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
98	0.005208	0.1855	b4174	hflK	-10.42	0.116019	265 -- 284	65 -- 83	modulator for HflB protease specific for phage lambda cII repressor		_____________264__________________285\n_____________\|____________________\|\n5'-AGA...ACCUG___G____U__G________GGAAA...GUC-3'\n______________GCG_CAAC_CU_AGGGAAAU\n______________\|\|\|_\|\|\|\|_\|:_\|\|\|\|\|\|\|\|\n______________CGC_GUUG_GG_UCCCUUUA\n3'-UUU...UAUGA___G____U___________GAACC...GUG-5'\n_____________\|____________________\|\n_____________84___________________64\n	278 -- 284	65 -- 71	-24.0318 kcal/mol	6.25533 kcal/mol	7.35968 kcal/mol	264 285@LB@ \| \|@LB@5'-AGA...ACCUG G U G GGAAA...GUC-3'@LB@ GCG CAAC CU AGGGAAAU@LB@ \|\|\| \|\|\|\| \|: \|\|\|\|\|\|\|\|@LB@ CGC GUUG GG UCCCUUUA@LB@3'-UUU...UAUGA G U GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -24.0318 kcal/mol@LB@Unfolding Energy - mRNA 6.25533 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 265 -- 284@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 65 -- 71@LB@
187	0.01114	0.2089	b0801	ybiC	-12.72	0.041489	266 -- 279	27 -- 40	putative dehydrogenase	b0517	_____________265____________280\n_____________\|______________\|\n5'-GCU...CGUCA_______A______AACAA...UUG-3'\n______________GAUGGGU_GCGAGG\n______________\|\|\|\|:\|\|_:\|:\|\|\|\n______________CUACUCA_UGUUCC\n3'-UUU...UAAUA_______A______CGUGU...GUG-5'\n_____________\|______________\|\n_____________41_____________26\n	266 -- 272	34 -- 40	-18.8068 kcal/mol	3.48138 kcal/mol	2.60767 kcal/mol	265 280@LB@ \| \|@LB@5'-GCU...CGUCA A AACAA...UUG-3'@LB@ GAUGGGU GCGAGG@LB@ \|\|\|\|:\|\| :\|:\|\|\|@LB@ CUACUCA UGUUCC@LB@3'-UUU...UAAUA A CGUGU...GUG-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -12.72 kcal/mol@LB@Hybridization Energy -18.8068 kcal/mol@LB@Unfolding Energy - mRNA 3.48138 kcal/mol@LB@Unfolding Energy - sRNA 2.60767 kcal/mol@LB@@LB@Position - mRNA 266 -- 279@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 34 -- 40@LB@
186	0.01109	0.2089	b3234	degQ	-11.96	0.058310	267 -- 277	3 -- 13	serine endoprotease periplasmic		_____________266_________278\n_____________\|___________\|\n5'-CUG...CGUCA___________CGCGU...UUG-3'\n______________UUUCAGGCCGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AAAGUCCGGCG\n3'-UUU...GACAA___________UG-5'\n_____________\|___________\|\n_____________14__________2\n	271 -- 277	3 -- 9	-19.4081 kcal/mol	1.79109 kcal/mol	5.63489 kcal/mol	266 278@LB@ \| \|@LB@5'-CUG...CGUCA CGCGU...UUG-3'@LB@ UUUCAGGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AAAGUCCGGCG@LB@3'-UUU...GACAA UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -11.96 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 5.63489 kcal/mol@LB@@LB@Position - mRNA 267 -- 277@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 3 -- 9@LB@
150	0.008837	0.2059	b0453	ybaY	-11.57	0.069675	268 -- 294	71 -- 94	outer membrane lipoprotein		_____________267_________________________295\n_____________\|___________________________\|\n5'-AAG...UAAAA___________CA_A____________CUGCAA-3'\n______________GCGCGGAUAUU__G_CGCCAGCACCGG\n______________\|\|\|\|\|:\|\|\|:\|__\|_\|\|\|\|\|:\|\|\|\|:\|\n______________CGCGCUUAUGA__C_GCGGUUGUGGUC\n3'-UUU...CCCCA___________________________CCUUU...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________70\n	283 -- 289	76 -- 82	-36.9875 kcal/mol	12.3701 kcal/mol	13.0144 kcal/mol	267 295@LB@ \| \|@LB@5'-AAG...UAAAA CA A CUGCAA-3'@LB@ GCGCGGAUAUU G CGCCAGCACCGG@LB@ \|\|\|\|\|:\|\|\|:\| \| \|\|\|\|\|:\|\|\|\|:\|@LB@ CGCGCUUAUGA C GCGGUUGUGGUC@LB@3'-UUU...CCCCA CCUUU...GUG-5'@LB@ \| \|@LB@ 95 70@LB@@LB@@LB@Energy -11.57 kcal/mol@LB@Hybridization Energy -36.9875 kcal/mol@LB@Unfolding Energy - mRNA 12.3701 kcal/mol@LB@Unfolding Energy - sRNA 13.0144 kcal/mol@LB@@LB@Position - mRNA 268 -- 294@LB@Position - sRNA 71 -- 94@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 76 -- 82@LB@
175	0.01031	0.2074	b1834	yebT	-10.32	0.121003	270 -- 282	51 -- 62	MCE domain protein		_____________269___________283\n_____________\|_____________\|\n5'-UCU...CUUUC_______U_____UCAUC...UUG-3'\n______________UGGCUGC_GCCGU\n______________\|\|\|\|\|\|\|_\|\|\|\|\|\n______________ACCGACG_CGGCA\n3'-UUU...UUAGA_____________UUUAA...GUG-5'\n_____________\|_____________\|\n_____________63____________50\n	270 -- 276	56 -- 62	-21.4836 kcal/mol	6.28034 kcal/mol	4.8826 kcal/mol	269 283@LB@ \| \|@LB@5'-UCU...CUUUC U UCAUC...UUG-3'@LB@ UGGCUGC GCCGU@LB@ \|\|\|\|\|\|\| \|\|\|\|\|@LB@ ACCGACG CGGCA@LB@3'-UUU...UUAGA UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -21.4836 kcal/mol@LB@Unfolding Energy - mRNA 6.28034 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 270 -- 282@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 56 -- 62@LB@
185	0.01108	0.2089	b0662	ubiF	-8.33	0.279302	272 -- 292	6 -- 27	2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase		_____________271____________________293\n_____________\|______________________\|\n5'-AAU...GGGCU____________GA___GC___AACGGUGA-3'\n______________GGCACAGCAC_G__UUU__GGU\n______________\|\|\|\|\|\|\|\|\|\|_\|__\|\|\|__\|\|:\n______________CCGUGUCGUG_C__AAA__CCG\n3'-UUU...UGUUC__________A_AA___GU___GCGUG-5'\n_____________\|______________________\|\n_____________28_____________________5\n	275 -- 281	18 -- 24	-24.5826 kcal/mol	6.14687 kcal/mol	10.1088 kcal/mol	271 293@LB@ \| \|@LB@5'-AAU...GGGCU GA GC AACGGUGA-3'@LB@ GGCACAGCAC G UUU GGU@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\| \|\|:@LB@ CCGUGUCGUG C AAA CCG@LB@3'-UUU...UGUUC A AA GU GCGUG-5'@LB@ \| \|@LB@ 28 5@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -24.5826 kcal/mol@LB@Unfolding Energy - mRNA 6.14687 kcal/mol@LB@Unfolding Energy - sRNA 10.1088 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 6 -- 27@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 18 -- 24@LB@
54	0.002681	0.1727	b3201	lptB	-14.37	0.019597	275 -- 293	64 -- 82	lipopolysaccharide export ABC transporter ATPase		_____________274_________________294\n_____________\|___________________\|\n5'-UUC...CUGAC_______U___________GUCGGUC-3'\n______________CGUCAAC_CCGGGGAAAUU\n______________\|\|:\|\|\|\|_\|\|:\|\|\|\|\|\|\|:\n______________GCGGUUG_GGUCCCUUUAG\n3'-UUU...AUGAC_______U___________AACCG...GUG-5'\n_____________\|___________________\|\n_____________83__________________63\n	287 -- 293	64 -- 70	-27.6824 kcal/mol	6.24463 kcal/mol	7.07066 kcal/mol	274 294@LB@ \| \|@LB@5'-UUC...CUGAC U GUCGGUC-3'@LB@ CGUCAAC CCGGGGAAAUU@LB@ \|\|:\|\|\|\| \|\|:\|\|\|\|\|\|\|:@LB@ GCGGUUG GGUCCCUUUAG@LB@3'-UUU...AUGAC U AACCG...GUG-5'@LB@ \| \|@LB@ 83 63@LB@@LB@@LB@Energy -14.37 kcal/mol@LB@Hybridization Energy -27.6824 kcal/mol@LB@Unfolding Energy - mRNA 6.24463 kcal/mol@LB@Unfolding Energy - sRNA 7.07066 kcal/mol@LB@@LB@Position - mRNA 275 -- 293@LB@Position - sRNA 64 -- 82@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 64 -- 70@LB@
99	0.005465	0.1855	b0767	pgl	-9.37	0.182441	275 -- 291	70 -- 86	6-phosphogluconolactonase		_____________274________________292\n_____________\|__________________\|\n5'-UCA...GGCGC____A_____________UUGUC...AUG-3'\n______________ACUG_CGCUGACA_CAGG\n______________\|\|\|\|_\|\|\|::\|\|\|_\|\|\|\|\n______________UGAC_GCGGUUGU_GUCC\n3'-UUU...GCUUA_____________G____CUUUA...GUG-5'\n_____________\|__________________\|\n_____________87_________________69\n	281 -- 287	75 -- 81	-21.4952 kcal/mol	4.85205 kcal/mol	7.27772 kcal/mol	274 292@LB@ \| \|@LB@5'-UCA...GGCGC A UUGUC...AUG-3'@LB@ ACUG CGCUGACA CAGG@LB@ \|\|\|\| \|\|\|::\|\|\| \|\|\|\|@LB@ UGAC GCGGUUGU GUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -21.4952 kcal/mol@LB@Unfolding Energy - mRNA 4.85205 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 75 -- 81@LB@
122	0.006658	0.1913	b0600	ybdL	-10.23	0.125775	275 -- 297	68 -- 86	methionine aminotransferase PLP-dependent		_____________274_____________________298\n_____________\|_______________________\|\n5'-UCA...AGCGC___G____AG__________C__UUA-3'\n______________GCU_GCGC__CAACACCAGG_GA\n______________:\|\|_\|\|\|\|__\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UGA_CGCG__GUUGUGGUCC_CU\n3'-UUU...GCUUA_______________________UUAGA...GUG-5'\n_____________\|_______________________\|\n_____________87______________________67\n	288 -- 294	70 -- 76	-27.7616 kcal/mol	10.1544 kcal/mol	7.37523 kcal/mol	274 298@LB@ \| \|@LB@5'-UCA...AGCGC G AG C UUA-3'@LB@ GCU GCGC CAACACCAGG GA@LB@ :\|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UGA CGCG GUUGUGGUCC CU@LB@3'-UUU...GCUUA UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.7616 kcal/mol@LB@Unfolding Energy - mRNA 10.1544 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 275 -- 297@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
59	0.002989	0.1727	b2713	hydN	-12.16	0.053402	276 -- 298	54 -- 76	formate dehydrogenase-H [4Fe-4S] ferredoxin subunit	b3573	_____________275______________________299\n_____________\|________________________\|\n5'-CUU...UUUCU_______A_____A___A______AU-3'\n______________CAUCAGG_AAAUC__GG_CUGUGC\n______________\|\|:\|\|\|\|_\|\|\|\|\|__\|\|_\|\|\|:\|\|\n______________GUGGUCC_UUUAG__CC_GACGCG\n3'-UUU...CGGUU_______C_____AA_________GCAUU...GUG-5'\n_____________\|________________________\|\n_____________77_______________________53\n	276 -- 282	70 -- 76	-25.5609 kcal/mol	4.47784 kcal/mol	8.92391 kcal/mol	275 299@LB@ \| \|@LB@5'-CUU...UUUCU A A A AU-3'@LB@ CAUCAGG AAAUC GG CUGUGC@LB@ \|\|:\|\|\|\| \|\|\|\|\| \|\| \|\|\|:\|\|@LB@ GUGGUCC UUUAG CC GACGCG@LB@3'-UUU...CGGUU C AA GCAUU...GUG-5'@LB@ \| \|@LB@ 77 53@LB@@LB@@LB@Energy -12.16 kcal/mol@LB@Hybridization Energy -25.5609 kcal/mol@LB@Unfolding Energy - mRNA 4.47784 kcal/mol@LB@Unfolding Energy - sRNA 8.92391 kcal/mol@LB@@LB@Position - mRNA 276 -- 298@LB@Position - sRNA 54 -- 76@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 70 -- 76@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