Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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	Additional homologs
105	0.005654	0.1855	b0004	thrC	-10.56	0.108775	227 -- 299	1 -- 79	L-threonine synthase		_____________226_____________________________________________________________________________________300\n_____________\|_______________________________________________________________________________________\|\n5'-CGC...GAUCA____G_G____UCAG____U__GCAA_______CCCAG____________________AAAAU___GG___________________G-3'\n______________CAAC_A_CAGG_____CUU_GC____GCCGUAA___________GGGUU____GGGCA_____CAG__GCUGUUUUUU___CCGCAC\n______________\|\|\|\|_\|_\|\|\|\|_____\|\|\|_\|\|____\|\|\|\|\|\|\|___________\|:\|\|\|____\|\|\|\|\|_____\|\|\|__:\|\|\|\|\|\|\|\|:___\|\|\|\|\|\|\n______________GUUG_U_GUCC_____GAA_CG____CGGCAUU___________CUCAA____CCCGU_____GUC__UGACAAAAAG___GGCGUG\n3'-UUU...ACGCG______G____CUUUA___C__ACG________UAAUAAUACUA_____UGUU_____________G___________UCC______-5'\n_____________\|______________________________________________________________________________________\|\n_____________80_____________________________________________________________________________________1\n	287 -- 293	10 -- 16	-55.9039 kcal/mol	22.5864 kcal/mol	22.7537 kcal/mol	226 300@LB@ \| \|@LB@5'-CGC...GAUCA G G UCAG U GCAA CCCAG AAAAU GG G-3'@LB@ CAAC A CAGG CUU GC GCCGUAA GGGUU GGGCA CAG GCUGUUUUUU CCGCAC@LB@ \|\|\|\| \| \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|: \|\|\|\|\|\|@LB@ GUUG U GUCC GAA CG CGGCAUU CUCAA CCCGU GUC UGACAAAAAG GGCGUG@LB@3'-UUU...ACGCG G CUUUA C ACG UAAUAAUACUA UGUU G UCC -5'@LB@ \| \|@LB@ 80 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -55.9039 kcal/mol@LB@Unfolding Energy - mRNA 22.5864 kcal/mol@LB@Unfolding Energy - sRNA 22.7537 kcal/mol@LB@@LB@Position - mRNA 227 -- 299@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 10 -- 16@LB@
112	0.005982	0.1855	b1820	yobD	-7.30	0.411799	229 -- 243	1 -- 14	UPF0266 family inner membrane protein		_____________228_____________244\n_____________\|_______________\|\n5'-ACC...GAUUC______UC_______UCCUG...CCC-3'\n______________UUUUCA__GCCGCAC\n______________\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________AAAAGU__CGGCGUG\n3'-UUU...UGACA______C________-5'\n_____________\|______________\|\n_____________15_____________1\n	237 -- 243	1 -- 7	-17.9899 kcal/mol	4.95197 kcal/mol	5.72803 kcal/mol	228 244@LB@ \| \|@LB@5'-ACC...GAUUC UC UCCUG...CCC-3'@LB@ UUUUCA GCCGCAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ AAAAGU CGGCGUG@LB@3'-UUU...UGACA C -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -17.9899 kcal/mol@LB@Unfolding Energy - mRNA 4.95197 kcal/mol@LB@Unfolding Energy - sRNA 5.72803 kcal/mol@LB@@LB@Position - mRNA 229 -- 243@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
145	0.008374	0.2033	b0068	thiB	-7.61	0.367750	229 -- 244	73 -- 87	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein		_____________228______________245\n_____________\|________________\|\n5'-UUU...GCUGU________A_______CGUUU...ACU-3'\n______________UGCUGUGC_CAGCGCC\n______________\|:\|\|\|:\|\|_\|\|:\|:\|\|\n______________AUGACGCG_GUUGUGG\n3'-UUU...CGCUU________________UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	230 -- 236	80 -- 86	-23.483 kcal/mol	8.91653 kcal/mol	6.95602 kcal/mol	228 245@LB@ \| \|@LB@5'-UUU...GCUGU A CGUUU...ACU-3'@LB@ UGCUGUGC CAGCGCC@LB@ \|:\|\|\|:\|\| \|\|:\|:\|\|@LB@ AUGACGCG GUUGUGG@LB@3'-UUU...CGCUU UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -23.483 kcal/mol@LB@Unfolding Energy - mRNA 8.91653 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 229 -- 244@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 80 -- 86@LB@
152	0.009044	0.2059	b1448	mnaT	-7.00	0.457084	229 -- 266	50 -- 86	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________228____________________________________267\n_____________\|______________________________________\|\n5'-CGC...AGCCG_________C_____C________AUAACCA_______UUGUA...CGG-3'\n______________ACUGUGCUG_CAUUG_GGAAAUUU_______CGCCGUG\n______________\|\|\|\|:\|\|::_\|\|:::_\|\|\|\|\|\|:\|_______\|\|\|\|\|\|:\n______________UGACGCGGU_GUGGU_CCUUUAGA_______GCGGCAU\n3'-UUU...GCUUA_________U_____C________ACCGAC________UUAAU...GUG-5'\n_____________\|______________________________________\|\n_____________87_____________________________________49\n	260 -- 266	50 -- 56	-33.8437 kcal/mol	9.99136 kcal/mol	16.8518 kcal/mol	228 267@LB@ \| \|@LB@5'-CGC...AGCCG C C AUAACCA UUGUA...CGG-3'@LB@ ACUGUGCUG CAUUG GGAAAUUU CGCCGUG@LB@ \|\|\|\|:\|\|:: \|\|::: \|\|\|\|\|\|:\| \|\|\|\|\|\|:@LB@ UGACGCGGU GUGGU CCUUUAGA GCGGCAU@LB@3'-UUU...GCUUA U C ACCGAC UUAAU...GUG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -7.00 kcal/mol@LB@Hybridization Energy -33.8437 kcal/mol@LB@Unfolding Energy - mRNA 9.99136 kcal/mol@LB@Unfolding Energy - sRNA 16.8518 kcal/mol@LB@@LB@Position - mRNA 229 -- 266@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 50 -- 56@LB@
141	0.008132	0.2031	b3412	bioH	-10.51	0.111302	230 -- 255	56 -- 74	pimeloyl-ACP methyl ester carboxylesterase		_____________229________________________256\n_____________\|__________________________\|\n5'-GGC...AAAGG________AUGUUC______U_____UGCAC...ACG-3'\n______________UCAGGGGA______AUCUUG_GCUGC\n______________:\|\|\|\|\|:\|______\|\|\|\|\|\|_\|\|\|\|\|\n______________GGUCCCUU______UAGAAC_CGACG\n3'-UUU...GUUGU__________________________CGGCA...GUG-5'\n_____________\|__________________________\|\n_____________75_________________________55\n	231 -- 237	67 -- 73	-25.2186 kcal/mol	6.56983 kcal/mol	8.13729 kcal/mol	229 256@LB@ \| \|@LB@5'-GGC...AAAGG AUGUUC U UGCAC...ACG-3'@LB@ UCAGGGGA AUCUUG GCUGC@LB@ :\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ GGUCCCUU UAGAAC CGACG@LB@3'-UUU...GUUGU CGGCA...GUG-5'@LB@ \| \|@LB@ 75 55@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -25.2186 kcal/mol@LB@Unfolding Energy - mRNA 6.56983 kcal/mol@LB@Unfolding Energy - sRNA 8.13729 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 56 -- 74@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 67 -- 73@LB@
159	0.009346	0.2062	b3661	nlpA	-7.63	0.365650	232 -- 240	1 -- 9	cytoplasmic membrane lipoprotein-28		_____________231_______241\n_____________\|_________\|\n5'-UGU...GACAG_________UAUUG...ACA-3'\n______________GGGCCGCAU\n______________:\|\|\|\|\|\|\|:\n______________UCCGGCGUG\n3'-UUU...AAAAG_________-5'\n_____________\|________\|\n_____________10_______1\n	234 -- 240	1 -- 7	-16.6231 kcal/mol	3.46198 kcal/mol	5.10726 kcal/mol	231 241@LB@ \| \|@LB@5'-UGU...GACAG UAUUG...ACA-3'@LB@ GGGCCGCAU@LB@ :\|\|\|\|\|\|\|:@LB@ UCCGGCGUG@LB@3'-UUU...AAAAG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -16.6231 kcal/mol@LB@Unfolding Energy - mRNA 3.46198 kcal/mol@LB@Unfolding Energy - sRNA 5.10726 kcal/mol@LB@@LB@Position - mRNA 232 -- 240@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@LB@
5	5.466e-05	0.03849	b0713	ybgL	-10.83	0.096857	234 -- 242	53 -- 61	UPF0271 family protein		_____________233_______243\n_____________\|_________\|\n5'-GCC...GCGAA_________AGCGA...AUG-3'\n______________GGCUGCGCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCGACGCGG\n3'-UUU...UAGAA_________CAUUU...GUG-5'\n_____________\|_________\|\n_____________62________52\n	236 -- 242	53 -- 59	-22.2033 kcal/mol	6.50503 kcal/mol	4.87107 kcal/mol	233 243@LB@ \| \|@LB@5'-GCC...GCGAA AGCGA...AUG-3'@LB@ GGCUGCGCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCGACGCGG@LB@3'-UUU...UAGAA CAUUU...GUG-5'@LB@ \| \|@LB@ 62 52@LB@@LB@@LB@Energy -10.83 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 6.50503 kcal/mol@LB@Unfolding Energy - sRNA 4.87107 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 53 -- 61@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 53 -- 59@LB@
21	0.001192	0.1727	b2526	hscA	-14.48	0.018641	235 -- 259	63 -- 88	DnaK-like molecular chaperone specific for IscU		_____________234________________________260\n_____________\|__________________________\|\n5'-AGC...UUUGA__________________C_UC____GGCGG...UGG-3'\n______________GUGCUGCGCC_GCAUCAG_G__GUCU\n______________:\|:\|\|\|\|\|\|\|_:\|\|:\|\|\|_\|__:\|\|\|\n______________UAUGACGCGG_UGUGGUC_C__UAGA\n3'-UUU...GCGCU__________U_______C_UU____ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________62\n	245 -- 251	71 -- 77	-31.0682 kcal/mol	9.20475 kcal/mol	7.38674 kcal/mol	234 260@LB@ \| \|@LB@5'-AGC...UUUGA C UC GGCGG...UGG-3'@LB@ GUGCUGCGCC GCAUCAG G GUCU@LB@ :\|:\|\|\|\|\|\|\| :\|\|:\|\|\| \| :\|\|\|@LB@ UAUGACGCGG UGUGGUC C UAGA@LB@3'-UUU...GCGCU U C UU ACCGA...GUG-5'@LB@ \| \|@LB@ 89 62@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -31.0682 kcal/mol@LB@Unfolding Energy - mRNA 9.20475 kcal/mol@LB@Unfolding Energy - sRNA 7.38674 kcal/mol@LB@@LB@Position - mRNA 235 -- 259@LB@Position - sRNA 63 -- 88@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 71 -- 77@LB@
130	0.007275	0.1966	b1638	pdxH	-11.04	0.087983	237 -- 249	47 -- 59	pyridoxine 5'-phosphate oxidase		_____________236___________250\n_____________\|_____________\|\n5'-UCU...CGCAU_____________ACACC...CCC-3'\n______________CUGCGCCGUGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________GACGCGGCAUUUA\n3'-UUU...GAACC_____________AUAAU...GUG-5'\n_____________\|_____________\|\n_____________60____________46\n	243 -- 249	47 -- 53	-22.1181 kcal/mol	4.88729 kcal/mol	6.18672 kcal/mol	236 250@LB@ \| \|@LB@5'-UCU...CGCAU ACACC...CCC-3'@LB@ CUGCGCCGUGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ GACGCGGCAUUUA@LB@3'-UUU...GAACC AUAAU...GUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.1181 kcal/mol@LB@Unfolding Energy - mRNA 4.88729 kcal/mol@LB@Unfolding Energy - sRNA 6.18672 kcal/mol@LB@@LB@Position - mRNA 237 -- 249@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching