Viral miRNA display CGI

miRNA display CGI

Results 1 - 19 of 19 are showing below:
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ID	Location	Perfect MFE.*	RefSeq Acc.	strand	Start Position	R_P_ratio#	P value
ID	Predicted miRNA align pattern
16487	5'	-53.3	NC_004084.1	+	12219	0.66	0.840351
16487	Target: 5'- cGACGCaucCGaCGACGAUCUCgCCGc---- -3' miRNA: 3'- -UUGCGa--GC-GCUGCUAGAG-GGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	23002	0.66	0.831352
16487	Target: 5'- gAGCGagaUCGaCGACGAUgaCCCGUcggUCg -3' miRNA: 3'- -UUGCg--AGC-GCUGCUAgaGGGCAua-AG- -5'
16487	5'	-53.3	NC_004084.1	+	3883	0.66	0.793306
16487	Target: 5'- cAGCGC-CG-GACGAUCUCgCCGUc--- -3' miRNA: 3'- -UUGCGaGCgCUGCUAGAG-GGCAuaag -5'
16487	5'	-53.3	NC_004084.1	+	48162	0.66	0.793306
16487	Target: 5'- aGugGCUCGaUGACuGUCUUCCG-GUUCu -3' miRNA: 3'- -UugCGAGC-GCUGcUAGAGGGCaUAAG- -5'
16487	5'	-53.3	NC_004084.1	+	49342	0.67	0.773202
16487	Target: 5'- cGGCGUacCGCGGCGAUCUCCgaacGUUCc -3' miRNA: 3'- -UUGCGa-GCGCUGCUAGAGGgca-UAAG- -5'
16487	5'	-53.3	NC_004084.1	+	39576	0.67	0.762919
16487	Target: 5'- gAGCaGCUCGuCGACGAggUCCCGg---- -3' miRNA: 3'- -UUG-CGAGC-GCUGCUagAGGGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	41755	0.67	0.762919
16487	Target: 5'- cGACGC-CgGCGACGAggacCUCCCGgacgacgUCg -3' miRNA: 3'- -UUGCGaG-CGCUGCUa---GAGGGCaua----AG- -5'
16487	5'	-53.3	NC_004084.1	+	52519	0.67	0.752499
16487	Target: 5'- --aGCUCGUacggcgucagGACGAUC-CCCGUGgcggUCu -3' miRNA: 3'- uugCGAGCG----------CUGCUAGaGGGCAUa---AG- -5'
16487	5'	-53.3	NC_004084.1	+	53588	0.67	0.752499
16487	Target: 5'- -gUGCUCGCGACGAUCggcgagcuuugaUCUCGa---- -3' miRNA: 3'- uuGCGAGCGCUGCUAG------------AGGGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	39520	0.68	0.709675
16487	Target: 5'- -uCGUUCGCGACGuccucgaggAUCUCCuCGUGa-- -3' miRNA: 3'- uuGCGAGCGCUGC---------UAGAGG-GCAUaag -5'
16487	5'	-53.3	NC_004084.1	+	40268	0.68	0.709675
16487	Target: 5'- cACGCUCGCGcUGAUCgaCCCGg---- -3' miRNA: 3'- uUGCGAGCGCuGCUAGa-GGGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	17998	0.68	0.698744
16487	Target: 5'- gAGCGUUCGUGAaGGUCUCUCGg---- -3' miRNA: 3'- -UUGCGAGCGCUgCUAGAGGGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	44142	0.68	0.697646
16487	Target: 5'- -cCGCUCGCGACGAcgaggaccUCcaccuggUCCCGg--UCg -3' miRNA: 3'- uuGCGAGCGCUGCU--------AG-------AGGGCauaAG- -5'
16487	5'	-53.3	NC_004084.1	+	20025	0.69	0.676693
16487	Target: 5'- cGGCGCUCGaggaCGACGAUCgcgUCUCGUcagUCg -3' miRNA: 3'- -UUGCGAGC----GCUGCUAG---AGGGCAua-AG- -5'
16487	5'	-53.3	NC_004084.1	+	22461	0.69	0.636623
16487	Target: 5'- gGGCGCUCGCGACGGcugcgugguggcggCUCCa--GUUCg -3' miRNA: 3'- -UUGCGAGCGCUGCUa-------------GAGGgcaUAAG- -5'
16487	5'	-53.3	NC_004084.1	+	56235	0.7	0.609849
16487	Target: 5'- uGGCGCagaucCGUGACGA-CUCCCGUGc-- -3' miRNA: 3'- -UUGCGa----GCGCUGCUaGAGGGCAUaag -5'
16487	5'	-53.3	NC_004084.1	+	2491	0.71	0.52211
16487	Target: 5'- -gUGUUCGCGACGAUCgcauUCCCGa---- -3' miRNA: 3'- uuGCGAGCGCUGCUAG----AGGGCauaag -5'
16487	5'	-53.3	NC_004084.1	+	19918	0.72	0.45962
16487	Target: 5'- cGAUGCUCGCGACGAUCgagggcgaggaUCCGU--UCa -3' miRNA: 3'- -UUGCGAGCGCUGCUAGa----------GGGCAuaAG- -5'
16487	5'	-53.3	NC_004084.1	+	52089	1.07	0.002384
16487	Target: 5'- gAACGCUCGCGACGAUCUCCCGUAUUCc -3' miRNA: 3'- -UUGCGAGCGCUGCUAGAGGGCAUAAG- -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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