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	Additional homologs
56	0.01109	0.5385	b0425	panE	-9.95	0.107741	273 -- 289	74 -- 89	2-dehydropantoate reductase NADPH-specific		_____________272_______________290\n_____________\|_________________\|\n5'-AUC...GUCAU________G_GC_____GCGCG...CGC-3'\n______________GAAGUUCA_G__UGGCU\n______________:\|\|\|\|\|\|\|_\|__\|\|\|\|\|\n______________UUUCAAGU_C__ACCGA\n3'-CGC...GGCGU________G_A______AAUCA...AAG-5'\n_____________\|_________________\|\n_____________90________________73\n	274 -- 280	82 -- 88	-18.2046 kcal/mol	7.73441 kcal/mol	0.517373 kcal/mol	272 290@LB@ \| \|@LB@5'-AUC...GUCAU G GC GCGCG...CGC-3'@LB@ GAAGUUCA G UGGCU@LB@ :\|\|\|\|\|\|\| \| \|\|\|\|\|@LB@ UUUCAAGU C ACCGA@LB@3'-CGC...GGCGU G A AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -9.95 kcal/mol@LB@Hybridization Energy -18.2046 kcal/mol@LB@Unfolding Energy - mRNA 7.73441 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 273 -- 289@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 82 -- 88@LB@
195	0.03428	0.5559	b0434	yajG	-10.30	0.093744	131 -- 149	66 -- 84	putative lipoprotein		_____________130__________________150\n_____________\|____________________\|\n5'-UGG...UCCCC___C_______AAU______GAUGG...UGC-3'\n______________UCG_CGUUGGC____GUUAU\n______________\|\|:_\|\|\|\|\|\|\|____\|\|\|\|\|\n______________AGU_GCAACCG____CAAUA\n3'-CGC...UUUCA___________AAAU_____AGCUC...AAG-5'\n_____________\|____________________\|\n_____________85___________________65\n	135 -- 141	75 -- 81	-17.0927 kcal/mol	6.21917 kcal/mol	0.5705 kcal/mol	130 150@LB@ \| \|@LB@5'-UGG...UCCCC C AAU GAUGG...UGC-3'@LB@ UCG CGUUGGC GUUAU@LB@ \|\|: \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AGU GCAACCG CAAUA@LB@3'-CGC...UUUCA AAAU AGCUC...AAG-5'@LB@ \| \|@LB@ 85 65@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -17.0927 kcal/mol@LB@Unfolding Energy - mRNA 6.21917 kcal/mol@LB@Unfolding Energy - sRNA 0.5705 kcal/mol@LB@@LB@Position - mRNA 131 -- 149@LB@Position - sRNA 66 -- 84@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 75 -- 81@LB@
101	0.01678	0.5385	b0452	tesB	-11.66	0.054224	159 -- 170	73 -- 84	acyl-CoA thioesterase 2		_____________158__________171\n_____________\|____________\|\n5'-CAA...UCAAC____U_______GCUGC...AGG-3'\n______________UCAC_UUGGCUU\n______________\|\|\|\|_\|\|\|\|\|\|\|\n______________AGUG_AACCGAA\n3'-CGC...UUUCA____C_______AUCAA...AAG-5'\n_____________\|____________\|\n_____________85___________72\n	164 -- 170	73 -- 79	-14.9501 kcal/mol	2.7795 kcal/mol	0.508835 kcal/mol	158 171@LB@ \| \|@LB@5'-CAA...UCAAC U GCUGC...AGG-3'@LB@ UCAC UUGGCUU@LB@ \|\|\|\| \|\|\|\|\|\|\|@LB@ AGUG AACCGAA@LB@3'-CGC...UUUCA C AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -14.9501 kcal/mol@LB@Unfolding Energy - mRNA 2.7795 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 73 -- 79@LB@
22	0.004141	0.5385	b0462	acrB	-13.08	0.030428	256 -- 265	75 -- 84	multidrug efflux system protein		_____________255________266\n_____________\|__________\|\n5'-AAG...UAUCA__________AGGGG...CGC-3'\n______________UCAUGUUGGC\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUGCAACCG\n3'-CGC...UUUCA__________AAAUC...AAG-5'\n_____________\|__________\|\n_____________85_________74\n	259 -- 265	75 -- 81	-16.8887 kcal/mol	3.30616 kcal/mol	0.505918 kcal/mol	255 266@LB@ \| \|@LB@5'-AAG...UAUCA AGGGG...CGC-3'@LB@ UCAUGUUGGC@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -13.08 kcal/mol@LB@Hybridization Energy -16.8887 kcal/mol@LB@Unfolding Energy - mRNA 3.30616 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 256 -- 265@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 75 -- 81@LB@
162	0.02861	0.5559	b0564	appY	-9.53	0.127084	148 -- 162	62 -- 79	global transcriptional activator; DLP12 prophage	b1499 b3515 b4116 b0566 b3516	_____________147________________163\n_____________\|__________________\|\n5'-AAA...UUUAA__________________CUACU...UAA-3'\n______________UUGGUU___GUUAUUUGA\n______________\|\|\|\|:\|___\|\|\|\|\|\|:\|\|\n______________AACCGA___CAAUAAGCU\n3'-CGC...AGUGC______AAU_________CAACU...AAG-5'\n_____________\|__________________\|\n_____________80_________________61\n	156 -- 162	62 -- 68	-13.1987 kcal/mol	2.92728 kcal/mol	0.737706 kcal/mol	147 163@LB@ \| \|@LB@5'-AAA...UUUAA CUACU...UAA-3'@LB@ UUGGUU GUUAUUUGA@LB@ \|\|\|\|:\| \|\|\|\|\|\|:\|\|@LB@ AACCGA CAAUAAGCU@LB@3'-CGC...AGUGC AAU CAACU...AAG-5'@LB@ \| \|@LB@ 80 61@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -13.1987 kcal/mol@LB@Unfolding Energy - mRNA 2.92728 kcal/mol@LB@Unfolding Energy - sRNA 0.737706 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 62 -- 79@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 62 -- 68@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@
86	0.01521	0.5385	b0605	ahpC	-11.47	0.058587	74 -- 93	73 -- 89	alkyl hydroperoxide reductase C22 subunit		_____________73___________________94\n_____________\|____________________\|\n5'-ACC...GGUGC_________AAA____U___ACGAA...GGA-3'\n______________AAAGUUCAC___GUUG_CUU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|_\|\|\|\n______________UUUCAAGUG___CAAC_GAA\n3'-CGC...GGCGU________________C___AUCAA...AAG-5'\n_____________\|____________________\|\n_____________90___________________72\n	76 -- 82	81 -- 87	-14.6327 kcal/mol	2.64398 kcal/mol	0.517627 kcal/mol	73 94@LB@ \| \|@LB@5'-ACC...GGUGC AAA U ACGAA...GGA-3'@LB@ AAAGUUCAC GUUG CUU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUCAAGUG CAAC GAA@LB@3'-CGC...GGCGU C AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -14.6327 kcal/mol@LB@Unfolding Energy - mRNA 2.64398 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 74 -- 93@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 81 -- 87@LB@
105	0.01788	0.5385	b0619	citA	-6.78	0.351941	4 -- 24	64 -- 89	sensory histidine kinase in two-component regulatory system with CitB		_____________3__________________________25\n_____________\|__________________________\|\n________5'-CAU______AG__________________AUUUA...UCA-3'\n______________AGAGUU_____UGGUUUU__UUAUUU\n______________\|:\|\|\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|:\n______________UUUCAA_____ACCGAAA__AAUAAG\n3'-CGC...GGCGU______GUGCA_______UC______CUCAA...AAG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	12 -- 18	72 -- 78	-10.9037 kcal/mol	3.54899 kcal/mol	0.576654 kcal/mol	3 25@LB@ \| \|@LB@ 5'-CAU AG AUUUA...UCA-3'@LB@ AGAGUU UGGUUUU UUAUUU@LB@ \|:\|\|\|\| \|\|\|:\|\|\| \|\|\|\|\|:@LB@ UUUCAA ACCGAAA AAUAAG@LB@3'-CGC...GGCGU GUGCA UC CUCAA...AAG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -10.9037 kcal/mol@LB@Unfolding Energy - mRNA 3.54899 kcal/mol@LB@Unfolding Energy - sRNA 0.576654 kcal/mol@LB@@LB@Position - mRNA 4 -- 24@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 12 -- 18@LB@Position Seed - sRNA 72 -- 78@LB@
48	0.009918	0.5385	b0641	lptE	-9.88	0.110832	177 -- 184	74 -- 81	LPS assembly OM complex LptDE lipoprotein component		_____________176______185\n_____________\|________\|\n5'-ACG...CUGGU________AAGCG...UGA-3'\n______________CGUUGGCU\n______________\|\|\|\|\|\|\|\|\n______________GCAACCGA\n3'-CGC...CAAGU________AAUCA...AAG-5'\n_____________\|________\|\n_____________82_______73\n	178 -- 184	74 -- 80	-13.2047 kcal/mol	2.99134 kcal/mol	0.332056 kcal/mol	176 185@LB@ \| \|@LB@5'-ACG...CUGGU AAGCG...UGA-3'@LB@ CGUUGGCU@LB@ \|\|\|\|\|\|\|\|@LB@ GCAACCGA@LB@3'-CGC...CAAGU AAUCA...AAG-5'@LB@ \| \|@LB@ 82 73@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.2047 kcal/mol@LB@Unfolding Energy - mRNA 2.99134 kcal/mol@LB@Unfolding Energy - sRNA 0.332056 kcal/mol@LB@@LB@Position - mRNA 177 -- 184@LB@Position - sRNA 74 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 74 -- 80@LB@
50	0.0104	0.5385	b0661	miaB	-10.15	0.099644	35 -- 45	74 -- 85	tRNA-i(6)A37 methylthiotransferase		_____________34___________46\n_____________\|____________\|\n5'-CGC...GCAAU____________GAUUU...AAC-3'\n______________UUC_CGUUGGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________AAG_GCAACCGA\n3'-CGC...UUUUC___U________AAUCA...AAG-5'\n_____________\|____________\|\n_____________86___________73\n	39 -- 45	74 -- 80	-13.4892 kcal/mol	2.82751 kcal/mol	0.512001 kcal/mol	34 46@LB@ \| \|@LB@5'-CGC...GCAAU GAUUU...AAC-3'@LB@ UUC CGUUGGUU@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ AAG GCAACCGA@LB@3'-CGC...UUUUC U AAUCA...AAG-5'@LB@ \| \|@LB@ 86 73@LB@@LB@@LB@Energy -10.15 kcal/mol@LB@Hybridization Energy -13.4892 kcal/mol@LB@Unfolding Energy - mRNA 2.82751 kcal/mol@LB@Unfolding Energy - sRNA 0.512001 kcal/mol@LB@@LB@Position - mRNA 35 -- 45@LB@Position - sRNA 74 -- 85@LB@Position Seed - mRNA 39 -- 45@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)

Job resubmission

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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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