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
84	0.004676	0.1855	b0526	cysS	-14.43	0.019007	256 -- 269	64 -- 77	cysteinyl-tRNA synthetase		_____________255____________270\n_____________\|______________\|\n5'-GCC...UAUUC______________GGCAU...ACG-3'\n______________ACGCCGGGGAAGUC\n______________\|\|:\|\|:\|\|\|\|\|:\|\|\n______________UGUGGUCCCUUUAG\n3'-UUU...GCGGU______________AACCG...GUG-5'\n_____________\|______________\|\n_____________78_____________63\n	263 -- 269	64 -- 70	-23.2043 kcal/mol	4.03864 kcal/mol	4.72709 kcal/mol	255 270@LB@ \| \|@LB@5'-GCC...UAUUC GGCAU...ACG-3'@LB@ ACGCCGGGGAAGUC@LB@ \|\|:\|\|:\|\|\|\|\|:\|\|@LB@ UGUGGUCCCUUUAG@LB@3'-UUU...GCGGU AACCG...GUG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -23.2043 kcal/mol@LB@Unfolding Energy - mRNA 4.03864 kcal/mol@LB@Unfolding Energy - sRNA 4.72709 kcal/mol@LB@@LB@Position - mRNA 256 -- 269@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 64 -- 70@LB@
48	0.002388	0.1727	b2198	ccmD	-12.59	0.043972	250 -- 282	36 -- 77	cytochrome c biogenesis protein; heme export ABC transporter holo-CcmE release factor		_____________249________________________________________283\n_____________\|__________________________________________\|\n5'-UGG...CGGUU_____UUUUUU_____________G_________________CCGUU...UGG-3'\n______________ACGCC______GUC_UGGCUG_GC_GUG_______GUGAUGA\n______________\|\|:\|\|______:\|\|_\|\|\|\|\|\|_\|\|_\|\|:_______:\|\|\|\|\|\|\n______________UGUGG______UAG_ACCGAC_CG_CAU_______UACUACU\n3'-UUU...GCGGU_____UCCCUU___A______G__G___UUAAUAA_______CAAUG...GUG-5'\n_____________\|__________________________________________\|\n_____________78_________________________________________35\n	276 -- 282	36 -- 42	-31.2682 kcal/mol	9.31707 kcal/mol	9.36195 kcal/mol	249 283@LB@ \| \|@LB@5'-UGG...CGGUU UUUUUU G CCGUU...UGG-3'@LB@ ACGCC GUC UGGCUG GC GUG GUGAUGA@LB@ \|\|:\|\| :\|\| \|\|\|\|\|\| \|\| \|\|: :\|\|\|\|\|\|@LB@ UGUGG UAG ACCGAC CG CAU UACUACU@LB@3'-UUU...GCGGU UCCCUU A G G UUAAUAA CAAUG...GUG-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -31.2682 kcal/mol@LB@Unfolding Energy - mRNA 9.31707 kcal/mol@LB@Unfolding Energy - sRNA 9.36195 kcal/mol@LB@@LB@Position - mRNA 250 -- 282@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 36 -- 42@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@
76	0.003978	0.182	b0336	codB	-6.71	0.504284	39 -- 48	1 -- 11	cytosine transporter		_____________38__________49\n_____________\|___________\|\n5'-CCA...UCUUA___________CCACU...UUU-3'\n______________UCAGGCC_UAC\n______________\|\|\|\|\|\|\|_:\|\|\n______________AGUCCGG_GUG\n3'-UUU...CAAAA_______C___-5'\n_____________\|__________\|\n_____________12_________1\n	39 -- 45	5 -- 11	-14.8291 kcal/mol	2.46298 kcal/mol	5.60325 kcal/mol	38 49@LB@ \| \|@LB@5'-CCA...UCUUA CCACU...UUU-3'@LB@ UCAGGCC UAC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ AGUCCGG GUG@LB@3'-UUU...CAAAA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -6.71 kcal/mol@LB@Hybridization Energy -14.8291 kcal/mol@LB@Unfolding Energy - mRNA 2.46298 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 5 -- 11@LB@
95	0.005084	0.1855	b3182	dacB	-12.18	0.052827	253 -- 263	2 -- 12	D-alanyl-D-alanine carboxypeptidase		_____________252_________264\n_____________\|___________\|\n5'-CCG...CAGUG___________AAUGU...GUG-3'\n______________UUCAGGCCGCA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AAGUCCGGCGU\n3'-UUU...ACAAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	257 -- 263	2 -- 8	-21.5619 kcal/mol	3.68722 kcal/mol	5.66926 kcal/mol	252 264@LB@ \| \|@LB@5'-CCG...CAGUG AAUGU...GUG-3'@LB@ UUCAGGCCGCA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AAGUCCGGCGU@LB@3'-UUU...ACAAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -21.5619 kcal/mol@LB@Unfolding Energy - mRNA 3.68722 kcal/mol@LB@Unfolding Energy - sRNA 5.66926 kcal/mol@LB@@LB@Position - mRNA 253 -- 263@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 2 -- 8@LB@
171	0.01011	0.2071	b4086	alsC	-10.38	0.118114	189 -- 207	53 -- 70	D-allose ABC transporter permease		_____________188_________________208\n_____________\|___________________\|\n5'-CGC...GAAGA_______A____A__G___UUACC...CGA-3'\n______________GGAGAUU_UGGC_UG_GCU\n______________\|\|\|:\|\|:_\|\|\|\|_\|\|_\|\|:\n______________CCUUUAG_ACCG_AC_CGG\n3'-UUU...UGGUC_______A_______G___CAUUU...GUG-5'\n_____________\|___________________\|\n_____________71__________________52\n	189 -- 195	64 -- 70	-21.9341 kcal/mol	4.72392 kcal/mol	6.83419 kcal/mol	188 208@LB@ \| \|@LB@5'-CGC...GAAGA A A G UUACC...CGA-3'@LB@ GGAGAUU UGGC UG GCU@LB@ \|\|\|:\|\|: \|\|\|\| \|\| \|\|:@LB@ CCUUUAG ACCG AC CGG@LB@3'-UUU...UGGUC A G CAUUU...GUG-5'@LB@ \| \|@LB@ 71 52@LB@@LB@@LB@Energy -10.38 kcal/mol@LB@Hybridization Energy -21.9341 kcal/mol@LB@Unfolding Energy - mRNA 4.72392 kcal/mol@LB@Unfolding Energy - sRNA 6.83419 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 53 -- 70@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 64 -- 70@LB@
70	0.003478	0.1727	b1919	dcyD	-7.16	0.432573	249 -- 279	53 -- 83	D-cysteine desulfhydrase PLP-dependent		_____________248_______________________________280\n_____________\|_________________________________\|\n5'-CUG...UCGGC____________CUC___U________C_____UUUCU...GGG-3'\n______________GCGCCAACGCCG___GAA_AUCU__GC_GCGCU\n______________\|\|\|\|\|\|\|\|:\|\|:___\|\|\|_\|\|\|\|__\|\|_\|\|\|\|:\n______________CGCGGUUGUGGU___CUU_UAGA__CG_CGCGG\n3'-UUU...UAUGA____________CC_________AC__A_____CAUUU...GUG-5'\n_____________\|_________________________________\|\n_____________84________________________________52\n	252 -- 258	74 -- 80	-36.5845 kcal/mol	12.956 kcal/mol	16.4685 kcal/mol	248 280@LB@ \| \|@LB@5'-CUG...UCGGC CUC U C UUUCU...GGG-3'@LB@ GCGCCAACGCCG GAA AUCU GC GCGCU@LB@ \|\|\|\|\|\|\|\|:\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|:@LB@ CGCGGUUGUGGU CUU UAGA CG CGCGG@LB@3'-UUU...UAUGA CC AC A CAUUU...GUG-5'@LB@ \| \|@LB@ 84 52@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -36.5845 kcal/mol@LB@Unfolding Energy - mRNA 12.956 kcal/mol@LB@Unfolding Energy - sRNA 16.4685 kcal/mol@LB@@LB@Position - mRNA 249 -- 279@LB@Position - sRNA 53 -- 83@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 74 -- 80@LB@
2	1.572e-09	2.767e-06	b3749	rbsA	-20.95	0.000983	43 -- 64	65 -- 86	D-ribose ABC transporter ATPase		_____________42_____________________65\n_____________\|______________________\|\n5'-UAA...GAGCA_____AAA______________ACCAU...UGG-3'\n______________GCUGC___AACACCAGGGAAAU\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGACG___UUGUGGUCCCUUUA\n3'-UUU...GCUUA_____CGG______________GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	58 -- 64	65 -- 71	-31.8331 kcal/mol	3.49898 kcal/mol	7.38332 kcal/mol	42 65@LB@ \| \|@LB@5'-UAA...GAGCA AAA ACCAU...UGG-3'@LB@ GCUGC AACACCAGGGAAAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGACG UUGUGGUCCCUUUA@LB@3'-UUU...GCUUA CGG GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -20.95 kcal/mol@LB@Hybridization Energy -31.8331 kcal/mol@LB@Unfolding Energy - mRNA 3.49898 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 43 -- 64@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 65 -- 71@LB@
146	0.008611	0.2059	b3750	rbsC	-8.88	0.223197	137 -- 159	56 -- 77	D-ribose ABC transporter permease		_____________136_______________________160\n_____________\|_________________________\|\n5'-GAU...AGGCC_____________G_UAA_______CGCUG...UCU-3'\n______________AC_CCA_GGAAGU_U___UGGCUGC\n______________\|\|_\|\|\|_\|\|\|\|:\|_\|___\|\|\|\|\|\|\|\n______________UG_GGU_CCUUUA_A___ACCGACG\n3'-UUU...GCGGU__U___C______G___________CGGCA...GUG-5'\n_____________\|_________________________\|\n_____________78________________________55\n	153 -- 159	56 -- 62	-22.4095 kcal/mol	5.11916 kcal/mol	8.4081 kcal/mol	136 160@LB@ \| \|@LB@5'-GAU...AGGCC G UAA CGCUG...UCU-3'@LB@ AC CCA GGAAGU U UGGCUGC@LB@ \|\| \|\|\| \|\|\|\|:\| \| \|\|\|\|\|\|\|@LB@ UG GGU CCUUUA A ACCGACG@LB@3'-UUU...GCGGU U C G CGGCA...GUG-5'@LB@ \| \|@LB@ 78 55@LB@@LB@@LB@Energy -8.88 kcal/mol@LB@Hybridization Energy -22.4095 kcal/mol@LB@Unfolding Energy - mRNA 5.11916 kcal/mol@LB@Unfolding Energy - sRNA 8.4081 kcal/mol@LB@@LB@Position - mRNA 137 -- 159@LB@Position - sRNA 56 -- 77@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 56 -- 62@LB@
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 24 -- 30@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