Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
120	0.004053	0.119	b2441	eutB	-6.09	0.606518	293 -- 299	73 -- 79	ethanolamine ammonia-lyase large subunit heavy chain		_____________292_____300\n_____________\|_______\|\n5'-CUG...GGGGA_______G-3'\n______________UGUGCUG\n______________\|\|\|\|\|\|:\n______________ACACGAU\n3'-UUU...AGUUA_______ACGUC...ACG-5'\n_____________\|_______\|\n_____________80______72\n	293 -- 299	73 -- 79	-8.7652 kcal/mol	1.34517 kcal/mol	1.33434 kcal/mol	292 300@LB@ \| \|@LB@5'-CUG...GGGGA G-3'@LB@ UGUGCUG@LB@ \|\|\|\|\|\|:@LB@ ACACGAU@LB@3'-UUU...AGUUA ACGUC...ACG-5'@LB@ \| \|@LB@ 80 72@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.7652 kcal/mol@LB@Unfolding Energy - mRNA 1.34517 kcal/mol@LB@Unfolding Energy - sRNA 1.33434 kcal/mol@LB@@LB@Position - mRNA 293 -- 299@LB@Position - sRNA 73 -- 79@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 73 -- 79@LB@
19	4.82e-05	0.008725	b2452	eutH	-15.86	0.002353	187 -- 206	37 -- 56	ethanolamine transporter		_____________186___________________207\n_____________\|_____________________\|\n5'-UUG...CUAAC_______A_____________AUUAA...UCC-3'\n______________AGGGAGU_AAGGCGAUG_GGA\n______________\|\|\|:\|\|\|_\|\|\|:\|:\|\|:_\|\|\|\n______________UCCUUCA_UUCUGUUAU_CCU\n3'-UUU...UUUUU_________________A___CGCGU...ACG-5'\n_____________\|_____________________\|\n_____________57____________________36\n	197 -- 203	41 -- 47	-22.1606 kcal/mol	2.59538 kcal/mol	3.6645 kcal/mol	186 207@LB@ \| \|@LB@5'-UUG...CUAAC A AUUAA...UCC-3'@LB@ AGGGAGU AAGGCGAUG GGA@LB@ \|\|\|:\|\|\| \|\|\|:\|:\|\|: \|\|\|@LB@ UCCUUCA UUCUGUUAU CCU@LB@3'-UUU...UUUUU A CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -15.86 kcal/mol@LB@Hybridization Energy -22.1606 kcal/mol@LB@Unfolding Energy - mRNA 2.59538 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 187 -- 206@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 41 -- 47@LB@
61	0.001027	0.05816	b0443	fadM	-9.40	0.151451	193 -- 205	69 -- 81	long-chain acyl-CoA thioesterase III		_____________192___________206\n_____________\|_____________\|\n5'-GUU...AGGUU____C________AACAC...AUG-3'\n______________AUUG_GCUAUGCA\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\n______________UAAC_CGAUACGU\n3'-UUU...UUAGU____A________CAUUA...ACG-5'\n_____________\|_____________\|\n_____________82____________68\n	199 -- 205	69 -- 75	-15.9471 kcal/mol	4.72824 kcal/mol	1.82028 kcal/mol	192 206@LB@ \| \|@LB@5'-GUU...AGGUU C AACAC...AUG-3'@LB@ AUUG GCUAUGCA@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAAC CGAUACGU@LB@3'-UUU...UUAGU A CAUUA...ACG-5'@LB@ \| \|@LB@ 82 68@LB@@LB@@LB@Energy -9.40 kcal/mol@LB@Hybridization Energy -15.9471 kcal/mol@LB@Unfolding Energy - mRNA 4.72824 kcal/mol@LB@Unfolding Energy - sRNA 1.82028 kcal/mol@LB@@LB@Position - mRNA 193 -- 205@LB@Position - sRNA 69 -- 81@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
23	8.752e-05	0.01341	b1476	fdnI	-10.32	0.092280	170 -- 193	36 -- 57	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________169_______________________194\n_____________\|_________________________\|\n5'-CGU...CGAAU_________________ACGA____GAUCA...UUU-3'\n______________AAGGAAGU_GGACGAUG____GGAG\n______________\|\|\|\|\|\|\|\|_:\|\|\|:\|\|:____\|\|\|\|\n______________UUCCUUCA_UCUGUUAU____CCUC\n3'-UUU...GUUUU________U________A_______GCGUU...ACG-5'\n_____________\|_________________________\|\n_____________58________________________35\n	179 -- 185	41 -- 47	-22.1274 kcal/mol	8.02585 kcal/mol	3.74338 kcal/mol	169 194@LB@ \| \|@LB@5'-CGU...CGAAU ACGA GAUCA...UUU-3'@LB@ AAGGAAGU GGACGAUG GGAG@LB@ \|\|\|\|\|\|\|\| :\|\|\|:\|\|: \|\|\|\|@LB@ UUCCUUCA UCUGUUAU CCUC@LB@3'-UUU...GUUUU U A GCGUU...ACG-5'@LB@ \| \|@LB@ 58 35@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -22.1274 kcal/mol@LB@Unfolding Energy - mRNA 8.02585 kcal/mol@LB@Unfolding Energy - sRNA 3.74338 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 36 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 41 -- 47@LB@
153	0.00596	0.1368	b3892	fdoI	-11.89	0.036676	181 -- 200	31 -- 53	formate dehydrogenase-O cytochrome b556 subunit		_____________180_____________________201\n_____________\|_______________________\|\n5'-CCA...ACGAA___A___________________AUGAA...UGG-3'\n______________GAG_AAGACGA___GGAGCGCAA\n______________:\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|\|\|\|\n______________UUC_UUCUGUU___CCUCGCGUU\n3'-UUU...UUUCC___A_______AUA_________GCGGG...ACG-5'\n_____________\|_______________________\|\n_____________54______________________30\n	194 -- 200	31 -- 37	-24.6235 kcal/mol	2.95491 kcal/mol	9.77014 kcal/mol	180 201@LB@ \| \|@LB@5'-CCA...ACGAA A AUGAA...UGG-3'@LB@ GAG AAGACGA GGAGCGCAA@LB@ :\|\| \|\|\|\|\|:\| \|\|\|\|\|\|\|\|\|@LB@ UUC UUCUGUU CCUCGCGUU@LB@3'-UUU...UUUCC A AUA GCGGG...ACG-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -24.6235 kcal/mol@LB@Unfolding Energy - mRNA 2.95491 kcal/mol@LB@Unfolding Energy - sRNA 9.77014 kcal/mol@LB@@LB@Position - mRNA 181 -- 200@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 31 -- 37@LB@
55	0.0007336	0.04699	b0585	fes	-14.13	0.008457	197 -- 228	46 -- 77	enterobactin/ferrienterobactin esterase		_____________196________________________________229\n_____________\|__________________________________\|\n5'-CAU...GGUUA__G____A___CG_________U___________GCUGG...GGU-3'\n______________UG_UGUG_CGG____UUAAAAG_AGGAAGUGAGA\n______________\|\|_\|:\|\|_\|:\|____\|:\|\|\|\|:_\|\|\|\|\|\|\|:\|\|\|\n______________AC_AUAC_GUC____AGUUUUU_UCCUUCAUUCU\n3'-UUU...UUAAC__G________AUUA___________________GUUAU...ACG-5'\n_____________\|__________________________________\|\n_____________78_________________________________45\n	222 -- 228	46 -- 52	-26.4508 kcal/mol	7.03406 kcal/mol	5.29333 kcal/mol	196 229@LB@ \| \|@LB@5'-CAU...GGUUA G A CG U GCUGG...GGU-3'@LB@ UG UGUG CGG UUAAAAG AGGAAGUGAGA@LB@ \|\| \|:\|\| \|:\| \|:\|\|\|\|: \|\|\|\|\|\|\|:\|\|\|@LB@ AC AUAC GUC AGUUUUU UCCUUCAUUCU@LB@3'-UUU...UUAAC G AUUA GUUAU...ACG-5'@LB@ \| \|@LB@ 78 45@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -26.4508 kcal/mol@LB@Unfolding Energy - mRNA 7.03406 kcal/mol@LB@Unfolding Energy - sRNA 5.29333 kcal/mol@LB@@LB@Position - mRNA 197 -- 228@LB@Position - sRNA 46 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 46 -- 52@LB@
38	0.0003163	0.02889	b4315	fimI	-9.52	0.141947	182 -- 216	45 -- 80	fimbrial protein involved in type 1 pilus biosynthesis		_____________181___________________________________217\n_____________\|_____________________________________\|\n5'-UGC...CACCC______GAUAAAAAUAACGAU________________UAUUU...AAU-3'\n______________UUGUGC_______________GAAAAGGAAG__AGAU\n______________\|\|\|\|\|\|_______________:\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________AACACG_______________UUUUUCCUUC__UCUG\n3'-UUU...UAGUU______AUACGUCAUUAAGU___________AU____UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________81____________________________________44\n	206 -- 212	51 -- 57	-20.4045 kcal/mol	5.26447 kcal/mol	5.61905 kcal/mol	181 217@LB@ \| \|@LB@5'-UGC...CACCC GAUAAAAAUAACGAU UAUUU...AAU-3'@LB@ UUGUGC GAAAAGGAAG AGAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ AACACG UUUUUCCUUC UCUG@LB@3'-UUU...UAGUU AUACGUCAUUAAGU AU UUAUA...ACG-5'@LB@ \| \|@LB@ 81 44@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -20.4045 kcal/mol@LB@Unfolding Energy - mRNA 5.26447 kcal/mol@LB@Unfolding Energy - sRNA 5.61905 kcal/mol@LB@@LB@Position - mRNA 182 -- 216@LB@Position - sRNA 45 -- 80@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 51 -- 57@LB@
104	0.00334	0.1114	b1923	fliC	-7.97	0.300066	194 -- 205	75 -- 89	flagellar filament structural protein (flagellin)		_____________193_____________206\n_____________\|_______________\|\n5'-GUU...GGAUA_______________ACAAG...CUU-3'\n______________ACGAAUCA__UG_GC\n______________\|\|\|\|\|\|\|\|__\|\|_\|\|\n______________UGCUUAGU__AC_CG\n3'-UUU...CAGCA________UA__A__AUACG...ACG-5'\n_____________\|_______________\|\n_____________90______________74\n	195 -- 201	82 -- 88	-12.363 kcal/mol	2.14901 kcal/mol	2.24483 kcal/mol	193 206@LB@ \| \|@LB@5'-GUU...GGAUA ACAAG...CUU-3'@LB@ ACGAAUCA UG GC@LB@ \|\|\|\|\|\|\|\| \|\| \|\|@LB@ UGCUUAGU AC CG@LB@3'-UUU...CAGCA UA A AUACG...ACG-5'@LB@ \| \|@LB@ 90 74@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -12.363 kcal/mol@LB@Unfolding Energy - mRNA 2.14901 kcal/mol@LB@Unfolding Energy - sRNA 2.24483 kcal/mol@LB@@LB@Position - mRNA 194 -- 205@LB@Position - sRNA 75 -- 89@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 82 -- 88@LB@
98	0.003129	0.1114	b0357	frmR	-9.19	0.168108	184 -- 207	25 -- 48	regulator protein that represses frmRAB operon		_____________183______________________208\n_____________\|________________________\|\n5'-CUG...CAUGC________A__U___AA_______GUACU...CCG-3'\n______________AGAUGAUG_GG_GCG__AUGCCCA\n______________\|\|\|::\|\|:_\|\|_\|\|\|__\|:\|\|\|\|\|\n______________UCUGUUAU_CC_CGC__UGCGGGU\n3'-UUU...UUCAU________A__U___GU_______AGCGA...ACG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	201 -- 207	25 -- 31	-27.7971 kcal/mol	6.33291 kcal/mol	12.271 kcal/mol	183 208@LB@ \| \|@LB@5'-CUG...CAUGC A U AA GUACU...CCG-3'@LB@ AGAUGAUG GG GCG AUGCCCA@LB@ \|\|\|::\|\|: \|\| \|\|\| \|:\|\|\|\|\|@LB@ UCUGUUAU CC CGC UGCGGGU@LB@3'-UUU...UUCAU A U GU AGCGA...ACG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -27.7971 kcal/mol@LB@Unfolding Energy - mRNA 6.33291 kcal/mol@LB@Unfolding Energy - sRNA 12.271 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 25 -- 31@LB@
142	0.005444	0.1351	b3950	frwB	-10.99	0.063119	13 -- 50	47 -- 86	putative enzyme IIB component of PTS	b3899	_____________12__________________________________________51\n_____________\|___________________________________________\|\n5'-GCA...GGGGU____U__________C__________________C___C____UUAUA...GGG-3'\n______________GGUC_GAUUGUGCUG__CGGUGGUU____GAAGG_AAG_UGGG\n______________::\|\|_:\|\|\|\|\|\|\|\|:__\|:\|\|::\|\|____:\|\|\|\|_\|\|\|_\|::\|\n______________UUAG_UUAACACGAU__GUCAUUAA____UUUCC_UUC_AUUC\n3'-UUU...CAUGC_______________AC________GUUU______________UGUUA...ACG-5'\n_____________\|___________________________________________\|\n_____________87__________________________________________46\n	30 -- 36	63 -- 69	-27.1662 kcal/mol	11.4404 kcal/mol	4.74035 kcal/mol	12 51@LB@ \| \|@LB@5'-GCA...GGGGU U C C C UUAUA...GGG-3'@LB@ GGUC GAUUGUGCUG CGGUGGUU GAAGG AAG UGGG@LB@ ::\|\| :\|\|\|\|\|\|\|\|: \|:\|\|::\|\| :\|\|\|\| \|\|\| \|::\|@LB@ UUAG UUAACACGAU GUCAUUAA UUUCC UUC AUUC@LB@3'-UUU...CAUGC AC GUUU UGUUA...ACG-5'@LB@ \| \|@LB@ 87 46@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -27.1662 kcal/mol@LB@Unfolding Energy - mRNA 11.4404 kcal/mol@LB@Unfolding Energy - sRNA 4.74035 kcal/mol@LB@@LB@Position - mRNA 13 -- 50@LB@Position - sRNA 47 -- 86@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 63 -- 69@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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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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