Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
60	0.01169	0.5385	b2441	eutB	-14.17	0.019414	238 -- 261	12 -- 34	ethanolamine ammonia-lyase large subunit heavy chain	_____________237______________________262\n_____________\|________________________\|\n5'-CUG...AUAUC_G_______AUG____________UGGCU...UGG-3'\n______________A_UUUAAGG___UAAAAGAGGUGC\n______________\|_\|\|:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\n______________U_AAGUUCC___AUUUUCUCCACG\n3'-CGC...GUCAC_G_______CA_____________GCGAG...AAG-5'\n_____________\|________________________\|\n_____________35_______________________11\n	255 -- 261	12 -- 18	-24.3693 kcal/mol	4.39141 kcal/mol	5.80707 kcal/mol	237 262@LB@ \| \|@LB@5'-CUG...AUAUC G AUG UGGCU...UGG-3'@LB@ A UUUAAGG UAAAAGAGGUGC@LB@ \| \|\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|@LB@ U AAGUUCC AUUUUCUCCACG@LB@3'-CGC...GUCAC G CA GCGAG...AAG-5'@LB@ \| \|@LB@ 35 11@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -24.3693 kcal/mol@LB@Unfolding Energy - mRNA 4.39141 kcal/mol@LB@Unfolding Energy - sRNA 5.80707 kcal/mol@LB@@LB@Position - mRNA 238 -- 261@LB@Position - sRNA 12 -- 34@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 12 -- 18@LB@
141	0.02331	0.5385	b1844	exoX	-7.22	0.302733	200 -- 217	62 -- 83	exodeoxyribonuclease 10; DNA exonuclease X	_____________199_____________________218\n_____________\|_______________________\|\n5'-UUA...CAUGC_______C__A____________UACAG...UGA-3'\n______________CAUGUUG_GC_UUA_____UCGA\n______________\|\|:\|\|\|\|_\|\|_\|\|\|_____\|\|\|\|\n______________GUGCAAC_CG_AAU_____AGCU\n3'-CGC...UUCAA__________A___CAAUA____CAACU...AAG-5'\n_____________\|_______________________\|\n_____________84______________________61\n	200 -- 206	77 -- 83	-13.618 kcal/mol	4.77882 kcal/mol	1.62352 kcal/mol	199 218@LB@ \| \|@LB@5'-UUA...CAUGC C A UACAG...UGA-3'@LB@ CAUGUUG GC UUA UCGA@LB@ \|\|:\|\|\|\| \|\| \|\|\| \|\|\|\|@LB@ GUGCAAC CG AAU AGCU@LB@3'-CGC...UUCAA A CAAUA CAACU...AAG-5'@LB@ \| \|@LB@ 84 61@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -13.618 kcal/mol@LB@Unfolding Energy - mRNA 4.77882 kcal/mol@LB@Unfolding Energy - sRNA 1.62352 kcal/mol@LB@@LB@Position - mRNA 200 -- 217@LB@Position - sRNA 62 -- 83@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 77 -- 83@LB@
20	0.003438	0.5385	b3093	exuT	-11.51	0.057623	213 -- 228	75 -- 90	hexuronate transporter	_____________212______________229\n_____________\|________________\|\n5'-GGA...AAAUU_____G__________AUAUG...CGC-3'\n______________AAAGG_UUACGUUGGU\n______________\|\|\|:\|_\|:\|\|\|\|\|\|\|:\n______________UUUUC_AGUGCAACCG\n3'-CGC...AGGCG_____A__________AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	222 -- 228	75 -- 81	-17.0017 kcal/mol	4.97243 kcal/mol	0.517251 kcal/mol	212 229@LB@ \| \|@LB@5'-GGA...AAAUU G AUAUG...CGC-3'@LB@ AAAGG UUACGUUGGU@LB@ \|\|\|:\| \|:\|\|\|\|\|\|\|:@LB@ UUUUC AGUGCAACCG@LB@3'-CGC...AGGCG A AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -17.0017 kcal/mol@LB@Unfolding Energy - mRNA 4.97243 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 213 -- 228@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 75 -- 81@LB@
196	0.0344	0.5559	b0954	fabA	-7.50	0.274211	100 -- 110	74 -- 84	beta-hydroxydecanoyl thioester dehydrase	_____________99__________111\n_____________\|___________\|\n5'-GUG...GGCCA___________GAACU...ACA-3'\n______________UUACGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGA\n3'-CGC...UUUCA___________AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	104 -- 110	74 -- 80	-16.8122 kcal/mol	8.80896 kcal/mol	0.508159 kcal/mol	99 111@LB@ \| \|@LB@5'-GUG...GGCCA GAACU...ACA-3'@LB@ UUACGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGA@LB@3'-CGC...UUUCA AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -16.8122 kcal/mol@LB@Unfolding Energy - mRNA 8.80896 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 100 -- 110@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 74 -- 80@LB@
150	0.02548	0.5485	b0180	fabZ	-10.02	0.104939	240 -- 263	1 -- 24	(3R)-hydroxymyristol acyl carrier protein dehydratase	_____________239______________________264\n_____________\|________________________\|\n5'-AAA...AGAUU______CUUC______A_______CCGUU...AAG-3'\n______________UUAGAA____UGCCGC_CCGUUUC\n______________\|\|\|:\|\|____\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________AAUUUU____ACGGCG_GGCAAAG\n3'-CGC...UUCCC______CUCC______A_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	257 -- 263	1 -- 7	-23.7452 kcal/mol	3.39044 kcal/mol	10.3355 kcal/mol	239 264@LB@ \| \|@LB@5'-AAA...AGAUU CUUC A CCGUU...AAG-3'@LB@ UUAGAA UGCCGC CCGUUUC@LB@ \|\|\|:\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAUUUU ACGGCG GGCAAAG@LB@3'-CGC...UUCCC CUCC A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.02 kcal/mol@LB@Hybridization Energy -23.7452 kcal/mol@LB@Unfolding Energy - mRNA 3.39044 kcal/mol@LB@Unfolding Energy - sRNA 10.3355 kcal/mol@LB@@LB@Position - mRNA 240 -- 263@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 1 -- 7@LB@
169	0.03038	0.5559	b2912	fau	-9.38	0.135051	85 -- 98	22 -- 35	5-formyltetrahydrofolate cyclo-ligase family protein	_____________84_____________99\n_____________\|______________\|\n5'-GAA...ACCAA__G___________CAGCC...UGG-3'\n______________GG_UUCAAGGGUUA\n______________\|:_\|\|\|\|\|\|\|\|\|\|\|\n______________CU_AAGUUCCCAAU\n3'-CGC...CGUCA__G___________UUUCU...AAG-5'\n_____________\|______________\|\n_____________36_____________21\n	92 -- 98	22 -- 28	-18.6025 kcal/mol	5.89438 kcal/mol	3.32987 kcal/mol	84 99@LB@ \| \|@LB@5'-GAA...ACCAA G CAGCC...UGG-3'@LB@ GG UUCAAGGGUUA@LB@ \|: \|\|\|\|\|\|\|\|\|\|\|@LB@ CU AAGUUCCCAAU@LB@3'-CGC...CGUCA G UUUCU...AAG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -18.6025 kcal/mol@LB@Unfolding Energy - mRNA 5.89438 kcal/mol@LB@Unfolding Energy - sRNA 3.32987 kcal/mol@LB@@LB@Position - mRNA 85 -- 98@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 22 -- 28@LB@
160	0.02795	0.5559	b1475	fdnH	-7.98	0.230122	69 -- 80	24 -- 35	formate dehydrogenase-N Fe-S (beta) subunit nitrate-inducible	_____________68___________81\n_____________\|____________\|\n5'-CGC...ACUGG____________GUCGC...UUA-3'\n______________GGCUUUGAGGGU\n______________\|:\|\|\|::\|\|\|\|\|\n______________CUGAAGUUCCCA\n3'-CGC...CGUCA____________AUUUU...AAG-5'\n_____________\|____________\|\n_____________36___________23\n	74 -- 80	24 -- 30	-17.8377 kcal/mol	6.53052 kcal/mol	3.32971 kcal/mol	68 81@LB@ \| \|@LB@5'-CGC...ACUGG GUCGC...UUA-3'@LB@ GGCUUUGAGGGU@LB@ \|:\|\|\|::\|\|\|\|\|@LB@ CUGAAGUUCCCA@LB@3'-CGC...CGUCA AUUUU...AAG-5'@LB@ \| \|@LB@ 36 23@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -17.8377 kcal/mol@LB@Unfolding Energy - mRNA 6.53052 kcal/mol@LB@Unfolding Energy - sRNA 3.32971 kcal/mol@LB@@LB@Position - mRNA 69 -- 80@LB@Position - sRNA 24 -- 35@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 24 -- 30@LB@
47	0.009854	0.5385	b3408	feoA	-10.27	0.095129	159 -- 188	52 -- 83	ferrous iron transporter protein A	_____________158_________________________________189\n_____________\|___________________________________\|\n5'-AGC...CGCCC____A_______________C___UAA________AAGUA...CUG-3'\n______________CAUG__GGU___AGUUA_UC_AGU___UGAGAAAC\n______________\|\|:\|__\|\|:___\|\|\|\|\|_\|\|_\|\|\|___\|\|\|\|\|\|\|\|\n______________GUGC__CCG___UCAAU_AG_UCA___ACUCUUUG\n3'-CGC...UUCAA____AA___AAA_____A__C______________AGAGC...AAG-5'\n_____________\|___________________________________\|\n_____________84__________________________________51\n	182 -- 188	52 -- 58	-20.9255 kcal/mol	6.25891 kcal/mol	4.4004 kcal/mol	158 189@LB@ \| \|@LB@5'-AGC...CGCCC A C UAA AAGUA...CUG-3'@LB@ CAUG GGU AGUUA UC AGU UGAGAAAC@LB@ \|\|:\| \|\|: \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUGC CCG UCAAU AG UCA ACUCUUUG@LB@3'-CGC...UUCAA AA AAA A C AGAGC...AAG-5'@LB@ \| \|@LB@ 84 51@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -20.9255 kcal/mol@LB@Unfolding Energy - mRNA 6.25891 kcal/mol@LB@Unfolding Energy - sRNA 4.4004 kcal/mol@LB@@LB@Position - mRNA 159 -- 188@LB@Position - sRNA 52 -- 83@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 52 -- 58@LB@
65	0.01282	0.5385	b0589	fepG	-12.08	0.045738	8 -- 17	74 -- 83	iron-enterobactin ABC transporter permease	_____________7__________18\n_____________\|__________\|\n____5'-CAUAUGG__________GGUGG...CGC-3'\n______________CGCGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\n______________GUGCAACCGA\n3'-CGC...UUCAA__________AAUCA...AAG-5'\n_____________\|__________\|\n_____________84_________73\n	11 -- 17	74 -- 80	-17.1529 kcal/mol	4.57841 kcal/mol	0.494551 kcal/mol	7 18@LB@ \| \|@LB@ 5'-CAUAUGG GGUGG...CGC-3'@LB@ CGCGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ GUGCAACCGA@LB@3'-CGC...UUCAA AAUCA...AAG-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -17.1529 kcal/mol@LB@Unfolding Energy - mRNA 4.57841 kcal/mol@LB@Unfolding Energy - sRNA 0.494551 kcal/mol@LB@@LB@Position - mRNA 8 -- 17@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 74 -- 80@LB@
98	0.0165	0.5385	b0151	fhuC	-12.15	0.044517	184 -- 202	66 -- 85	iron(3+)-hydroxamate import ABC transporter ATPase	_____________183____________________203\n_____________\|______________________\|\n5'-CUG...CCCAU_____AA_______________GCAGG...CCU-3'\n______________UUCAC__GUUGGCU___GUUAU\n______________\|\|\|\|\|__\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAGUG__CAACCGA___CAAUA\n3'-CGC...UUUUC______________AAU_____AGCUC...AAG-5'\n_____________\|______________________\|\n_____________86_____________________65\n	191 -- 197	74 -- 80	-16.912 kcal/mol	4.1925 kcal/mol	0.573112 kcal/mol	183 203@LB@ \| \|@LB@5'-CUG...CCCAU AA GCAGG...CCU-3'@LB@ UUCAC GUUGGCU GUUAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAGUG CAACCGA CAAUA@LB@3'-CGC...UUUUC AAU AGCUC...AAG-5'@LB@ \| \|@LB@ 86 65@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -16.912 kcal/mol@LB@Unfolding Energy - mRNA 4.1925 kcal/mol@LB@Unfolding Energy - sRNA 0.573112 kcal/mol@LB@@LB@Position - mRNA 184 -- 202@LB@Position - sRNA 66 -- 85@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 74 -- 80@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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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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