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
31	0.001906	0.2067	b0198	metI	-9.82	0.132421	237 -- 257	48 -- 68	DL-methionine transporter subunit	_____________236____________________258\n_____________\|______________________\|\n5'-UCA...GUGGC__A__________C________ACCUU...CGG-3'\n______________GU_UGGGAAA_CG_UGGCAAUG\n______________\|\|_\|\|\|:\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CA_ACCUUUU_GU_ACCGUUAC\n3'-UUU...AUAUA__________A__C________GUUAC...UUG-5'\n_____________\|______________________\|\n_____________69_____________________47\n	251 -- 257	48 -- 54	-20.2902 kcal/mol	6.26471 kcal/mol	4.20468 kcal/mol	236 258@LB@ \| \|@LB@5'-UCA...GUGGC A C ACCUU...CGG-3'@LB@ GU UGGGAAA CG UGGCAAUG@LB@ \|\| \|\|\|:\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CA ACCUUUU GU ACCGUUAC@LB@3'-UUU...AUAUA A C GUUAC...UUG-5'@LB@ \| \|@LB@ 69 47@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -20.2902 kcal/mol@LB@Unfolding Energy - mRNA 6.26471 kcal/mol@LB@Unfolding Energy - sRNA 4.20468 kcal/mol@LB@@LB@Position - mRNA 237 -- 257@LB@Position - sRNA 48 -- 68@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 48 -- 54@LB@
62	0.004714	0.2539	b0973	hyaB	-9.08	0.185506	169 -- 187	48 -- 64	hydrogenase 1 large subunit	_____________168_________________188\n_____________\|___________________\|\n5'-GGU...AAACC___C_____CCA_______AGGAU...GCG-3'\n______________GAA_AUCAG___GGCAAUG\n______________\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUU_UAGUC___CCGUUAC\n3'-UUU...ACAAC___U_____A_________GUUAC...UUG-5'\n_____________\|___________________\|\n_____________65__________________47\n	181 -- 187	48 -- 54	-17.0784 kcal/mol	4.02672 kcal/mol	3.97302 kcal/mol	168 188@LB@ \| \|@LB@5'-GGU...AAACC C CCA AGGAU...GCG-3'@LB@ GAA AUCAG GGCAAUG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUU UAGUC CCGUUAC@LB@3'-UUU...ACAAC U A GUUAC...UUG-5'@LB@ \| \|@LB@ 65 47@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -17.0784 kcal/mol@LB@Unfolding Energy - mRNA 4.02672 kcal/mol@LB@Unfolding Energy - sRNA 3.97302 kcal/mol@LB@@LB@Position - mRNA 169 -- 187@LB@Position - sRNA 48 -- 64@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 48 -- 54@LB@
122	0.01263	0.3462	b0537	intD	-10.49	0.096065	54 -- 80	48 -- 76	DLP12 prophage; putative phage integrase	_____________53____________________________81\n_____________\|_____________________________\|\n5'-GAG...AUUGG____________________A________ACGCA...AAG-3'\n______________UUUUGUAU_UUGGGGAG_CA_UGGCGAUG\n______________\|\|\|\|:\|\|\|_\|\|\|\|::\|:_\|\|_\|\|\|\|:\|\|\|\n______________AAAAUAUA_AACCUUUU_GU_ACCGUUAC\n3'-UUU...ACAGA________C________A__C________GUUAC...UUG-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	74 -- 80	48 -- 54	-25.3626 kcal/mol	9.83015 kcal/mol	5.0412 kcal/mol	53 81@LB@ \| \|@LB@5'-GAG...AUUGG A ACGCA...AAG-3'@LB@ UUUUGUAU UUGGGGAG CA UGGCGAUG@LB@ \|\|\|\|:\|\|\| \|\|\|\|::\|: \|\| \|\|\|\|:\|\|\|@LB@ AAAAUAUA AACCUUUU GU ACCGUUAC@LB@3'-UUU...ACAGA C A C GUUAC...UUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -25.3626 kcal/mol@LB@Unfolding Energy - mRNA 9.83015 kcal/mol@LB@Unfolding Energy - sRNA 5.0412 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 74 -- 80@LB@Position Seed - sRNA 48 -- 54@LB@
154	0.01792	0.3828	b2610	ffh	-8.53	0.234957	246 -- 258	48 -- 60	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)	_____________245___________259\n_____________\|_____________\|\n5'-AGG...GCAAU_________C___GACGC...AAG-3'\n______________AUCAGUGGC_GUG\n______________\|\|\|\|\|\|\|\|\|_:\|\|\n______________UAGUCACCG_UAC\n3'-UUU...CCUUU_________U___GUUAC...UUG-5'\n_____________\|_____________\|\n_____________61____________47\n	248 -- 254	52 -- 58	-18.214 kcal/mol	6.29175 kcal/mol	3.39422 kcal/mol	245 259@LB@ \| \|@LB@5'-AGG...GCAAU C GACGC...AAG-3'@LB@ AUCAGUGGC GUG@LB@ \|\|\|\|\|\|\|\|\| :\|\|@LB@ UAGUCACCG UAC@LB@3'-UUU...CCUUU U GUUAC...UUG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.214 kcal/mol@LB@Unfolding Energy - mRNA 6.29175 kcal/mol@LB@Unfolding Energy - sRNA 3.39422 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 52 -- 58@LB@
188	0.02326	0.4145	b2501	ppk	-10.84	0.080977	186 -- 203	48 -- 65	polyphosphate kinase component of RNA degradosome	_____________185________________204\n_____________\|__________________\|\n5'-CGC...AAAAC____UAAA__________GGUCA...UUG-3'\n______________GGAG____AGUGGUAAUG\n______________\|\|\|:____\|\|\|\|\|:\|\|\|\|\n______________CCUU____UCACCGUUAC\n3'-UUU...UACAA____UUAG__________GUUAC...UUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	197 -- 203	48 -- 54	-18.775 kcal/mol	3.93073 kcal/mol	4.00814 kcal/mol	185 204@LB@ \| \|@LB@5'-CGC...AAAAC UAAA GGUCA...UUG-3'@LB@ GGAG AGUGGUAAUG@LB@ \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ CCUU UCACCGUUAC@LB@3'-UUU...UACAA UUAG GUUAC...UUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -10.84 kcal/mol@LB@Hybridization Energy -18.775 kcal/mol@LB@Unfolding Energy - mRNA 3.93073 kcal/mol@LB@Unfolding Energy - sRNA 4.00814 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 48 -- 54@LB@
120	0.01191	0.3337	b0354	yaiL	-10.86	0.080118	189 -- 207	50 -- 67	DUF2058 family protein	_____________188_________________208\n_____________\|___________________\|\n5'-GUA...CGGGU_______CAA__A______AACUU...UUC-3'\n______________UUGGAAA___AG_UGGCAA\n______________\|\|\|\|\|\|\|___\|\|_\|\|\|\|\|\|\n______________AACCUUU___UC_ACCGUU\n3'-UUU...UAUAC_______UAG_________ACGUU...UUG-5'\n_____________\|___________________\|\n_____________68__________________49\n	189 -- 195	61 -- 67	-16.0374 kcal/mol	2.05851 kcal/mol	3.12147 kcal/mol	188 208@LB@ \| \|@LB@5'-GUA...CGGGU CAA A AACUU...UUC-3'@LB@ UUGGAAA AG UGGCAA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ AACCUUU UC ACCGUU@LB@3'-UUU...UAUAC UAG ACGUU...UUG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -16.0374 kcal/mol@LB@Unfolding Energy - mRNA 2.05851 kcal/mol@LB@Unfolding Energy - sRNA 3.12147 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 61 -- 67@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@
8	0.0003008	0.1262	b3191	mlaB	-9.66	0.142648	16 -- 23	51 -- 58	ABC transporter maintaining OM lipid asymmetry cytoplasmic STAS component	_____________15_______24\n_____________\|________\|\n5'-GUG...ACUUC________UAAAA...AGG-3'\n______________CAGUGGCG\n______________\|\|\|\|\|\|\|:\n______________GUCACCGU\n3'-UUU...UUUUA________UACGU...UUG-5'\n_____________\|________\|\n_____________59_______50\n	17 -- 23	51 -- 57	-13.9143 kcal/mol	1.55672 kcal/mol	2.69685 kcal/mol	15 24@LB@ \| \|@LB@5'-GUG...ACUUC UAAAA...AGG-3'@LB@ CAGUGGCG@LB@ \|\|\|\|\|\|\|:@LB@ GUCACCGU@LB@3'-UUU...UUUUA UACGU...UUG-5'@LB@ \| \|@LB@ 59 50@LB@@LB@@LB@Energy -9.66 kcal/mol@LB@Hybridization Energy -13.9143 kcal/mol@LB@Unfolding Energy - mRNA 1.55672 kcal/mol@LB@Unfolding Energy - sRNA 2.69685 kcal/mol@LB@@LB@Position - mRNA 16 -- 23@LB@Position - sRNA 51 -- 58@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 51 -- 57@LB@
10	0.0004066	0.1262	b3429	glgA	-9.74	0.137242	173 -- 185	51 -- 64	glycogen synthase	_____________172____________186\n_____________\|______________\|\n5'-GUA...GCUAC______________UAAAC...ACG-3'\n______________GGAAGUUAG_GGCA\n______________\|:\|\|:\|:\|\|_\|\|\|\|\n______________CUUUUAGUC_CCGU\n3'-UUU...ACAAC_________A____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	175 -- 181	56 -- 62	-15.3924 kcal/mol	2.76007 kcal/mol	2.8882 kcal/mol	172 186@LB@ \| \|@LB@5'-GUA...GCUAC UAAAC...ACG-3'@LB@ GGAAGUUAG GGCA@LB@ \|:\|\|:\|:\|\| \|\|\|\|@LB@ CUUUUAGUC CCGU@LB@3'-UUU...ACAAC A UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -15.3924 kcal/mol@LB@Unfolding Energy - mRNA 2.76007 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 173 -- 185@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 56 -- 62@LB@
29	0.001819	0.2065	b3648	gmk	-8.89	0.201842	236 -- 243	51 -- 58	guanylate kinase	_____________235______244\n_____________\|________\|\n5'-GUG...GCCCC________CGGGU...CCC-3'\n______________CAGUGGCG\n______________\|\|\|\|\|\|\|:\n______________GUCACCGU\n3'-UUU...UUUUA________UACGU...UUG-5'\n_____________\|________\|\n_____________59_______50\n	237 -- 243	51 -- 57	-13.8917 kcal/mol	2.3096 kcal/mol	2.69685 kcal/mol	235 244@LB@ \| \|@LB@5'-GUG...GCCCC CGGGU...CCC-3'@LB@ CAGUGGCG@LB@ \|\|\|\|\|\|\|:@LB@ GUCACCGU@LB@3'-UUU...UUUUA UACGU...UUG-5'@LB@ \| \|@LB@ 59 50@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -13.8917 kcal/mol@LB@Unfolding Energy - mRNA 2.3096 kcal/mol@LB@Unfolding Energy - sRNA 2.69685 kcal/mol@LB@@LB@Position - mRNA 236 -- 243@LB@Position - sRNA 51 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@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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