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
12733	5'	-53.9	NC_003356.1	+	34578	0.66	0.724652
	Target:  5'- cCGGCACUUgaCAGUGUgA-CUGcCAGCa -3' miRNA:   3'- -GCCGUGAA--GUUACGgUgGACaGUCGc -5'
12733	5'	-53.9	NC_003356.1	+	7556	0.67	0.61181
	Target:  5'- gCGGCAUUUCuuguUGCauuuCCUGUUGGUGc -3' miRNA:   3'- -GCCGUGAAGuu--ACGgu--GGACAGUCGC- -5'
12733	5'	-53.9	NC_003356.1	+	26501	0.69	0.544252
	Target:  5'- uGGCAuaaccgccauCUUCAucauUGcCCACCUG-CAGCGc -3' miRNA:   3'- gCCGU----------GAAGUu---AC-GGUGGACaGUCGC- -5'
12733	5'	-53.9	NC_003356.1	+	12219	0.69	0.522229
	Target:  5'- uGGauaUUCug-GCCACaCUGUCGGCGg -3' miRNA:   3'- gCCgugAAGuuaCGGUG-GACAGUCGC- -5'
12733	5'	-53.9	NC_003356.1	+	26387	0.69	0.489874
	Target:  5'- uGGCaACUUUAuuuugcGUGCCGCCUGcCGGaCGc -3' miRNA:   3'- gCCG-UGAAGU------UACGGUGGACaGUC-GC- -5'
12733	5'	-53.9	NC_003356.1	+	31398	0.7	0.479296
	Target:  5'- gCGGgauaUAUUUCAGUGCCACCUGgcugucCAGUu -3' miRNA:   3'- -GCC----GUGAAGUUACGGUGGACa-----GUCGc -5'
12733	5'	-53.9	NC_003356.1	+	30943	1.1	0.000838
	Target:  5'- uCGGCACUUCAAUGCCACCUGUCAGCGa -3' miRNA:   3'- -GCCGUGAAGUUACGGUGGACAGUCGC- -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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