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

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA 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/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
4	0.0002658	0.2138	b1040	csgD	-11.06	0.024985	185 -- 199	38 -- 52	csgBAC operon transcriptional regulator	_____________184_____________200\n_____________\|_______________\|\n5'-UUA...UAAAA____C__________CAUGU...CGC-3'\n______________AAAG_GGGGUUUCAU\n______________\|\|\|\|_\|\|::\|\|\|\|\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	193 -- 199	38 -- 44	-14.3947 kcal/mol	2.26766 kcal/mol	1.0693 kcal/mol	184 200@LB@ \| \|@LB@5'-UUA...UAAAA C CAUGU...CGC-3'@LB@ AAAG GGGGUUUCAU@LB@ \|\|\|\| \|\|::\|\|\|\|\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -14.3947 kcal/mol@LB@Unfolding Energy - mRNA 2.26766 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 185 -- 199@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 38 -- 44@LB@
10	0.001925	0.593	b2910	zapA	-12.97	0.010115	44 -- 65	38 -- 56	FtsZ stabilizer	_____________43_____________________66\n_____________\|______________________\|\n5'-GUU...UUCGU______AG________A_____GAUAU...AUC-3'\n______________CGUCAA__GGAGGAAU_UUCAU\n______________\|\|\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GCAGUU__UCUCCUUA_AAGUA\n3'-UUU...ACCGG______________________AAAAA...ACA-5'\n_____________\|______________________\|\n_____________57_____________________37\n	53 -- 59	43 -- 49	-19.9082 kcal/mol	5.76295 kcal/mol	1.17918 kcal/mol	43 66@LB@ \| \|@LB@5'-GUU...UUCGU AG A GAUAU...AUC-3'@LB@ CGUCAA GGAGGAAU UUCAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GCAGUU UCUCCUUA AAGUA@LB@3'-UUU...ACCGG AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -19.9082 kcal/mol@LB@Unfolding Energy - mRNA 5.76295 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 44 -- 65@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 43 -- 49@LB@
25	0.004737	0.5992	b1093	fabG	-11.25	0.022809	188 -- 202	38 -- 52	3-oxoacyl-[acyl-carrier-protein] reductase	_____________187_____________203\n_____________\|_______________\|\n5'-UAC...CUUUA_________AA____GAAUU...UUG-3'\n______________AAAGAGGAA__UCAU\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UUUCUCCUU__AGUA\n3'-UUU...GGCAG_________AA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	190 -- 196	44 -- 50	-14.2885 kcal/mol	1.96871 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-UAC...CUUUA AA GAAUU...UUG-3'@LB@ AAAGAGGAA UCAU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUCCUU AGUA@LB@3'-UUU...GGCAG AA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -14.2885 kcal/mol@LB@Unfolding Energy - mRNA 1.96871 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
41	0.008018	0.6129	b1740	nadE	-11.27	0.022577	258 -- 272	38 -- 52	NAD synthetase NH3/glutamine-dependent	_____________257_____________273\n_____________\|_______________\|\n5'-UUC...AUGCU_________A_____CGUAG...ACC-3'\n______________GAAGAGGAA_UUCGU\n______________:\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________UUUCUCCUU_AAGUA\n3'-UUU...GGCAG_________A_____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	260 -- 266	44 -- 50	-15.8385 kcal/mol	3.49717 kcal/mol	1.0693 kcal/mol	257 273@LB@ \| \|@LB@5'-UUC...AUGCU A CGUAG...ACC-3'@LB@ GAAGAGGAA UUCGU@LB@ :\|\|\|\|\|\|\|\| \|\|\|:\|@LB@ UUUCUCCUU AAGUA@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -15.8385 kcal/mol@LB@Unfolding Energy - mRNA 3.49717 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 44 -- 50@LB@
47	0.009275	0.6129	b3412	bioH	-9.55	0.050822	229 -- 245	38 -- 55	pimeloyl-ACP methyl ester carboxylesterase	_____________228_________________246\n_____________\|___________________\|\n5'-GGC...CAAAG_____________G_____CUUGU...ACG-3'\n______________GUC__AGGGGAAU_UUCAU\n______________\|\|\|__\|\|:\|\|\|\|\|_\|\|\|\|\|\n______________CAG__UCUCCUUA_AAGUA\n3'-UUU...CCGGG___UU______________AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	233 -- 239	43 -- 49	-15.7204 kcal/mol	5.00086 kcal/mol	1.17036 kcal/mol	228 246@LB@ \| \|@LB@5'-GGC...CAAAG G CUUGU...ACG-3'@LB@ GUC AGGGGAAU UUCAU@LB@ \|\|\| \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ CAG UCUCCUUA AAGUA@LB@3'-UUU...CCGGG UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.55 kcal/mol@LB@Hybridization Energy -15.7204 kcal/mol@LB@Unfolding Energy - mRNA 5.00086 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 229 -- 245@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 43 -- 49@LB@
61	0.01292	0.6177	b4154	frdA	-9.46	0.053105	187 -- 202	38 -- 54	anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit	_____________186_______________203\n_____________\|_________________\|\n5'-UAA...AACAA__U_________G____GCAAA...UCG-3'\n______________UC__GGAGGAAU_UCGU\n______________\|\|__:\|\|\|\|\|\|\|_\|\|:\|\n______________AG__UCUCCUUA_AGUA\n3'-UUU...CGGGC__UU________A____AAAAA...ACA-5'\n_____________\|_________________\|\n_____________55________________37\n	191 -- 197	43 -- 49	-14.1575 kcal/mol	3.5319 kcal/mol	1.17036 kcal/mol	186 203@LB@ \| \|@LB@5'-UAA...AACAA U G GCAAA...UCG-3'@LB@ UC GGAGGAAU UCGU@LB@ \|\| :\|\|\|\|\|\|\| \|\|:\|@LB@ AG UCUCCUUA AGUA@LB@3'-UUU...CGGGC UU A AAAAA...ACA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -14.1575 kcal/mol@LB@Unfolding Energy - mRNA 3.5319 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 187 -- 202@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 43 -- 49@LB@
79	0.01695	0.6177	b0435	bolA	-9.02	0.064980	184 -- 202	38 -- 55	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________183_________________203\n_____________\|___________________\|\n5'-UGA...GCGUU___G______AU_______GAUGA...CCG-3'\n______________GUC_GAGGAG__AUUUCAU\n______________\|\|\|_:\|:\|\|\|__\|\|\|\|\|\|\|\n______________CAG_UUUCUC__UAAAGUA\n3'-UUU...CCGGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________37\n	196 -- 202	38 -- 44	-15.2358 kcal/mol	5.04311 kcal/mol	1.17036 kcal/mol	183 203@LB@ \| \|@LB@5'-UGA...GCGUU G AU GAUGA...CCG-3'@LB@ GUC GAGGAG AUUUCAU@LB@ \|\|\| :\|:\|\|\| \|\|\|\|\|\|\|@LB@ CAG UUUCUC UAAAGUA@LB@3'-UUU...CCGGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.2358 kcal/mol@LB@Unfolding Energy - mRNA 5.04311 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
86	0.01794	0.6177	b3260	dusB	-7.53	0.128932	119 -- 138	38 -- 55	tRNA-dihydrouridine synthase B	_____________118__________________139\n_____________\|____________________\|\n5'-ACU...GAUUG_______UUU__CC______CUCGU...GAG-3'\n______________GUCAAAG___GG__UUUCAU\n______________\|\|\|\|\|\|\|___\|\|__\|\|\|\|\|\|\n______________CAGUUUC___CC__AAAGUA\n3'-UUU...CCGGG_______U____UU______AAAAA...ACA-5'\n_____________\|____________________\|\n_____________56___________________37\n	119 -- 125	49 -- 55	-13.3869 kcal/mol	4.6894 kcal/mol	1.17036 kcal/mol	118 139@LB@ \| \|@LB@5'-ACU...GAUUG UUU CC CUCGU...GAG-3'@LB@ GUCAAAG GG UUUCAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ CAGUUUC CC AAAGUA@LB@3'-UUU...CCGGG U UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -13.3869 kcal/mol@LB@Unfolding Energy - mRNA 4.6894 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 119 -- 138@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 49 -- 55@LB@
96	0.01897	0.6177	b2422	cysA	-7.76	0.115977	190 -- 202	38 -- 50	sulfate/thiosulfate transporter subunit	_____________189___________203\n_____________\|_____________\|\n5'-GGU...CAGCA_______CA____GAGCA...UGC-3'\n______________GGAGGAA__UCAU\n______________:\|\|\|\|\|\|__\|\|\|\|\n______________UCUCCUU__AGUA\n3'-UUU...CAGUU_______AA____AAAAA...ACA-5'\n_____________\|_____________\|\n_____________51____________37\n	190 -- 196	44 -- 50	-11.8687 kcal/mol	3.04673 kcal/mol	1.0603 kcal/mol	189 203@LB@ \| \|@LB@5'-GGU...CAGCA CA GAGCA...UGC-3'@LB@ GGAGGAA UCAU@LB@ :\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCUU AGUA@LB@3'-UUU...CAGUU AA AAAAA...ACA-5'@LB@ \| \|@LB@ 51 37@LB@@LB@@LB@Energy -7.76 kcal/mol@LB@Hybridization Energy -11.8687 kcal/mol@LB@Unfolding Energy - mRNA 3.04673 kcal/mol@LB@Unfolding Energy - sRNA 1.0603 kcal/mol@LB@@LB@Position - mRNA 190 -- 202@LB@Position - sRNA 38 -- 50@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
106	0.02162	0.6177	b1831	proQ	-7.28	0.143813	159 -- 202	38 -- 75	RNA chaperone putative ProP translation regulator	_____________158_____________________________________________203\n_____________\|_______________________________________________\|\n5'-UUA...UUCAU___UG______U________A____CGUUGU__UC___A________GGAAA...CGC-3'\n______________GCC_____CGC_UGUUGGCU_CGUC______AA__AGG_AAUUUCAU\n______________\|\|\|_____\|\|\|_\|:\|\|\|\|\|:_\|\|\|\|______\|\|__\|\|\|_\|\|\|\|\|\|\|\|\n______________CGG_____GCG_AUAACCGG_GCAG______UU__UCC_UUAAAGUA\n3'-UUU...UUUAC___UUAUA_________________________UC____________AAAAA...ACA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________37\n	196 -- 202	38 -- 44	-31.8607 kcal/mol	10.974 kcal/mol	13.6034 kcal/mol	158 203@LB@ \| \|@LB@5'-UUA...UUCAU UG U A CGUUGU UC A GGAAA...CGC-3'@LB@ GCC CGC UGUUGGCU CGUC AA AGG AAUUUCAU@LB@ \|\|\| \|\|\| \|:\|\|\|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CGG GCG AUAACCGG GCAG UU UCC UUAAAGUA@LB@3'-UUU...UUUAC UUAUA UC AAAAA...ACA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -31.8607 kcal/mol@LB@Unfolding Energy - mRNA 10.974 kcal/mol@LB@Unfolding Energy - sRNA 13.6034 kcal/mol@LB@@LB@Position - mRNA 159 -- 202@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@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