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
13266	5'	-54.9	NC_003401.1	+	132690	0.66	0.916611
	Target:  5'- gGCuuguGGGGccccGG-GCCCGgGGGGCGUCGGg -3' miRNA:   3'- -UGu---CCUC----UCaCGGGCgUUCUGUAGCU- -5'
13266	5'	-54.9	NC_003401.1	+	118706	0.66	0.904347
	Target:  5'- -gGGGAaAGUGCUCaCAAGACAUCc- -3' miRNA:   3'- ugUCCUcUCACGGGcGUUCUGUAGcu -5'
13266	5'	-54.9	NC_003401.1	+	69347	0.69	0.764973
	Target:  5'- gGCAGGuGGAaggGUCCGCG-GGCGUCGAu -3' miRNA:   3'- -UGUCC-UCUca-CGGGCGUuCUGUAGCU- -5'
13266	5'	-54.9	NC_003401.1	+	28	0.7	0.705102
	Target:  5'- gACAGGGGAcggcgugugcGUGCuuGUGAGACAcCGGg -3' miRNA:   3'- -UGUCCUCU----------CACGggCGUUCUGUaGCU- -5'
13266	5'	-54.9	NC_003401.1	+	132763	0.7	0.705102
	Target:  5'- gACAGGGGAcggcgugugcGUGCuuGUGAGACAcCGGg -3' miRNA:   3'- -UGUCCUCU----------CACGggCGUUCUGUaGCU- -5'
13266	5'	-54.9	NC_003401.1	+	73012	0.72	0.590742
	Target:  5'- cACAGGAGGcGUGCCCGUuccuguaGUCGAg -3' miRNA:   3'- -UGUCCUCU-CACGGGCGuucug--UAGCU- -5'
13266	5'	-54.9	NC_003401.1	+	118584	1.08	0.003218
	Target:  5'- gACAGGAGAGUGCCCGCAAGACAUCGAc -3' miRNA:   3'- -UGUCCUCUCACGGGCGUUCUGUAGCU- -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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