Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5344133

Input and runtime details for job 5344133 (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 5344133 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:28:43 CET 2018
?Processing Started@ Fri Feb 16 20:36:11 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:15:51 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:15:58 CET 2018
?Job Completed@ Sat Feb 17 02:16:29 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

The job description you specified

RybB


Output download complete results [zip]

Downloadable files

[csv]
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heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

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 0 0 b3752 rbsK -20.54 0.000534 137 -- 155 1 -- 21 ribokinase  
2 5.107e-11 8.961e-08 b2314 dedD -25.37 0.000001 176 -- 205 1 -- 30 membrane-anchored periplasmic protein involved in septation  
3 3.973e-07 0.0004647 b0081 mraZ -16.47 0.011640 172 -- 200 1 -- 32 RsmH methytransferase inhibitor  
4 1.99e-05 0.01653 b4255 rraB -17.36 0.006479 180 -- 205 1 -- 23 protein inhibitor of RNase E  
5 2.356e-05 0.01653 b1123 potD -19.53 0.001282 190 -- 207 9 -- 25 spermidine/putrescine ABC transporter periplasmic binding protein  
6 9.344e-05 0.05465 b2215 ompC -14.72 0.032428 133 -- 159 1 -- 28 outer membrane porin protein C b0929 b0241 b1377
7 0.0001218 0.05555 b1811 yoaH -21.30 0.000256 259 -- 293 1 -- 35 UPF0181 family protein  
8 0.0001267 0.05555 b2697 alaS -16.66 0.010303 247 -- 274 1 -- 35 alanyl-tRNA synthetase  
9 0.0002541 0.09908 b4000 hupA -15.77 0.017828 82 -- 110 1 -- 35 HU DNA-binding transcriptional regulator alpha subunit  
10 0.0003274 0.1087 b1020 phoH -9.93 0.281763 74 -- 85 48 -- 59 ATP-binding protein; putative PhoH family P-loop ATPase  

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)

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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