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
31416	5'	-48.3	NC_006635.1	+	1173	0.66	0.863601
	Target:  5'- gGCugGUCCUUUggaggugcagUGGUagugGUAGAGCu -3' miRNA:   3'- aUGugCGGGAAA----------ACCGaaa-CGUUUCG- -5'
31416	5'	-48.3	NC_006635.1	+	24785	0.7	0.663329
	Target:  5'- uUAUACGCCCUUUUGGCa--------- -3' miRNA:   3'- -AUGUGCGGGAAAACCGaaacguuucg -5'
31416	5'	-48.3	NC_006635.1	+	26722	0.71	0.613974
	Target:  5'- -cUACGgCCUUUUGGCUUUGgAAAu- -3' miRNA:   3'- auGUGCgGGAAAACCGAAACgUUUcg -5'
31416	5'	-48.3	NC_006635.1	+	26650	0.76	0.328097
	Target:  5'- uUAUACGCCCUUUUGGCUUUa------ -3' miRNA:   3'- -AUGUGCGGGAAAACCGAAAcguuucg -5'
31416	5'	-48.3	NC_006635.1	+	24745	0.77	0.29367
	Target:  5'- aAUACGCCCUUUUGGCauuagGCAc-GCg -3' miRNA:   3'- aUGUGCGGGAAAACCGaaa--CGUuuCG- -5'
31416	5'	-48.3	NC_006635.1	+	26852	0.78	0.254685
	Target:  5'- uUAUACGCCCUUUUGGCauuagGCAc-GCg -3' miRNA:   3'- -AUGUGCGGGAAAACCGaaa--CGUuuCG- -5'
31416	5'	-48.3	NC_006635.1	+	26806	0.99	0.009216
	Target:  5'- uUAUACGCCCUcUUGGCUUUGCAAAGCc -3' miRNA:   3'- -AUGUGCGGGAaAACCGAAACGUUUCG- -5'
31416	5'	-48.3	NC_006635.1	+	26876	1.1	0.00151
	Target:  5'- uUACACGCCCUUUUGGCUUUGCAAAGCc -3' miRNA:   3'- -AUGUGCGGGAAAACCGAAACGUUUCG- -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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