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
22419	3'	-53.6	NC_005056.1	+	26305	0.66	0.61516
	Target:  5'- --cCGGUAaACGCCUUaccgGUGCCuGCgGCAa -3' miRNA:   3'- uuaGUCAU-UGCGGAG----UACGGuCG-CGU- -5'
22419	3'	-53.6	NC_005056.1	+	3864	0.66	0.60806
	Target:  5'- -cUCAGUGGCGCUcaguuuuuccugcaCAUGCuCAGCGaCAg -3' miRNA:   3'- uuAGUCAUUGCGGa-------------GUACG-GUCGC-GU- -5'
22419	3'	-53.6	NC_005056.1	+	17814	0.66	0.579768
	Target:  5'- cGGUCAGcauUggUGCCgUCAUGCgCGGCaGCAc -3' miRNA:   3'- -UUAGUC---AuuGCGG-AGUACG-GUCG-CGU- -5'
22419	3'	-53.6	NC_005056.1	+	18748	0.67	0.54252
	Target:  5'- -cUCGGUGAcaauacugcCGCCUCGgcggaugaugcaGCCGGUGCAc -3' miRNA:   3'- uuAGUCAUU---------GCGGAGUa-----------CGGUCGCGU- -5'
22419	3'	-53.6	NC_005056.1	+	28436	0.69	0.404139
	Target:  5'- --aCGGUcGCGCCaCGcGCCAGCGCc -3' miRNA:   3'- uuaGUCAuUGCGGaGUaCGGUCGCGu -5'
22419	3'	-53.6	NC_005056.1	+	24446	0.7	0.375028
	Target:  5'- uGGUCGGUuauaaAACGCCUCucguaCAGCGCGa -3' miRNA:   3'- -UUAGUCA-----UUGCGGAGuacg-GUCGCGU- -5'
22419	3'	-53.6	NC_005056.1	+	26942	1.06	0.00085
	Target:  5'- cAAUCAGUAACGCCUCAUGCCAGCGCAu -3' miRNA:   3'- -UUAGUCAUUGCGGAGUACGGUCGCGU- -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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