Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
6	0.0002023	0.1081	b1884	cheR	-8.31	0.257615	184 -- 205	1 -- 21	chemotaxis regulator protein-glutamate methyltransferase	_____________183____________________206\n_____________\|______________________\|\n5'-GCC...CUGAA_____UGA_______C______UUCAU...UGA-3'\n______________GUGAU___GAAGGCG_UAUGAC\n______________\|\|\|\|:___:\|\|\|\|\|:_\|\|\|:\|\|\n______________CACUG___UUUCCGU_AUAUUG\n3'-UUU...UUAGA_____UUA______________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	192 -- 198	7 -- 13	-19.9838 kcal/mol	7.26541 kcal/mol	4.41334 kcal/mol	183 206@LB@ \| \|@LB@5'-GCC...CUGAA UGA C UUCAU...UGA-3'@LB@ GUGAU GAAGGCG UAUGAC@LB@ \|\|\|\|: :\|\|\|\|\|: \|\|\|:\|\|@LB@ CACUG UUUCCGU AUAUUG@LB@3'-UUU...UUAGA UUA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -19.9838 kcal/mol@LB@Unfolding Energy - mRNA 7.26541 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 184 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 7 -- 13@LB@
80	0.006956	0.2822	b1914	uvrY	-9.02	0.189987	260 -- 281	5 -- 24	response regulator in two-component regulatory system with BarA	_____________259____________________282\n_____________\|______________________\|\n5'-UUC...CGCAU____GAA____UA_________AAAGU...CAU-3'\n______________UCUG___GAUA__AAGGGUAUA\n______________\|\|\|\|___\|\|:\|__\|\|:\|\|:\|\|\|\n______________AGAC___CUGU__UUUCCGUAU\n3'-UUU...AUUUU____A______UA_________AUUG-5'\n_____________\|______________________\|\n_____________25_____________________4\n	275 -- 281	5 -- 11	-15.9126 kcal/mol	2.27135 kcal/mol	4.61703 kcal/mol	259 282@LB@ \| \|@LB@5'-UUC...CGCAU GAA UA AAAGU...CAU-3'@LB@ UCUG GAUA AAGGGUAUA@LB@ \|\|\|\| \|\|:\| \|\|:\|\|:\|\|\|@LB@ AGAC CUGU UUUCCGUAU@LB@3'-UUU...AUUUU A UA AUUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.9126 kcal/mol@LB@Unfolding Energy - mRNA 2.27135 kcal/mol@LB@Unfolding Energy - sRNA 4.61703 kcal/mol@LB@@LB@Position - mRNA 260 -- 281@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 5 -- 11@LB@
156	0.01801	0.3828	b1942	fliJ	-11.30	0.063944	187 -- 254	7 -- 65	flagellar protein	_____________186______________________________________________________________________255\n_____________\|________________________________________________________________________\|\n5'-UUC...ACCCA_____UAACGG___A_____GAACAUG_____C____GACCCU______________GCAGA__A_______GAGGA...AGC-3'\n______________GGAGA______CAG_UGGCA_______GUGCG_UGGC______GAAA____GAUCUG_____AA_AGAGGUA\n______________\|\|\|:\|______\|\|\|_\|\|\|\|\|_______:\|\|\|:_\|\|\|\|______\|\|\|\|____:\|\|\|\|\|_____\|\|_\|:\|\|\|:\|\n______________CCUUU______GUC_ACCGU_______UACGU_ACCG______CUUU____UUAGAC_____UU_UUUCCGU\n3'-UUU...UACAA_____UA_________________________U____GGUUGU____UAUU______ACUG___A_______AUAUUG-5'\n_____________\|________________________________________________________________________\|\n_____________66_______________________________________________________________________6\n	248 -- 254	7 -- 13	-39.8056 kcal/mol	16.3505 kcal/mol	12.1538 kcal/mol	186 255@LB@ \| \|@LB@5'-UUC...ACCCA UAACGG A GAACAUG C GACCCU GCAGA A GAGGA...AGC-3'@LB@ GGAGA CAG UGGCA GUGCG UGGC GAAA GAUCUG AA AGAGGUA@LB@ \|\|\|:\| \|\|\| \|\|\|\|\| :\|\|\|: \|\|\|\| \|\|\|\| :\|\|\|\|\| \|\| \|:\|\|\|:\|@LB@ CCUUU GUC ACCGU UACGU ACCG CUUU UUAGAC UU UUUCCGU@LB@3'-UUU...UACAA UA U GGUUGU UAUU ACUG A AUAUUG-5'@LB@ \| \|@LB@ 66 6@LB@@LB@@LB@Energy -11.30 kcal/mol@LB@Hybridization Energy -39.8056 kcal/mol@LB@Unfolding Energy - mRNA 16.3505 kcal/mol@LB@Unfolding Energy - sRNA 12.1538 kcal/mol@LB@@LB@Position - mRNA 187 -- 254@LB@Position - sRNA 7 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 7 -- 13@LB@
167	0.01994	0.3993	b1982	amn	-7.06	0.411594	174 -- 215	8 -- 54	AMP nucleosidase	_____________173______________________________________________216\n_____________\|________________________________________________\|\n5'-UUU...UGUGC_____U____________________CACACA___A____________UCCGG...GCA-3'\n______________GGUAA_UGU_AUGG___AACAGGAGA_______UG__AUAAUAAGGGC\n______________\|\|:\|\|_\|\|:_\|\|\|\|___\|\|\|\|\|:\|:\|_______\|\|__\|:\|\|\|\|\|:\|\|\|\n______________CCGUU_ACG_UACC___UUGUCUUUU_______AC__UGUUAUUUCCG\n3'-UUU...AGUCA_________U____GGG_________AUUUUAG__AC___________UAUAUUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________7\n	209 -- 215	8 -- 14	-29.9928 kcal/mol	10.9089 kcal/mol	12.019 kcal/mol	173 216@LB@ \| \|@LB@5'-UUU...UGUGC U CACACA A UCCGG...GCA-3'@LB@ GGUAA UGU AUGG AACAGGAGA UG AUAAUAAGGGC@LB@ \|\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|:\|:\| \|\| \|:\|\|\|\|\|:\|\|\|@LB@ CCGUU ACG UACC UUGUCUUUU AC UGUUAUUUCCG@LB@3'-UUU...AGUCA U GGG AUUUUAG AC UAUAUUG-5'@LB@ \| \|@LB@ 55 7@LB@@LB@@LB@Energy -7.06 kcal/mol@LB@Hybridization Energy -29.9928 kcal/mol@LB@Unfolding Energy - mRNA 10.9089 kcal/mol@LB@Unfolding Energy - sRNA 12.019 kcal/mol@LB@@LB@Position - mRNA 174 -- 215@LB@Position - sRNA 8 -- 54@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 8 -- 14@LB@
199	0.02539	0.4256	b2094	gatA	-8.91	0.199733	27 -- 47	1 -- 21	galactitol-specific enzyme IIA component of PTS	_____________26_____________________48\n_____________\|______________________\|\n5'-UUA...UGAUG____AUCU______________AUCCC...AUG-3'\n______________GUGA____UGAAGGCGUG_GAC\n______________\|\|\|\|____\|:\|\|\|\|\|:\|:_:\|\|\n______________CACU____AUUUCCGUAU_UUG\n3'-UUU...UUAGA____GUU___________A___-5'\n_____________\|_____________________\|\n_____________22____________________1\n	38 -- 44	5 -- 11	-17.7737 kcal/mol	4.45083 kcal/mol	4.41334 kcal/mol	26 48@LB@ \| \|@LB@5'-UUA...UGAUG AUCU AUCCC...AUG-3'@LB@ GUGA UGAAGGCGUG GAC@LB@ \|\|\|\| \|:\|\|\|\|\|:\|: :\|\|@LB@ CACU AUUUCCGUAU UUG@LB@3'-UUU...UUAGA GUU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -17.7737 kcal/mol@LB@Unfolding Energy - mRNA 4.45083 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 27 -- 47@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
131	0.01428	0.3654	b2099	yegU	-10.27	0.106798	246 -- 258	42 -- 54	ADP-ribosylglycohydrolase family protein	_____________245___________259\n_____________\|_____________\|\n5'-GUG...CGUUA__G__________GGAUG...CAC-3'\n______________GG_GAUGCGAUGG\n______________\|\|_:\|\|\|\|:\|\|\|\|\n______________CC_UUACGUUACC\n3'-UUU...AGUCA__G__________GGGUU...UUG-5'\n_____________\|_____________\|\n_____________55____________41\n	252 -- 258	42 -- 48	-19.8763 kcal/mol	6.10373 kcal/mol	3.49932 kcal/mol	245 259@LB@ \| \|@LB@5'-GUG...CGUUA G GGAUG...CAC-3'@LB@ GG GAUGCGAUGG@LB@ \|\| :\|\|\|\|:\|\|\|\|@LB@ CC UUACGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -19.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.10373 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 42 -- 48@LB@
101	0.009525	0.3118	b2101	yegW	-12.09	0.042153	47 -- 73	39 -- 66	putative DNA-binding transcriptional regulator	_____________46____________________________74\n_____________\|_____________________________\|\n5'-CGG...GACCG____CAGG___A_____U___________GGUGG...AAA-3'\n______________UGGA____UAG_UGGCA___CAAUGGUCC\n______________\|\|\|\|____:\|\|_\|\|\|\|\|___\|\|\|\|\|\|:\|\|\n______________ACCU____GUC_ACCGU___GUUACCGGG\n3'-UUU...AUACA____UUUA_________UAC_________UUGUC...UUG-5'\n_____________\|_____________________________\|\n_____________67____________________________38\n	67 -- 73	39 -- 45	-28.0375 kcal/mol	9.27172 kcal/mol	6.67256 kcal/mol	46 74@LB@ \| \|@LB@5'-CGG...GACCG CAGG A U GGUGG...AAA-3'@LB@ UGGA UAG UGGCA CAAUGGUCC@LB@ \|\|\|\| :\|\| \|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ ACCU GUC ACCGU GUUACCGGG@LB@3'-UUU...AUACA UUUA UAC UUGUC...UUG-5'@LB@ \| \|@LB@ 67 38@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -28.0375 kcal/mol@LB@Unfolding Energy - mRNA 9.27172 kcal/mol@LB@Unfolding Energy - sRNA 6.67256 kcal/mol@LB@@LB@Position - mRNA 47 -- 73@LB@Position - sRNA 39 -- 66@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 39 -- 45@LB@
139	0.0159	0.3828	b2108	yehA	-9.84	0.131393	50 -- 60	55 -- 65	putative fimbrial-like adhesin protein	_____________49__________61\n_____________\|___________\|\n5'-GUU...GGCCA___________UAUUU...UUG-3'\n______________GGGAAGUCAGU\n______________\|\|:\|\|:\|\|\|\|\|\n______________CCUUUUAGUCA\n3'-UUU...UACAA___________CCGUU...UUG-5'\n_____________\|___________\|\n_____________66__________54\n	54 -- 60	55 -- 61	-13.8721 kcal/mol	3.08221 kcal/mol	0.952476 kcal/mol	49 61@LB@ \| \|@LB@5'-GUU...GGCCA UAUUU...UUG-3'@LB@ GGGAAGUCAGU@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ CCUUUUAGUCA@LB@3'-UUU...UACAA CCGUU...UUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -9.84 kcal/mol@LB@Hybridization Energy -13.8721 kcal/mol@LB@Unfolding Energy - mRNA 3.08221 kcal/mol@LB@Unfolding Energy - sRNA 0.952476 kcal/mol@LB@@LB@Position - mRNA 50 -- 60@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 55 -- 61@LB@
112	0.0105	0.3154	b2136	yohD	-14.01	0.014269	227 -- 295	6 -- 72	DedA family inner membrane protein	_____________226_____________________________________________________________________296\n_____________\|_______________________________________________________________________\|\n5'-GAU...UCACA_____GUUAUGCCG__C____________A____________________C_____UUUGCUG________UGCGG-3'\n______________AUAUG_________CG_UGGUGAU_CGGU_GCCUGGCGGAAGGUGAAA_C_GUGAC_______GGAGGCGU\n______________\|\|\|\|\|_________\|:_\|\|\|::\|\|_\|::\|_\|\|\|:::\|:\|\|\|::\|:\|\|\|_\|_\|\|\|\|\|_______::\|\|\|\|:\|\n______________UAUAC_________GU_ACCGUUA_GUUA_CGGGUUGUCUUUUAUUUU_G_CACUG_______UUUCCGUA\n3'-UUU...AAAAA_____AACCUUUUA__C_______C____C__________________A_A_____UUA____________UAUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________73______________________________________________________________________5\n	289 -- 295	6 -- 12	-51.7055 kcal/mol	25.533 kcal/mol	12.1614 kcal/mol	226 296@LB@ \| \|@LB@5'-GAU...UCACA GUUAUGCCG C A C UUUGCUG UGCGG-3'@LB@ AUAUG CG UGGUGAU CGGU GCCUGGCGGAAGGUGAAA C GUGAC GGAGGCGU@LB@ \|\|\|\|\| \|: \|\|\|::\|\| \|::\| \|\|\|:::\|:\|\|\|::\|:\|\|\| \| \|\|\|\|\| ::\|\|\|\|:\|@LB@ UAUAC GU ACCGUUA GUUA CGGGUUGUCUUUUAUUUU G CACUG UUUCCGUA@LB@3'-UUU...AAAAA AACCUUUUA C C C A A UUA UAUUG-5'@LB@ \| \|@LB@ 73 5@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -51.7055 kcal/mol@LB@Unfolding Energy - mRNA 25.533 kcal/mol@LB@Unfolding Energy - sRNA 12.1614 kcal/mol@LB@@LB@Position - mRNA 227 -- 295@LB@Position - sRNA 6 -- 72@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 6 -- 12@LB@
179	0.02223	0.4143	b2167	fruA	-7.15	0.399094	192 -- 200	5 -- 13	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________191_______201\n_____________\|_________\|\n5'-CGC...GCAGG_________AUGAA...AAA-3'\n______________AGAGGCAUA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCCGUAU\n3'-UUU...UGUUA_________AUUG-5'\n_____________\|_________\|\n_____________14________4\n	194 -- 200	5 -- 11	-11.8443 kcal/mol	1.8873 kcal/mol	2.80332 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...GCAGG AUGAA...AAA-3'@LB@ AGAGGCAUA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCCGUAU@LB@3'-UUU...UGUUA AUUG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -11.8443 kcal/mol@LB@Unfolding Energy - mRNA 1.8873 kcal/mol@LB@Unfolding Energy - sRNA 2.80332 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@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

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usability assessment

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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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