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
136	0.01308	0.3087	b0131	panD	-6.12	0.181240	260 -- 282	17 -- 40	aspartate 1-decarboxylase	_____________259______________________283\n_____________\|________________________\|\n5'-AUU...GACCU_____AU_________________UUGAC...UUG-3'\n______________GCACU__GAAGGUUC_UUGCGCCA\n______________\|\|\|\|\|__:\|\|::\|\|\|_\|\|:\|:\|\|\|\n______________CGUGA__UUUUUAAG_AAUGUGGU\n3'-UUU...UUCUU_____AU________C________CCUUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________16\n	268 -- 274	26 -- 32	-23.1255 kcal/mol	7.80932 kcal/mol	9.19627 kcal/mol	259 283@LB@ \| \|@LB@5'-AUU...GACCU AU UUGAC...UUG-3'@LB@ GCACU GAAGGUUC UUGCGCCA@LB@ \|\|\|\|\| :\|\|::\|\|\| \|\|:\|:\|\|\|@LB@ CGUGA UUUUUAAG AAUGUGGU@LB@3'-UUU...UUCUU AU C CCUUU...CAA-5'@LB@ \| \|@LB@ 41 16@LB@@LB@@LB@Energy -6.12 kcal/mol@LB@Hybridization Energy -23.1255 kcal/mol@LB@Unfolding Energy - mRNA 7.80932 kcal/mol@LB@Unfolding Energy - sRNA 9.19627 kcal/mol@LB@@LB@Position - mRNA 260 -- 282@LB@Position - sRNA 17 -- 40@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 26 -- 32@LB@
131	0.01234	0.3033	b4139	aspA	-5.03	0.315570	237 -- 252	26 -- 41	aspartate ammonia-lyase	_____________236______________253\n_____________\|________________\|\n5'-GAU...UGUUG_____CA_________CAGCU...ACU-3'\n______________GGUAC__GGGAAGUUC\n______________:\|:\|\|__:::\|\|:\|\|\|\n______________UCGUG__UUUUUUAAG\n3'-UUU...GUUCU_____AA_________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	246 -- 252	26 -- 32	-10.8102 kcal/mol	4.127 kcal/mol	1.64829 kcal/mol	236 253@LB@ \| \|@LB@5'-GAU...UGUUG CA CAGCU...ACU-3'@LB@ GGUAC GGGAAGUUC@LB@ :\|:\|\| :::\|\|:\|\|\|@LB@ UCGUG UUUUUUAAG@LB@3'-UUU...GUUCU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -10.8102 kcal/mol@LB@Unfolding Energy - mRNA 4.127 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 237 -- 252@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 26 -- 32@LB@
72	0.003773	0.1688	b1860	ruvB	-7.81	0.067658	103 -- 111	38 -- 46	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________102_______112\n_____________\|_________\|\n5'-ACG...AACCA_________AGCCG...GUC-3'\n______________CAAGAAGCA\n______________\|\|\|\|\|\|\|\|\|\n______________GUUCUUCGU\n3'-UUU...AAUUC_________GAAUU...CAA-5'\n_____________\|_________\|\n_____________47________37\n	105 -- 111	38 -- 44	-11.4188 kcal/mol	0.978333 kcal/mol	2.62609 kcal/mol	102 112@LB@ \| \|@LB@5'-ACG...AACCA AGCCG...GUC-3'@LB@ CAAGAAGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ GUUCUUCGU@LB@3'-UUU...AAUUC GAAUU...CAA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -11.4188 kcal/mol@LB@Unfolding Energy - mRNA 0.978333 kcal/mol@LB@Unfolding Energy - sRNA 2.62609 kcal/mol@LB@@LB@Position - mRNA 103 -- 111@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 38 -- 44@LB@
23	0.000685	0.09021	b3780	rhlB	-7.99	0.060609	254 -- 278	29 -- 60	ATP-dependent RNA helicase	_____________253______________________________279\n_____________\|________________________________\|\n5'-UCG...CAUCC____G_________________C_________AAAGG...CGC-3'\n______________GAAG_UUGU_______AGAAGC_CUUGAAAAA\n______________\|\|\|:_\|\|\|:_______\|\|\|\|\|\|_\|\|\|:\|\|\|\|\|\n______________CUUU_AACG_______UCUUCG_GAAUUUUUU\n3'-UUU...CCCUA____G____AAUUCGU______U_________AAGCA...CAA-5'\n_____________\|________________________________\|\n_____________61_______________________________28\n	270 -- 276	31 -- 37	-19.7636 kcal/mol	5.50064 kcal/mol	6.27092 kcal/mol	253 279@LB@ \| \|@LB@5'-UCG...CAUCC G C AAAGG...CGC-3'@LB@ GAAG UUGU AGAAGC CUUGAAAAA@LB@ \|\|\|: \|\|\|: \|\|\|\|\|\| \|\|\|:\|\|\|\|\|@LB@ CUUU AACG UCUUCG GAAUUUUUU@LB@3'-UUU...CCCUA G AAUUCGU U AAGCA...CAA-5'@LB@ \| \|@LB@ 61 28@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -19.7636 kcal/mol@LB@Unfolding Energy - mRNA 5.50064 kcal/mol@LB@Unfolding Energy - sRNA 6.27092 kcal/mol@LB@@LB@Position - mRNA 254 -- 278@LB@Position - sRNA 29 -- 60@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 31 -- 37@LB@
66	0.003432	0.1645	b0882	clpA	-7.45	0.084488	282 -- 290	34 -- 42	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity	_____________281_______291\n_____________\|_________\|\n5'-UUU...CCGUC_________UUACU...CGC-3'\n______________GAGCACUUG\n______________:\|\|\|\|\|\|\|:\n______________UUCGUGAAU\n3'-UUU...CGUUC_________UUUUU...CAA-5'\n_____________\|_________\|\n_____________43________33\n	284 -- 290	34 -- 40	-10.5586 kcal/mol	1.49281 kcal/mol	1.61613 kcal/mol	281 291@LB@ \| \|@LB@5'-UUU...CCGUC UUACU...CGC-3'@LB@ GAGCACUUG@LB@ :\|\|\|\|\|\|\|:@LB@ UUCGUGAAU@LB@3'-UUU...CGUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 43 33@LB@@LB@@LB@Energy -7.45 kcal/mol@LB@Hybridization Energy -10.5586 kcal/mol@LB@Unfolding Energy - mRNA 1.49281 kcal/mol@LB@Unfolding Energy - sRNA 1.61613 kcal/mol@LB@@LB@Position - mRNA 282 -- 290@LB@Position - sRNA 34 -- 42@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 34 -- 40@LB@
80	0.005376	0.2146	b1520	yneE	-6.66	0.134465	278 -- 284	34 -- 40	bestrophin family putative inner membrane protein	_____________277_____285\n_____________\|_______\|\n5'-CGU...UCCUC_______CUACU...UCU-3'\n______________GCGCUUA\n______________\|\|:\|\|\|\|\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	278 -- 284	34 -- 40	-8.65652 kcal/mol	0.386276 kcal/mol	1.61352 kcal/mol	277 285@LB@ \| \|@LB@5'-CGU...UCCUC CUACU...UCU-3'@LB@ GCGCUUA@LB@ \|\|:\|\|\|\|@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -6.66 kcal/mol@LB@Hybridization Energy -8.65652 kcal/mol@LB@Unfolding Energy - mRNA 0.386276 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 278 -- 284@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 34 -- 40@LB@
68	0.003533	0.1645	b3650	spoT	-9.27	0.026581	116 -- 140	36 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase	_____________115________________________141\n_____________\|__________________________\|\n5'-UAG...CGCCA_____A___AA___________C___GAAUU...CUC-3'\n______________GGAAC__GC__GAGCAGGAAGC_GCU\n______________\|:\|\|\|__\|\|__:\|\|\|\|:\|\|\|\|\|_:\|\|\n______________CUUUG__CG__UUCGUUCUUCG_UGA\n3'-UUU...CCCUA_____AA__AA_______________AUUUU...CAA-5'\n_____________\|__________________________\|\n_____________61_________________________35\n	130 -- 136	39 -- 45	-24.6059 kcal/mol	9.08429 kcal/mol	6.24973 kcal/mol	115 141@LB@ \| \|@LB@5'-UAG...CGCCA A AA C GAAUU...CUC-3'@LB@ GGAAC GC GAGCAGGAAGC GCU@LB@ \|:\|\|\| \|\| :\|\|\|\|:\|\|\|\|\| :\|\|@LB@ CUUUG CG UUCGUUCUUCG UGA@LB@3'-UUU...CCCUA AA AA AUUUU...CAA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -24.6059 kcal/mol@LB@Unfolding Energy - mRNA 9.08429 kcal/mol@LB@Unfolding Energy - sRNA 6.24973 kcal/mol@LB@@LB@Position - mRNA 116 -- 140@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 39 -- 45@LB@
89	0.006302	0.2266	b3208	mtgA	-4.90	0.336213	28 -- 47	28 -- 47	biosynthetic peptidoglycan transglycosylase	_____________27____________________48\n_____________\|_____________________\|\n5'-UUG...AUACC____________GG_______GGGCG...UGU-3'\n______________GC_AGAAGUGCU__AAGAGAU\n______________\|\|_\|\|\|\|\|::\|\|__\|\|:\|:\|\|\n______________CG_UCUUCGUGA__UUUUUUA\n3'-UUU...GAAUU__U_________A________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________48____________________27\n	32 -- 38	36 -- 42	-15.6239 kcal/mol	4.50128 kcal/mol	6.22212 kcal/mol	27 48@LB@ \| \|@LB@5'-UUG...AUACC GG GGGCG...UGU-3'@LB@ GC AGAAGUGCU AAGAGAU@LB@ \|\| \|\|\|\|\|::\|\| \|\|:\|:\|\|@LB@ CG UCUUCGUGA UUUUUUA@LB@3'-UUU...GAAUU U A AGCAA...CAA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -4.90 kcal/mol@LB@Hybridization Energy -15.6239 kcal/mol@LB@Unfolding Energy - mRNA 4.50128 kcal/mol@LB@Unfolding Energy - sRNA 6.22212 kcal/mol@LB@@LB@Position - mRNA 28 -- 47@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 36 -- 42@LB@
74	0.004124	0.1795	b2599	pheA	-8.54	0.042758	34 -- 48	29 -- 42	chorismate mutase and prephenate dehydratase P-protein	_____________33______________49\n_____________\|_______________\|\n5'-UGA...UACUA___U___________ACAAA...UCG-3'\n______________AAG_CACUUAAGGAA\n______________\|\|\|_\|\|\|\|\|\|\|::\|\|\n______________UUC_GUGAAUUUUUU\n3'-UUU...CGUUC_______________AAGCA...CAA-5'\n_____________\|_______________\|\n_____________43______________28\n	42 -- 48	29 -- 35	-11.0993 kcal/mol	0.931405 kcal/mol	1.62369 kcal/mol	33 49@LB@ \| \|@LB@5'-UGA...UACUA U ACAAA...UCG-3'@LB@ AAG CACUUAAGGAA@LB@ \|\|\| \|\|\|\|\|\|\|::\|\|@LB@ UUC GUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -11.0993 kcal/mol@LB@Unfolding Energy - mRNA 0.931405 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 34 -- 48@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 29 -- 35@LB@
96	0.007122	0.239	b2060	wzc	-5.51	0.249431	285 -- 291	37 -- 43	colanic acid production tyrosine-protein kinase; autokinase; Ugd phosphorylase	_____________284_____292\n_____________\|_______\|\n5'-GAA...UCAUU_______GCUGG...GGG-3'\n______________GAAGCGC\n______________\|\|\|\|\|:\|\n______________CUUCGUG\n3'-UUU...UCGUU_______AAUUU...CAA-5'\n_____________\|_______\|\n_____________44______36\n	285 -- 291	37 -- 43	-9.9751 kcal/mol	0.803081 kcal/mol	3.6595 kcal/mol	284 292@LB@ \| \|@LB@5'-GAA...UCAUU GCUGG...GGG-3'@LB@ GAAGCGC@LB@ \|\|\|\|\|:\|@LB@ CUUCGUG@LB@3'-UUU...UCGUU AAUUU...CAA-5'@LB@ \| \|@LB@ 44 36@LB@@LB@@LB@Energy -5.51 kcal/mol@LB@Hybridization Energy -9.9751 kcal/mol@LB@Unfolding Energy - mRNA 0.803081 kcal/mol@LB@Unfolding Energy - sRNA 3.6595 kcal/mol@LB@@LB@Position - mRNA 285 -- 291@LB@Position - sRNA 37 -- 43@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 37 -- 43@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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