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
17040	5'	-55.3	NC_004333.2	+	9632	0.66	0.624388
	Target:  5'- -gGCUGCCGgCggCgcgccUGCGCCCg -3' miRNA:   3'- aaUGACGGCgGaaGaacacACGCGGG- -5'
17040	5'	-55.3	NC_004333.2	+	43209	0.67	0.568206
	Target:  5'- -cGCUGCCGCaaggCUcGgccauUGCGCCCu -3' miRNA:   3'- aaUGACGGCGgaa-GAaCac---ACGCGGG- -5'
17040	5'	-55.3	NC_004333.2	+	18873	0.67	0.568206
	Target:  5'- -cAUUGCCGCCg----Gg--GCGCCCa -3' miRNA:   3'- aaUGACGGCGGaagaaCacaCGCGGG- -5'
17040	5'	-55.3	NC_004333.2	+	35416	0.67	0.557098
	Target:  5'- aUugUGCCGCCUgugaUgUUGgcGUGCGCa- -3' miRNA:   3'- aAugACGGCGGA----AgAACa-CACGCGgg -5'
17040	5'	-55.3	NC_004333.2	+	27993	1.1	0.000528
	Target:  5'- aUUACUGCCGCCUUCUUGUGUGCGCCCg -3' miRNA:   3'- -AAUGACGGCGGAAGAACACACGCGGG- -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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