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
41	0.00828	0.5385	b2246	rhmT	-13.65	0.023999	257 -- 273	69 -- 86	putative L-rhamnonate transporter	_____________256________________274\n_____________\|__________________\|\n5'-ACG...AUUCC____________GCU___AUGUG...CGA-3'\n______________GUUUAUGUUGGC____GU\n______________\|\|\|:\|:\|\|\|\|\|\|____\|\|\n______________CAAGUGCAACCG____CA\n3'-CGC...GUUUU____________AAAU__AUAAG...AAG-5'\n_____________\|__________________\|\n_____________87_________________68\n	262 -- 268	75 -- 81	-18.6828 kcal/mol	4.45929 kcal/mol	0.568509 kcal/mol	256 274@LB@ \| \|@LB@5'-ACG...AUUCC GCU AUGUG...CGA-3'@LB@ GUUUAUGUUGGC GU@LB@ \|\|\|:\|:\|\|\|\|\|\| \|\|@LB@ CAAGUGCAACCG CA@LB@3'-CGC...GUUUU AAAU AUAAG...AAG-5'@LB@ \| \|@LB@ 87 68@LB@@LB@@LB@Energy -13.65 kcal/mol@LB@Hybridization Energy -18.6828 kcal/mol@LB@Unfolding Energy - mRNA 4.45929 kcal/mol@LB@Unfolding Energy - sRNA 0.568509 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 69 -- 86@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 75 -- 81@LB@
42	0.008798	0.5385	b0087	mraY	-9.88	0.111048	142 -- 153	79 -- 90	phospho-N-acetylmuramoyl-pentapeptide transferase	_____________141__________154\n_____________\|____________\|\n5'-GAC...UAGUU____________AGUGC...CGC-3'\n______________AAGGGUUCACGU\n______________\|\|::\|\|\|\|\|\|\|\|\n______________UUUUCAAGUGCA\n3'-CGC...AGGCG____________ACCGA...AAG-5'\n_____________\|____________\|\n_____________91___________78\n	147 -- 153	79 -- 85	-14.1224 kcal/mol	3.73912 kcal/mol	0.506924 kcal/mol	141 154@LB@ \| \|@LB@5'-GAC...UAGUU AGUGC...CGC-3'@LB@ AAGGGUUCACGU@LB@ \|\|::\|\|\|\|\|\|\|\|@LB@ UUUUCAAGUGCA@LB@3'-CGC...AGGCG ACCGA...AAG-5'@LB@ \| \|@LB@ 91 78@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -14.1224 kcal/mol@LB@Unfolding Energy - mRNA 3.73912 kcal/mol@LB@Unfolding Energy - sRNA 0.506924 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 79 -- 90@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 79 -- 85@LB@
43	0.009109	0.5385	b2531	iscR	-9.39	0.134324	275 -- 298	62 -- 87	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________274________________________299\n_____________\|__________________________\|\n5'-AUG...GGCCC___A__________GAUAUUUC____AC-3'\n______________GGU_C_CGUUGGCU_________CGA\n______________:\|\|_\|_\|\|\|\|\|\|\|\|_________\|\|\|\n______________UCA_G_GCAACCGA_________GCU\n3'-CGC...CGUUU___A_U________AAUCAAUAA___CAACU...AAG-5'\n_____________\|__________________________\|\n_____________88_________________________61\n	281 -- 287	74 -- 80	-16.3089 kcal/mol	5.20915 kcal/mol	1.70771 kcal/mol	274 299@LB@ \| \|@LB@5'-AUG...GGCCC A GAUAUUUC AC-3'@LB@ GGU C CGUUGGCU CGA@LB@ :\|\| \| \|\|\|\|\|\|\|\| \|\|\|@LB@ UCA G GCAACCGA GCU@LB@3'-CGC...CGUUU A U AAUCAAUAA CAACU...AAG-5'@LB@ \| \|@LB@ 88 61@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -16.3089 kcal/mol@LB@Unfolding Energy - mRNA 5.20915 kcal/mol@LB@Unfolding Energy - sRNA 1.70771 kcal/mol@LB@@LB@Position - mRNA 275 -- 298@LB@Position - sRNA 62 -- 87@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 74 -- 80@LB@
44	0.009138	0.5385	b4148	sugE	-12.73	0.035076	273 -- 288	62 -- 77	multidrug efflux system protein	_____________272______________289\n_____________\|________________\|\n5'-CGC...CCCAC_________C______CGCCG...UUA-3'\n______________GGCUUUAGU_GUUUGA\n______________\|\|\|\|\|\|\|\|\|_:\|\|:\|\|\n______________CCGAAAUCA_UAAGCU\n3'-CGC...UGCAA_________A______CAACU...AAG-5'\n_____________\|________________\|\n_____________78_______________61\n	275 -- 281	69 -- 75	-18.0703 kcal/mol	4.60455 kcal/mol	0.736118 kcal/mol	272 289@LB@ \| \|@LB@5'-CGC...CCCAC C CGCCG...UUA-3'@LB@ GGCUUUAGU GUUUGA@LB@ \|\|\|\|\|\|\|\|\| :\|\|:\|\|@LB@ CCGAAAUCA UAAGCU@LB@3'-CGC...UGCAA A CAACU...AAG-5'@LB@ \| \|@LB@ 78 61@LB@@LB@@LB@Energy -12.73 kcal/mol@LB@Hybridization Energy -18.0703 kcal/mol@LB@Unfolding Energy - mRNA 4.60455 kcal/mol@LB@Unfolding Energy - sRNA 0.736118 kcal/mol@LB@@LB@Position - mRNA 273 -- 288@LB@Position - sRNA 62 -- 77@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 69 -- 75@LB@
45	0.009513	0.5385	b2513	yfgM	-9.58	0.124672	177 -- 189	15 -- 27	ancillary SecYEG translocon subunit; putative anti-RcsB factor	_____________176___________190\n_____________\|_____________\|\n5'-GGC...UUACU_________A___AGAAG...UUG-3'\n______________GGGUUAAGG_AGG\n______________\|\|\|\|\|\|\|::_\|\|\|\n______________CCCAAUUUU_UCC\n3'-CGC...AAGUU_________C___ACGGC...AAG-5'\n_____________\|_____________\|\n_____________28____________14\n	179 -- 185	19 -- 25	-14.0675 kcal/mol	1.24912 kcal/mol	3.23583 kcal/mol	176 190@LB@ \| \|@LB@5'-GGC...UUACU A AGAAG...UUG-3'@LB@ GGGUUAAGG AGG@LB@ \|\|\|\|\|\|\|:: \|\|\|@LB@ CCCAAUUUU UCC@LB@3'-CGC...AAGUU C ACGGC...AAG-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.0675 kcal/mol@LB@Unfolding Energy - mRNA 1.24912 kcal/mol@LB@Unfolding Energy - sRNA 3.23583 kcal/mol@LB@@LB@Position - mRNA 177 -- 189@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 19 -- 25@LB@
46	0.009803	0.5385	b1418	cybB	-9.32	0.138160	281 -- 295	73 -- 89	cytochrome b561	_____________280_______________296\n_____________\|_________________\|\n5'-AAC...GCAAU_________________CUUCC-3'\n______________GGAGUUU_CG_UGGUUU\n______________::\|\|\|\|:_\|\|_\|\|\|:\|\|\n______________UUUCAAG_GC_ACCGAA\n3'-CGC...GGCGU_______U__A______AUCAA...AAG-5'\n_____________\|_________________\|\n_____________90________________72\n	281 -- 287	83 -- 89	-12.2046 kcal/mol	2.36714 kcal/mol	0.517627 kcal/mol	280 296@LB@ \| \|@LB@5'-AAC...GCAAU CUUCC-3'@LB@ GGAGUUU CG UGGUUU@LB@ ::\|\|\|\|: \|\| \|\|\|:\|\|@LB@ UUUCAAG GC ACCGAA@LB@3'-CGC...GGCGU U A AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -12.2046 kcal/mol@LB@Unfolding Energy - mRNA 2.36714 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 281 -- 295@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 83 -- 89@LB@
47	0.009854	0.5385	b3408	feoA	-10.27	0.095129	159 -- 188	52 -- 83	ferrous iron transporter protein A	_____________158_________________________________189\n_____________\|___________________________________\|\n5'-AGC...CGCCC____A_______________C___UAA________AAGUA...CUG-3'\n______________CAUG__GGU___AGUUA_UC_AGU___UGAGAAAC\n______________\|\|:\|__\|\|:___\|\|\|\|\|_\|\|_\|\|\|___\|\|\|\|\|\|\|\|\n______________GUGC__CCG___UCAAU_AG_UCA___ACUCUUUG\n3'-CGC...UUCAA____AA___AAA_____A__C______________AGAGC...AAG-5'\n_____________\|___________________________________\|\n_____________84__________________________________51\n	182 -- 188	52 -- 58	-20.9255 kcal/mol	6.25891 kcal/mol	4.4004 kcal/mol	158 189@LB@ \| \|@LB@5'-AGC...CGCCC A C UAA AAGUA...CUG-3'@LB@ CAUG GGU AGUUA UC AGU UGAGAAAC@LB@ \|\|:\| \|\|: \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GUGC CCG UCAAU AG UCA ACUCUUUG@LB@3'-CGC...UUCAA AA AAA A C AGAGC...AAG-5'@LB@ \| \|@LB@ 84 51@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -20.9255 kcal/mol@LB@Unfolding Energy - mRNA 6.25891 kcal/mol@LB@Unfolding Energy - sRNA 4.4004 kcal/mol@LB@@LB@Position - mRNA 159 -- 188@LB@Position - sRNA 52 -- 83@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 52 -- 58@LB@
48	0.009918	0.5385	b0641	lptE	-9.88	0.110832	177 -- 184	74 -- 81	LPS assembly OM complex LptDE lipoprotein component	_____________176______185\n_____________\|________\|\n5'-ACG...CUGGU________AAGCG...UGA-3'\n______________CGUUGGCU\n______________\|\|\|\|\|\|\|\|\n______________GCAACCGA\n3'-CGC...CAAGU________AAUCA...AAG-5'\n_____________\|________\|\n_____________82_______73\n	178 -- 184	74 -- 80	-13.2047 kcal/mol	2.99134 kcal/mol	0.332056 kcal/mol	176 185@LB@ \| \|@LB@5'-ACG...CUGGU AAGCG...UGA-3'@LB@ CGUUGGCU@LB@ \|\|\|\|\|\|\|\|@LB@ GCAACCGA@LB@3'-CGC...CAAGU AAUCA...AAG-5'@LB@ \| \|@LB@ 82 73@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -13.2047 kcal/mol@LB@Unfolding Energy - mRNA 2.99134 kcal/mol@LB@Unfolding Energy - sRNA 0.332056 kcal/mol@LB@@LB@Position - mRNA 177 -- 184@LB@Position - sRNA 74 -- 81@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 74 -- 80@LB@
49	0.01016	0.5385	b3354	yheU	-13.31	0.027656	105 -- 118	71 -- 84	UPF0270 family protein	_____________104____________119\n_____________\|______________\|\n5'-CUG...GGCGG______________UUGGC...GUA-3'\n______________UCAUGUUGGCUUUA\n______________\|\|\|:\|\|\|\|\|\|\|\|\|\|\n______________AGUGCAACCGAAAU\n3'-CGC...UUUCA______________CAAUA...AAG-5'\n_____________\|______________\|\n_____________85_____________70\n	112 -- 118	71 -- 77	-20.4483 kcal/mol	6.58199 kcal/mol	0.5567 kcal/mol	104 119@LB@ \| \|@LB@5'-CUG...GGCGG UUGGC...GUA-3'@LB@ UCAUGUUGGCUUUA@LB@ \|\|\|:\|\|\|\|\|\|\|\|\|\|@LB@ AGUGCAACCGAAAU@LB@3'-CGC...UUUCA CAAUA...AAG-5'@LB@ \| \|@LB@ 85 70@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -20.4483 kcal/mol@LB@Unfolding Energy - mRNA 6.58199 kcal/mol@LB@Unfolding Energy - sRNA 0.5567 kcal/mol@LB@@LB@Position - mRNA 105 -- 118@LB@Position - sRNA 71 -- 84@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 71 -- 77@LB@
50	0.0104	0.5385	b0661	miaB	-10.15	0.099644	35 -- 45	74 -- 85	tRNA-i(6)A37 methylthiotransferase	_____________34___________46\n_____________\|____________\|\n5'-CGC...GCAAU____________GAUUU...AAC-3'\n______________UUC_CGUUGGUU\n______________\|\|\|_\|\|\|\|\|\|:\|\n______________AAG_GCAACCGA\n3'-CGC...UUUUC___U________AAUCA...AAG-5'\n_____________\|____________\|\n_____________86___________73\n	39 -- 45	74 -- 80	-13.4892 kcal/mol	2.82751 kcal/mol	0.512001 kcal/mol	34 46@LB@ \| \|@LB@5'-CGC...GCAAU GAUUU...AAC-3'@LB@ UUC CGUUGGUU@LB@ \|\|\| \|\|\|\|\|\|:\|@LB@ AAG GCAACCGA@LB@3'-CGC...UUUUC U AAUCA...AAG-5'@LB@ \| \|@LB@ 86 73@LB@@LB@@LB@Energy -10.15 kcal/mol@LB@Hybridization Energy -13.4892 kcal/mol@LB@Unfolding Energy - mRNA 2.82751 kcal/mol@LB@Unfolding Energy - sRNA 0.512001 kcal/mol@LB@@LB@Position - mRNA 35 -- 45@LB@Position - sRNA 74 -- 85@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 74 -- 80@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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