Input and runtime details for job 8257533 (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 8257533 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:34:31 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:34:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:30:38 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:30:45 CET 2018
	Job Completed		@ Fri Feb 16 22:31:01 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=8257533&toolName=CopraRNA ( 30 days expiry )

Description of the job

LhrA2

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_003210 Listeria monocytogenes EGD-e

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
8	0.001816	0.4469	lmo1666	N/A	-21.94	0.003684	151 -- 207	157 -- 207	peptidoglycan-linked protein	lmo0333	_____________150____________208\n_____________\|______________\|\n5'-GUG...AGAUG______________GUAAA...CUC-3'\n______________GGGAUGAAUGAAAA\n______________\|:\|\|\|\|\|\|\|\|\|\|\|\|\n______________CUCUACUUACUUUU\n3'-GUU...GGUUA______________GUUUA...GGA-5'\n_____________\|______________\|\n_____________208____________156\n	201 -- 207	157 -- 163	-18.267 kcal/mol	1.529 kcal/mol	0.904482 kcal/mol	150 208@LB@ \| \|@LB@5'-GUG...AGAUG GUAAA...CUC-3'@LB@ GGGAUGAAUGAAAA@LB@ \|:\|\|\|\|\|\|\|\|\|\|\|\|@LB@ CUCUACUUACUUUU@LB@3'-GUU...GGUUA GUUUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -21.94 kcal/mol@LB@Hybridization Energy -18.267 kcal/mol@LB@Unfolding Energy - mRNA 1.529 kcal/mol@LB@Unfolding Energy - sRNA 0.904482 kcal/mol@LB@@LB@Position - mRNA 151 -- 207@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
23	0.00382	0.4469	lmo1572	accA	-20.61	0.007329	192 -- 226	157 -- 188	acetyl-CoA carboxylase carboxyltransferase subunit alpha		_____________191______________________________________________________________________________227\n_____________\|________________________________________________________________________________\|\n5'-AGG...UUUAA__AU______GAAA__A____GA_____________A__UG__________________G___________AUU______ACCGA...CCA-3'\n______________GC__UCAUGU____GC_CCUG___GUAG_GGGGUGA_GU_______________AUGGC_AAUGAGAUGGA___UGAGAA\n______________\|\|__\|\|\|\|\|\|____\|\|_\|\|\|:___:\|\|:_\|\|\|:\|\|\|_\|:_______________\|:\|\|\|_\|\|\|\|\|\|\|\|\|:\|___\|\|\|:\|\|\n______________CG__AGUACA____CG_GGAU___UAUU_CCCUACU_CG_______________UGCCG_UUACUCUACUU___ACUUUU\n3'-GUU...CGCAA__GU______AGCC__C____ACG____G_______C__UAUCUGUACUUGAUG_____G____________________GUUUA...GGA-5'\n_____________\|________________________________________________________________________________\|\n_____________189______________________________________________________________________________156\n	211 -- 217	163 -- 169	-59.1532 kcal/mol	18.9584 kcal/mol	22.6787 kcal/mol	191 227@LB@ \| \|@LB@5'-AGG...UUUAA AU GAAA A GA A UG G AUU ACCGA...CCA-3'@LB@ GC UCAUGU GC CCUG GUAG GGGGUGA GU AUGGC AAUGAGAUGGA UGAGAA@LB@ \|\| \|\|\|\|\|\| \|\| \|\|\|: :\|\|: \|\|\|:\|\|\| \|: \|:\|\|\| \|\|\|\|\|\|\|\|\|:\| \|\|\|:\|\|@LB@ CG AGUACA CG GGAU UAUU CCCUACU CG UGCCG UUACUCUACUU ACUUUU@LB@3'-GUU...CGCAA GU AGCC C ACG G C UAUCUGUACUUGAUG G GUUUA...GGA-5'@LB@ \| \|@LB@ 189 156@LB@@LB@@LB@Energy -20.61 kcal/mol@LB@Hybridization Energy -59.1532 kcal/mol@LB@Unfolding Energy - mRNA 18.9584 kcal/mol@LB@Unfolding Energy - sRNA 22.6787 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 157 -- 188@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 163 -- 169@LB@
41	0.008795	0.5772	lmo1984	ilvB	-19.06	0.015768	187 -- 229	157 -- 201	acetolactate synthase		_____________186____________________________________________230\n_____________\|______________________________________________\|\n5'-AUU...AAAAA_______G___A______UUG_____A_________CA________AGCGA...ACA-3'\n______________AUGAGGU_AUA_GCGUGA___AUACG__CGA__AGA__AAUGAAAA\n______________\|\|\|\|\|\|:_\|\|\|_:\|:\|\|\|___\|:\|\|\|__\|:\|__\|\|\|__\|\|\|\|\|\|\|\|\n______________UACUCCG_UAU_UGUACU___UGUGC__GUU__UCU__UUACUUUU\n3'-GUU...UGCCC___________C______UGA_____CG___AC___AC________GUUUA...GGA-5'\n_____________\|______________________________________________\|\n_____________202____________________________________________156\n	223 -- 229	157 -- 163	-31.6948 kcal/mol	5.6221 kcal/mol	13.9999 kcal/mol	186 230@LB@ \| \|@LB@5'-AUU...AAAAA G A UUG A CA AGCGA...ACA-3'@LB@ AUGAGGU AUA GCGUGA AUACG CGA AGA AAUGAAAA@LB@ \|\|\|\|\|\|: \|\|\| :\|:\|\|\| \|:\|\|\| \|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ UACUCCG UAU UGUACU UGUGC GUU UCU UUACUUUU@LB@3'-GUU...UGCCC C UGA CG AC AC GUUUA...GGA-5'@LB@ \| \|@LB@ 202 156@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -31.6948 kcal/mol@LB@Unfolding Energy - mRNA 5.6221 kcal/mol@LB@Unfolding Energy - sRNA 13.9999 kcal/mol@LB@@LB@Position - mRNA 187 -- 229@LB@Position - sRNA 157 -- 201@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 157 -- 163@LB@
45	0.0103	0.599	lmo0066	N/A	-17.00	0.040990	179 -- 207	157 -- 199	toxin		_____________178___________208\n_____________\|_____________\|\n5'-AAA...AGGCC_____________AAGUC...AUU-3'\n______________AGAUGAAUGAAAG\n______________\|\|\|\|\|\|\|\|\|\|\|\|:\n______________UCUACUUACUUUU\n3'-GUU...GUUAC_____________GUUUA...GGA-5'\n_____________\|_____________\|\n_____________200___________156\n	201 -- 207	157 -- 163	-14.7839 kcal/mol	1.76886 kcal/mol	0.884237 kcal/mol	178 208@LB@ \| \|@LB@5'-AAA...AGGCC AAGUC...AUU-3'@LB@ AGAUGAAUGAAAG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|:@LB@ UCUACUUACUUUU@LB@3'-GUU...GUUAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -14.7839 kcal/mol@LB@Unfolding Energy - mRNA 1.76886 kcal/mol@LB@Unfolding Energy - sRNA 0.884237 kcal/mol@LB@@LB@Position - mRNA 179 -- 207@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 157 -- 163@LB@
48	0.01096	0.599	lmo0184	N/A	-18.00	0.026009	159 -- 211	157 -- 203	oligo-1 6-glucosidase		_____________158_____212\n_____________\|_______\|\n5'-ACG...ACAAG_______AUUUA...GAA-3'\n______________GGCGGGA\n______________::\|\|\|\|\|\n______________UUGCCCU\n3'-GUU...ACGUA_______ACUCC...GGA-5'\n_____________\|_______\|\n_____________204_____156\n	185 -- 191	201 -- 207	-10.9952 kcal/mol	1.94403 kcal/mol	0.326294 kcal/mol	158 212@LB@ \| \|@LB@5'-ACG...ACAAG AUUUA...GAA-3'@LB@ GGCGGGA@LB@ ::\|\|\|\|\|@LB@ UUGCCCU@LB@3'-GUU...ACGUA ACUCC...GGA-5'@LB@ \| \|@LB@ 204 156@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -10.9952 kcal/mol@LB@Unfolding Energy - mRNA 1.94403 kcal/mol@LB@Unfolding Energy - sRNA 0.326294 kcal/mol@LB@@LB@Position - mRNA 159 -- 211@LB@Position - sRNA 157 -- 203@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 201 -- 207@LB@
49	0.01139	0.599	lmo0181	N/A	-18.25	0.023109	147 -- 168	157 -- 179	sugar ABC transporter substrate-binding protein		_____________146________________169\n_____________\|__________________\|\n5'-AAG...AAUGG_______CG_________AAUAA...UUA-3'\n______________CAAUGAG__GAAUGAAAG\n______________\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\|:\n______________GUUACUC__CUUACUUUU\n3'-GUU...UGCCG_______UA_________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________180________________156\n	162 -- 168	157 -- 163	-17.3464 kcal/mol	2.46271 kcal/mol	0.933292 kcal/mol	146 169@LB@ \| \|@LB@5'-AAG...AAUGG CG AAUAA...UUA-3'@LB@ CAAUGAG GAAUGAAAG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|:@LB@ GUUACUC CUUACUUUU@LB@3'-GUU...UGCCG UA GUUUA...GGA-5'@LB@ \| \|@LB@ 180 156@LB@@LB@@LB@Energy -18.25 kcal/mol@LB@Hybridization Energy -17.3464 kcal/mol@LB@Unfolding Energy - mRNA 2.46271 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 147 -- 168@LB@Position - sRNA 157 -- 179@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 157 -- 163@LB@
77	0.02006	0.6733	lmo1400	N/A	-17.16	0.038248	136 -- 215	157 -- 223	N-acetyltransferase		_____________135_____________216\n_____________\|_______________\|\n5'-AAA...GUUUU_______________AUUUU...AAG-3'\n______________UGAG_UGAGUGGAAA\n______________\|\|\|\|_\|\|\|:\|\|:\|\|\|\n______________ACUC_ACUUACUUUU\n3'-GUU...CGGUU____U__________GUUUA...GGA-5'\n_____________\|_______________\|\n_____________224_____________156\n	209 -- 215	157 -- 163	-14.2437 kcal/mol	2.95971 kcal/mol	0.905109 kcal/mol	135 216@LB@ \| \|@LB@5'-AAA...GUUUU AUUUU...AAG-3'@LB@ UGAG UGAGUGGAAA@LB@ \|\|\|\| \|\|\|:\|\|:\|\|\|@LB@ ACUC ACUUACUUUU@LB@3'-GUU...CGGUU U GUUUA...GGA-5'@LB@ \| \|@LB@ 224 156@LB@@LB@@LB@Energy -17.16 kcal/mol@LB@Hybridization Energy -14.2437 kcal/mol@LB@Unfolding Energy - mRNA 2.95971 kcal/mol@LB@Unfolding Energy - sRNA 0.905109 kcal/mol@LB@@LB@Position - mRNA 136 -- 215@LB@Position - sRNA 157 -- 223@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 157 -- 163@LB@
98	0.02549	0.6733	lmo2155	N/A	-16.07	0.061955	240 -- 298	157 -- 207	ribonucleotide-diphosphate reductase subunit alpha		_____________239________299\n_____________\|__________\|\n5'-UAU...UAAAA__________AACAG...AAA-3'\n______________GACGGGG_GA\n______________:\|\|\|\|\|:_\|\|\n______________UUGCCCU_CU\n3'-GUU...ACGUA_______A__CCGUA...GGA-5'\n_____________\|__________\|\n_____________208________156\n	240 -- 246	201 -- 207	-11.5149 kcal/mol	1.00175 kcal/mol	0.374399 kcal/mol	239 299@LB@ \| \|@LB@5'-UAU...UAAAA AACAG...AAA-3'@LB@ GACGGGG GA@LB@ :\|\|\|\|\|: \|\|@LB@ UUGCCCU CU@LB@3'-GUU...ACGUA A CCGUA...GGA-5'@LB@ \| \|@LB@ 208 156@LB@@LB@@LB@Energy -16.07 kcal/mol@LB@Hybridization Energy -11.5149 kcal/mol@LB@Unfolding Energy - mRNA 1.00175 kcal/mol@LB@Unfolding Energy - sRNA 0.374399 kcal/mol@LB@@LB@Position - mRNA 240 -- 298@LB@Position - sRNA 157 -- 207@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 201 -- 207@LB@
104	0.02699	0.6733	lmo1327	rbfA	-16.36	0.054483	188 -- 240	157 -- 199	ribosome-binding factor A		_____________187________________241\n_____________\|__________________\|\n5'-ACA...CGUGU_______CA_________AAGAA...CUG-3'\n______________CAGUGAG___AAUGAAAA\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\n______________GUUACUC___UUACUUUU\n3'-GUU...UGCCG_______UAC________GUUUA...GGA-5'\n_____________\|__________________\|\n_____________200________________156\n	234 -- 240	157 -- 163	-12.7883 kcal/mol	2.00785 kcal/mol	0.933292 kcal/mol	187 241@LB@ \| \|@LB@5'-ACA...CGUGU CA AAGAA...CUG-3'@LB@ CAGUGAG AAUGAAAA@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GUUACUC UUACUUUU@LB@3'-GUU...UGCCG UAC GUUUA...GGA-5'@LB@ \| \|@LB@ 200 156@LB@@LB@@LB@Energy -16.36 kcal/mol@LB@Hybridization Energy -12.7883 kcal/mol@LB@Unfolding Energy - mRNA 2.00785 kcal/mol@LB@Unfolding Energy - sRNA 0.933292 kcal/mol@LB@@LB@Position - mRNA 188 -- 240@LB@Position - sRNA 157 -- 199@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 157 -- 163@LB@
138	0.03642	0.6968	lmo0509	prs	-15.18	0.090372	180 -- 241	157 -- 211	phosphoribosyl pyrophosphate synthetase		_____________179____________________________________242\n_____________\|______________________________________\|\n5'-AAC...GAAGA_____G______G__AG_____A_C_____C_______AUGAA...UCC-3'\n______________AAUUA_UAUGGC_GA__GAGAU_G_AAUGG_AGGCAAA\n______________\|\|:\|\|_:\|:\|\|\|_:\|__\|\|\|\|\|_\|_\|\|\|\|:_\|::\|\|\|\|\n______________UUGAU_GUGCCG_UU__CUCUA_C_UUACU_UUUGUUU\n3'-GUU...UGUAC____________G__A______________________AUUAC...GGA-5'\n_____________\|______________________________________\|\n_____________212____________________________________156\n	206 -- 212	153 -- 159	-24.2745 kcal/mol	6.00947 kcal/mol	10.6652 kcal/mol	179 242@LB@ \| \|@LB@5'-AAC...GAAGA G G AG A C C AUGAA...UCC-3'@LB@ AAUUA UAUGGC GA GAGAU G AAUGG AGGCAAA@LB@ \|\|:\|\| :\|:\|\|\| :\| \|\|\|\|\| \| \|\|\|\|: \|::\|\|\|\|@LB@ UUGAU GUGCCG UU CUCUA C UUACU UUUGUUU@LB@3'-GUU...UGUAC G A AUUAC...GGA-5'@LB@ \| \|@LB@ 212 156@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -24.2745 kcal/mol@LB@Unfolding Energy - mRNA 6.00947 kcal/mol@LB@Unfolding Energy - sRNA 10.6652 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 157 -- 211@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 153 -- 159@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