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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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
141 0.007251 0.182 stm2325 nuoE -19.46 0.021521 159 -- 233 56 -- 129 NADH-quinone oxidoreductase subunit E  
142 0.007269 0.182 stm4341 frdC -12.15 0.319206 131 -- 234 54 -- 160 fumarate reductase subunit C  
143 0.007336 0.182 stm2276 ubiG -14.65 0.134291 225 -- 278 36 -- 81 2-octaprenyl-6-hydroxy phenol methylase  
144 0.00736 0.182 stm4559 yjjG -11.80 0.356804 189 -- 218 128 -- 159 putative haloacid dehalogenase-like hydrolase  
145 0.007435 0.1826 stm1822 yoaB -15.17 0.110813 243 -- 269 162 -- 185 similar to E. coli orf hypothetical protein (AAC74879.1); Blastp hit to AAC74879.1 (130 aa) 92% identity in aa 17 - 130  
146 0.007509 0.1831 stm1510 ydfH -14.80 0.126744 211 -- 261 32 -- 88 GntR family transcriptional regulator  
147 0.007823 0.1845 stm3477 cysG -15.08 0.114738 192 -- 245 61 -- 111 uroporphyrinogen-III C-methyltransferase  
148 0.007836 0.1845 stm2318 nuoL -12.84 0.254324 144 -- 178 37 -- 76 NADH-quinone oxidoreductase subunit L  
149 0.007892 0.1845 stm2071 hisG -15.61 0.094042 166 -- 245 36 -- 100 ATP phosphoribosyltransferase  
150 0.007945 0.1845 stm2555 glyA -15.42 0.100951 252 -- 282 137 -- 168 serine hydroxymethyltransferase  

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