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
51	0.002326	0.1469	b2780	pyrG	-6.37	0.158020	19 -- 28	33 -- 42	CTP synthetase	_____________18_________29\n_____________\|__________\|\n5'-UGU...AUGAC__________UUUGC...GCC-3'\n______________AAGCGCUUGA\n______________\|\|\|\|:\|\|\|:\|\n______________UUCGUGAAUU\n3'-UUU...CGUUC__________UUUUA...CAA-5'\n_____________\|__________\|\n_____________43_________32\n	22 -- 28	33 -- 39	-10.9983 kcal/mol	3.00927 kcal/mol	1.61944 kcal/mol	18 29@LB@ \| \|@LB@5'-UGU...AUGAC UUUGC...GCC-3'@LB@ AAGCGCUUGA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UUCGUGAAUU@LB@3'-UUU...CGUUC UUUUA...CAA-5'@LB@ \| \|@LB@ 43 32@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -10.9983 kcal/mol@LB@Unfolding Energy - mRNA 3.00927 kcal/mol@LB@Unfolding Energy - sRNA 1.61944 kcal/mol@LB@@LB@Position - mRNA 19 -- 28@LB@Position - sRNA 33 -- 42@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 33 -- 39@LB@
109	0.009396	0.2693	b1958	yedI	-10.22	0.013950	83 -- 110	33 -- 54	DUF808 family inner membrane protein	_____________82_____________________________111\n_____________\|______________________________\|\n5'-AAA...CAUUC______________AUAUAAUU________UUGUU...CCG-3'\n______________UGCU__GGCGAGAG________GCACUUGA\n______________\|\|\|\|__:\|\|:\|\|\|:________\|\|\|\|\|\|:\|\n______________ACGA__UCGUUCUU________CGUGAAUU\n3'-UUU...UUUGA____AU________________________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________55_____________________________32\n	104 -- 110	33 -- 39	-21.3805 kcal/mol	4.98239 kcal/mol	6.17798 kcal/mol	82 111@LB@ \| \|@LB@5'-AAA...CAUUC AUAUAAUU UUGUU...CCG-3'@LB@ UGCU GGCGAGAG GCACUUGA@LB@ \|\|\|\| :\|\|:\|\|\|: \|\|\|\|\|\|:\|@LB@ ACGA UCGUUCUU CGUGAAUU@LB@3'-UUU...UUUGA AU UUUUA...CAA-5'@LB@ \| \|@LB@ 55 32@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 4.98239 kcal/mol@LB@Unfolding Energy - sRNA 6.17798 kcal/mol@LB@@LB@Position - mRNA 83 -- 110@LB@Position - sRNA 33 -- 54@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 33 -- 39@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein	_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@LB@
182	0.02157	0.3768	b0887	cydD	-7.84	0.066788	30 -- 38	33 -- 41	glutathione/cysteine ABC transporter export permease/ATPase	_____________29________39\n_____________\|_________\|\n5'-AUU...AUGGC_________UGCGG...UGA-3'\n______________AGCACUUGA\n______________\|\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	32 -- 38	33 -- 39	-10.6359 kcal/mol	1.18174 kcal/mol	1.6188 kcal/mol	29 39@LB@ \| \|@LB@5'-AUU...AUGGC UGCGG...UGA-3'@LB@ AGCACUUGA@LB@ \|\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -10.6359 kcal/mol@LB@Unfolding Energy - mRNA 1.18174 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 30 -- 38@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 33 -- 39@LB@
57	0.002825	0.1597	b2233	yfaL	-10.30	0.013161	220 -- 233	34 -- 47	adhesin	_____________219____________234\n_____________\|______________\|\n5'-UAU...UCUAC______________UCUUU...CAU-3'\n______________GCAAGGAGUAUUUA\n______________\|\|\|\|\|:\|\|:\|:\|\|\|\n______________CGUUCUUCGUGAAU\n3'-UUU...GAAUU______________UUUUU...CAA-5'\n_____________\|______________\|\n_____________48_____________33\n	227 -- 233	34 -- 40	-18.4969 kcal/mol	2.11117 kcal/mol	6.08192 kcal/mol	219 234@LB@ \| \|@LB@5'-UAU...UCUAC UCUUU...CAU-3'@LB@ GCAAGGAGUAUUUA@LB@ \|\|\|\|\|:\|\|:\|:\|\|\|@LB@ CGUUCUUCGUGAAU@LB@3'-UUU...GAAUU UUUUU...CAA-5'@LB@ \| \|@LB@ 48 33@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -18.4969 kcal/mol@LB@Unfolding Energy - mRNA 2.11117 kcal/mol@LB@Unfolding Energy - sRNA 6.08192 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 34 -- 47@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 34 -- 40@LB@
62	0.00332	0.1645	b1305	pspB	-5.29	0.278747	189 -- 201	34 -- 46	psp operon transcription co-activator	_____________188___________202\n_____________\|_____________\|\n5'-AUU...UCGUC_____________UGAGC...GUG-3'\n______________UAAGGAGUACUUA\n______________:\|\|\|:\|\|:\|\|\|\|\|\n______________GUUCUUCGUGAAU\n3'-UUU...AAUUC_____________UUUUU...CAA-5'\n_____________\|_____________\|\n_____________47____________33\n	195 -- 201	34 -- 40	-14.7021 kcal/mol	3.41245 kcal/mol	5.99897 kcal/mol	188 202@LB@ \| \|@LB@5'-AUU...UCGUC UGAGC...GUG-3'@LB@ UAAGGAGUACUUA@LB@ :\|\|\|:\|\|:\|\|\|\|\|@LB@ GUUCUUCGUGAAU@LB@3'-UUU...AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 47 33@LB@@LB@@LB@Energy -5.29 kcal/mol@LB@Hybridization Energy -14.7021 kcal/mol@LB@Unfolding Energy - mRNA 3.41245 kcal/mol@LB@Unfolding Energy - sRNA 5.99897 kcal/mol@LB@@LB@Position - mRNA 189 -- 201@LB@Position - sRNA 34 -- 46@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@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@
79	0.005218	0.2128	b1264	trpE	-7.84	0.066605	225 -- 250	34 -- 59	component I of anthranilate synthase	_____________224__________________________251\n_____________\|____________________________\|\n5'-UGU...CUCUC_________AACCU______________UCGCG...CGG-3'\n______________GAAC_UGCU_____GCGA_AGGCGCUUA\n______________:\|\|\|_\|\|\|\|_____\|\|:\|_\|:\|\|:\|\|\|\|\n______________UUUG_ACGA_____CGUU_UUCGUGAAU\n3'-UUU...CCUAC____A____AUU______C_________UUUUU...CAA-5'\n_____________\|____________________________\|\n_____________60___________________________33\n	244 -- 250	34 -- 40	-20.2106 kcal/mol	6.10702 kcal/mol	6.26371 kcal/mol	224 251@LB@ \| \|@LB@5'-UGU...CUCUC AACCU UCGCG...CGG-3'@LB@ GAAC UGCU GCGA AGGCGCUUA@LB@ :\|\|\| \|\|\|\| \|\|:\| \|:\|\|:\|\|\|\|@LB@ UUUG ACGA CGUU UUCGUGAAU@LB@3'-UUU...CCUAC A AUU C UUUUU...CAA-5'@LB@ \| \|@LB@ 60 33@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -20.2106 kcal/mol@LB@Unfolding Energy - mRNA 6.10702 kcal/mol@LB@Unfolding Energy - sRNA 6.26371 kcal/mol@LB@@LB@Position - mRNA 225 -- 250@LB@Position - sRNA 34 -- 59@LB@Position Seed - mRNA 244 -- 250@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@
108	0.009338	0.2693	b0639	nadD	-9.48	0.023112	42 -- 61	34 -- 53	nicotinic acid mononucleotide adenylyltransferase NAD(P)-dependent	_____________41___________________62\n_____________\|____________________\|\n5'-AUG...AAAUC________C___C___G___CGUCA...CGC-3'\n______________GCUUAAGU_AGA_GCA_UUA\n______________\|\|\|\|\|\|\|:_\|\|\|_\|\|\|_\|\|\|\n______________CGAAUUCG_UCU_CGU_AAU\n3'-UUU...UUGAA________U___U___G___UUUUU...CAA-5'\n_____________\|____________________\|\n_____________54___________________33\n	42 -- 48	47 -- 53	-20.1483 kcal/mol	4.55179 kcal/mol	6.11529 kcal/mol	41 62@LB@ \| \|@LB@5'-AUG...AAAUC C C G CGUCA...CGC-3'@LB@ GCUUAAGU AGA GCA UUA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\| \|\|\|@LB@ CGAAUUCG UCU CGU AAU@LB@3'-UUU...UUGAA U U G UUUUU...CAA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -20.1483 kcal/mol@LB@Unfolding Energy - mRNA 4.55179 kcal/mol@LB@Unfolding Energy - sRNA 6.11529 kcal/mol@LB@@LB@Position - mRNA 42 -- 61@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 47 -- 53@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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