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
27947	3'	-57.3	NC_005886.2	+	22890	0.66	0.592338
	Target:  5'- gGCGauagCGUGCCGGUGCUcACcGcGcUGCa -3' miRNA:   3'- -CGCa---GCGCGGCCACGAcUGuCaC-ACG- -5'
27947	3'	-57.3	NC_005886.2	+	35320	0.66	0.581493
	Target:  5'- cGUGcUCGCGCCaGUucGCUGACA---UGCa -3' miRNA:   3'- -CGC-AGCGCGGcCA--CGACUGUcacACG- -5'
27947	3'	-57.3	NC_005886.2	+	16208	0.71	0.315615
	Target:  5'- cGgGUuaCGCGCCGGU-CUGACGGUagguUGCg -3' miRNA:   3'- -CgCA--GCGCGGCCAcGACUGUCAc---ACG- -5'
27947	3'	-57.3	NC_005886.2	+	7162	0.71	0.307978
	Target:  5'- uGCGUCgaucgccacgGUGCCGGUGCUcgcgcuCGGUGgcgGCg -3' miRNA:   3'- -CGCAG----------CGCGGCCACGAcu----GUCACa--CG- -5'
27947	3'	-57.3	NC_005886.2	+	41569	0.72	0.258468
	Target:  5'- gGCGUCaGCGCCGGacGUUG-CGGccgGUGCg -3' miRNA:   3'- -CGCAG-CGCGGCCa-CGACuGUCa--CACG- -5'
27947	3'	-57.3	NC_005886.2	+	1727	0.72	0.24557
	Target:  5'- cCGUUGCgGCgGGUGC-GGCAGUG-GCa -3' miRNA:   3'- cGCAGCG-CGgCCACGaCUGUCACaCG- -5'
27947	3'	-57.3	NC_005886.2	+	41347	1.14	0.000255
	Target:  5'- gGCGUCGCGCCGGUGCUGACAGUGUGCg -3' miRNA:   3'- -CGCAGCGCGGCCACGACUGUCACACG- -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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