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
14	0.0002995	0.06692	b4195	ulaC	-9.74	0.019405	182 -- 212	24 -- 54	L-ascorbate-specific enzyme IIA component of PTS	_____________181_______________________________213\n_____________\|_________________________________\|\n5'-GCG...CAGGA___G__________C____CAU_______A___GAUUC...UGG-3'\n______________UGU__AAGUAAGGA_GCGC____GAAAUU_CGU\n______________\|\|:__\|\|\|:\|\|\|:\|_\|\|:\|____:\|\|\|\|\|_\|\|\|\n______________ACG__UUCGUUCUU_CGUG____UUUUAA_GCA\n3'-UUU...UUUGA___AA______________AAUU__________AUGUG...CAA-5'\n_____________\|_________________________________\|\n_____________55________________________________23\n	187 -- 193	42 -- 48	-22.0137 kcal/mol	6.00518 kcal/mol	6.26866 kcal/mol	181 213@LB@ \| \|@LB@5'-GCG...CAGGA G C CAU A GAUUC...UGG-3'@LB@ UGU AAGUAAGGA GCGC GAAAUU CGU@LB@ \|\|: \|\|\|:\|\|\|:\| \|\|:\| :\|\|\|\|\| \|\|\|@LB@ ACG UUCGUUCUU CGUG UUUUAA GCA@LB@3'-UUU...UUUGA AA AAUU AUGUG...CAA-5'@LB@ \| \|@LB@ 55 23@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -22.0137 kcal/mol@LB@Unfolding Energy - mRNA 6.00518 kcal/mol@LB@Unfolding Energy - sRNA 6.26866 kcal/mol@LB@@LB@Position - mRNA 182 -- 212@LB@Position - sRNA 24 -- 54@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 42 -- 48@LB@
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@LB@
106	0.009044	0.2693	b3360	pabA	-9.65	0.020637	134 -- 165	7 -- 41	aminodeoxychorismate synthase subunit II	_____________133_________________________________166\n_____________\|___________________________________\|\n5'-GCG...UAUUU____AAGUGGUAAG___AA________________GUAAA...CGU-3'\n______________AGCA___________CG____GCCGGGGAAUCUGA\n______________\|\|\|\|___________\|\|____:\|\|:\|\|:\|\|\|\|\|\|\|\n______________UCGU___________GC____UGGUCCUUUAGACU\n3'-UUU...GUUCU____GAAUUUUUUAA__AAUG______________ACACAA-5'\n_____________\|___________________________________\|\n_____________42__________________________________6\n	156 -- 162	10 -- 16	-26.3396 kcal/mol	7.46958 kcal/mol	9.22092 kcal/mol	133 166@LB@ \| \|@LB@5'-GCG...UAUUU AAGUGGUAAG AA GUAAA...CGU-3'@LB@ AGCA CG GCCGGGGAAUCUGA@LB@ \|\|\|\| \|\| :\|\|:\|\|:\|\|\|\|\|\|\|@LB@ UCGU GC UGGUCCUUUAGACU@LB@3'-UUU...GUUCU GAAUUUUUUAA AAUG ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -26.3396 kcal/mol@LB@Unfolding Energy - mRNA 7.46958 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 134 -- 165@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 10 -- 16@LB@
196	0.02353	0.3864	b1948	fliP	-9.61	0.021211	171 -- 185	45 -- 59	flagellar biosynthesis protein	_____________170_____________186\n_____________\|_______________\|\n5'-AUU...AUGAA_______________UAGCG...GCG-3'\n______________AAAUUUGCUUAAGCG\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|:\n______________UUUGAACGAAUUCGU\n3'-UUU...CCUAC_______________UCUUC...CAA-5'\n_____________\|_______________\|\n_____________60______________44\n	178 -- 184	46 -- 52	-18.3894 kcal/mol	2.75936 kcal/mol	6.02152 kcal/mol	170 186@LB@ \| \|@LB@5'-AUU...AUGAA UAGCG...GCG-3'@LB@ AAAUUUGCUUAAGCG@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|:@LB@ UUUGAACGAAUUCGU@LB@3'-UUU...CCUAC UCUUC...CAA-5'@LB@ \| \|@LB@ 60 44@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -18.3894 kcal/mol@LB@Unfolding Energy - mRNA 2.75936 kcal/mol@LB@Unfolding Energy - sRNA 6.02152 kcal/mol@LB@@LB@Position - mRNA 171 -- 185@LB@Position - sRNA 45 -- 59@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 46 -- 52@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@
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@
5	2.271e-05	0.01463	b0476	aes	-9.47	0.023317	2 -- 45	10 -- 53	acetyl esterase	_____________1______________________________________________46\n_____________\|______________________________________________\|\n__________5'-C_____CG_________AUGUUU_____UA_________________UCAUG...CAA-3'\n______________GUUUA___GGGAAGUA______GGAUU__CGUU_UACCGGGAAAUU\n______________\|:\|\|\|___::\|\|\|\|:\|______::\|\|\|__\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:\n______________CGAAU___UUCUUCGU______UUUAA__GCAA_GUGGUCCUUUAG\n3'-UUU...UUGAA_____UCG________GAAUUU___________U____________ACUAC...CAA-5'\n_____________\|______________________________________________\|\n_____________54_____________________________________________9\n	39 -- 45	10 -- 16	-31.5647 kcal/mol	8.26599 kcal/mol	13.8307 kcal/mol	1 46@LB@ \| \|@LB@ 5'-C CG AUGUUU UA UCAUG...CAA-3'@LB@ GUUUA GGGAAGUA GGAUU CGUU UACCGGGAAAUU@LB@ \|:\|\|\| ::\|\|\|\|:\| ::\|\|\| \|\|\|\| :\|\|\|:\|\|\|\|\|\|:@LB@ CGAAU UUCUUCGU UUUAA GCAA GUGGUCCUUUAG@LB@3'-UUU...UUGAA UCG GAAUUU U ACUAC...CAA-5'@LB@ \| \|@LB@ 54 9@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -31.5647 kcal/mol@LB@Unfolding Energy - mRNA 8.26599 kcal/mol@LB@Unfolding Energy - sRNA 13.8307 kcal/mol@LB@@LB@Position - mRNA 2 -- 45@LB@Position - sRNA 10 -- 53@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 10 -- 16@LB@
86	0.005829	0.217	b2399	yfeD	-9.44	0.023742	136 -- 182	13 -- 56	DUF1323 family putative DNA-binding protein	_____________135______________________________________________183\n_____________\|________________________________________________\|\n5'-UGA...ACAUC_______CU________G_A___UC____________ACGC_______UUCGC...GGA-3'\n______________CUUGCUU__GCGGGAAG_G_UUA__GGAUU_GUUACA____UUAGGGA\n______________\|\|\|\|\|\|\|__\|\|::\|\|\|\|_:_\|\|\|__::\|\|\|_\|\|\|\|\|\|____::\|\|\|:\|\n______________GAACGAA__CGUUCUUC_U_AAU__UUUAA_CAAUGU____GGUCCUU\n3'-UUU...ACUUU_______UU________G_G___UU_____G_________________UAGAC...CAA-5'\n_____________\|________________________________________________\|\n_____________57_______________________________________________12\n	146 -- 152	40 -- 46	-35.8501 kcal/mol	12.5789 kcal/mol	13.8302 kcal/mol	135 183@LB@ \| \|@LB@5'-UGA...ACAUC CU G A UC ACGC UUCGC...GGA-3'@LB@ CUUGCUU GCGGGAAG G UUA GGAUU GUUACA UUAGGGA@LB@ \|\|\|\|\|\|\| \|\|::\|\|\|\| : \|\|\| ::\|\|\| \|\|\|\|\|\| ::\|\|\|:\|@LB@ GAACGAA CGUUCUUC U AAU UUUAA CAAUGU GGUCCUU@LB@3'-UUU...ACUUU UU G G UU G UAGAC...CAA-5'@LB@ \| \|@LB@ 57 12@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -35.8501 kcal/mol@LB@Unfolding Energy - mRNA 12.5789 kcal/mol@LB@Unfolding Energy - sRNA 13.8302 kcal/mol@LB@@LB@Position - mRNA 136 -- 182@LB@Position - sRNA 13 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 40 -- 46@LB@
193	0.0233	0.3864	b1563	relE	-9.36	0.025073	16 -- 27	29 -- 40	Qin prophage; toxin of the RelE-RelB toxin-antitoxin system	_____________15___________28\n_____________\|____________\|\n5'-GCG...ACGCC____________AUGGG...UAC-3'\n______________GCGCUUGAAAAA\n______________\|\|:\|\|\|:\|\|\|\|\|\n______________CGUGAAUUUUUU\n3'-UUU...UUCUU____________AAGCA...CAA-5'\n_____________\|____________\|\n_____________41___________28\n	21 -- 27	29 -- 35	-12.3855 kcal/mol	1.40487 kcal/mol	1.62106 kcal/mol	15 28@LB@ \| \|@LB@5'-GCG...ACGCC AUGGG...UAC-3'@LB@ GCGCUUGAAAAA@LB@ \|\|:\|\|\|:\|\|\|\|\|@LB@ CGUGAAUUUUUU@LB@3'-UUU...UUCUU AAGCA...CAA-5'@LB@ \| \|@LB@ 41 28@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -12.3855 kcal/mol@LB@Unfolding Energy - mRNA 1.40487 kcal/mol@LB@Unfolding Energy - sRNA 1.62106 kcal/mol@LB@@LB@Position - mRNA 16 -- 27@LB@Position - sRNA 29 -- 40@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 29 -- 35@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@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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