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]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[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
21 0.000482 0.08173 stm1057 pepN -18.92 0.026522 201 -- 244 36 -- 81 aminopeptidase N  
22 0.0005859 0.08814 stm1976 fliM -14.91 0.122150 23 -- 60 38 -- 69 flagellar motor switch protein FliM  
23 0.0005914 0.08814 stm3466 crp -13.97 0.171291 272 -- 288 36 -- 50 transcriptional regulator Crp  
24 0.000609 0.08814 stm3510 yhgH -18.34 0.033208 106 -- 153 42 -- 84 DNA utilization protein GntX  
25 0.0006298 0.08814 stm3161 metC -13.21 0.223681 190 -- 249 35 -- 90 cystathionine beta-lyase  
26 0.0006768 0.08814 stm1365 ydiJ -17.55 0.045121 78 -- 116 57 -- 91 similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017  
27 0.0006872 0.08814 stm1806 nhaB -13.59 0.196266 64 -- 136 66 -- 135 Na+/H+ antiporter NhaB  
28 0.0007333 0.08814 stm0376 sbmA -15.26 0.107034 68 -- 102 55 -- 90 peptide transporter  
29 0.0007392 0.08814 stm3096 yqgE -16.45 0.068552 198 -- 251 37 -- 84 DUF179 domain-containing protein  
30 0.0007612 0.08814 stm3909 ilvC -21.15 0.011132 166 -- 188 66 -- 89 ketol-acid reductoisomerase  

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

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2