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]
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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
1 0 0 stm2982 gcvA -98.53 0.000000 1 -- 73 1 -- 73 transcriptional regulator GcvA  
32 0.001017 0.1132 stm1874 N/A -30.35 0.000300 5 -- 53 36 -- 83 putative inner membrane protein  
8 9.263e-05 0.04123 stm0369 prpC -29.42 0.000431 202 -- 269 31 -- 91 2-methylcitrate synthase  
156 0.008228 0.1845 stm1715 yciN -28.69 0.000575 104 -- 163 36 -- 90 similar to E. coli orf hypothetical protein (AAC74355.1); Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83  
84 0.003893 0.1596 stm2015 erfK -27.15 0.001054 109 -- 172 35 -- 90 L D-transpeptidase  
5 6.363e-05 0.04123 stm0399 brnQ -24.27 0.003272 169 -- 224 36 -- 81 branched-chain amino acid transport system II carrier protein  
7 8.283e-05 0.04123 stm1953 yedO -23.64 0.004188 172 -- 228 31 -- 88 D-cysteine desulfhydrase  
17 0.0003055 0.06194 stm2694 N/A -22.95 0.005498 261 -- 295 52 -- 90 Fels-2 prophage protein  
85 0.003998 0.1596 stm1098 hpaC -22.15 0.007534 132 -- 187 37 -- 90 4-hydroxyphenylacetate 3-monooxygenase reductase component  
37 0.001263 0.1215 stm2511 guaB -22.14 0.007548 255 -- 298 35 -- 73 IMP dehydrogenase  

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