Viral miRNA display CGI

miRNA display CGI

Results 1 - 14 of 14 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	3'	-52.6	NC_004084.1	+	12054	0.66	0.867258
16487	Target: 5'- gGGCGUCGGuGuccUGGACgaaaccCACAguugGGCGa -3' miRNA: 3'- -CCGCAGCC-Cu--ACCUGaua---GUGU----UCGU- -5'
16487	3'	-52.6	NC_004084.1	+	55972	0.66	0.850512
16487	Target: 5'- cGGCGaCGcGGAgGGGCUgaucgccgAUgGCGAGCAu -3' miRNA: 3'- -CCGCaGC-CCUaCCUGA--------UAgUGUUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	50250	0.67	0.832826
16487	Target: 5'- aGGCGUCGcuGGAgcGGGCUGgucggCACGaccaGGCGa -3' miRNA: 3'- -CCGCAGC--CCUa-CCUGAUa----GUGU----UCGU- -5'
16487	3'	-52.6	NC_004084.1	+	35911	0.67	0.823653
16487	Target: 5'- cGuCGUCGaGGAU-GACgcguUCACGAGCAu -3' miRNA: 3'- cC-GCAGC-CCUAcCUGau--AGUGUUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	18127	0.67	0.794936
16487	Target: 5'- cGCGaUCcGGAUGGACUggaacgacGUCGCcGGCGa -3' miRNA: 3'- cCGC-AGcCCUACCUGA--------UAGUGuUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	11703	0.68	0.773881
16487	Target: 5'- cGGCGUCGGaagccaucgaagaGAUGGGCgcugagCAguGGCGc -3' miRNA: 3'- -CCGCAGCC-------------CUACCUGaua---GUguUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	15871	0.68	0.743739
16487	Target: 5'- -uCGUCGGG-UGGACaGUCGaucCGAGCGg -3' miRNA: 3'- ccGCAGCCCuACCUGaUAGU---GUUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	51724	0.69	0.733104
16487	Target: 5'- cGGCGUUGaccucgaGAUGGAC-GUCGuCGAGCAg -3' miRNA: 3'- -CCGCAGCc------CUACCUGaUAGU-GUUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	29142	0.69	0.678609
16487	Target: 5'- cGGUGUCGGcGGugcUGGugUGgucgCGCGGGCc -3' miRNA: 3'- -CCGCAGCC-CU---ACCugAUa---GUGUUCGu -5'
16487	3'	-52.6	NC_004084.1	+	10689	0.71	0.5896
16487	Target: 5'- uGGCGgucaUCGGGAcaaaucUGGACUA-CGCgGAGCAc -3' miRNA: 3'- -CCGC----AGCCCU------ACCUGAUaGUG-UUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	16432	0.74	0.40312
16487	Target: 5'- cGGCGUCGauGUGGGCaucgGUUACGGGCAu -3' miRNA: 3'- -CCGCAGCccUACCUGa---UAGUGUUCGU- -5'
16487	3'	-52.6	NC_004084.1	+	35792	0.76	0.324839
16487	Target: 5'- aGGCGcCGGGAaGGACgcgcucgGUCAUGAGCu -3' miRNA: 3'- -CCGCaGCCCUaCCUGa------UAGUGUUCGu -5'
16487	3'	-52.6	NC_004084.1	+	20965	0.78	0.251789
16487	Target: 5'- cGGgGUCGGGAUgcGGACUcuUCGCGAGUg -3' miRNA: 3'- -CCgCAGCCCUA--CCUGAu-AGUGUUCGu -5'
16487	3'	-52.6	NC_004084.1	+	52053	1.12	0.001314
16487	Target: 5'- cGGCGUCGGGAUGGACUAUCACAAGCAg -3' miRNA: 3'- -CCGCAGCCCUACCUGAUAGUGUUCGU- -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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