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
155	0.01672	0.3455	b1686	menI	-4.77	0.356790	227 -- 235	36 -- 44	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________226_______236\n_____________\|_________\|\n5'-GGC...ACCCU_________GAAUG...AUG-3'\n______________GGAAGCACU\n______________:\|\|\|\|\|\|\|\|\n______________UCUUCGUGA\n3'-UUU...UUCGU_________AUUUU...CAA-5'\n_____________\|_________\|\n_____________45________35\n	229 -- 235	36 -- 42	-13.4239 kcal/mol	4.1512 kcal/mol	4.5009 kcal/mol	226 236@LB@ \| \|@LB@5'-GGC...ACCCU GAAUG...AUG-3'@LB@ GGAAGCACU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUUCGUGA@LB@3'-UUU...UUCGU AUUUU...CAA-5'@LB@ \| \|@LB@ 45 35@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -13.4239 kcal/mol@LB@Unfolding Energy - mRNA 4.1512 kcal/mol@LB@Unfolding Energy - sRNA 4.5009 kcal/mol@LB@@LB@Position - mRNA 227 -- 235@LB@Position - sRNA 36 -- 44@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
31	0.0009469	0.09599	b0166	dapD	-11.60	0.005180	96 -- 124	11 -- 40	2 3 4 5-tetrahydropyridine-2-carboxylate N-succinyltransferase	_____________95_____________________________125\n_____________\|______________________________\|\n5'-UUG...GGCGU________UAACGA_______G________GCAUC...AGG-3'\n______________GCGCUUAA_______GUUGCA_CAGGAAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|:\|\|_\|\|\|\|\|\|:\|\n______________CGUGAAUU_______CAAUGU_GUCCUUUA\n3'-UUU...UUCUU________UUUUAAG______G________GACUA...CAA-5'\n_____________\|______________________________\|\n_____________41_____________________________10\n	97 -- 103	33 -- 39	-29.7713 kcal/mol	8.96001 kcal/mol	9.20882 kcal/mol	95 125@LB@ \| \|@LB@5'-UUG...GGCGU UAACGA G GCAUC...AGG-3'@LB@ GCGCUUAA GUUGCA CAGGAAGU@LB@ \|\|:\|\|\|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ CGUGAAUU CAAUGU GUCCUUUA@LB@3'-UUU...UUCUU UUUUAAG G GACUA...CAA-5'@LB@ \| \|@LB@ 41 10@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -29.7713 kcal/mol@LB@Unfolding Energy - mRNA 8.96001 kcal/mol@LB@Unfolding Energy - sRNA 9.20882 kcal/mol@LB@@LB@Position - mRNA 96 -- 124@LB@Position - sRNA 11 -- 40@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 33 -- 39@LB@
126	0.01159	0.2964	b3693	dgoK	-8.44	0.045823	138 -- 160	34 -- 54	2-oxo-3-deoxygalactonate kinase	_____________137_____________________161\n_____________\|_______________________\|\n5'-CAG...GGCGA___GGCA_______C________CCAUG...CAG-3'\n______________UGC____GAGCAGG_GGCGCUUA\n______________\|\|\|____:\|\|\|\|:\|_:\|\|:\|\|\|\|\n______________ACG____UUCGUUC_UCGUGAAU\n3'-UUU...UUUGA___AA_________U________UUUUU...CAA-5'\n_____________\|_______________________\|\n_____________55______________________33\n	154 -- 160	34 -- 40	-23.026 kcal/mol	8.41527 kcal/mol	6.17478 kcal/mol	137 161@LB@ \| \|@LB@5'-CAG...GGCGA GGCA C CCAUG...CAG-3'@LB@ UGC GAGCAGG GGCGCUUA@LB@ \|\|\| :\|\|\|\|:\| :\|\|:\|\|\|\|@LB@ ACG UUCGUUC UCGUGAAU@LB@3'-UUU...UUUGA AA U UUUUU...CAA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -23.026 kcal/mol@LB@Unfolding Energy - mRNA 8.41527 kcal/mol@LB@Unfolding Energy - sRNA 6.17478 kcal/mol@LB@@LB@Position - mRNA 138 -- 160@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 34 -- 40@LB@
53	0.002646	0.1597	b1704	aroH	-6.03	0.190589	111 -- 120	31 -- 40	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase tryptophan repressible	_____________110________121\n_____________\|__________\|\n5'-CCA...ACCUC__________UCAGC...CCC-3'\n______________GCACUUGAAA\n______________\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUU\n3'-UUU...UUCUU__________UUAAG...CAA-5'\n_____________\|__________\|\n_____________41_________30\n	114 -- 120	31 -- 37	-11.574 kcal/mol	3.92769 kcal/mol	1.61955 kcal/mol	110 121@LB@ \| \|@LB@5'-CCA...ACCUC UCAGC...CCC-3'@LB@ GCACUUGAAA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUU@LB@3'-UUU...UUCUU UUAAG...CAA-5'@LB@ \| \|@LB@ 41 30@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -11.574 kcal/mol@LB@Unfolding Energy - mRNA 3.92769 kcal/mol@LB@Unfolding Energy - sRNA 1.61955 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 31 -- 40@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 31 -- 37@LB@
149	0.01515	0.3274	b4196	ulaD	-9.50	0.022893	140 -- 153	36 -- 49	3-keto-L-gulonate 6-phosphate decarboxylase	_____________139____________154\n_____________\|______________\|\n5'-CGA...GUACC______________GGAUC...AAG-3'\n______________GAGCAGGAAGUACU\n______________:\|\|\|\|:\|\|\|\|:\|\|\|\n______________UUCGUUCUUCGUGA\n3'-UUU...ACGAA______________AUUUU...CAA-5'\n_____________\|______________\|\n_____________50_____________35\n	147 -- 153	36 -- 42	-21.0071 kcal/mol	5.47534 kcal/mol	6.03645 kcal/mol	139 154@LB@ \| \|@LB@5'-CGA...GUACC GGAUC...AAG-3'@LB@ GAGCAGGAAGUACU@LB@ :\|\|\|\|:\|\|\|\|:\|\|\|@LB@ UUCGUUCUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -21.0071 kcal/mol@LB@Unfolding Energy - mRNA 5.47534 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 140 -- 153@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 36 -- 42@LB@
181	0.0215	0.3768	b3843	ubiD	-7.81	0.067872	2 -- 28	14 -- 40	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C_______CAGUACA___AA_________UUGCA...UGG-3'\n______________GCGCUUG________GU__AUACCAGGA\n______________\|\|:\|\|\|:________\|\|__\|:\|\|\|\|\|\|\|\n______________CGUGAAU________CA__UGUGGUCCU\n3'-UUU...UUCUU_______UUUUUAAG__A__________UUAGA...CAA-5'\n_____________\|____________________________\|\n_____________41___________________________13\n	22 -- 28	14 -- 20	-21.9915 kcal/mol	4.97788 kcal/mol	9.20436 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C CAGUACA AA UUGCA...UGG-3'@LB@ GCGCUUG GU AUACCAGGA@LB@ \|\|:\|\|\|: \|\| \|:\|\|\|\|\|\|\|@LB@ CGUGAAU CA UGUGGUCCU@LB@3'-UUU...UUCUU UUUUUAAG A UUAGA...CAA-5'@LB@ \| \|@LB@ 41 13@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -21.9915 kcal/mol@LB@Unfolding Energy - mRNA 4.97788 kcal/mol@LB@Unfolding Energy - sRNA 9.20436 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 14 -- 40@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 14 -- 20@LB@
134	0.01281	0.308	b3316	rpsS	-8.71	0.038435	274 -- 288	39 -- 53	30S ribosomal subunit protein S19	_____________273______________289\n_____________\|________________\|\n5'-GCG...GGAAA__G____A________CCCUG...CUU-3'\n______________GC__GAG_CAAGAAGC\n______________\|\|__:\|\|_\|\|\|\|\|\|\|\|\n______________CG__UUC_GUUCUUCG\n3'-UUU...UUGAA__AA____________UGAAU...CAA-5'\n_____________\|________________\|\n_____________54_______________38\n	282 -- 288	39 -- 45	-16.1876 kcal/mol	1.46049 kcal/mol	6.01745 kcal/mol	273 289@LB@ \| \|@LB@5'-GCG...GGAAA G A CCCUG...CUU-3'@LB@ GC GAG CAAGAAGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|\|@LB@ CG UUC GUUCUUCG@LB@3'-UUU...UUGAA AA UGAAU...CAA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -16.1876 kcal/mol@LB@Unfolding Energy - mRNA 1.46049 kcal/mol@LB@Unfolding Energy - sRNA 6.01745 kcal/mol@LB@@LB@Position - mRNA 274 -- 288@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 39 -- 45@LB@
187	0.02188	0.3768	b3065	rpsU	-8.54	0.042773	188 -- 200	37 -- 49	30S ribosomal subunit protein S21	_____________187___________201\n_____________\|_____________\|\n5'-GAC...AUCAA_____________AUGCC...GUC-3'\n______________AGGUGAGAGGCAC\n______________\|:\|::\|\|\|:\|\|\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	194 -- 200	37 -- 43	-18.635 kcal/mol	4.05763 kcal/mol	6.03369 kcal/mol	187 201@LB@ \| \|@LB@5'-GAC...AUCAA AUGCC...GUC-3'@LB@ AGGUGAGAGGCAC@LB@ \|:\|::\|\|\|:\|\|\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -18.635 kcal/mol@LB@Unfolding Energy - mRNA 4.05763 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 37 -- 43@LB@
123	0.0108	0.2828	b2606	rplS	-6.81	0.122900	220 -- 252	37 -- 58	50S ribosomal subunit protein L19	_____________219_______________________________253\n_____________\|_________________________________\|\n5'-AUA...UAAGC______AACAAGAGCAGAUG________C____CUUCC...UUG-3'\n______________AACUUG______________AAGCAGGA_GUAC\n______________\|\|\|\|\|\|______________\|\|\|\|\|:\|\|_\|:\|\|\n______________UUGAAC______________UUCGUUCU_CGUG\n3'-UUU...CUACU______GAA___________________U____AAUUU...CAA-5'\n_____________\|_________________________________\|\n_____________59________________________________36\n	241 -- 247	42 -- 48	-17.5998 kcal/mol	4.54246 kcal/mol	6.24354 kcal/mol	219 253@LB@ \| \|@LB@5'-AUA...UAAGC AACAAGAGCAGAUG C CUUCC...UUG-3'@LB@ AACUUG AAGCAGGA GUAC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\| \|:\|\|@LB@ UUGAAC UUCGUUCU CGUG@LB@3'-UUU...CUACU GAA U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -17.5998 kcal/mol@LB@Unfolding Energy - mRNA 4.54246 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 220 -- 252@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 42 -- 48@LB@
191	0.02253	0.38	b3186	rplU	-5.10	0.305418	95 -- 102	34 -- 41	50S ribosomal subunit protein L21	_____________94_______103\n_____________\|________\|\n5'-UUA...ACUGU________UCAAA...UUG-3'\n______________AGCACUUG\n______________\|\|\|\|\|\|\|:\n______________UCGUGAAU\n3'-UUU...GUUCU________UUUUU...CAA-5'\n_____________\|________\|\n_____________42_______33\n	96 -- 102	34 -- 40	-9.60207 kcal/mol	2.88333 kcal/mol	1.6155 kcal/mol	94 103@LB@ \| \|@LB@5'-UUA...ACUGU UCAAA...UUG-3'@LB@ AGCACUUG@LB@ \|\|\|\|\|\|\|:@LB@ UCGUGAAU@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -9.60207 kcal/mol@LB@Unfolding Energy - mRNA 2.88333 kcal/mol@LB@Unfolding Energy - sRNA 1.6155 kcal/mol@LB@@LB@Position - mRNA 95 -- 102@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 34 -- 40@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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usability assessment

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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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