Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
13	0.0004028	0.1087	b1107	nagZ	-16.35	0.012500	184 -- 201	3 -- 21	beta N-acetyl-glucosaminidase		_____________183_________________202\n_____________\|___________________\|\n5'-AUU...AUAAA___AU______________UGGGU...CGC-3'\n______________ACA___AAGGAGAGCAGUG\n______________\|\|\|___\|\|\|:\|:\|\|\|\|\|\|\|\n______________UGU___UUCUUUUCGUCAC\n3'-UUU...ACCCC___AGU_____________CG-5'\n_____________\|___________________\|\n_____________22__________________2\n	195 -- 201	3 -- 9	-19.0842 kcal/mol	1.22154 kcal/mol	1.5107 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...AUAAA AU UGGGU...CGC-3'@LB@ ACA AAGGAGAGCAGUG@LB@ \|\|\| \|\|\|:\|:\|\|\|\|\|\|\|@LB@ UGU UUCUUUUCGUCAC@LB@3'-UUU...ACCCC AGU CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -19.0842 kcal/mol@LB@Unfolding Energy - mRNA 1.22154 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 3 -- 9@LB@
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@LB@
139	0.01022	0.2504	b3163	nlpI	-13.31	0.067339	19 -- 42	4 -- 21	lipoprotein involved in osmotic sensitivity and filamentation		_____________18_______________________43\n_____________\|________________________\|\n5'-AGG...UCUGA___________GCGACU_______CUCAA...CAU-3'\n______________GCAUUAAAGAA______GAGCAGU\n______________:\|\|\|:\|\|\|\|\|\|______:\|\|\|\|\|\|\n______________UGUAGUUUCUU______UUCGUCA\n3'-UUU...ACCCC________________________CCG-5'\n_____________\|________________________\|\n_____________22_______________________3\n	36 -- 42	4 -- 10	-18.4935 kcal/mol	3.67449 kcal/mol	1.51 kcal/mol	18 43@LB@ \| \|@LB@5'-AGG...UCUGA GCGACU CUCAA...CAU-3'@LB@ GCAUUAAAGAA GAGCAGU@LB@ :\|\|\|:\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCUU UUCGUCA@LB@3'-UUU...ACCCC CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -18.4935 kcal/mol@LB@Unfolding Energy - mRNA 3.67449 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 19 -- 42@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 4 -- 10@LB@
64	0.003422	0.1851	b4238	nrdD	-18.31	0.003326	69 -- 106	1 -- 34	anaerobic ribonucleoside-triphosphate reductase		_____________68_____________________________________107\n_____________\|______________________________________\|\n5'-UAU...GCUCC________AA__U_C_______U___U______A____GAUUG...UCG-3'\n______________CCACGAAA__GG_G_GGCGUUG_GGA_AAGCGG_UGGC\n______________\|\|\|\|:\|\|\|__\|\|_\|_\|:\|:\|::_:\|\|_\|\|\|\|:\|_\|\|\|\|\n______________GGUGUUUU__CC_C_CUGUAGU_UCU_UUCGUC_ACCG\n3'-UUU...CCCGA________A_____________U___U___________-5'\n_____________\|_____________________________________\|\n_____________35____________________________________1\n	84 -- 90	16 -- 22	-34.2754 kcal/mol	11.6957 kcal/mol	4.26884 kcal/mol	68 107@LB@ \| \|@LB@5'-UAU...GCUCC AA U C U U A GAUUG...UCG-3'@LB@ CCACGAAA GG G GGCGUUG GGA AAGCGG UGGC@LB@ \|\|\|\|:\|\|\| \|\| \| \|:\|:\|:: :\|\| \|\|\|\|:\| \|\|\|\|@LB@ GGUGUUUU CC C CUGUAGU UCU UUCGUC ACCG@LB@3'-UUU...CCCGA A U U -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -18.31 kcal/mol@LB@Hybridization Energy -34.2754 kcal/mol@LB@Unfolding Energy - mRNA 11.6957 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 69 -- 106@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
141	0.01037	0.2504	b2161	nupX	-15.31	0.023296	54 -- 80	1 -- 26	nucleoside permease	b2164	_____________53____________________________81\n_____________\|_____________________________\|\n5'-UUG...GGUUC_______UA_________U_______C__GGCUA...GCG-3'\n______________UGGGGAU__GUCGAAGAG__GC_GUG_GC\n______________\|\|\|\|\|\|:__:\|\|:\|\|\|\|:__\|\|_\|\|\|_\|\|\n______________ACCCCUG__UAGUUUCUU__CG_CAC_CG\n3'-UUU...GUUUU__________________UU__U______-5'\n_____________\|____________________________\|\n_____________27___________________________1\n	65 -- 71	11 -- 17	-27.7009 kcal/mol	9.87339 kcal/mol	2.51842 kcal/mol	53 81@LB@ \| \|@LB@5'-UUG...GGUUC UA U C GGCUA...GCG-3'@LB@ UGGGGAU GUCGAAGAG GC GUG GC@LB@ \|\|\|\|\|\|: :\|\|:\|\|\|\|: \|\| \|\|\| \|\|@LB@ ACCCCUG UAGUUUCUU CG CAC CG@LB@3'-UUU...GUUUU UU U -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.7009 kcal/mol@LB@Unfolding Energy - mRNA 9.87339 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 11 -- 17@LB@
47	0.002271	0.1648	b3169	nusA	-13.61	0.058009	55 -- 79	4 -- 28	transcription termination/antitermination L factor		_____________54__________________________80\n_____________\|___________________________\|\n5'-UUG...UCGUA_____CA________UC__________AGACG...CAG-3'\n______________AAUGG__GGGCGUUA____AAAGCGGU\n______________\|\|\|\|\|__\|\|:\|:\|:\|____\|\|\|\|\|:\|\|\n______________UUACC__CCUGUAGU____UUUCGUCA\n3'-UUU...GUGUU_______________UUCU________CCG-5'\n_____________\|___________________________\|\n_____________29__________________________3\n	73 -- 79	4 -- 10	-21.8237 kcal/mol	5.69952 kcal/mol	2.51457 kcal/mol	54 80@LB@ \| \|@LB@5'-UUG...UCGUA CA UC AGACG...CAG-3'@LB@ AAUGG GGGCGUUA AAAGCGGU@LB@ \|\|\|\|\| \|\|:\|:\|:\| \|\|\|\|\|:\|\|@LB@ UUACC CCUGUAGU UUUCGUCA@LB@3'-UUU...GUGUU UUCU CCG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -21.8237 kcal/mol@LB@Unfolding Energy - mRNA 5.69952 kcal/mol@LB@Unfolding Energy - sRNA 2.51457 kcal/mol@LB@@LB@Position - mRNA 55 -- 79@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
137	0.0102	0.2504	b0957	ompA	-10.25	0.250752	198 -- 232	1 -- 30	outer membrane protein A (3a;II*;G;d)		_____________197_________________________________233\n_____________\|___________________________________\|\n5'-CUU...CGCAA______AAAAA____GCUAUCGC__UU________ACUGG...AAC-3'\n______________AAAAUG_____GACA________GA__GCAGUGGC\n______________\|\|\|\|\|\|_____\|\|\|\|________:\|__\|\|\|\|\|\|\|\|\n______________UUUUAC_____CUGU________UU__CGUCACCG\n3'-UUU...AGGUG______CC_______AGUUUC____UU________-5'\n_____________\|__________________________________\|\n_____________31_________________________________1\n	226 -- 232	1 -- 7	-21.624 kcal/mol	8.85247 kcal/mol	2.51911 kcal/mol	197 233@LB@ \| \|@LB@5'-CUU...CGCAA AAAAA GCUAUCGC UU ACUGG...AAC-3'@LB@ AAAAUG GACA GA GCAGUGGC@LB@ \|\|\|\|\|\| \|\|\|\| :\| \|\|\|\|\|\|\|\|@LB@ UUUUAC CUGU UU CGUCACCG@LB@3'-UUU...AGGUG CC AGUUUC UU -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.624 kcal/mol@LB@Unfolding Energy - mRNA 8.85247 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 198 -- 232@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 1 -- 7@LB@
6	9.344e-05	0.05465	b2215	ompC	-14.72	0.032428	133 -- 159	1 -- 28	outer membrane porin protein C	b0929 b0241 b1377	_____________132____________________________160\n_____________\|______________________________\|\n5'-AUC...UGAUU____A___UUA_____UAU___________AUAAA...AUC-3'\n______________AAUG_GGG___AUCAG______GCAGUGGC\n______________\|\|\|\|_\|\|\|___\|\|\|\|:______\|\|\|\|\|\|\|\|\n______________UUAC_CCC___UAGUU______CGUCACCG\n3'-UUU...GUGUU________UG______UCUUUU________-5'\n_____________\|_____________________________\|\n_____________29____________________________1\n	153 -- 159	1 -- 7	-26.8714 kcal/mol	9.63393 kcal/mol	2.519 kcal/mol	132 160@LB@ \| \|@LB@5'-AUC...UGAUU A UUA UAU AUAAA...AUC-3'@LB@ AAUG GGG AUCAG GCAGUGGC@LB@ \|\|\|\| \|\|\| \|\|\|\|: \|\|\|\|\|\|\|\|@LB@ UUAC CCC UAGUU CGUCACCG@LB@3'-UUU...GUGUU UG UCUUUU -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -14.72 kcal/mol@LB@Hybridization Energy -26.8714 kcal/mol@LB@Unfolding Energy - mRNA 9.63393 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 133 -- 159@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 1 -- 7@LB@
93	0.00579	0.2147	b1256	ompW	-13.14	0.073154	206 -- 220	1 -- 16	outer membrane protein W		_____________205______________221\n_____________\|________________\|\n5'-GAC...AUGAA____UU__________GGCUU...CUG-3'\n______________AAAG__AA_CAGUGGC\n______________\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUC__UU_GUCACCG\n3'-UUU...UGUAG____UU__C_______-5'\n_____________\|_______________\|\n_____________17______________1\n	214 -- 220	1 -- 7	-16.0357 kcal/mol	1.55126 kcal/mol	1.34555 kcal/mol	205 221@LB@ \| \|@LB@5'-GAC...AUGAA UU GGCUU...CUG-3'@LB@ AAAG AA CAGUGGC@LB@ \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC UU GUCACCG@LB@3'-UUU...UGUAG UU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.0357 kcal/mol@LB@Unfolding Energy - mRNA 1.55126 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 206 -- 220@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@LB@
62	0.003256	0.1843	b1243	oppA	-14.22	0.042360	208 -- 232	1 -- 21	oligopeptide ABC transporter periplasmic binding protein		_____________207_______________________233\n_____________\|_________________________\|\n5'-UGU...GACCA______CC_________UU___A__AGCUG...UCA-3'\n______________ACAUCA__AAGAGAAGU__AGU_GC\n______________\|\|\|\|\|\|__\|\|\|\|:\|\|\|:__\|\|\|_\|\|\n______________UGUAGU__UUCUUUUCG__UCA_CG\n3'-UUU...ACCCC______________________C__-5'\n_____________\|________________________\|\n_____________22_______________________1\n	218 -- 224	7 -- 13	-18.9529 kcal/mol	3.22094 kcal/mol	1.51103 kcal/mol	207 233@LB@ \| \|@LB@5'-UGU...GACCA CC UU A AGCUG...UCA-3'@LB@ ACAUCA AAGAGAAGU AGU GC@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|: \|\|\| \|\|@LB@ UGUAGU UUCUUUUCG UCA CG@LB@3'-UUU...ACCCC C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -18.9529 kcal/mol@LB@Unfolding Energy - mRNA 3.22094 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 208 -- 232@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 7 -- 13@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