Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3202356

Input and runtime details for job 3202356 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 3202356 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:02 CET 2018
?Processing Started@ Fri Feb 16 15:24:35 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:03:47 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:03:55 CET 2018
?Job Completed@ Sat Feb 17 02:04:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

GcvB


Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
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[txt] [svg]


heatmap

? Conserved, identified interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
171 0.009384 0.1945 stm1741 N/A -12.47 0.287408 104 -- 168 71 -- 131 transporter  
172 0.009395 0.1945 stm3373 mreC -15.91 0.084075 179 -- 229 45 -- 87 rod shape-determining protein MreC  
173 0.009489 0.1945 stm3985 yigZ -14.68 0.132642 77 -- 135 33 -- 90 YigZ family protein  
174 0.009594 0.1945 stm1955 fliZ -12.61 0.274939 261 -- 282 33 -- 59 flagellar regulatory protein FliZ  
175 0.009595 0.1945 stm0268 N/A -12.50 0.284574 64 -- 117 80 -- 130 type VI secretion protein  
176 0.009613 0.1945 stm3378 N/A -14.56 0.138793 155 -- 243 45 -- 125 sulfoxide reductase heme-binding subunit YedZ  
177 0.009665 0.1945 stm0079 yaaU -14.30 0.152587 187 -- 218 40 -- 79 MFS transporter  
178 0.009774 0.1951 stm2667 pheA -14.20 0.157815 177 -- 228 36 -- 93 chorismate mutase  
179 0.009806 0.1951 stm3912 rep -13.00 0.240883 219 -- 287 22 -- 83 ATP-dependent DNA helicase Rep  
180 0.009911 0.1961 stm0199 stfF -15.44 0.100302 89 -- 133 44 -- 87 fimbrial protein  

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

		

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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Feeds the job parameters to the input page to resubmit the job.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2