Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1765463

Input and runtime details for job 1765463 (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 1765463 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:41:59 CET 2018
?Processing Started@ Fri Feb 16 15:42:13 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 19:57:45 CET 2018
?Post-Processing Finished@ Fri Feb 16 19:57:53 CET 2018
?Job Completed@ Fri Feb 16 19:58:19 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

The job description you specified

5 ChiX sequences


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
1 0 0 b0481 ybaK -91.37 0.000000 1 -- 79 1 -- 79 Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase  
2 6.241e-06 0.01004 b1737 chbC -18.35 0.000789 134 -- 152 38 -- 56 N N'-diacetylchitobiose-specific enzyme IIC component of PTS  
3 9.453e-06 0.01014 b0681 chiP -16.40 0.001982 182 -- 193 45 -- 56 chitoporin uptake of chitosugars  
4 0.0002658 0.2138 b1040 csgD -11.06 0.024985 185 -- 199 38 -- 52 csgBAC operon transcriptional regulator  
5 0.0004437 0.2856 b0847 ybjL -12.50 0.012601 224 -- 253 26 -- 55 putative transporter  
6 0.0006545 0.351 b1857 znuA -11.78 0.017745 58 -- 67 45 -- 54 zinc ABC transporter periplasmic binding protein  
7 0.001184 0.5444 b0817 mntR -11.99 0.016054 285 -- 294 46 -- 55 Mn(2+)-responsive manganese regulon transcriptional regulator  
8 0.001474 0.5928 b1048 opgG -11.67 0.018726 159 -- 168 44 -- 53 OPG biosynthetic periplasmic beta-1 6 branching glycosyltransferase  
9 0.001801 0.593 b1276 acnA -10.22 0.037037 184 -- 198 44 -- 55 aconitate hydratase 1; aconitase A  
10 0.001925 0.593 b2910 zapA -12.97 0.010115 44 -- 65 38 -- 56 FtsZ stabilizer  

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