Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
153	0.016	0.3359	b2167	fruA	-4.10	0.476180	191 -- 199	37 -- 45	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________190_______200\n_____________\|_________\|\n5'-CGC...AGCAG_________AAUGA...AAA-3'\n______________GAGAGGCAU\n______________:\|\|\|:\|\|\|:\n______________UUCUUCGUG\n3'-UUU...AUUCG_________AAUUU...CAA-5'\n_____________\|_________\|\n_____________46________36\n	193 -- 199	37 -- 43	-10.9543 kcal/mol	1.97714 kcal/mol	4.8783 kcal/mol	190 200@LB@ \| \|@LB@5'-CGC...AGCAG AAUGA...AAA-3'@LB@ GAGAGGCAU@LB@ :\|\|\|:\|\|\|:@LB@ UUCUUCGUG@LB@3'-UUU...AUUCG AAUUU...CAA-5'@LB@ \| \|@LB@ 46 36@LB@@LB@@LB@Energy -4.10 kcal/mol@LB@Hybridization Energy -10.9543 kcal/mol@LB@Unfolding Energy - mRNA 1.97714 kcal/mol@LB@Unfolding Energy - sRNA 4.8783 kcal/mol@LB@@LB@Position - mRNA 191 -- 199@LB@Position - sRNA 37 -- 45@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 37 -- 43@LB@
198	0.02375	0.3864	b3946	fsaB	-8.18	0.053967	105 -- 117	26 -- 40	fructose-6-phosphate aldolase 2	_____________104_____________118\n_____________\|_______________\|\n5'-UGG...AUCAU_______________CGUAA...CUG-3'\n______________GCAC__GAAGAAUUC\n______________\|\|\|\|__:\|\|:\|\|\|\|\|\n______________CGUG__UUUUUUAAG\n3'-UUU...UUCUU____AA_________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	111 -- 117	26 -- 32	-11.851 kcal/mol	2.02524 kcal/mol	1.64811 kcal/mol	104 118@LB@ \| \|@LB@5'-UGG...AUCAU CGUAA...CUG-3'@LB@ GCAC GAAGAAUUC@LB@ \|\|\|\| :\|\|:\|\|\|\|\|@LB@ CGUG UUUUUUAAG@LB@3'-UUU...UUCUU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.18 kcal/mol@LB@Hybridization Energy -11.851 kcal/mol@LB@Unfolding Energy - mRNA 2.02524 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 105 -- 117@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 26 -- 32@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
152	0.01589	0.3359	b3428	glgP	-3.42	0.610648	252 -- 258	36 -- 42	glycogen phosphorylase	_____________251_____259\n_____________\|_______\|\n5'-CCA...CUCUU_______CUAUC...CGG-3'\n______________AAGCACU\n______________\|\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	252 -- 258	36 -- 42	-8.34293 kcal/mol	3.32239 kcal/mol	1.60154 kcal/mol	251 259@LB@ \| \|@LB@5'-CCA...CUCUU CUAUC...CGG-3'@LB@ AAGCACU@LB@ \|\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -3.42 kcal/mol@LB@Hybridization Energy -8.34293 kcal/mol@LB@Unfolding Energy - mRNA 3.32239 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 252 -- 258@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 36 -- 42@LB@
173	0.01972	0.3669	b3426	glpD	-5.91	0.203159	207 -- 224	3 -- 20	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding	_____________206_________________225\n_____________\|___________________\|\n5'-AAC...UGGAA____A_________U____AUAGG...AGG-3'\n______________ACCA__AGAUCUGA_UGUG\n______________\|\|\|\|__\|:\|\|\|\|\|\|_\|\|\|\|\n______________UGGU__UUUAGACU_ACAC\n3'-UUU...CAAUG____CC_____________AA-5'\n_____________\|___________________\|\n_____________21__________________2\n	213 -- 219	7 -- 13	-16.1802 kcal/mol	2.74973 kcal/mol	7.52321 kcal/mol	206 225@LB@ \| \|@LB@5'-AAC...UGGAA A U AUAGG...AGG-3'@LB@ ACCA AGAUCUGA UGUG@LB@ \|\|\|\| \|:\|\|\|\|\|\| \|\|\|\|@LB@ UGGU UUUAGACU ACAC@LB@3'-UUU...CAAUG CC AA-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -16.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.74973 kcal/mol@LB@Unfolding Energy - sRNA 7.52321 kcal/mol@LB@@LB@Position - mRNA 207 -- 224@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 7 -- 13@LB@
137	0.01315	0.3087	b2239	glpQ	-7.04	0.107729	242 -- 248	36 -- 42	periplasmic glycerophosphodiester phosphodiesterase	_____________241_____249\n_____________\|_______\|\n5'-CGG...AUGAU_______AUAGU...UCA-3'\n______________GAGCACU\n______________:\|\|\|\|\|\|\n______________UUCGUGA\n3'-UUU...CGUUC_______AUUUU...CAA-5'\n_____________\|_______\|\n_____________43______35\n	242 -- 248	36 -- 42	-9.09813 kcal/mol	0.455964 kcal/mol	1.60154 kcal/mol	241 249@LB@ \| \|@LB@5'-CGG...AUGAU AUAGU...UCA-3'@LB@ GAGCACU@LB@ :\|\|\|\|\|\|@LB@ UUCGUGA@LB@3'-UUU...CGUUC AUUUU...CAA-5'@LB@ \| \|@LB@ 43 35@LB@@LB@@LB@Energy -7.04 kcal/mol@LB@Hybridization Energy -9.09813 kcal/mol@LB@Unfolding Energy - mRNA 0.455964 kcal/mol@LB@Unfolding Energy - sRNA 1.60154 kcal/mol@LB@@LB@Position - mRNA 242 -- 248@LB@Position - sRNA 36 -- 42@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 36 -- 42@LB@
162	0.01764	0.3508	b0654	gltJ	-6.81	0.123116	18 -- 45	15 -- 42	glutamate/aspartate ABC transporter permease	_____________17___________________________46\n_____________\|____________________________\|\n5'-CAA...UGACA_______GAACU____ACAAGA______GGCGG...UCG-3'\n______________AGGCACU_____AAUU______ACCAGG\n______________\|:\|\|\|\|\|_____\|\|\|\|______\|\|\|\|\|\|\n______________UUCGUGA_____UUAA______UGGUCC\n3'-UUU...CGUUC_______AUUUU____GCAAUG______UUUAG...CAA-5'\n_____________\|____________________________\|\n_____________43___________________________14\n	18 -- 24	36 -- 42	-19.3193 kcal/mol	3.30421 kcal/mol	9.20431 kcal/mol	17 46@LB@ \| \|@LB@5'-CAA...UGACA GAACU ACAAGA GGCGG...UCG-3'@LB@ AGGCACU AAUU ACCAGG@LB@ \|:\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|@LB@ UUCGUGA UUAA UGGUCC@LB@3'-UUU...CGUUC AUUUU GCAAUG UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -19.3193 kcal/mol@LB@Unfolding Energy - mRNA 3.30421 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 36 -- 42@LB@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@LB@
114	0.009652	0.2693	b2614	grpE	-8.47	0.044767	262 -- 275	27 -- 41	heat shock protein	_____________261_____________276\n_____________\|_______________\|\n5'-GAG...GGAUC_____G_________GAGGC...CUG-3'\n______________AGCAC__AAGAGAUU\n______________\|\|\|\|\|__\|\|:\|:\|\|\|\n______________UCGUG__UUUUUUAA\n3'-UUU...GUUCU_____AA________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	269 -- 275	27 -- 33	-11.1078 kcal/mol	0.992631 kcal/mol	1.6427 kcal/mol	261 276@LB@ \| \|@LB@5'-GAG...GGAUC G GAGGC...CUG-3'@LB@ AGCAC AAGAGAUU@LB@ \|\|\|\|\| \|\|:\|:\|\|\|@LB@ UCGUG UUUUUUAA@LB@3'-UUU...GUUCU AA GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.1078 kcal/mol@LB@Unfolding Energy - mRNA 0.992631 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 262 -- 275@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@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