Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 8257533

Input and runtime details for job 8257533 (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 8257533 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:34:31 CET 2018
?Processing Started@ Fri Feb 16 15:34:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:30:38 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:30:45 CET 2018
?Job Completed@ Fri Feb 16 22:31:01 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

The job description you specified

LhrA2


Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
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[html] [pdf]
[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_003210 Listeria monocytogenes EGD-e

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
1 1.731e-05 0.04657 lmo1883 N/A -26.54 0.000269 199 -- 265 114 -- 169 chitinase  
2 0.0002774 0.3688 lmo1666 N/A -21.94 0.003684 151 -- 207 157 -- 207 peptidoglycan-linked protein lmo0333
3 0.0004111 0.3688 lmo0196 N/A -23.83 0.001321 198 -- 256 156 -- 209 regulatory protein SpoVG  
4 0.0009641 0.4469 lmo0851 N/A -23.35 0.001728 188 -- 220 172 -- 201 lmo0851  
5 0.001245 0.4469 lmo1835 carB -22.95 0.002153 176 -- 228 154 -- 207 carbamoyl-phosphate synthetase  
6 0.001395 0.4469 lmo2078 N/A -19.77 0.011149 188 -- 240 154 -- 207    
7 0.001816 0.4469 lmo1666 N/A -21.94 0.003684 151 -- 207 157 -- 207 peptidoglycan-linked protein lmo0333
8 0.001816 0.4469 lmo1666 N/A -21.94 0.003684 151 -- 207 157 -- 207 peptidoglycan-linked protein lmo0333
9 0.002066 0.4469 lmo0669 N/A -20.91 0.006284 33 -- 77 156 -- 211 oxidoreductase  
10 0.002311 0.4469 lmo2106 N/A -20.89 0.006356 172 -- 222 159 -- 207    

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