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
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase	_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@LB@
135	0.01294	0.3087	b3785	wzzE	-4.46	0.409883	275 -- 291	39 -- 56	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein	_____________274_________________292\n_____________\|___________________\|\n5'-GCU...CGUAC___________U_______UAUGG...UUA-3'\n______________CUUGU__GGGC_GGGAAGC\n______________\|\|\|\|:__::\|\|_::\|\|\|\|\|\n______________GAACG__UUCG_UUCUUCG\n3'-UUU...ACUUU_____AA____________UGAAU...CAA-5'\n_____________\|___________________\|\n_____________57__________________38\n	285 -- 291	39 -- 45	-16.5835 kcal/mol	6.01236 kcal/mol	6.11167 kcal/mol	274 292@LB@ \| \|@LB@5'-GCU...CGUAC U UAUGG...UUA-3'@LB@ CUUGU GGGC GGGAAGC@LB@ \|\|\|\|: ::\|\| ::\|\|\|\|\|@LB@ GAACG UUCG UUCUUCG@LB@3'-UUU...ACUUU AA UGAAU...CAA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -4.46 kcal/mol@LB@Hybridization Energy -16.5835 kcal/mol@LB@Unfolding Energy - mRNA 6.01236 kcal/mol@LB@Unfolding Energy - sRNA 6.11167 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 39 -- 45@LB@
183	0.02165	0.3768	b4201	priB	-4.41	0.419305	289 -- 298	45 -- 54	primosomal protein N	_____________288________299\n_____________\|__________\|\n5'-AGG...GUUCG__________UC-3'\n______________UGCUUGAGCA\n______________\|\|\|\|\|:\|\|\|\|\n______________ACGAAUUCGU\n3'-UUU...UUUGA__________UCUUC...CAA-5'\n_____________\|__________\|\n_____________55_________44\n	290 -- 296	47 -- 53	-14.7774 kcal/mol	4.46723 kcal/mol	5.90361 kcal/mol	288 299@LB@ \| \|@LB@5'-AGG...GUUCG UC-3'@LB@ UGCUUGAGCA@LB@ \|\|\|\|\|:\|\|\|\|@LB@ ACGAAUUCGU@LB@3'-UUU...UUUGA UCUUC...CAA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -4.41 kcal/mol@LB@Hybridization Energy -14.7774 kcal/mol@LB@Unfolding Energy - mRNA 4.46723 kcal/mol@LB@Unfolding Energy - sRNA 5.90361 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 47 -- 53@LB@
65	0.003382	0.1645	b1739	osmE	-4.35	0.428849	173 -- 228	7 -- 58	osmotically-inducible lipoprotein	_____________172______________________________________________________229\n_____________\|________________________________________________________\|\n5'-GAA...UAUCU___AC___GA___A_______A__GAAUAUGAACAAGAA____G______U_____GUGCA...AGC-3'\n______________AAC__GCU__UAA_CAAGAGG_CG_______________UAUG_CAGGAA_UCUGA\n______________\|\|\|__\|\|\|__\|\|\|_\|\|\|\|\|:\|_\|:_______________\|\|::_\|\|\|\|\|\|_\|\|\|\|\|\n______________UUG__CGA__AUU_GUUCUUC_GU_______________AUGU_GUCCUU_AGACU\n3'-UUU...CUACU___AA________C__________GAAUUUUUUAAGCA_____G______U_____ACACAA-5'\n_____________\|________________________________________________________\|\n_____________59_______________________________________________________6\n	187 -- 193	40 -- 46	-28.7812 kcal/mol	10.5809 kcal/mol	13.8467 kcal/mol	172 229@LB@ \| \|@LB@5'-GAA...UAUCU AC GA A A GAAUAUGAACAAGAA G U GUGCA...AGC-3'@LB@ AAC GCU UAA CAAGAGG CG UAUG CAGGAA UCUGA@LB@ \|\|\| \|\|\| \|\|\| \|\|\|\|\|:\| \|: \|\|:: \|\|\|\|\|\| \|\|\|\|\|@LB@ UUG CGA AUU GUUCUUC GU AUGU GUCCUU AGACU@LB@3'-UUU...CUACU AA C GAAUUUUUUAAGCA G U ACACAA-5'@LB@ \| \|@LB@ 59 6@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -28.7812 kcal/mol@LB@Unfolding Energy - mRNA 10.5809 kcal/mol@LB@Unfolding Energy - sRNA 13.8467 kcal/mol@LB@@LB@Position - mRNA 173 -- 228@LB@Position - sRNA 7 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@LB@
138	0.01322	0.3087	b1523	yneG	-4.22	0.452951	267 -- 281	24 -- 41	DUF4186 family protein	_____________266________________282\n_____________\|__________________\|\n5'-AUG...GUCUG_____________G____CAGUA...AAG-3'\n______________GGCA__UGAAAGA__CGU\n______________:\|\|\|__\|:\|\|\|:\|__\|\|\|\n______________UCGU__AUUUUUU__GCA\n3'-UUU...GUUCU____GA_______AA___AUGUG...CAA-5'\n_____________\|__________________\|\n_____________42_________________23\n	271 -- 277	29 -- 35	-8.58312 kcal/mol	2.71204 kcal/mol	1.64881 kcal/mol	266 282@LB@ \| \|@LB@5'-AUG...GUCUG G CAGUA...AAG-3'@LB@ GGCA UGAAAGA CGU@LB@ :\|\|\| \|:\|\|\|:\| \|\|\|@LB@ UCGU AUUUUUU GCA@LB@3'-UUU...GUUCU GA AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -4.22 kcal/mol@LB@Hybridization Energy -8.58312 kcal/mol@LB@Unfolding Energy - mRNA 2.71204 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 267 -- 281@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 29 -- 35@LB@
99	0.007347	0.239	b4348	hsdS	-4.18	0.460078	133 -- 139	70 -- 76	specificity determinant for hsdM and hsdR	_____________132_____140\n_____________\|_______\|\n5'-CUG...GUGAA_______CGAGC...UAA-3'\n______________CUGGGGG\n______________\|\|\|:\|\|\|\n______________GACUCCC\n3'-UUU...GCUGG_______CCAGC...CAA-5'\n_____________\|_______\|\n_____________77______69\n	133 -- 139	70 -- 76	-10.3039 kcal/mol	2.51492 kcal/mol	3.60488 kcal/mol	132 140@LB@ \| \|@LB@5'-CUG...GUGAA CGAGC...UAA-3'@LB@ CUGGGGG@LB@ \|\|\|:\|\|\|@LB@ GACUCCC@LB@3'-UUU...GCUGG CCAGC...CAA-5'@LB@ \| \|@LB@ 77 69@LB@@LB@@LB@Energy -4.18 kcal/mol@LB@Hybridization Energy -10.3039 kcal/mol@LB@Unfolding Energy - mRNA 2.51492 kcal/mol@LB@Unfolding Energy - sRNA 3.60488 kcal/mol@LB@@LB@Position - mRNA 133 -- 139@LB@Position - sRNA 70 -- 76@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 70 -- 76@LB@
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@
87	0.005861	0.217	b3083	higB	-4.01	0.492619	220 -- 233	28 -- 42	mRNA interferase toxin of the HigB-HigA toxin-antitoxin system	_____________219_____________234\n_____________\|_______________\|\n5'-GCA...UCAAA_______________GCUGC...GAU-3'\n______________AAGCAUU_GAAAGAU\n______________\|\|\|\|\|:\|_:\|\|\|:\|\|\n______________UUCGUGA_UUUUUUA\n3'-UUU...CGUUC_______A_______AGCAA...CAA-5'\n_____________\|_______________\|\n_____________43______________27\n	220 -- 226	36 -- 42	-9.16043 kcal/mol	3.51035 kcal/mol	1.63711 kcal/mol	219 234@LB@ \| \|@LB@5'-GCA...UCAAA GCUGC...GAU-3'@LB@ AAGCAUU GAAAGAU@LB@ \|\|\|\|\|:\| :\|\|\|:\|\|@LB@ UUCGUGA UUUUUUA@LB@3'-UUU...CGUUC A AGCAA...CAA-5'@LB@ \| \|@LB@ 43 27@LB@@LB@@LB@Energy -4.01 kcal/mol@LB@Hybridization Energy -9.16043 kcal/mol@LB@Unfolding Energy - mRNA 3.51035 kcal/mol@LB@Unfolding Energy - sRNA 1.63711 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 28 -- 42@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 36 -- 42@LB@
140	0.01344	0.3093	b0426	yajQ	-3.92	0.510019	240 -- 246	37 -- 43	phage Phi6 host factor ATP/GTP binding protein	_____________239_____247\n_____________\|_______\|\n5'-UAA...UUCAG_______GUAAC...GUA-3'\n______________GAAGCAC\n______________\|\|\|\|\|\|\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	240 -- 246	37 -- 43	-10.1802 kcal/mol	2.59742 kcal/mol	3.6595 kcal/mol	239 247@LB@ \| \|@LB@5'-UAA...UUCAG GUAAC...GUA-3'@LB@ GAAGCAC@LB@ \|\|\|\|\|\|\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -3.92 kcal/mol@LB@Hybridization Energy -10.1802 kcal/mol@LB@Unfolding Energy - mRNA 2.59742 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 240 -- 246@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 37 -- 43@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@

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