Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
4	8.9e-06	0.006694	b3281	aroE	-13.87	0.039990	230 -- 259	45 -- 75	dehydroshikimate reductase NAD(P)-binding		_____________229_____________________________260\n_____________\|_______________________________\|\n5'-UUU...AAUCC___A__C________A___CCA_________UCAGC...AUG-3'\n______________GAU_GC_CACAGCAA_UCG____UUCAUUCA\n______________\|\|:_:\|_\|\|\|\|\|\|\|\|_\|\|\|____\|\|\|\|:\|\|\|\n______________CUG_UG_GUGUCGUU_AGC____AAGUGAGU\n3'-UUU...CGUUU___A__U________A___AACA________CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	253 -- 259	45 -- 51	-26.2723 kcal/mol	8.66309 kcal/mol	3.74078 kcal/mol	229 260@LB@ \| \|@LB@5'-UUU...AAUCC A C A CCA UCAGC...AUG-3'@LB@ GAU GC CACAGCAA UCG UUCAUUCA@LB@ \|\|: :\| \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|\|\|@LB@ CUG UG GUGUCGUU AGC AAGUGAGU@LB@3'-UUU...CGUUU A U A AACA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -26.2723 kcal/mol@LB@Unfolding Energy - mRNA 8.66309 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 45 -- 51@LB@
72	0.002899	0.1417	b3688	yidQ	-12.98	0.064171	231 -- 261	39 -- 71	DUF1375 family outer membrane protein		_____________230_______________________________262\n_____________\|_________________________________\|\n5'-AUG...UCAUG___________AAUGACA__________A____GCUCC...GAA-3'\n______________AUAUGCAGCGG_________UUACUCGG_GGAU\n______________\|:\|::\|\|\|\|::_________\|:\|\|\|\|:\|_\|\|\|\|\n______________UGUGUGUCGUU_________AGUGAGUC_CCUA\n3'-UUU...UCUGA___________AAGCAACAA________C____AAGGU...GCA-5'\n_____________\|_________________________________\|\n_____________72________________________________38\n	250 -- 256	44 -- 50	-25.1937 kcal/mol	7.46905 kcal/mol	4.74947 kcal/mol	230 262@LB@ \| \|@LB@5'-AUG...UCAUG AAUGACA A GCUCC...GAA-3'@LB@ AUAUGCAGCGG UUACUCGG GGAU@LB@ \|:\|::\|\|\|\|:: \|:\|\|\|\|:\| \|\|\|\|@LB@ UGUGUGUCGUU AGUGAGUC CCUA@LB@3'-UUU...UCUGA AAGCAACAA C AAGGU...GCA-5'@LB@ \| \|@LB@ 72 38@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -25.1937 kcal/mol@LB@Unfolding Energy - mRNA 7.46905 kcal/mol@LB@Unfolding Energy - sRNA 4.74947 kcal/mol@LB@@LB@Position - mRNA 231 -- 261@LB@Position - sRNA 39 -- 71@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 44 -- 50@LB@
166	0.008074	0.1711	b2158	yeiH	-9.26	0.321503	233 -- 257	41 -- 72	UPF0324 family inner membrane protein		_____________232_______________________________258\n_____________\|_________________________________\|\n5'-CAC...CAUCG_____UG_____________________C____UUAGC...GUG-3'\n______________UACAC__UGGCA________UUUUAUUC_GGGG\n______________\|\|\|\|\|__::\|\|\|________\|\|\|:\|:\|\|_\|\|\|\|\n______________AUGUG__GUCGU________AAAGUGAG_CCCC\n3'-UUU...UUCUG_____U______UAAGCAAC________U____UAAAG...GCA-5'\n_____________\|_________________________________\|\n_____________73________________________________40\n	246 -- 252	46 -- 52	-21.8619 kcal/mol	7.84401 kcal/mol	4.75632 kcal/mol	232 258@LB@ \| \|@LB@5'-CAC...CAUCG UG C UUAGC...GUG-3'@LB@ UACAC UGGCA UUUUAUUC GGGG@LB@ \|\|\|\|\| ::\|\|\| \|\|\|:\|:\|\| \|\|\|\|@LB@ AUGUG GUCGU AAAGUGAG CCCC@LB@3'-UUU...UUCUG U UAAGCAAC U UAAAG...GCA-5'@LB@ \| \|@LB@ 73 40@LB@@LB@@LB@Energy -9.26 kcal/mol@LB@Hybridization Energy -21.8619 kcal/mol@LB@Unfolding Energy - mRNA 7.84401 kcal/mol@LB@Unfolding Energy - sRNA 4.75632 kcal/mol@LB@@LB@Position - mRNA 233 -- 257@LB@Position - sRNA 41 -- 72@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 46 -- 52@LB@
71	0.002886	0.1417	b2431	yfeX	-11.26	0.145044	235 -- 277	40 -- 74	porphyrinogen oxidase cytoplasmic		_____________234_________________________________________278\n_____________\|___________________________________________\|\n5'-AUU...AGAAC____C______________GAUCGAA__CAACGUGAA______AGUUG...CCA-3'\n______________AUUG_CGCGCGGCGAUUUG_______GC_________AGGGGA\n______________\|:\|:_\|:\|:\|:\|\|:\|\|\|:\|_______:\|_________\|\|\|\|\|\|\n______________UGAU_GUGUGUCGUUAAGC_______UG_________UCCCCU\n3'-UUU...GUUUC___________________AACAAAG__AG_____________AAAGG...GCA-5'\n_____________\|___________________________________________\|\n_____________75__________________________________________39\n	246 -- 252	58 -- 64	-30.0675 kcal/mol	14.0273 kcal/mol	4.77707 kcal/mol	234 278@LB@ \| \|@LB@5'-AUU...AGAAC C GAUCGAA CAACGUGAA AGUUG...CCA-3'@LB@ AUUG CGCGCGGCGAUUUG GC AGGGGA@LB@ \|:\|: \|:\|:\|:\|\|:\|\|\|:\| :\| \|\|\|\|\|\|@LB@ UGAU GUGUGUCGUUAAGC UG UCCCCU@LB@3'-UUU...GUUUC AACAAAG AG AAAGG...GCA-5'@LB@ \| \|@LB@ 75 39@LB@@LB@@LB@Energy -11.26 kcal/mol@LB@Hybridization Energy -30.0675 kcal/mol@LB@Unfolding Energy - mRNA 14.0273 kcal/mol@LB@Unfolding Energy - sRNA 4.77707 kcal/mol@LB@@LB@Position - mRNA 235 -- 277@LB@Position - sRNA 40 -- 74@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
179	0.009001	0.1747	b2725	hycA	-11.58	0.125812	239 -- 264	43 -- 70	regulator of the transcriptional regulator FhlA		_____________238_____________________________265\n_____________\|_______________________________\|\n5'-UUA...UACAU__________CA____________CUA____ACCAG...AGG-3'\n______________CGCACAGCGG__UCG_____UCGC___CAGG\n______________\|:\|\|\|\|\|\|::__\|\|\|_____\|\|:\|___\|\|\|\|\n______________GUGUGUCGUU__AGC_____AGUG___GUCC\n3'-UUU...CUGAU__________A____AACAA____A______CCUAA...GCA-5'\n_____________\|_______________________________\|\n_____________71______________________________42\n	242 -- 248	61 -- 67	-23.0547 kcal/mol	7.15003 kcal/mol	4.32399 kcal/mol	238 265@LB@ \| \|@LB@5'-UUA...UACAU CA CUA ACCAG...AGG-3'@LB@ CGCACAGCGG UCG UCGC CAGG@LB@ \|:\|\|\|\|\|\|:: \|\|\| \|\|:\| \|\|\|\|@LB@ GUGUGUCGUU AGC AGUG GUCC@LB@3'-UUU...CUGAU A AACAA A CCUAA...GCA-5'@LB@ \| \|@LB@ 71 42@LB@@LB@@LB@Energy -11.58 kcal/mol@LB@Hybridization Energy -23.0547 kcal/mol@LB@Unfolding Energy - mRNA 7.15003 kcal/mol@LB@Unfolding Energy - sRNA 4.32399 kcal/mol@LB@@LB@Position - mRNA 239 -- 264@LB@Position - sRNA 43 -- 70@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 61 -- 67@LB@
192	0.00979	0.1776	b3879	yihR	-14.50	0.028125	239 -- 282	38 -- 72	putative sulphoquinovose mutarotase		_____________238__________________________________________283\n_____________\|____________________________________________\|\n5'-CAU...ACCAA_______U_____GGACAGACC________UGCCG_________AUCAC...UGA-3'\n______________UAUGCAU_GCAGU_________GUUUCACU_____CGGGGGAUU\n______________\|\|::\|\|:_\|\|\|:\|_________\|\|\|\|\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________AUGUGUG_CGUUA_________CAAAGUGA_____GUCCCCUAA\n3'-UUU...UUCUG_______U_____AGCAA__________________________AGGUA...GCA-5'\n_____________\|____________________________________________\|\n_____________73___________________________________________37\n	276 -- 282	38 -- 44	-32.397 kcal/mol	13.138 kcal/mol	4.76382 kcal/mol	238 283@LB@ \| \|@LB@5'-CAU...ACCAA U GGACAGACC UGCCG AUCAC...UGA-3'@LB@ UAUGCAU GCAGU GUUUCACU CGGGGGAUU@LB@ \|\|::\|\|: \|\|\|:\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ AUGUGUG CGUUA CAAAGUGA GUCCCCUAA@LB@3'-UUU...UUCUG U AGCAA AGGUA...GCA-5'@LB@ \| \|@LB@ 73 37@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -32.397 kcal/mol@LB@Unfolding Energy - mRNA 13.138 kcal/mol@LB@Unfolding Energy - sRNA 4.76382 kcal/mol@LB@@LB@Position - mRNA 239 -- 282@LB@Position - sRNA 38 -- 72@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 38 -- 44@LB@
35	0.0005607	0.05638	b1434	ydcN	-11.45	0.133710	242 -- 253	62 -- 74	putative DNA-binding transcriptional regulator	b1508 b1299	_____________241___________254\n_____________\|_____________\|\n5'-CGG...AAACA_____________GCGCG...CUA-3'\n______________ACUACGC_CAGCA\n______________\|\|\|\|\|:\|_\|\|\|\|\|\n______________UGAUGUG_GUCGU\n3'-UUU...GUUUC_______U_____UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	242 -- 248	68 -- 74	-17.054 kcal/mol	2.36402 kcal/mol	3.24359 kcal/mol	241 254@LB@ \| \|@LB@5'-CGG...AAACA GCGCG...CUA-3'@LB@ ACUACGC CAGCA@LB@ \|\|\|\|\|:\| \|\|\|\|\|@LB@ UGAUGUG GUCGU@LB@3'-UUU...GUUUC U UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -17.054 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 68 -- 74@LB@
163	0.007762	0.1668	b0394	mak	-14.23	0.032787	242 -- 265	40 -- 75	manno(fructo)kinase		_____________241__________________________________266\n_____________\|____________________________________\|\n5'-GUU...GAAGU________UG______G___________________GCAGU...GUG-3'\n______________GAUUGCAC__GGCGAU_____________CAGGGGA\n______________\|\|:\|:\|\|\|__:\|\|:\|\|_____________\|\|\|\|\|\|\|\n______________CUGAUGUG__UCGUUA_____________GUCCCCU\n3'-UUU...CGUUU________UG______AGCAACAAAGUGA_______AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	259 -- 265	40 -- 46	-27.5886 kcal/mol	8.58508 kcal/mol	4.77786 kcal/mol	241 266@LB@ \| \|@LB@5'-GUU...GAAGU UG G GCAGU...GUG-3'@LB@ GAUUGCAC GGCGAU CAGGGGA@LB@ \|\|:\|:\|\|\| :\|\|:\|\| \|\|\|\|\|\|\|@LB@ CUGAUGUG UCGUUA GUCCCCU@LB@3'-UUU...CGUUU UG AGCAACAAAGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -14.23 kcal/mol@LB@Hybridization Energy -27.5886 kcal/mol@LB@Unfolding Energy - mRNA 8.58508 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 242 -- 265@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 40 -- 46@LB@
106	0.004704	0.1538	b0995	torR	-15.76	0.013096	243 -- 292	33 -- 70	response regulator in two-component regulatory system with TorS		_____________242_________________________________________________293\n_____________\|___________________________________________________\|\n5'-CCA...UUACC__G_________ACAAUCCUAC__________A__GGUAUACC________UACGGCGA-3'\n______________CA_GC_GCGAUU__________UUCACUCAGG_GG________GUUUCCGU\n______________\|\|_:\|_\|\|:\|\|\|__________\|\|\|\|\|\|\|\|\|\|_\|\|________:\|\|\|\|\|:\|\n______________GU_UG_CGUUAA__________AAGUGAGUCC_CC________UAAAGGUA\n3'-UUU...CUGAU__G__U______GCAACA_________________________________CGAAU...GCA-5'\n_____________\|___________________________________________________\|\n_____________71__________________________________________________32\n	286 -- 292	33 -- 39	-31.2367 kcal/mol	10.6838 kcal/mol	4.7924 kcal/mol	242 293@LB@ \| \|@LB@5'-CCA...UUACC G ACAAUCCUAC A GGUAUACC UACGGCGA-3'@LB@ CA GC GCGAUU UUCACUCAGG GG GUUUCCGU@LB@ \|\| :\| \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\| \|\| :\|\|\|\|\|:\|@LB@ GU UG CGUUAA AAGUGAGUCC CC UAAAGGUA@LB@3'-UUU...CUGAU G U GCAACA CGAAU...GCA-5'@LB@ \| \|@LB@ 71 32@LB@@LB@@LB@Energy -15.76 kcal/mol@LB@Hybridization Energy -31.2367 kcal/mol@LB@Unfolding Energy - mRNA 10.6838 kcal/mol@LB@Unfolding Energy - sRNA 4.7924 kcal/mol@LB@@LB@Position - mRNA 243 -- 292@LB@Position - sRNA 33 -- 70@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 33 -- 39@LB@
123	0.005464	0.1553	b3746	ravA	-13.51	0.048673	243 -- 263	41 -- 65	hexameric AAA+ MoxR family ATPase putative molecular chaperone		_____________242_______________________264\n_____________\|_________________________\|\n5'-UGA...GCCUG____________GAAA_________CUUUA...UAU-3'\n______________AGCAGUUCGUUG________AGGGG\n______________\|\|\|\|:\|\|\|\|\|\|\|________\|\|\|\|\|\n______________UCGUUAAGCAAC________UCCCC\n3'-UUU...GUGUG____________AAAGUGAG_____UAAAG...GCA-5'\n_____________\|_________________________\|\n_____________66________________________40\n	248 -- 254	54 -- 60	-25.3509 kcal/mol	7.14336 kcal/mol	4.70281 kcal/mol	242 264@LB@ \| \|@LB@5'-UGA...GCCUG GAAA CUUUA...UAU-3'@LB@ AGCAGUUCGUUG AGGGG@LB@ \|\|\|\|:\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCGUUAAGCAAC UCCCC@LB@3'-UUU...GUGUG AAAGUGAG UAAAG...GCA-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -13.51 kcal/mol@LB@Hybridization Energy -25.3509 kcal/mol@LB@Unfolding Energy - mRNA 7.14336 kcal/mol@LB@Unfolding Energy - sRNA 4.70281 kcal/mol@LB@@LB@Position - mRNA 243 -- 263@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 54 -- 60@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

Use the following button if you want to resubmit the job with altered input or parameterization:

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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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