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
23082	5'	-56.8	NC_005178.1	+	28489	0.66	0.488807
	Target:  5'- uUCUGGAggccggugaCCGCGAGCGCgGCGCg--- -3' miRNA:   3'- cAGACCUg--------GGCGUUCGUG-UGCGacuu -5'
23082	5'	-56.8	NC_005178.1	+	36701	0.66	0.478199
	Target:  5'- ---cGGuuCUGUggGUGCGCGCUGAAa -3' miRNA:   3'- cagaCCugGGCGuuCGUGUGCGACUU- -5'
23082	5'	-56.8	NC_005178.1	+	20752	0.66	0.447083
	Target:  5'- -cCUGGGCCgGCAGGCugGCcagcacCUGGu -3' miRNA:   3'- caGACCUGGgCGUUCGugUGc-----GACUu -5'
23082	5'	-56.8	NC_005178.1	+	16430	0.67	0.417126
	Target:  5'- -aCUGGcugcggauGCCCGCcAGCucgccgcCACGCUGAGu -3' miRNA:   3'- caGACC--------UGGGCGuUCGu------GUGCGACUU- -5'
23082	5'	-56.8	NC_005178.1	+	17889	0.67	0.407416
	Target:  5'- -cCUGGACCCGguAcGCcaGCGCGcCUGGc -3' miRNA:   3'- caGACCUGGGCguU-CG--UGUGC-GACUu -5'
23082	5'	-56.8	NC_005178.1	+	30981	0.68	0.357507
	Target:  5'- aGUCUGGAa-CGCuuauuucaguccGCGCACGCUGAc -3' miRNA:   3'- -CAGACCUggGCGuu----------CGUGUGCGACUu -5'
23082	5'	-56.8	NC_005178.1	+	4843	1.06	0.00051
	Target:  5'- cGUCUGGACCCGCAAGCACACGCUGAAg -3' miRNA:   3'- -CAGACCUGGGCGUUCGUGUGCGACUU- -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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