Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

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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
118 0.006444 0.1913 b0189 rof -9.63 0.163299 226 -- 241 29 -- 45 modulator of Rho-dependent transcription termination  
9 0.0003241 0.1198 b1110 ycfJ -9.50 0.172514 224 -- 251 52 -- 76 uncharacterized protein  
131 0.007315 0.1966 b3824 rhtB -9.48 0.174149 77 -- 100 63 -- 87 homoserine homoserine lactone and S-methyl-methionine efflux pump  
182 0.01083 0.2089 b0314 betT -9.44 0.176432 217 -- 228 66 -- 77 choline transporter of high affinity  
151 0.008943 0.2059 b1284 yciT -9.40 0.179701 94 -- 109 63 -- 77 global regulator of transcription; DeoR family  
99 0.005465 0.1855 b0767 pgl -9.37 0.182441 275 -- 291 70 -- 86 6-phosphogluconolactonase  
3 3.071e-06 0.003055 b2100 yegV -9.35 0.183884 5 -- 14 51 -- 60 putative kinase  
192 0.01187 0.2159 b2600 tyrA -9.34 0.184498 136 -- 155 70 -- 86 fused chorismate mutase T/prephenate dehydrogenase  
88 0.004799 0.1855 b2213 ada -9.32 0.185618 222 -- 245 63 -- 86 fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase  
128 0.007127 0.1961 b0696 kdpC -9.30 0.187437 90 -- 106 44 -- 60 potassium translocating ATPase subunit C  

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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Results are computed with CopraRNA version 2.1.2