Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
117	0.0126	0.3585	b2200	ccmB	-15.87	0.019639	270 -- 292	1 -- 22	heme export ABC transporter permease	_____________269_____________________293\n_____________\|_______________________\|\n5'-CGU...CCAAC____U_U__U_____________AAUUACCC-3'\n______________CCGC_G_GG_UCUUCCUGAUUGU\n______________\|\|\|\|_\|_\|\|_\|\|\|\|\|\|\|\|\|\|:\|:\n______________GGCG_C_CC_AGAAGGACUAGCG\n3'-UUU...CAAGA______U__C_____________-5'\n_____________\|______________________\|\n_____________23_____________________1\n	286 -- 292	1 -- 7	-31.2771 kcal/mol	7.85543 kcal/mol	7.55214 kcal/mol	269 293@LB@ \| \|@LB@5'-CGU...CCAAC U U U AAUUACCC-3'@LB@ CCGC G GG UCUUCCUGAUUGU@LB@ \|\|\|\| \| \|\| \|\|\|\|\|\|\|\|\|\|:\|:@LB@ GGCG C CC AGAAGGACUAGCG@LB@3'-UUU...CAAGA U C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -31.2771 kcal/mol@LB@Unfolding Energy - mRNA 7.85543 kcal/mol@LB@Unfolding Energy - sRNA 7.55214 kcal/mol@LB@@LB@Position - mRNA 270 -- 292@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.006788	0.3082	b3525	yhjH	-16.42	0.015793	272 -- 288	44 -- 60	cyclic-di-GMP phosphodiesterase FlhDC-regulated	_____________271_______________289\n_____________\|_________________\|\n5'-UUA...CGUUU____UU___________GUGCU...CCU-3'\n______________UUGG__GCAGUGUGAGC\n______________:\|\|\|__\|\|\|:\|\|\|\|\|\|\|\n______________GACC__CGUUACACUCG\n3'-UUU...AUUAU____UU___________UUACA...GCG-5'\n_____________\|_________________\|\n_____________61________________43\n	279 -- 285	47 -- 53	-25.6078 kcal/mol	5.89114 kcal/mol	3.2985 kcal/mol	271 289@LB@ \| \|@LB@5'-UUA...CGUUU UU GUGCU...CCU-3'@LB@ UUGG GCAGUGUGAGC@LB@ :\|\|\| \|\|\|:\|\|\|\|\|\|\|@LB@ GACC CGUUACACUCG@LB@3'-UUU...AUUAU UU UUACA...GCG-5'@LB@ \| \|@LB@ 61 43@LB@@LB@@LB@Energy -16.42 kcal/mol@LB@Hybridization Energy -25.6078 kcal/mol@LB@Unfolding Energy - mRNA 5.89114 kcal/mol@LB@Unfolding Energy - sRNA 3.2985 kcal/mol@LB@@LB@Position - mRNA 272 -- 288@LB@Position - sRNA 44 -- 60@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 47 -- 53@LB@
132	0.01454	0.37	b1083	flgL	-7.54	0.428067	272 -- 293	37 -- 57	flagellar hook-filament junction protein	_____________271____________________294\n_____________\|______________________\|\n5'-UUG...UGGAU______CG_C__ACA_______ACGGGUA-3'\n______________GAAGUA__G_GA___GAUGUCG\n______________\|\|\|\|:\|__\|_\|\|___:\|\|\|\|\|\|\n______________CUUCGU__C_CU___UUACAGC\n3'-UUU...AUGAC______UA_A__CG________ACGAA...GCG-5'\n_____________\|______________________\|\n_____________58_____________________36\n	287 -- 293	37 -- 43	-16.4529 kcal/mol	5.68525 kcal/mol	3.2267 kcal/mol	271 294@LB@ \| \|@LB@5'-UUG...UGGAU CG C ACA ACGGGUA-3'@LB@ GAAGUA G GA GAUGUCG@LB@ \|\|\|\|:\| \| \|\| :\|\|\|\|\|\|@LB@ CUUCGU C CU UUACAGC@LB@3'-UUU...AUGAC UA A CG ACGAA...GCG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -7.54 kcal/mol@LB@Hybridization Energy -16.4529 kcal/mol@LB@Unfolding Energy - mRNA 5.68525 kcal/mol@LB@Unfolding Energy - sRNA 3.2267 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
197	0.02501	0.4226	b2947	gshB	-10.62	0.150229	274 -- 293	36 -- 62	glutathione synthetase	_____________273_________________________294\n_____________\|___________________________\|\n5'-UGC...UAUGU_____________________C_____GGUUACG-3'\n______________UGCUGGAAGCA_______CAG_GUCGU\n______________\|:\|\|\|\|\|\|\|\|\|_______\|\|:_\|\|\|\|\|\n______________AUGACCUUCGU_______GUU_CAGCA\n3'-UUU...UCAUU___________UACACUC___A_____CGAAA...GCG-5'\n_____________\|___________________________\|\n_____________63__________________________35\n	278 -- 284	52 -- 58	-23.3786 kcal/mol	9.45801 kcal/mol	3.30265 kcal/mol	273 294@LB@ \| \|@LB@5'-UGC...UAUGU C GGUUACG-3'@LB@ UGCUGGAAGCA CAG GUCGU@LB@ \|:\|\|\|\|\|\|\|\|\| \|\|: \|\|\|\|\|@LB@ AUGACCUUCGU GUU CAGCA@LB@3'-UUU...UCAUU UACACUC A CGAAA...GCG-5'@LB@ \| \|@LB@ 63 35@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -23.3786 kcal/mol@LB@Unfolding Energy - mRNA 9.45801 kcal/mol@LB@Unfolding Energy - sRNA 3.30265 kcal/mol@LB@@LB@Position - mRNA 274 -- 293@LB@Position - sRNA 36 -- 62@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 52 -- 58@LB@
139	0.01578	0.3813	b3386	rpe	-11.91	0.092481	276 -- 300	34 -- 60	D-ribulose-5-phosphate 3-epimerase	_____________275_________________________300\n_____________\|___________________________\|\n5'-CGC...AAGCC____C_________C__U__________-3'\n______________CUGG_AGC__UG_G_GC_GAUGUCGUGC\n______________\|\|\|\|_\|\|\|__\|\|_\|_\|\|_:\|\|\|\|\|\|\|\|\|\n______________GACC_UCG__AC_C_CG_UUACAGCACG\n3'-UUU...AUUAU____U___UU__A_U_____________AAAGU...GCG-5'\n_____________\|____________________________\|\n_____________61___________________________33\n	294 -- 300	34 -- 40	-27.2321 kcal/mol	8.55668 kcal/mol	6.76671 kcal/mol	275 300@LB@ \| \|@LB@5'-CGC...AAGCC C C U -3'@LB@ CUGG AGC UG G GC GAUGUCGUGC@LB@ \|\|\|\| \|\|\| \|\| \| \|\| :\|\|\|\|\|\|\|\|\|@LB@ GACC UCG AC C CG UUACAGCACG@LB@3'-UUU...AUUAU U UU A U AAAGU...GCG-5'@LB@ \| \|@LB@ 61 33@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -27.2321 kcal/mol@LB@Unfolding Energy - mRNA 8.55668 kcal/mol@LB@Unfolding Energy - sRNA 6.76671 kcal/mol@LB@@LB@Position - mRNA 276 -- 300@LB@Position - sRNA 34 -- 60@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 34 -- 40@LB@
129	0.01401	0.3627	b0696	kdpC	-11.63	0.102829	282 -- 295	49 -- 63	potassium translocating ATPase subunit C	_____________281_____________296\n_____________\|_______________\|\n5'-GCG...CCACC_______________GUGGU-3'\n______________GUACUGG_GGCAAUG\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\n______________UAUGACC_UCGUUAC\n3'-UUU...UUCAU_______U_______ACUCG...GCG-5'\n_____________\|_______________\|\n_____________64______________48\n	289 -- 295	49 -- 55	-18.0603 kcal/mol	3.42021 kcal/mol	3.01015 kcal/mol	281 296@LB@ \| \|@LB@5'-GCG...CCACC GUGGU-3'@LB@ GUACUGG GGCAAUG@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UAUGACC UCGUUAC@LB@3'-UUU...UUCAU U ACUCG...GCG-5'@LB@ \| \|@LB@ 64 48@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -18.0603 kcal/mol@LB@Unfolding Energy - mRNA 3.42021 kcal/mol@LB@Unfolding Energy - sRNA 3.01015 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 49 -- 63@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 49 -- 55@LB@
151	0.01843	0.4072	b4028	yjbG	-13.08	0.058794	282 -- 297	40 -- 55	extracellular polysaccharide export OMA protein	_____________281______________298\n_____________\|________________\|\n5'-AAA...UGUUC_______GC_______AGG-3'\n______________AGCAAUG__AGCAGUG\n______________\|\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________UCGUUAC__UCGUUAC\n3'-UUU...GACCU_______AC_______AGCAC...GCG-5'\n_____________\|________________\|\n_____________56_______________39\n	291 -- 297	40 -- 46	-18.8155 kcal/mol	2.52344 kcal/mol	3.20849 kcal/mol	281 298@LB@ \| \|@LB@5'-AAA...UGUUC GC AGG-3'@LB@ AGCAAUG AGCAGUG@LB@ \|\|\|\|\|\|\| \|\|\|\|:\|\|@LB@ UCGUUAC UCGUUAC@LB@3'-UUU...GACCU AC AGCAC...GCG-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -18.8155 kcal/mol@LB@Unfolding Energy - mRNA 2.52344 kcal/mol@LB@Unfolding Energy - sRNA 3.20849 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 40 -- 46@LB@
40	0.003423	0.2776	b3901	rhaM	-14.12	0.039141	284 -- 296	49 -- 61	L-rhamnose mutarotase	_____________283___________297\n_____________\|_____________\|\n5'-ACG...CCAGA_____________CUGA-3'\n______________ACUGGAAGCAGUG\n______________\|\|\|\|\|\|\|\|\|\|:\|\|\n______________UGACCUUCGUUAC\n3'-UUU...CAUUA_____________ACUCG...GCG-5'\n_____________\|_____________\|\n_____________62____________48\n	290 -- 296	49 -- 55	-21.3506 kcal/mol	4.21776 kcal/mol	3.00866 kcal/mol	283 297@LB@ \| \|@LB@5'-ACG...CCAGA CUGA-3'@LB@ ACUGGAAGCAGUG@LB@ \|\|\|\|\|\|\|\|\|\|:\|\|@LB@ UGACCUUCGUUAC@LB@3'-UUU...CAUUA ACUCG...GCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -14.12 kcal/mol@LB@Hybridization Energy -21.3506 kcal/mol@LB@Unfolding Energy - mRNA 4.21776 kcal/mol@LB@Unfolding Energy - sRNA 3.00866 kcal/mol@LB@@LB@Position - mRNA 284 -- 296@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 49 -- 55@LB@
49	0.004671	0.2905	b3184	yhbE	-14.90	0.028775	284 -- 299	49 -- 64	EamA family inner membrane putative transporter	_____________283______________300\n_____________\|________________\|\n5'-AAG...AAGCA________________G-3'\n______________GGUGCUGGAGGUGAUG\n______________::\|:\|\|\|\|\|:\|::\|\|\|\n______________UUAUGACCUUCGUUAC\n3'-UUU...AUUCA________________ACUCG...GCG-5'\n_____________\|________________\|\n_____________65_______________48\n	293 -- 299	49 -- 55	-22.6177 kcal/mol	4.70237 kcal/mol	3.01036 kcal/mol	283 300@LB@ \| \|@LB@5'-AAG...AAGCA G-3'@LB@ GGUGCUGGAGGUGAUG@LB@ ::\|:\|\|\|\|\|:\|::\|\|\|@LB@ UUAUGACCUUCGUUAC@LB@3'-UUU...AUUCA ACUCG...GCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -22.6177 kcal/mol@LB@Unfolding Energy - mRNA 4.70237 kcal/mol@LB@Unfolding Energy - sRNA 3.01036 kcal/mol@LB@@LB@Position - mRNA 284 -- 299@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 49 -- 55@LB@
194	0.02479	0.4226	b1260	trpA	-8.29	0.338830	290 -- 297	41 -- 48	tryptophan synthase alpha subunit	_____________289______298\n_____________\|________\|\n5'-GCC...GGCAU________CAU-3'\n______________UGAGCAGU\n______________\|\|\|\|\|\|:\|\n______________ACUCGUUA\n3'-UUU...GUUAC________CAGCA...GCG-5'\n_____________\|________\|\n_____________49_______40\n	291 -- 297	41 -- 47	-10.1831 kcal/mol	0.772851 kcal/mol	1.11967 kcal/mol	289 298@LB@ \| \|@LB@5'-GCC...GGCAU CAU-3'@LB@ UGAGCAGU@LB@ \|\|\|\|\|\|:\|@LB@ ACUCGUUA@LB@3'-UUU...GUUAC CAGCA...GCG-5'@LB@ \| \|@LB@ 49 40@LB@@LB@@LB@Energy -8.29 kcal/mol@LB@Hybridization Energy -10.1831 kcal/mol@LB@Unfolding Energy - mRNA 0.772851 kcal/mol@LB@Unfolding Energy - sRNA 1.11967 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 41 -- 48@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 41 -- 47@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)

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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

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