Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
132	0.01257	0.3067	b2516	rodZ	-8.98	0.032240	231 -- 240	34 -- 43	MreB assembly cytoskeletal protein	_____________230________241\n_____________\|__________\|\n5'-UAA...AAAAU__________CUACC...UUG-3'\n______________GAAGCACUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CUUCGUGAAU\n3'-UUU...UCGUU__________UUUUU...CAA-5'\n_____________\|__________\|\n_____________44_________33\n	234 -- 240	34 -- 40	-13.7965 kcal/mol	1.10051 kcal/mol	3.71643 kcal/mol	230 241@LB@ \| \|@LB@5'-UAA...AAAAU CUACC...UUG-3'@LB@ GAAGCACUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CUUCGUGAAU@LB@3'-UUU...UCGUU UUUUU...CAA-5'@LB@ \| \|@LB@ 44 33@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -13.7965 kcal/mol@LB@Unfolding Energy - mRNA 1.10051 kcal/mol@LB@Unfolding Energy - sRNA 3.71643 kcal/mol@LB@@LB@Position - mRNA 231 -- 240@LB@Position - sRNA 34 -- 43@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 34 -- 40@LB@
87	0.005861	0.217	b3083	higB	-4.01	0.492619	220 -- 233	28 -- 42	mRNA interferase toxin of the HigB-HigA toxin-antitoxin system	_____________219_____________234\n_____________\|_______________\|\n5'-GCA...UCAAA_______________GCUGC...GAU-3'\n______________AAGCAUU_GAAAGAU\n______________\|\|\|\|\|:\|_:\|\|\|:\|\|\n______________UUCGUGA_UUUUUUA\n3'-UUU...CGUUC_______A_______AGCAA...CAA-5'\n_____________\|_______________\|\n_____________43______________27\n	220 -- 226	36 -- 42	-9.16043 kcal/mol	3.51035 kcal/mol	1.63711 kcal/mol	219 234@LB@ \| \|@LB@5'-GCA...UCAAA GCUGC...GAU-3'@LB@ AAGCAUU GAAAGAU@LB@ \|\|\|\|\|:\| :\|\|\|:\|\|@LB@ UUCGUGA UUUUUUA@LB@3'-UUU...CGUUC A AGCAA...CAA-5'@LB@ \| \|@LB@ 43 27@LB@@LB@@LB@Energy -4.01 kcal/mol@LB@Hybridization Energy -9.16043 kcal/mol@LB@Unfolding Energy - mRNA 3.51035 kcal/mol@LB@Unfolding Energy - sRNA 1.63711 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 28 -- 42@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 36 -- 42@LB@
119	0.01022	0.2766	b0123	cueO	-7.29	0.093095	47 -- 59	29 -- 41	multicopper oxidase (laccase)	_____________46____________60\n_____________\|_____________\|\n5'-CUG...UACCA__G__________GAUAA...CGU-3'\n______________GG_GCUUAAAGAA\n______________:\|_:\|\|\|\|\|\|:\|\|\n______________UC_UGAAUUUUUU\n3'-UUU...GUUCU__G__________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	53 -- 59	29 -- 35	-11.0144 kcal/mol	2.10364 kcal/mol	1.62306 kcal/mol	46 60@LB@ \| \|@LB@5'-CUG...UACCA G GAUAA...CGU-3'@LB@ GG GCUUAAAGAA@LB@ :\| :\|\|\|\|\|\|:\|\|@LB@ UC UGAAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -11.0144 kcal/mol@LB@Unfolding Energy - mRNA 2.10364 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 47 -- 59@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 29 -- 35@LB@
27	0.0008083	0.09021	b2711	norW	-10.17	0.014477	99 -- 112	13 -- 26	NADH:flavorubredoxin oxidoreductase	_____________98_____________113\n_____________\|______________\|\n5'-GAA...CAGGA______________CGCCG...UUG-3'\n______________CGUUGCGCCAGGAA\n______________\|\|\|\|:\|:\|\|\|\|\|\|\|\n______________GCAAUGUGGUCCUU\n3'-UUU...UUUAA______________UAGAC...CAA-5'\n_____________\|______________\|\n_____________27_____________12\n	106 -- 112	13 -- 19	-23.5838 kcal/mol	5.14562 kcal/mol	8.27144 kcal/mol	98 113@LB@ \| \|@LB@5'-GAA...CAGGA CGCCG...UUG-3'@LB@ CGUUGCGCCAGGAA@LB@ \|\|\|\|:\|:\|\|\|\|\|\|\|@LB@ GCAAUGUGGUCCUU@LB@3'-UUU...UUUAA UAGAC...CAA-5'@LB@ \| \|@LB@ 27 12@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -23.5838 kcal/mol@LB@Unfolding Energy - mRNA 5.14562 kcal/mol@LB@Unfolding Energy - sRNA 8.27144 kcal/mol@LB@@LB@Position - mRNA 99 -- 112@LB@Position - sRNA 13 -- 26@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 13 -- 19@LB@
8	5.642e-05	0.02272	b2282	nuoH	-5.33	0.272754	189 -- 221	13 -- 44	NADH:ubiquinone oxidoreductase membrane subunit H	_____________188________________________________222\n_____________\|__________________________________\|\n5'-CUC...CUCAA________AACAAU_____G_A__U_________CUGAU...GCU-3'\n______________GGAGGCAC______GAGUU_G_UA_CACC_GGAA\n______________:\|\|:\|\|\|\|______:\|:\|\|_\|_\|\|_\|\|\|\|_\|\|\|\|\n______________UCUUCGUG______UUUAA_C_AU_GUGG_CCUU\n3'-UUU...UUCGU________AAUUU______G_A_______U____UAGAC...CAA-5'\n_____________\|__________________________________\|\n_____________45_________________________________12\n	190 -- 196	37 -- 43	-24.1154 kcal/mol	6.60325 kcal/mol	12.1776 kcal/mol	188 222@LB@ \| \|@LB@5'-CUC...CUCAA AACAAU G A U CUGAU...GCU-3'@LB@ GGAGGCAC GAGUU G UA CACC GGAA@LB@ :\|\|:\|\|\|\| :\|:\|\| \| \|\| \|\|\|\| \|\|\|\|@LB@ UCUUCGUG UUUAA C AU GUGG CCUU@LB@3'-UUU...UUCGU AAUUU G A U UAGAC...CAA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -5.33 kcal/mol@LB@Hybridization Energy -24.1154 kcal/mol@LB@Unfolding Energy - mRNA 6.60325 kcal/mol@LB@Unfolding Energy - sRNA 12.1776 kcal/mol@LB@@LB@Position - mRNA 189 -- 221@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 37 -- 43@LB@
108	0.009338	0.2693	b0639	nadD	-9.48	0.023112	42 -- 61	34 -- 53	nicotinic acid mononucleotide adenylyltransferase NAD(P)-dependent	_____________41___________________62\n_____________\|____________________\|\n5'-AUG...AAAUC________C___C___G___CGUCA...CGC-3'\n______________GCUUAAGU_AGA_GCA_UUA\n______________\|\|\|\|\|\|\|:_\|\|\|_\|\|\|_\|\|\|\n______________CGAAUUCG_UCU_CGU_AAU\n3'-UUU...UUGAA________U___U___G___UUUUU...CAA-5'\n_____________\|____________________\|\n_____________54___________________33\n	42 -- 48	47 -- 53	-20.1483 kcal/mol	4.55179 kcal/mol	6.11529 kcal/mol	41 62@LB@ \| \|@LB@5'-AUG...AAAUC C C G CGUCA...CGC-3'@LB@ GCUUAAGU AGA GCA UUA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\| \|\|\|@LB@ CGAAUUCG UCU CGU AAU@LB@3'-UUU...UUGAA U U G UUUUU...CAA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -20.1483 kcal/mol@LB@Unfolding Energy - mRNA 4.55179 kcal/mol@LB@Unfolding Energy - sRNA 6.11529 kcal/mol@LB@@LB@Position - mRNA 42 -- 61@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 47 -- 53@LB@
22	0.0006536	0.09021	b1245	oppC	-8.46	0.045181	270 -- 288	37 -- 58	oligopeptide ABC transporter permease	_____________269____________________289\n_____________\|______________________\|\n5'-GGU...GGCGC_________________C____GUCGA...UUA-3'\n______________AGCUUGU___GGCAGGA_GCAC\n______________\|:\|\|\|\|:___:\|\|\|:\|\|_\|\|\|\|\n______________UUGAACG___UCGUUCU_CGUG\n3'-UUU...CUACU_______AAU_______U____AAUUU...CAA-5'\n_____________\|______________________\|\n_____________59_____________________36\n	277 -- 283	42 -- 48	-22.602 kcal/mol	7.90039 kcal/mol	6.24354 kcal/mol	269 289@LB@ \| \|@LB@5'-GGU...GGCGC C GUCGA...UUA-3'@LB@ AGCUUGU GGCAGGA GCAC@LB@ \|:\|\|\|\|: :\|\|\|:\|\| \|\|\|\|@LB@ UUGAACG UCGUUCU CGUG@LB@3'-UUU...CUACU AAU U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -22.602 kcal/mol@LB@Unfolding Energy - mRNA 7.90039 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 270 -- 288@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
73	0.004067	0.1794	b1244	oppB	-5.52	0.247965	106 -- 113	36 -- 43	oligopeptide ABC transporter permease	_____________105______114\n_____________\|________\|\n5'-UCC...AUUGU________AAUGG...GCC-3'\n______________GAAGCACU\n______________\|\|\|\|\|\|\|\|\n______________CUUCGUGA\n3'-UUU...UCGUU________AUUUU...CAA-5'\n_____________\|________\|\n_____________44_______35\n	107 -- 113	36 -- 42	-11.7212 kcal/mol	2.50266 kcal/mol	3.69444 kcal/mol	105 114@LB@ \| \|@LB@5'-UCC...AUUGU AAUGG...GCC-3'@LB@ GAAGCACU@LB@ \|\|\|\|\|\|\|\|@LB@ CUUCGUGA@LB@3'-UUU...UCGUU AUUUU...CAA-5'@LB@ \| \|@LB@ 44 35@LB@@LB@@LB@Energy -5.52 kcal/mol@LB@Hybridization Energy -11.7212 kcal/mol@LB@Unfolding Energy - mRNA 2.50266 kcal/mol@LB@Unfolding Energy - sRNA 3.69444 kcal/mol@LB@@LB@Position - mRNA 106 -- 113@LB@Position - sRNA 36 -- 43@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 36 -- 42@LB@
112	0.009574	0.2693	b2494	bepA	-6.13	0.179960	208 -- 220	29 -- 41	OM protein maintenance and assembly metalloprotease and chaperone periplasmic	_____________207___________221\n_____________\|_____________\|\n5'-UGA...GUUCA____G________AAACC...UGC-3'\n______________GGCA_UUGAAAAA\n______________:\|\|\|_\|\|:\|\|\|\|\|\n______________UCGU_AAUUUUUU\n3'-UUU...GUUCU____G________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	214 -- 220	29 -- 35	-11.3192 kcal/mol	3.5632 kcal/mol	1.62306 kcal/mol	207 221@LB@ \| \|@LB@5'-UGA...GUUCA G AAACC...UGC-3'@LB@ GGCA UUGAAAAA@LB@ :\|\|\| \|\|:\|\|\|\|\|@LB@ UCGU AAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -6.13 kcal/mol@LB@Hybridization Energy -11.3192 kcal/mol@LB@Unfolding Energy - mRNA 3.5632 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 208 -- 220@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 29 -- 35@LB@
65	0.003382	0.1645	b1739	osmE	-4.35	0.428849	173 -- 228	7 -- 58	osmotically-inducible lipoprotein	_____________172______________________________________________________229\n_____________\|________________________________________________________\|\n5'-GAA...UAUCU___AC___GA___A_______A__GAAUAUGAACAAGAA____G______U_____GUGCA...AGC-3'\n______________AAC__GCU__UAA_CAAGAGG_CG_______________UAUG_CAGGAA_UCUGA\n______________\|\|\|__\|\|\|__\|\|\|_\|\|\|\|\|:\|_\|:_______________\|\|::_\|\|\|\|\|\|_\|\|\|\|\|\n______________UUG__CGA__AUU_GUUCUUC_GU_______________AUGU_GUCCUU_AGACU\n3'-UUU...CUACU___AA________C__________GAAUUUUUUAAGCA_____G______U_____ACACAA-5'\n_____________\|________________________________________________________\|\n_____________59_______________________________________________________6\n	187 -- 193	40 -- 46	-28.7812 kcal/mol	10.5809 kcal/mol	13.8467 kcal/mol	172 229@LB@ \| \|@LB@5'-GAA...UAUCU AC GA A A GAAUAUGAACAAGAA G U GUGCA...AGC-3'@LB@ AAC GCU UAA CAAGAGG CG UAUG CAGGAA UCUGA@LB@ \|\|\| \|\|\| \|\|\| \|\|\|\|\|:\| \|: \|\|:: \|\|\|\|\|\| \|\|\|\|\|@LB@ UUG CGA AUU GUUCUUC GU AUGU GUCCUU AGACU@LB@3'-UUU...CUACU AA C GAAUUUUUUAAGCA G U ACACAA-5'@LB@ \| \|@LB@ 59 6@LB@@LB@@LB@Energy -4.35 kcal/mol@LB@Hybridization Energy -28.7812 kcal/mol@LB@Unfolding Energy - mRNA 10.5809 kcal/mol@LB@Unfolding Energy - sRNA 13.8467 kcal/mol@LB@@LB@Position - mRNA 173 -- 228@LB@Position - sRNA 7 -- 58@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 40 -- 46@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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