Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
68	0.013	0.5385	b2823	ppdC	-12.74	0.034901	243 -- 262	69 -- 89	putative prepilin peptidase-dependent protein	_____________242___________________263\n_____________\|_____________________\|\n5'-ACG...UGCCG_____A_________GA____GUUGA...UCC-3'\n______________GAGGU__AUGUUGGC__UGGU\n______________:\|:\|\|__\|:\|\|\|\|\|\|__\|:\|\|\n______________UUUCA__UGCAACCG__AUCA\n3'-CGC...GGCGU_____AG________AA____AUAAG...AAG-5'\n_____________\|_____________________\|\n_____________90____________________68\n	250 -- 256	75 -- 81	-18.5568 kcal/mol	5.24273 kcal/mol	0.572143 kcal/mol	242 263@LB@ \| \|@LB@5'-ACG...UGCCG A GA GUUGA...UCC-3'@LB@ GAGGU AUGUUGGC UGGU@LB@ :\|:\|\| \|:\|\|\|\|\|\| \|:\|\|@LB@ UUUCA UGCAACCG AUCA@LB@3'-CGC...GGCGU AG AA AUAAG...AAG-5'@LB@ \| \|@LB@ 90 68@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -18.5568 kcal/mol@LB@Unfolding Energy - mRNA 5.24273 kcal/mol@LB@Unfolding Energy - sRNA 0.572143 kcal/mol@LB@@LB@Position - mRNA 243 -- 262@LB@Position - sRNA 69 -- 89@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 75 -- 81@LB@
197	0.0346	0.5559	b2829	ptsP	-9.94	0.108120	103 -- 113	80 -- 90	PEP-protein phosphotransferase enzyme I; GAF domain containing protein	_____________102_________114\n_____________\|___________\|\n5'-CCA...AAUGA___________AGUGU...UGG-3'\n______________AAGAGUUCGCG\n______________\|\|:\|\|\|\|\|:\|\|\n______________UUUUCAAGUGC\n3'-CGC...AGGCG___________AACCG...AAG-5'\n_____________\|___________\|\n_____________91__________79\n	107 -- 113	80 -- 86	-13.2227 kcal/mol	2.77203 kcal/mol	0.506776 kcal/mol	102 114@LB@ \| \|@LB@5'-CCA...AAUGA AGUGU...UGG-3'@LB@ AAGAGUUCGCG@LB@ \|\|:\|\|\|\|\|:\|\|@LB@ UUUUCAAGUGC@LB@3'-CGC...AGGCG AACCG...AAG-5'@LB@ \| \|@LB@ 91 79@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -13.2227 kcal/mol@LB@Unfolding Energy - mRNA 2.77203 kcal/mol@LB@Unfolding Energy - sRNA 0.506776 kcal/mol@LB@@LB@Position - mRNA 103 -- 113@LB@Position - sRNA 80 -- 90@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 80 -- 86@LB@
79	0.01412	0.5385	b2830	rppH	-5.99	0.454649	93 -- 100	64 -- 71	RNA pyrophosphohydrolase	_____________92_______101\n_____________\|________\|\n5'-UUC...CUGUG________AAUUG...GGC-3'\n______________AGUUAUUC\n______________\|\|\|\|\|\|\|\|\n______________UCAAUAAG\n3'-CGC...CGAAA________CUCAA...AAG-5'\n_____________\|________\|\n_____________72_______63\n	94 -- 100	64 -- 70	-7.84269 kcal/mol	1.74359 kcal/mol	0.11296 kcal/mol	92 101@LB@ \| \|@LB@5'-UUC...CUGUG AAUUG...GGC-3'@LB@ AGUUAUUC@LB@ \|\|\|\|\|\|\|\|@LB@ UCAAUAAG@LB@3'-CGC...CGAAA CUCAA...AAG-5'@LB@ \| \|@LB@ 72 63@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -7.84269 kcal/mol@LB@Unfolding Energy - mRNA 1.74359 kcal/mol@LB@Unfolding Energy - sRNA 0.11296 kcal/mol@LB@@LB@Position - mRNA 93 -- 100@LB@Position - sRNA 64 -- 71@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 64 -- 70@LB@
169	0.03038	0.5559	b2912	fau	-9.38	0.135051	85 -- 98	22 -- 35	5-formyltetrahydrofolate cyclo-ligase family protein	_____________84_____________99\n_____________\|______________\|\n5'-GAA...ACCAA__G___________CAGCC...UGG-3'\n______________GG_UUCAAGGGUUA\n______________\|:_\|\|\|\|\|\|\|\|\|\|\|\n______________CU_AAGUUCCCAAU\n3'-CGC...CGUCA__G___________UUUCU...AAG-5'\n_____________\|______________\|\n_____________36_____________21\n	92 -- 98	22 -- 28	-18.6025 kcal/mol	5.89438 kcal/mol	3.32987 kcal/mol	84 99@LB@ \| \|@LB@5'-GAA...ACCAA G CAGCC...UGG-3'@LB@ GG UUCAAGGGUUA@LB@ \|: \|\|\|\|\|\|\|\|\|\|\|@LB@ CU AAGUUCCCAAU@LB@3'-CGC...CGUCA G UUUCU...AAG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -18.6025 kcal/mol@LB@Unfolding Energy - mRNA 5.89438 kcal/mol@LB@Unfolding Energy - sRNA 3.32987 kcal/mol@LB@@LB@Position - mRNA 85 -- 98@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 22 -- 28@LB@
173	0.03066	0.5559	b2928	yggC	-11.87	0.049837	290 -- 298	75 -- 83	putative PanK family P-loop kinase	_____________289_______299\n_____________\|_________\|\n5'-GAA...CUGCA_________GG-3'\n______________CAUGUUGGC\n______________\|\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	292 -- 298	75 -- 81	-14.124 kcal/mol	1.76242 kcal/mol	0.492259 kcal/mol	289 299@LB@ \| \|@LB@5'-GAA...CUGCA GG-3'@LB@ CAUGUUGGC@LB@ \|\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -11.87 kcal/mol@LB@Hybridization Energy -14.124 kcal/mol@LB@Unfolding Energy - mRNA 1.76242 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 290 -- 298@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 75 -- 81@LB@
52	0.01055	0.5385	b2963	mltC	-16.80	0.006570	83 -- 101	12 -- 32	membrane-bound lytic murein transglycosylase C	_____________82____________________102\n_____________\|_____________________\|\n5'-CAU...UCCUG_____________________AUAUC...AUA-3'\n______________UUCGAGGGU__AAAGAGGUGC\n______________\|\|\|:\|\|\|\|\|__\|\|\|\|\|\|\|\|\|\|\n______________AAGUUCCCA__UUUCUCCACG\n3'-CGC...CACUG_________AU__________GCGAG...AAG-5'\n_____________\|_____________________\|\n_____________33____________________11\n	95 -- 101	12 -- 18	-28.8763 kcal/mol	6.26663 kcal/mol	5.80657 kcal/mol	82 102@LB@ \| \|@LB@5'-CAU...UCCUG AUAUC...AUA-3'@LB@ UUCGAGGGU AAAGAGGUGC@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ AAGUUCCCA UUUCUCCACG@LB@3'-CGC...CACUG AU GCGAG...AAG-5'@LB@ \| \|@LB@ 33 11@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -28.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.26663 kcal/mol@LB@Unfolding Energy - sRNA 5.80657 kcal/mol@LB@@LB@Position - mRNA 83 -- 101@LB@Position - sRNA 12 -- 32@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 12 -- 18@LB@
88	0.01545	0.5385	b3009	yghB	-9.13	0.148475	202 -- 216	61 -- 78	general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter	_____________201________________217\n_____________\|__________________\|\n5'-UCU...GUCCA_______________A__AUAUC...UUG-3'\n______________UGGCU___GUUAUUC_AG\n______________\|\|\|\|\|___\|\|\|\|\|\|\|_\|\|\n______________ACCGA___CAAUAAG_UC\n3'-CGC...GUGCA_____AAU_______C__AACUC...AAG-5'\n_____________\|__________________\|\n_____________79_________________60\n	207 -- 213	64 -- 70	-14.1767 kcal/mol	4.24529 kcal/mol	0.796888 kcal/mol	201 217@LB@ \| \|@LB@5'-UCU...GUCCA A AUAUC...UUG-3'@LB@ UGGCU GUUAUUC AG@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ ACCGA CAAUAAG UC@LB@3'-CGC...GUGCA AAU C AACUC...AAG-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -14.1767 kcal/mol@LB@Unfolding Energy - mRNA 4.24529 kcal/mol@LB@Unfolding Energy - sRNA 0.796888 kcal/mol@LB@@LB@Position - mRNA 202 -- 216@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 64 -- 70@LB@
140	0.02329	0.5385	b3026	qseC	-7.47	0.277092	174 -- 202	52 -- 78	quorum sensing sensory histidine kinase in two-component regulatory system with QseB	_____________173___________________________203\n_____________\|_____________________________\|\n5'-AAA...GUGCA____A_______CA_AUU__G________GAAAU...GGA-3'\n______________UGGU_UUGGUUA__C___AG_UGAGAAAU\n______________\|\|\|:_\|\|:\|\|\|\|__\|___\|\|_\|\|\|\|\|\|\|:\n______________ACCG_AAUCAAU__G___UC_ACUCUUUG\n3'-CGC...GUGCA____A_______AA_C____A________AGAGC...AAG-5'\n_____________\|_____________________________\|\n_____________79____________________________51\n	196 -- 202	52 -- 58	-18.6962 kcal/mol	6.8409 kcal/mol	4.38944 kcal/mol	173 203@LB@ \| \|@LB@5'-AAA...GUGCA A CA AUU G GAAAU...GGA-3'@LB@ UGGU UUGGUUA C AG UGAGAAAU@LB@ \|\|\|: \|\|:\|\|\|\| \| \|\| \|\|\|\|\|\|\|:@LB@ ACCG AAUCAAU G UC ACUCUUUG@LB@3'-CGC...GUGCA A AA C A AGAGC...AAG-5'@LB@ \| \|@LB@ 79 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -18.6962 kcal/mol@LB@Unfolding Energy - mRNA 6.8409 kcal/mol@LB@Unfolding Energy - sRNA 4.38944 kcal/mol@LB@@LB@Position - mRNA 174 -- 202@LB@Position - sRNA 52 -- 78@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 52 -- 58@LB@
26	0.00484	0.5385	b3033	yqiB	-11.20	0.065436	106 -- 117	15 -- 27	DUF1249 protein YqiB	_____________105___________118\n_____________\|_____________\|\n5'-UGG...CCAGU_____________GGAAA...GCG-3'\n______________GGG_UAGAAGAGG\n______________\|\|\|_\|\|:\|\|\|\|\|\|\n______________CCC_AUUUUCUCC\n3'-CGC...AAGUU___A_________ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	111 -- 117	15 -- 21	-17.3581 kcal/mol	2.92425 kcal/mol	3.23583 kcal/mol	105 118@LB@ \| \|@LB@5'-UGG...CCAGU GGAAA...GCG-3'@LB@ GGG UAGAAGAGG@LB@ \|\|\| \|\|:\|\|\|\|\|\|@LB@ CCC AUUUUCUCC@LB@3'-CGC...AAGUU A ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.3581 kcal/mol@LB@Unfolding Energy - mRNA 2.92425 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 106 -- 117@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 15 -- 21@LB@
127	0.02181	0.5385	b3057	bacA	-7.57	0.267037	62 -- 69	75 -- 82	undecaprenyl pyrophosphate phosphatase	_____________61_______70\n_____________\|________\|\n5'-UUC...GGCGA________GUAAU...UUG-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	63 -- 69	75 -- 81	-12.0605 kcal/mol	4.15225 kcal/mol	0.339284 kcal/mol	61 70@LB@ \| \|@LB@5'-UUC...GGCGA GUAAU...UUG-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -12.0605 kcal/mol@LB@Unfolding Energy - mRNA 4.15225 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 62 -- 69@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 75 -- 81@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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