Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
191	0.01886	0.3104	b3494	uspB	-6.32	0.440313	280 -- 286	5 -- 11	universal stress (ethanol tolerance) protein B	_____________279_____287\n_____________\|_______\|\n5'-AAU...ACUAC_______GUUAG...UGC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	280 -- 286	5 -- 11	-11.0709 kcal/mol	3.63469 kcal/mol	1.11145 kcal/mol	279 287@LB@ \| \|@LB@5'-AAU...ACUAC GUUAG...UGC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -11.0709 kcal/mol@LB@Unfolding Energy - mRNA 3.63469 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 280 -- 286@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 5 -- 11@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase	_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
188	0.0185	0.3104	b3364	tsgA	-7.52	0.300608	282 -- 299	12 -- 29	putative transporter	_____________281________________300\n_____________\|__________________\|\n5'-CCA...UCACC_____________G____A-3'\n______________GGGAUGGUGAUGG_AAAU\n______________\|\|\|\|\|\|:\|\|\|\|::_\|\|\|\|\n______________CCCUACUACUAUU_UUUA\n3'-UUU...UAAGU_____________G____CGCGC...AAG-5'\n_____________\|__________________\|\n_____________30_________________11\n	282 -- 288	23 -- 29	-23.3156 kcal/mol	8.39977 kcal/mol	7.39774 kcal/mol	281 300@LB@ \| \|@LB@5'-CCA...UCACC G A-3'@LB@ GGGAUGGUGAUGG AAAU@LB@ \|\|\|\|\|\|:\|\|\|\|:: \|\|\|\|@LB@ CCCUACUACUAUU UUUA@LB@3'-UUU...UAAGU G CGCGC...AAG-5'@LB@ \| \|@LB@ 30 11@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -23.3156 kcal/mol@LB@Unfolding Energy - mRNA 8.39977 kcal/mol@LB@Unfolding Energy - sRNA 7.39774 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 12 -- 29@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 23 -- 29@LB@
11	0.0003246	0.08948	b2299	yfcD	-11.11	0.078371	283 -- 295	5 -- 18	putative NUDIX hydrolase	_____________282____________296\n_____________\|______________\|\n5'-AGA...CCGGG__________G___ACAGU-3'\n______________AACAAAUGCG_G_C\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\n______________UUGUUUACGC_C_G\n3'-UUU...UACUA__________G_A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	286 -- 292	9 -- 15	-15.7313 kcal/mol	3.39963 kcal/mol	1.2243 kcal/mol	282 296@LB@ \| \|@LB@5'-AGA...CCGGG G ACAGU-3'@LB@ AACAAAUGCG G C@LB@ \|\|\|\|\|\|\|\|\|\| \| \|@LB@ UUGUUUACGC C G@LB@3'-UUU...UACUA G A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.7313 kcal/mol@LB@Unfolding Energy - mRNA 3.39963 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 9 -- 15@LB@
102	0.01008	0.3104	b3500	gor	-8.16	0.240292	285 -- 295	4 -- 15	glutathione oxidoreductase	_____________284__________296\n_____________\|____________\|\n5'-GGC...GCCAG____________GAUUG-3'\n______________AAAUGUGCG_CU\n______________\|\|\|\|\|:\|\|\|_\|\|\n______________UUUACGCGC_GA\n3'-UUU...UAUUG_________A__AAG-5'\n_____________\|____________\|\n_____________16___________3\n	287 -- 293	7 -- 13	-12.6909 kcal/mol	3.32128 kcal/mol	1.20666 kcal/mol	284 296@LB@ \| \|@LB@5'-GGC...GCCAG GAUUG-3'@LB@ AAAUGUGCG CU@LB@ \|\|\|\|\|:\|\|\| \|\|@LB@ UUUACGCGC GA@LB@3'-UUU...UAUUG A AAG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -12.6909 kcal/mol@LB@Unfolding Energy - mRNA 3.32128 kcal/mol@LB@Unfolding Energy - sRNA 1.20666 kcal/mol@LB@@LB@Position - mRNA 285 -- 295@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 7 -- 13@LB@
37	0.00241	0.2206	b2455	eutE	-11.61	0.064061	286 -- 298	3 -- 15	aldehyde oxidoreductase ethanolamine utilization protein	_____________285___________299\n_____________\|_____________\|\n5'-GGU...UCAUG_____G_______CG-3'\n______________AGAUG_GCGUUUU\n______________\|:\|\|\|_\|\|\|\|:\|\|\n______________UUUAC_CGCAGAA\n3'-UUU...UAUUG_____G_______AG-5'\n_____________\|_____________\|\n_____________16____________2\n	292 -- 298	3 -- 9	-14.5549 kcal/mol	1.73631 kcal/mol	1.20903 kcal/mol	285 299@LB@ \| \|@LB@5'-GGU...UCAUG G CG-3'@LB@ AGAUG GCGUUUU@LB@ \|:\|\|\| \|\|\|\|:\|\|@LB@ UUUAC CGCAGAA@LB@3'-UUU...UAUUG G AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -14.5549 kcal/mol@LB@Unfolding Energy - mRNA 1.73631 kcal/mol@LB@Unfolding Energy - sRNA 1.20903 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 3 -- 9@LB@
139	0.01337	0.3104	b1255	yciC	-11.25	0.074167	287 -- 299	1 -- 13	UPF0259 family inner membrane protein	_____________286___________300\n_____________\|_____________\|\n5'-AAU...UUGCU__________A__A-3'\n______________AUGUGCGUUU_UC\n______________\|\|\|:\|\|\|\|:\|_\|\|\n______________UACGCGCAGA_AG\n3'-UUU...UUGUU__________A__-5'\n_____________\|____________\|\n_____________14___________1\n	290 -- 296	4 -- 10	-15.0519 kcal/mol	2.63141 kcal/mol	1.17519 kcal/mol	286 300@LB@ \| \|@LB@5'-AAU...UUGCU A A-3'@LB@ AUGUGCGUUU UC@LB@ \|\|\|:\|\|\|\|:\| \|\|@LB@ UACGCGCAGA AG@LB@3'-UUU...UUGUU A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -15.0519 kcal/mol@LB@Unfolding Energy - mRNA 2.63141 kcal/mol@LB@Unfolding Energy - sRNA 1.17519 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 4 -- 10@LB@
63	0.0059	0.3087	b3834	ubiJ	-8.76	0.193647	289 -- 295	4 -- 10	aerobic ubiquinone synthesis protein SCP2 family protein	_____________288_____296\n_____________\|_______\|\n5'-GCU...CCGCU_______GCUGG-3'\n______________CGCGUCU\n______________\|\|\|\|\|\|\|\n______________GCGCAGA\n3'-UUU...UUUAC_______AAG-5'\n_____________\|_______\|\n_____________11______3\n	289 -- 295	4 -- 10	-11.2085 kcal/mol	1.2993 kcal/mol	1.14958 kcal/mol	288 296@LB@ \| \|@LB@5'-GCU...CCGCU GCUGG-3'@LB@ CGCGUCU@LB@ \|\|\|\|\|\|\|@LB@ GCGCAGA@LB@3'-UUU...UUUAC AAG-5'@LB@ \| \|@LB@ 11 3@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -11.2085 kcal/mol@LB@Unfolding Energy - mRNA 1.2993 kcal/mol@LB@Unfolding Energy - sRNA 1.14958 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 4 -- 10@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 4 -- 10@LB@
148	0.01421	0.3104	b2379	alaC	-8.54	0.209762	290 -- 297	5 -- 12	glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase	_____________289______298\n_____________\|________\|\n5'-UGU...AUGGC________GGC-3'\n______________UGCGCGUC\n______________\|\|\|\|\|\|\|\|\n______________ACGCGCAG\n3'-UUU...UGUUU________AAAG-5'\n_____________\|________\|\n_____________13_______4\n	291 -- 297	5 -- 11	-14.909 kcal/mol	5.25295 kcal/mol	1.11508 kcal/mol	289 298@LB@ \| \|@LB@5'-UGU...AUGGC GGC-3'@LB@ UGCGCGUC@LB@ \|\|\|\|\|\|\|\|@LB@ ACGCGCAG@LB@3'-UUU...UGUUU AAAG-5'@LB@ \| \|@LB@ 13 4@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -14.909 kcal/mol@LB@Unfolding Energy - mRNA 5.25295 kcal/mol@LB@Unfolding Energy - sRNA 1.11508 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 5 -- 12@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 5 -- 11@LB@
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein	_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@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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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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