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
15409	5'	-50.5	NC_003907.2	+	45511	0.66	0.914415
	Target:  5'- uCCGCAGcccagagcugGCGGGGGUUCcgaguaGUgUAUGAa -3' miRNA:   3'- -GGCGUCua--------CGUCCUCAAG------UAgAUGCU- -5'
15409	5'	-50.5	NC_003907.2	+	2584	0.66	0.900672
	Target:  5'- cCUGCuAGGUGCAGGuGcacaCAUCgACGAc -3' miRNA:   3'- -GGCG-UCUACGUCCuCaa--GUAGaUGCU- -5'
15409	5'	-50.5	NC_003907.2	+	2246	0.67	0.877872
	Target:  5'- gCCGUuguGAUagGCAGuGAGUUUGUCUAUGu -3' miRNA:   3'- -GGCGu--CUA--CGUC-CUCAAGUAGAUGCu -5'
15409	5'	-50.5	NC_003907.2	+	8469	0.67	0.84274
	Target:  5'- gCGUGGA-GCAGGGGcgagguugcgugcUUgGUCUACGAu -3' miRNA:   3'- gGCGUCUaCGUCCUC-------------AAgUAGAUGCU- -5'
15409	5'	-50.5	NC_003907.2	+	43133	0.73	0.527552
	Target:  5'- -aGCAGAUGCAGGuaaUUUGUCUGCa- -3' miRNA:   3'- ggCGUCUACGUCCuc-AAGUAGAUGcu -5'
15409	5'	-50.5	NC_003907.2	+	29784	0.75	0.432218
	Target:  5'- aCCaGCAGGUGCAGGcGacagCAUCUAUGGa -3' miRNA:   3'- -GG-CGUCUACGUCCuCaa--GUAGAUGCU- -5'
15409	5'	-50.5	NC_003907.2	+	9710	1.12	0.00159
	Target:  5'- aCCGCAGAUGCAGGAGUUCAUCUACGAu -3' miRNA:   3'- -GGCGUCUACGUCCUCAAGUAGAUGCU- -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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