5'	-55.3	NC_004689.1	+	16307	0.67	0.721144
	Target:  5'- uGuuGucUCGUAGGGCAGaagcgguGCGCCGUg -3' miRNA:   3'- cUggCuaAGCGUCCCGUU-------UGCGGCAg -5'
20882	5'	-55.3	NC_004689.1	+	42383	0.67	0.690327
	Target:  5'- uACUGc--UGCGGGGCAAcgagucuCGCCGUCu -3' miRNA:   3'- cUGGCuaaGCGUCCCGUUu------GCGGCAG- -5'
20882	5'	-55.3	NC_004689.1	+	40606	0.67	0.679581
	Target:  5'- uGCCG--UUGCugucGGUGAACGCCGUCa -3' miRNA:   3'- cUGGCuaAGCGuc--CCGUUUGCGGCAG- -5'
20882	5'	-55.3	NC_004689.1	+	41918	0.68	0.625395
	Target:  5'- cGACCGGcacggccaccUUCGCAGcGGCuu-CGUCGUg -3' miRNA:   3'- -CUGGCU----------AAGCGUC-CCGuuuGCGGCAg -5'
20882	5'	-55.3	NC_004689.1	+	56075	0.69	0.57134
	Target:  5'- aGCCGAcccacgUGCAGGGCcAACGUCGa- -3' miRNA:   3'- cUGGCUaa----GCGUCCCGuUUGCGGCag -5'
20882	5'	-55.3	NC_004689.1	+	9504	0.73	0.357471
	Target:  5'- -uCUGGUcaUCGUGGGGCAAugGCCGg- -3' miRNA:   3'- cuGGCUA--AGCGUCCCGUUugCGGCag -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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