Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
94	0.008385	0.3	b1804	rnd	-8.17	0.271836	224 -- 238	41 -- 54	ribonuclease D	_____________223_____________239\n_____________\|_______________\|\n5'-GUC...ACCAC__A_______C____UUCUU...GUA-3'\n______________GG_CGAUGCG_UGGC\n______________\|\|_\|:\|\|\|\|:_\|\|\|\|\n______________CC_GUUACGU_ACCG\n3'-UUU...AGUCA__________U____GGUUG...UUG-5'\n_____________\|_______________\|\n_____________55______________40\n	227 -- 233	46 -- 52	-18.0571 kcal/mol	5.99437 kcal/mol	3.89026 kcal/mol	223 239@LB@ \| \|@LB@5'-GUC...ACCAC A C UUCUU...GUA-3'@LB@ GG CGAUGCG UGGC@LB@ \|\| \|:\|\|\|\|: \|\|\|\|@LB@ CC GUUACGU ACCG@LB@3'-UUU...AGUCA U GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -18.0571 kcal/mol@LB@Unfolding Energy - mRNA 5.99437 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 224 -- 238@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 46 -- 52@LB@
136	0.01532	0.3774	b3054	ygiF	-8.05	0.285135	192 -- 208	38 -- 53	inorganic triphosphatase	_____________191_______________209\n_____________\|_________________\|\n5'-GGC...GAUAA____AG__C________GGAAA...CCG-3'\n______________GUAA__GC_AUGGCUCA\n______________\|:\|\|__\|\|_\|\|\|\|\|:\|\|\n______________CGUU__CG_UACCGGGU\n3'-UUU...GUCAC____A___U________UGUCU...UUG-5'\n_____________\|_________________\|\n_____________54________________37\n	202 -- 208	38 -- 44	-16.8567 kcal/mol	4.04422 kcal/mol	4.7597 kcal/mol	191 209@LB@ \| \|@LB@5'-GGC...GAUAA AG C GGAAA...CCG-3'@LB@ GUAA GC AUGGCUCA@LB@ \|:\|\| \|\| \|\|\|\|\|:\|\|@LB@ CGUU CG UACCGGGU@LB@3'-UUU...GUCAC A U UGUCU...UUG-5'@LB@ \| \|@LB@ 54 37@LB@@LB@@LB@Energy -8.05 kcal/mol@LB@Hybridization Energy -16.8567 kcal/mol@LB@Unfolding Energy - mRNA 4.04422 kcal/mol@LB@Unfolding Energy - sRNA 4.7597 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 38 -- 53@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 38 -- 44@LB@
132	0.0144	0.3654	b2381	ypdB	-7.98	0.293473	18 -- 39	11 -- 32	response regulator activating yhjX; pyruvate-responsive YpdAB two-component system	_____________17_____________________40\n_____________\|______________________\|\n5'-AUU...GAAGC_________GCCG_________AUUGG...ACG-3'\n______________GAAUGAAAU____GGCAAUAAA\n______________:\|\|\|:\|\|\|\|____\|:\|\|\|\|\|\|\|\n______________UUUAUUUUA____CUGUUAUUU\n3'-UUU...UGUCU_________GACA_________CCGUA...UUG-5'\n_____________\|______________________\|\n_____________33_____________________10\n	33 -- 39	11 -- 17	-14.9693 kcal/mol	2.07375 kcal/mol	4.91579 kcal/mol	17 40@LB@ \| \|@LB@5'-AUU...GAAGC GCCG AUUGG...ACG-3'@LB@ GAAUGAAAU GGCAAUAAA@LB@ :\|\|\|:\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ UUUAUUUUA CUGUUAUUU@LB@3'-UUU...UGUCU GACA CCGUA...UUG-5'@LB@ \| \|@LB@ 33 10@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -14.9693 kcal/mol@LB@Unfolding Energy - mRNA 2.07375 kcal/mol@LB@Unfolding Energy - sRNA 4.91579 kcal/mol@LB@@LB@Position - mRNA 18 -- 39@LB@Position - sRNA 11 -- 32@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 11 -- 17@LB@
15	0.0005657	0.1268	b3715	yieH	-7.91	0.301098	195 -- 204	4 -- 13	phosphoenolpyruvate and 6-phosphogluconate phosphatase	_____________194________205\n_____________\|__________\|\n5'-CUG...AAAGG__________CCCGG...UUG-3'\n______________AAAGGCAUGU\n______________\|\|\|\|\|\|\|\|:\|\n______________UUUCCGUAUA\n3'-UUU...UGUUA__________UUG-5'\n_____________\|__________\|\n_____________14_________3\n	198 -- 204	4 -- 10	-12.382 kcal/mol	1.66065 kcal/mol	2.80714 kcal/mol	194 205@LB@ \| \|@LB@5'-CUG...AAAGG CCCGG...UUG-3'@LB@ AAAGGCAUGU@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UUUCCGUAUA@LB@3'-UUU...UGUUA UUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -7.91 kcal/mol@LB@Hybridization Energy -12.382 kcal/mol@LB@Unfolding Energy - mRNA 1.66065 kcal/mol@LB@Unfolding Energy - sRNA 2.80714 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 4 -- 10@LB@
37	0.002433	0.2088	b2825	ppdB	-7.88	0.305516	133 -- 146	40 -- 54	putative prepilin peptidase-dependent protein	_____________132_____________147\n_____________\|_______________\|\n5'-CAU...CAACG_______________GGUGG...CGU-3'\n______________GGCGA_GUGGUGGCU\n______________\|\|\|:\|_\|:::\|\|\|\|:\n______________CCGUU_CGUUACCGG\n3'-UUU...AGUCA_____A_________GUUGU...UUG-5'\n_____________\|_______________\|\n_____________55______________39\n	140 -- 146	40 -- 46	-19.4494 kcal/mol	6.98652 kcal/mol	4.58617 kcal/mol	132 147@LB@ \| \|@LB@5'-CAU...CAACG GGUGG...CGU-3'@LB@ GGCGA GUGGUGGCU@LB@ \|\|\|:\| \|:::\|\|\|\|:@LB@ CCGUU CGUUACCGG@LB@3'-UUU...AGUCA A GUUGU...UUG-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -19.4494 kcal/mol@LB@Unfolding Energy - mRNA 6.98652 kcal/mol@LB@Unfolding Energy - sRNA 4.58617 kcal/mol@LB@@LB@Position - mRNA 133 -- 146@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 40 -- 46@LB@
152	0.01787	0.3828	b1659	ydhB	-7.85	0.308650	225 -- 251	41 -- 68	LysR family putative transcriptional regulator	_____________224__________________________252\n_____________\|____________________________\|\n5'-CGA...UCGAA____UU__UG____A___C_________AGUUU...UCA-3'\n______________GUUG__GA__CGGU_GCG__GUAAUGGU\n______________\|\|\|\|__:\|__\|:\|\|_\|\|:__\|:\|\|\|\|\|:\n______________CAAC__UU__GUCA_CGU__CGUUACCG\n3'-UUU...AUAUA____CU__UA____C___UA________GGUUG...UUG-5'\n_____________\|____________________________\|\n_____________69___________________________40\n	245 -- 251	41 -- 47	-21.9924 kcal/mol	7.69552 kcal/mol	6.44645 kcal/mol	224 252@LB@ \| \|@LB@5'-CGA...UCGAA UU UG A C AGUUU...UCA-3'@LB@ GUUG GA CGGU GCG GUAAUGGU@LB@ \|\|\|\| :\| \|:\|\| \|\|: \|:\|\|\|\|\|:@LB@ CAAC UU GUCA CGU CGUUACCG@LB@3'-UUU...AUAUA CU UA C UA GGUUG...UUG-5'@LB@ \| \|@LB@ 69 40@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -21.9924 kcal/mol@LB@Unfolding Energy - mRNA 7.69552 kcal/mol@LB@Unfolding Energy - sRNA 6.44645 kcal/mol@LB@@LB@Position - mRNA 225 -- 251@LB@Position - sRNA 41 -- 68@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 41 -- 47@LB@
182	0.02271	0.4143	b1686	menI	-7.81	0.313804	214 -- 222	57 -- 65	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________213_______223\n_____________\|_________\|\n5'-GGC...GAAAC_________CCCUG...AUG-3'\n______________GGAAAAUCA\n______________\|\|\|\|\|\|\|\|\|\n______________CCUUUUAGU\n3'-UUU...UACAA_________CACCG...UUG-5'\n_____________\|_________\|\n_____________66________56\n	216 -- 222	57 -- 63	-11.126 kcal/mol	2.47866 kcal/mol	0.839876 kcal/mol	213 223@LB@ \| \|@LB@5'-GGC...GAAAC CCCUG...AUG-3'@LB@ GGAAAAUCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCUUUUAGU@LB@3'-UUU...UACAA CACCG...UUG-5'@LB@ \| \|@LB@ 66 56@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -11.126 kcal/mol@LB@Unfolding Energy - mRNA 2.47866 kcal/mol@LB@Unfolding Energy - sRNA 0.839876 kcal/mol@LB@@LB@Position - mRNA 214 -- 222@LB@Position - sRNA 57 -- 65@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 57 -- 63@LB@
53	0.003903	0.237	b0946	zapC	-7.74	0.322468	177 -- 206	45 -- 76	FtsZ stabilizer	_____________176_________________________________207\n_____________\|___________________________________\|\n5'-AUU...UGCGG_______GG__AG______________A_______AUUAA...GUU-3'\n______________UUUUAUA__GU__GGGAGA_____GGC_GAUGCGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|:\|:\|_____\|\|\|_:\|\|\|\|:\|\n______________AAAAUAU__CA__CCUUUU_____CCG_UUACGUU\n3'-UUU...ACAGA_______A___A_______AGUCA___________ACCGG...UUG-5'\n_____________\|___________________________________\|\n_____________77__________________________________44\n	200 -- 206	45 -- 51	-19.1898 kcal/mol	6.23804 kcal/mol	5.21532 kcal/mol	176 207@LB@ \| \|@LB@5'-AUU...UGCGG GG AG A AUUAA...GUU-3'@LB@ UUUUAUA GU GGGAGA GGC GAUGCGA@LB@ \|\|\|\|\|\|\| \|\| \|\|:\|:\| \|\|\| :\|\|\|\|:\|@LB@ AAAAUAU CA CCUUUU CCG UUACGUU@LB@3'-UUU...ACAGA A A AGUCA ACCGG...UUG-5'@LB@ \| \|@LB@ 77 44@LB@@LB@@LB@Energy -7.74 kcal/mol@LB@Hybridization Energy -19.1898 kcal/mol@LB@Unfolding Energy - mRNA 6.23804 kcal/mol@LB@Unfolding Energy - sRNA 5.21532 kcal/mol@LB@@LB@Position - mRNA 177 -- 206@LB@Position - sRNA 45 -- 76@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 45 -- 51@LB@
193	0.02433	0.4239	b1125	potB	-7.71	0.326143	48 -- 60	50 -- 66	spermidine/putrescine ABC transporter permease	_____________47________________61\n_____________\|_________________\|\n5'-UCG...UGAAC_________________GAUGG...UUG-3'\n______________UGGAAAA____UGGCAA\n______________\|\|\|\|\|\|\|____\|\|\|\|\|\|\n______________ACCUUUU____ACCGUU\n3'-UUU...AUACA_______AGUC______ACGUU...UUG-5'\n_____________\|_________________\|\n_____________67________________49\n	48 -- 54	60 -- 66	-13.9172 kcal/mol	3.09187 kcal/mol	3.11877 kcal/mol	47 61@LB@ \| \|@LB@5'-UCG...UGAAC GAUGG...UUG-3'@LB@ UGGAAAA UGGCAA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACCUUUU ACCGUU@LB@3'-UUU...AUACA AGUC ACGUU...UUG-5'@LB@ \| \|@LB@ 67 49@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -13.9172 kcal/mol@LB@Unfolding Energy - mRNA 3.09187 kcal/mol@LB@Unfolding Energy - sRNA 3.11877 kcal/mol@LB@@LB@Position - mRNA 48 -- 60@LB@Position - sRNA 50 -- 66@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 60 -- 66@LB@
126	0.01341	0.3578	b3572	avtA	-7.69	0.327921	259 -- 267	58 -- 66	valine-pyruvate aminotransferase; transaminase C; alanine-valine transaminase	_____________258_______268\n_____________\|_________\|\n5'-UCG...GUUGA_________UGAAC...UUA-3'\n______________UGGAAGAUC\n______________\|\|\|\|\|:\|\|\|\n______________ACCUUUUAG\n3'-UUU...AUACA_________UCACC...UUG-5'\n_____________\|_________\|\n_____________67________57\n	261 -- 267	58 -- 64	-10.9576 kcal/mol	2.42155 kcal/mol	0.843879 kcal/mol	258 268@LB@ \| \|@LB@5'-UCG...GUUGA UGAAC...UUA-3'@LB@ UGGAAGAUC@LB@ \|\|\|\|\|:\|\|\|@LB@ ACCUUUUAG@LB@3'-UUU...AUACA UCACC...UUG-5'@LB@ \| \|@LB@ 67 57@LB@@LB@@LB@Energy -7.69 kcal/mol@LB@Hybridization Energy -10.9576 kcal/mol@LB@Unfolding Energy - mRNA 2.42155 kcal/mol@LB@Unfolding Energy - sRNA 0.843879 kcal/mol@LB@@LB@Position - mRNA 259 -- 267@LB@Position - sRNA 58 -- 66@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 58 -- 64@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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