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
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@
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@
144	0.01453	0.3231	b3614	yibQ	-4.49	0.404320	261 -- 267	34 -- 40	putative polysaccharide deacetylase	_____________260_____268\n_____________\|_______\|\n5'-UGG...CCCCC_______CUGGC...UUG-3'\n______________GUACUUG\n______________\|:\|\|\|\|:\n______________CGUGAAU\n3'-UUU...UUCUU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________41______33\n	261 -- 267	34 -- 40	-7.10274 kcal/mol	0.998159 kcal/mol	1.61352 kcal/mol	260 268@LB@ \| \|@LB@5'-UGG...CCCCC CUGGC...UUG-3'@LB@ GUACUUG@LB@ \|:\|\|\|\|:@LB@ CGUGAAU@LB@3'-UUU...UUCUU UUUUU...CAA-5'@LB@ \| \|@LB@ 41 33@LB@@LB@@LB@Energy -4.49 kcal/mol@LB@Hybridization Energy -7.10274 kcal/mol@LB@Unfolding Energy - mRNA 0.998159 kcal/mol@LB@Unfolding Energy - sRNA 1.61352 kcal/mol@LB@@LB@Position - mRNA 261 -- 267@LB@Position - sRNA 34 -- 40@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 34 -- 40@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@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
130	0.01234	0.3033	b2958	yggN	-5.61	0.236844	227 -- 233	35 -- 41	DUF2884 family putative periplasmic protein	_____________226_____234\n_____________\|_______\|\n5'-ACG...GCGGC_______UCAGU...UUG-3'\n______________AGCACUU\n______________\|\|\|\|\|\|\|\n______________UCGUGAA\n3'-UUU...GUUCU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________42______34\n	227 -- 233	35 -- 41	-8.1936 kcal/mol	0.976472 kcal/mol	1.6033 kcal/mol	226 234@LB@ \| \|@LB@5'-ACG...GCGGC UCAGU...UUG-3'@LB@ AGCACUU@LB@ \|\|\|\|\|\|\|@LB@ UCGUGAA@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 34@LB@@LB@@LB@Energy -5.61 kcal/mol@LB@Hybridization Energy -8.1936 kcal/mol@LB@Unfolding Energy - mRNA 0.976472 kcal/mol@LB@Unfolding Energy - sRNA 1.6033 kcal/mol@LB@@LB@Position - mRNA 227 -- 233@LB@Position - sRNA 35 -- 41@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 35 -- 41@LB@
189	0.02233	0.3796	b3417	malP	-8.63	0.040366	227 -- 245	35 -- 53	maltodextrin phosphorylase	_____________226_________________246\n_____________\|___________________\|\n5'-ACA...GAUAA__AAUUU____________UCACG...GCC-3'\n______________GC_____CAGGAAGCGCUU\n______________\|\|_____\|\|:\|\|\|\|\|:\|\|\|\n______________CG_____GUUCUUCGUGAA\n3'-UUU...UUGAA__AAUUC____________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	239 -- 245	35 -- 41	-18.4249 kcal/mol	3.68713 kcal/mol	6.10399 kcal/mol	226 246@LB@ \| \|@LB@5'-ACA...GAUAA AAUUU UCACG...GCC-3'@LB@ GC CAGGAAGCGCUU@LB@ \|\| \|\|:\|\|\|\|\|:\|\|\|@LB@ CG GUUCUUCGUGAA@LB@3'-UUU...UUGAA AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -18.4249 kcal/mol@LB@Unfolding Energy - mRNA 3.68713 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 227 -- 245@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 35 -- 41@LB@
4	1.769e-05	0.01424	b2105	rcnR	-7.88	0.065143	12 -- 26	36 -- 49	transcriptional repressor of rcnA	_____________11______________27\n_____________\|_______________\|\n5'-UGA...GCACC________U______GGGGA...ACG-3'\n______________AAGUAAGA_GGCGCU\n______________\|\|\|:\|\|\|\|_:\|\|:\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	13 -- 19	42 -- 48	-15.6635 kcal/mol	1.75127 kcal/mol	6.03645 kcal/mol	11 27@LB@ \| \|@LB@5'-UGA...GCACC U GGGGA...ACG-3'@LB@ AAGUAAGA GGCGCU@LB@ \|\|\|:\|\|\|\| :\|\|:\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -15.6635 kcal/mol@LB@Unfolding Energy - mRNA 1.75127 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 12 -- 26@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 42 -- 48@LB@
17	0.0004446	0.08107	b1976	mtfA	-9.25	0.026966	241 -- 268	36 -- 59	anti-repressor for DgsA(Mlc)	_____________240___________________________269\n_____________\|_____________________________\|\n5'-AUA...ACAUC________CCUUCCCU_____________AUCGA...AAC-3'\n______________AAAC_UGC________GGCAGGAAGCACU\n______________\|\|\|\|_\|\|\|________:\|\|\|:\|\|\|\|\|\|\|\|\n______________UUUG_ACG________UCGUUCUUCGUGA\n3'-UUU...CCUAC____A___AAU__________________AUUUU...CAA-5'\n_____________\|_____________________________\|\n_____________60____________________________35\n	262 -- 268	36 -- 42	-23.9855 kcal/mol	8.48573 kcal/mol	6.24948 kcal/mol	240 269@LB@ \| \|@LB@5'-AUA...ACAUC CCUUCCCU AUCGA...AAC-3'@LB@ AAAC UGC GGCAGGAAGCACU@LB@ \|\|\|\| \|\|\| :\|\|\|:\|\|\|\|\|\|\|\|@LB@ UUUG ACG UCGUUCUUCGUGA@LB@3'-UUU...CCUAC A AAU AUUUU...CAA-5'@LB@ \| \|@LB@ 60 35@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -23.9855 kcal/mol@LB@Unfolding Energy - mRNA 8.48573 kcal/mol@LB@Unfolding Energy - sRNA 6.24948 kcal/mol@LB@@LB@Position - mRNA 241 -- 268@LB@Position - sRNA 36 -- 59@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 36 -- 42@LB@
64	0.003339	0.1645	b3166	truB	-7.27	0.093914	187 -- 199	36 -- 48	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________186___________200\n_____________\|_____________\|\n5'-GGC...ACGAC_________G___AAUGA...AAC-3'\n______________AGCAAGGAG_ACU\n______________\|\|\|\|\|\|:\|\|_\|\|\|\n______________UCGUUCUUC_UGA\n3'-UUU...CGAAU_________G___AUUUU...CAA-5'\n_____________\|_____________\|\n_____________49____________35\n	189 -- 195	40 -- 46	-16.8762 kcal/mol	3.76451 kcal/mol	5.83861 kcal/mol	186 200@LB@ \| \|@LB@5'-GGC...ACGAC G AAUGA...AAC-3'@LB@ AGCAAGGAG ACU@LB@ \|\|\|\|\|\|:\|\| \|\|\|@LB@ UCGUUCUUC UGA@LB@3'-UUU...CGAAU G AUUUU...CAA-5'@LB@ \| \|@LB@ 49 35@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -16.8762 kcal/mol@LB@Unfolding Energy - mRNA 3.76451 kcal/mol@LB@Unfolding Energy - sRNA 5.83861 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 36 -- 48@LB@Position Seed - mRNA 189 -- 195@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)

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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