Input and runtime details for job 1786318 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA 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/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

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
77	0.00398	0.182	b2411	ligA	-14.36	0.019662	79 -- 95	70 -- 86	DNA ligase NAD(+)-dependent		_____________78________________96\n_____________\|_________________\|\n5'-GCA...CAGAA_______G_________ACAUC...CUG-3'\n______________AUUGCGC_AGUACCAGG\n______________\|:\|\|\|\|\|_\|::\|\|\|\|\|\|\n______________UGACGCG_UUGUGGUCC\n3'-UUU...GCUUA_______G_________CUUUA...GUG-5'\n_____________\|_________________\|\n_____________87________________69\n	89 -- 95	70 -- 76	-25.4632 kcal/mol	3.82569 kcal/mol	7.27772 kcal/mol	78 96@LB@ \| \|@LB@5'-GCA...CAGAA G ACAUC...CUG-3'@LB@ AUUGCGC AGUACCAGG@LB@ \|:\|\|\|\|\| \|::\|\|\|\|\|\|@LB@ UGACGCG UUGUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -25.4632 kcal/mol@LB@Unfolding Energy - mRNA 3.82569 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 79 -- 95@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 70 -- 76@LB@
86	0.004777	0.1855	b3157	yhbT	-11.83	0.061936	277 -- 294	70 -- 85	SCP-2 sterol transfer family protein		_____________276________________295\n_____________\|__________________\|\n5'-CUG...GCCAU________AA________UUCUUG-3'\n______________UUGCGCUA__ACGCCAGG\n______________:\|\|\|\|\|:\|__\|\|:\|\|\|\|\|\n______________GACGCGGU__UGUGGUCC\n3'-UUU...CUUAU__________________CUUUA...GUG-5'\n_____________\|__________________\|\n_____________86_________________69\n	288 -- 294	70 -- 76	-24.8001 kcal/mol	5.69349 kcal/mol	7.27689 kcal/mol	276 295@LB@ \| \|@LB@5'-CUG...GCCAU AA UUCUUG-3'@LB@ UUGCGCUA ACGCCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|\|@LB@ GACGCGGU UGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.8001 kcal/mol@LB@Unfolding Energy - mRNA 5.69349 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 277 -- 294@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
89	0.004811	0.1855	b4336	yjiN	-13.14	0.034257	120 -- 134	70 -- 84	zinc-type alcohol dehydrogenase-like protein		_____________119_____________135\n_____________\|_______________\|\n5'-GGU...UCGCG_______________CAGCC...CCA-3'\n______________UGCGCCAGCAUCAGG\n______________\|\|\|\|\|\|\|:\|\|:\|\|\|\|\n______________ACGCGGUUGUGGUCC\n3'-UUU...UUAUG_______________CUUUA...GUG-5'\n_____________\|_______________\|\n_____________85______________69\n	128 -- 134	70 -- 76	-28.7852 kcal/mol	8.39668 kcal/mol	7.24859 kcal/mol	119 135@LB@ \| \|@LB@5'-GGU...UCGCG CAGCC...CCA-3'@LB@ UGCGCCAGCAUCAGG@LB@ \|\|\|\|\|\|\|:\|\|:\|\|\|\|@LB@ ACGCGGUUGUGGUCC@LB@3'-UUU...UUAUG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -28.7852 kcal/mol@LB@Unfolding Energy - mRNA 8.39668 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 120 -- 134@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 70 -- 76@LB@
94	0.005015	0.1855	b2703	srlE	-7.35	0.404948	254 -- 271	70 -- 86	glucitol/sorbitol-specific enzyme IIB component of PTS		_____________253_________________272\n_____________\|___________________\|\n5'-GAA...CUUGA____AAA____________AAAAA...GUA-3'\n______________GCUG___GCC_ACGCCGGG\n______________:\|\|\|___\|\|\|_\|\|:\|\|:\|\|\n______________UGAC___CGG_UGUGGUCC\n3'-UUU...GCUUA____G_____U________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	265 -- 271	70 -- 76	-23.089 kcal/mol	8.46506 kcal/mol	7.27772 kcal/mol	253 272@LB@ \| \|@LB@5'-GAA...CUUGA AAA AAAAA...GUA-3'@LB@ GCUG GCC ACGCCGGG@LB@ :\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ UGAC CGG UGUGGUCC@LB@3'-UUU...GCUUA G U CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -23.089 kcal/mol@LB@Unfolding Energy - mRNA 8.46506 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 254 -- 271@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 70 -- 76@LB@
99	0.005465	0.1855	b0767	pgl	-9.37	0.182441	275 -- 291	70 -- 86	6-phosphogluconolactonase		_____________274________________292\n_____________\|__________________\|\n5'-UCA...GGCGC____A_____________UUGUC...AUG-3'\n______________ACUG_CGCUGACA_CAGG\n______________\|\|\|\|_\|\|\|::\|\|\|_\|\|\|\|\n______________UGAC_GCGGUUGU_GUCC\n3'-UUU...GCUUA_____________G____CUUUA...GUG-5'\n_____________\|__________________\|\n_____________87_________________69\n	281 -- 287	75 -- 81	-21.4952 kcal/mol	4.85205 kcal/mol	7.27772 kcal/mol	274 292@LB@ \| \|@LB@5'-UCA...GGCGC A UUGUC...AUG-3'@LB@ ACUG CGCUGACA CAGG@LB@ \|\|\|\| \|\|\|::\|\|\| \|\|\|\|@LB@ UGAC GCGGUUGU GUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -21.4952 kcal/mol@LB@Unfolding Energy - mRNA 4.85205 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 75 -- 81@LB@
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@LB@
125	0.006795	0.1914	b3003	yghA	-11.52	0.071261	264 -- 274	70 -- 80	putative oxidoreductase	b2902	_____________263_________275\n_____________\|___________\|\n5'-AAC...AACAA___________CAUCC...UAC-3'\n______________CCGACGCCAGG\n______________\|\|:\|\|:\|\|\|\|\|\n______________GGUUGUGGUCC\n3'-UUU...GACGC___________CUUUA...GUG-5'\n_____________\|___________\|\n_____________81__________69\n	268 -- 274	70 -- 76	-20.3781 kcal/mol	2.1599 kcal/mol	6.70146 kcal/mol	263 275@LB@ \| \|@LB@5'-AAC...AACAA CAUCC...UAC-3'@LB@ CCGACGCCAGG@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ GGUUGUGGUCC@LB@3'-UUU...GACGC CUUUA...GUG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -20.3781 kcal/mol@LB@Unfolding Energy - mRNA 2.1599 kcal/mol@LB@Unfolding Energy - sRNA 6.70146 kcal/mol@LB@@LB@Position - mRNA 264 -- 274@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 70 -- 76@LB@
136	0.007706	0.1993	b2188	yejM	-8.60	0.250530	107 -- 119	70 -- 83	essential inner membrane DUF3413 domain-containing protein; lipid A production and membrane permeability factor		_____________106____________120\n_____________\|______________\|\n5'-CGC...CCCCG______________CAAUU...UUG-3'\n______________GC_CCAACGCCAGG\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\n______________CG_GGUUGUGGUCC\n3'-UUU...UAUGA__C___________CUUUA...GUG-5'\n_____________\|______________\|\n_____________84_____________69\n	113 -- 119	70 -- 76	-22.9581 kcal/mol	7.21499 kcal/mol	7.14463 kcal/mol	106 120@LB@ \| \|@LB@5'-CGC...CCCCG CAAUU...UUG-3'@LB@ GC CCAACGCCAGG@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|@LB@ CG GGUUGUGGUCC@LB@3'-UUU...UAUGA C CUUUA...GUG-5'@LB@ \| \|@LB@ 84 69@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.9581 kcal/mol@LB@Unfolding Energy - mRNA 7.21499 kcal/mol@LB@Unfolding Energy - sRNA 7.14463 kcal/mol@LB@@LB@Position - mRNA 107 -- 119@LB@Position - sRNA 70 -- 83@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 70 -- 76@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon		_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase		_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - 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:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching