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
9567	3'	-54.6	NC_002554.1	+	5687	0.66	0.241317
	Target:  5'- cAGaaGGCGCGCGAUgaCGugAACUCu -3' miRNA:   3'- aUUgcCCGUGUGCUGgaGCugUUGGG- -5'
9567	3'	-54.6	NC_002554.1	+	1348	0.66	0.213707
	Target:  5'- gGGCGGGCGguCcacCCUCGcGCAACuCCa -3' miRNA:   3'- aUUGCCCGUguGcu-GGAGC-UGUUG-GG- -5'
9567	3'	-54.6	NC_002554.1	+	2748	0.67	0.177406
	Target:  5'- cUGACGGGCAaaggcUACuGGCCaaguUCGACGugUCg -3' miRNA:   3'- -AUUGCCCGU-----GUG-CUGG----AGCUGUugGG- -5'
9567	3'	-54.6	NC_002554.1	+	4322	0.68	0.163448
	Target:  5'- --uCGGGUguggACcggaagaaacucgagGCGACCUUGAcCAACCCg -3' miRNA:   3'- auuGCCCG----UG---------------UGCUGGAGCU-GUUGGG- -5'
9567	3'	-54.6	NC_002554.1	+	3388	0.68	0.161391
	Target:  5'- --gUGGGCGCGCuuCUUCGcGCAGCCa -3' miRNA:   3'- auuGCCCGUGUGcuGGAGC-UGUUGGg -5'
9567	3'	-54.6	NC_002554.1	+	8048	0.68	0.161391
	Target:  5'- ---gGGGCGCGCGACgC-CGugGgagugaaaaGCCCg -3' miRNA:   3'- auugCCCGUGUGCUG-GaGCugU---------UGGG- -5'
9567	3'	-54.6	NC_002554.1	+	1948	1.11	5.1e-05
	Target:  5'- gUAACGGGCACACGACCUCGACAACCCa -3' miRNA:   3'- -AUUGCCCGUGUGCUGGAGCUGUUGGG- -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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