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]
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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
158 0.00827 0.1845 stm1712 acnA -14.47 0.143385 236 -- 294 48 -- 104 aconitate hydratase 1  
129 0.006472 0.1774 stm0158 acnB -11.80 0.356459 140 -- 172 33 -- 60 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase  
137 0.006825 0.1774 stm1196 acpP -14.14 0.161333 197 -- 223 36 -- 60 acyl carrier protein  
19 0.0004167 0.0781 stm0475 acrB -19.12 0.024591 69 -- 114 139 -- 185 aminoglycoside/multidrug transporter permease  
170 0.009347 0.1945 stm0477 acrR -17.70 0.042454 229 -- 246 74 -- 91 DNA-binding transcriptional repressor AcrR  
13 0.0002148 0.05681 stm4275 acs -17.09 0.053801 176 -- 229 31 -- 87 acetate--CoA ligase  
131 0.006551 0.1774 stm3217 aer -17.88 0.039631 254 -- 298 36 -- 77 senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506  
126 0.006333 0.1774 stm1584 ansP -14.21 0.157463 122 -- 184 36 -- 93 amino acid permease  
181 0.01001 0.1966 stm2266 apbE -12.19 0.314808 267 -- 297 62 -- 90 FAD:protein FMN transferase ApbE  
2 2.663e-05 0.04123 stm2355 argT -17.69 0.042680 144 -- 202 34 -- 91 histidine ABC transporter substrate-binding protein HisJ  

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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Results are computed with CopraRNA version 2.1.2