Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
83	0.002775	0.1082	b2049	cpsB	-6.85	0.497101	286 -- 298	17 -- 31	mannose-1-phosphate guanyltransferase	_____________285_____________299\n_____________\|_______________\|\n5'-ACA...UCCCA_______________CC-3'\n______________AGC_AGU_UUUUAUG\n______________\|\|\|_\|\|:_\|\|\|\|\|\|\|\n______________UCG_UCG_AAAAUAC\n3'-UUU...CCAUG___A___U_______CCAAU...UCG-5'\n_____________\|_______________\|\n_____________32______________16\n	292 -- 298	17 -- 23	-8.99018 kcal/mol	0.716641 kcal/mol	1.4259 kcal/mol	285 299@LB@ \| \|@LB@5'-ACA...UCCCA CC-3'@LB@ AGC AGU UUUUAUG@LB@ \|\|\| \|\|: \|\|\|\|\|\|\|@LB@ UCG UCG AAAAUAC@LB@3'-UUU...CCAUG A U CCAAU...UCG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -8.99018 kcal/mol@LB@Unfolding Energy - mRNA 0.716641 kcal/mol@LB@Unfolding Energy - sRNA 1.4259 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 17 -- 23@LB@
166	0.008687	0.1759	b3210	arcB	-6.83	0.499810	260 -- 284	24 -- 46	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________259_______________________285\n_____________\|_________________________\|\n5'-UGC...GGUCU____C_C____CAAUGUU_______CUGGC...UUC-3'\n______________GGUG_G_UUCU_______GCUGGCG\n______________\|\|\|\|_\|_\|\|\|:_______\|\|\|:\|\|:\n______________CCAC_C_AAGG_______CGAUCGU\n3'-UUU...UUCCU___________ACCAUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	278 -- 284	24 -- 30	-17.917 kcal/mol	6.53164 kcal/mol	4.55813 kcal/mol	259 285@LB@ \| \|@LB@5'-UGC...GGUCU C C CAAUGUU CUGGC...UUC-3'@LB@ GGUG G UUCU GCUGGCG@LB@ \|\|\|\| \| \|\|\|: \|\|\|:\|\|:@LB@ CCAC C AAGG CGAUCGU@LB@3'-UUU...UUCCU ACCAUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -17.917 kcal/mol@LB@Unfolding Energy - mRNA 6.53164 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 260 -- 284@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 24 -- 30@LB@
192	0.01101	0.1919	b2478	dapA	-6.78	0.505920	248 -- 269	25 -- 47	dihydrodipicolinate synthase	_____________247_____________________270\n_____________\|_______________________\|\n5'-GGC...GAAAA____AAUG____UCG________UUGAA...CCA-3'\n______________AGGU____UCUG____GGCUAGC\n______________\|\|\|\|____:\|\|\|____:\|\|\|\|\|\|\n______________UCCA____GGAC____UCGAUCG\n3'-UUU...AUUCC____CCAA____CAUG_______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	263 -- 269	25 -- 31	-19.6963 kcal/mol	8.35751 kcal/mol	4.55753 kcal/mol	247 270@LB@ \| \|@LB@5'-GGC...GAAAA AAUG UCG UUGAA...CCA-3'@LB@ AGGU UCUG GGCUAGC@LB@ \|\|\|\| :\|\|\| :\|\|\|\|\|\|@LB@ UCCA GGAC UCGAUCG@LB@3'-UUU...AUUCC CCAA CAUG UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -19.6963 kcal/mol@LB@Unfolding Energy - mRNA 8.35751 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 25 -- 31@LB@
59	0.00143	0.08147	b0848	ybjM	-6.77	0.507403	86 -- 118	1 -- 33	inner membrane protein	_____________85_________________________________119\n_____________\|__________________________________\|\n5'-GAA...UAUCA___________GAAU__C____GCCUAUA_____AUGGA...GGG-3'\n______________ACGGCUA_UAU____UG_GUUG_______UUAGC\n______________\|\|:\|\|\|\|_:\|\|____\|\|_\|\|\|:_______\|:\|\|\|\n______________UGUCGAU_GUA____AC_CAAU_______AGUCG\n3'-UUU...GACCA_______C___AAAU__C____ACAAAA______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	86 -- 92	27 -- 33	-17.6492 kcal/mol	9.38597 kcal/mol	1.49313 kcal/mol	85 119@LB@ \| \|@LB@5'-GAA...UAUCA GAAU C GCCUAUA AUGGA...GGG-3'@LB@ ACGGCUA UAU UG GUUG UUAGC@LB@ \|\|:\|\|\|\| :\|\| \|\| \|\|\|: \|:\|\|\|@LB@ UGUCGAU GUA AC CAAU AGUCG@LB@3'-UUU...GACCA C AAAU C ACAAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -6.77 kcal/mol@LB@Hybridization Energy -17.6492 kcal/mol@LB@Unfolding Energy - mRNA 9.38597 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 86 -- 118@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 27 -- 33@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease	_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@
137	0.006165	0.1512	b1024	pgaA	-6.60	0.530802	267 -- 274	1 -- 8	biofilm adhesin polysaccharide PGA secretin; OM porin; poly-beta-1 6-N-acetyl-D-glucosamine export protein	_____________266______275\n_____________\|________\|\n5'-CUC...CCGCA________AGCGA...CUG-3'\n______________UUUUUAGC\n______________\|\|\|\|:\|\|\|\n______________AAAAGUCG\n3'-UUU...AUACA________-5'\n_____________\|_______\|\n_____________9_______1\n	268 -- 274	1 -- 7	-8.19691 kcal/mol	0.802454 kcal/mol	0.799201 kcal/mol	266 275@LB@ \| \|@LB@5'-CUC...CCGCA AGCGA...CUG-3'@LB@ UUUUUAGC@LB@ \|\|\|\|:\|\|\|@LB@ AAAAGUCG@LB@3'-UUU...AUACA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.60 kcal/mol@LB@Hybridization Energy -8.19691 kcal/mol@LB@Unfolding Energy - mRNA 0.802454 kcal/mol@LB@Unfolding Energy - sRNA 0.799201 kcal/mol@LB@@LB@Position - mRNA 267 -- 274@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 1 -- 7@LB@
144	0.006813	0.158	b0111	ampE	-6.38	0.559697	294 -- 300	1 -- 7	ampicillin resistance inner membrane protein; putative signaling protein in beta-lactamase regulation	_____________293____300\n_____________\|______\|\n5'-CUU...CGUUC_______-3'\n______________UUUCGGC\n______________\|\|\|\|:\|\|\n______________AAAGUCG\n3'-UUU...UACAA_______-5'\n_____________\|______\|\n_____________8______1\n	294 -- 300	1 -- 7	-7.27697 kcal/mol	0.0992979 kcal/mol	0.796773 kcal/mol	293 300@LB@ \| \|@LB@5'-CUU...CGUUC -3'@LB@ UUUCGGC@LB@ \|\|\|\|:\|\|@LB@ AAAGUCG@LB@3'-UUU...UACAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -7.27697 kcal/mol@LB@Unfolding Energy - mRNA 0.0992979 kcal/mol@LB@Unfolding Energy - sRNA 0.796773 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@LB@
177	0.009845	0.1869	b3241	aaeA	-6.34	0.565531	229 -- 235	29 -- 35	p-hydroxybenzoic acid efflux system component	_____________228_____236\n_____________\|_______\|\n5'-UCC...CUCCC_______CAUCA...CCG-3'\n______________GUACGGC\n______________\|\|\|\|:\|\|\n______________CAUGUCG\n3'-UUU...AGGAC_______AUCGU...UCG-5'\n_____________\|_______\|\n_____________36______28\n	229 -- 235	29 -- 35	-10.2139 kcal/mol	2.71034 kcal/mol	1.16584 kcal/mol	228 236@LB@ \| \|@LB@5'-UCC...CUCCC CAUCA...CCG-3'@LB@ GUACGGC@LB@ \|\|\|\|:\|\|@LB@ CAUGUCG@LB@3'-UUU...AGGAC AUCGU...UCG-5'@LB@ \| \|@LB@ 36 28@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.2139 kcal/mol@LB@Unfolding Energy - mRNA 2.71034 kcal/mol@LB@Unfolding Energy - sRNA 1.16584 kcal/mol@LB@@LB@Position - mRNA 229 -- 235@LB@Position - sRNA 29 -- 35@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 29 -- 35@LB@
200	0.01185	0.1975	b0025	ribF	-6.09	0.598433	35 -- 41	28 -- 34	bifunctional riboflavin kinase/FAD synthetase	_____________34______42\n_____________\|_______\|\n5'-UGG...GUGAA_______UUUCC...GCG-3'\n______________UACAGCU\n______________\|\|\|\|\|\|\|\n______________AUGUCGA\n3'-UUU...GGACC_______UCGUA...UCG-5'\n_____________\|_______\|\n_____________35______27\n	35 -- 41	28 -- 34	-8.9914 kcal/mol	1.72675 kcal/mol	1.17027 kcal/mol	34 42@LB@ \| \|@LB@5'-UGG...GUGAA UUUCC...GCG-3'@LB@ UACAGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGUCGA@LB@3'-UUU...GGACC UCGUA...UCG-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.9914 kcal/mol@LB@Unfolding Energy - mRNA 1.72675 kcal/mol@LB@Unfolding Energy - sRNA 1.17027 kcal/mol@LB@@LB@Position - mRNA 35 -- 41@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 28 -- 34@LB@
93	0.003115	0.1126	b2595	bamD	-5.90	0.625252	19 -- 35	31 -- 48	BamABCDE complex OM biogenesis lipoprotein	_____________18_________________36\n_____________\|__________________\|\n5'-CUG...UGACC___U_______C______CCGUU...AUG-3'\n______________GAG_UGGUUUU_GG_ACA\n______________\|\|\|_\|\|\|\|\|::_\|\|_\|\|\|\n______________CUC_ACCAAGG_CC_UGU\n3'-UUU...GAUUC___C_______A__A___CGAUC...UCG-5'\n_____________\|__________________\|\n_____________49_________________30\n	23 -- 29	38 -- 44	-14.3523 kcal/mol	5.2001 kcal/mol	3.25694 kcal/mol	18 36@LB@ \| \|@LB@5'-CUG...UGACC U C CCGUU...AUG-3'@LB@ GAG UGGUUUU GG ACA@LB@ \|\|\| \|\|\|\|\|:: \|\| \|\|\|@LB@ CUC ACCAAGG CC UGU@LB@3'-UUU...GAUUC C A A CGAUC...UCG-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -14.3523 kcal/mol@LB@Unfolding Energy - mRNA 5.2001 kcal/mol@LB@Unfolding Energy - sRNA 3.25694 kcal/mol@LB@@LB@Position - mRNA 19 -- 35@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 38 -- 44@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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