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
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@
111	0.005938	0.1855	b0962	helD	-11.18	0.082726	7 -- 19	71 -- 82	DNA helicase IV	_____________6_____________20\n_____________\|_____________\|\n_____5'-CAGAGU________G____CCCAG...GCC-3'\n______________CGCCAACA_CCAG\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\n______________GCGGUUGU_GGUC\n3'-UUU...AUGAC_____________CCUUU...GUG-5'\n_____________\|_____________\|\n_____________83____________70\n	8 -- 14	75 -- 81	-19.0718 kcal/mol	1.18849 kcal/mol	6.70061 kcal/mol	6 20@LB@ \| \|@LB@ 5'-CAGAGU G CCCAG...GCC-3'@LB@ CGCCAACA CCAG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|@LB@ GCGGUUGU GGUC@LB@3'-UUU...AUGAC CCUUU...GUG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.18 kcal/mol@LB@Hybridization Energy -19.0718 kcal/mol@LB@Unfolding Energy - mRNA 1.18849 kcal/mol@LB@Unfolding Energy - sRNA 6.70061 kcal/mol@LB@@LB@Position - mRNA 7 -- 19@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 8 -- 14@LB@Position Seed - sRNA 75 -- 81@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent	_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
33	0.001709	0.1727	b0023	rpsT	-12.95	0.037339	65 -- 78	72 -- 85	30S ribosomal subunit protein S20	_____________64_____________79\n_____________\|______________\|\n5'-UGA...GAAUC________U_____CGUAA...AGA-3'\n______________CUGCGCCA_CACUA\n______________\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________GACGCGGU_GUGGU\n3'-UUU...CUUAU________U_____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	66 -- 72	78 -- 84	-22.3173 kcal/mol	2.13275 kcal/mol	7.23443 kcal/mol	64 79@LB@ \| \|@LB@5'-UGA...GAAUC U CGUAA...AGA-3'@LB@ CUGCGCCA CACUA@LB@ \|\|\|\|\|\|\|\| \|\|\|:\|@LB@ GACGCGGU GUGGU@LB@3'-UUU...CUUAU U CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -22.3173 kcal/mol@LB@Unfolding Energy - mRNA 2.13275 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 65 -- 78@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 78 -- 84@LB@
168	0.009959	0.2071	b0727	sucB	-11.51	0.071542	30 -- 47	72 -- 88	dihydrolipoyltranssuccinase	_____________29_________________48\n_____________\|__________________\|\n5'-CAG...GCAUG_______A__________UUUCC...GUG-3'\n______________GUACUGC_GCCAGCAUCA\n______________:\|\|\|\|\|\|_\|\|\|\|:\|\|:\|\|\n______________UAUGACG_CGGUUGUGGU\n3'-UUU...GCGCU__________________CCCUU...GUG-5'\n_____________\|__________________\|\n_____________89_________________71\n	38 -- 44	75 -- 81	-25.7274 kcal/mol	6.97777 kcal/mol	7.24148 kcal/mol	29 48@LB@ \| \|@LB@5'-CAG...GCAUG A UUUCC...GUG-3'@LB@ GUACUGC GCCAGCAUCA@LB@ :\|\|\|\|\|\| \|\|\|\|:\|\|:\|\|@LB@ UAUGACG CGGUUGUGGU@LB@3'-UUU...GCGCU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -25.7274 kcal/mol@LB@Unfolding Energy - mRNA 6.97777 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 30 -- 47@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 75 -- 81@LB@
155	0.009115	0.2059	b1531	marA	-9.94	0.142609	213 -- 231	72 -- 89	multiple antibiotic resistance transcriptional regulator	_____________212_________________232\n_____________\|___________________\|\n5'-AAG...GACGC_______A_____U_____UUCAU...AGC-3'\n______________AAUACUG_CGCUA_UACCA\n______________\|\|\|\|\|\|\|_\|\|\|:\|_:\|\|\|\|\n______________UUAUGAC_GCGGU_GUGGU\n3'-UUU...CGCGC_____________U_____CCCUU...GUG-5'\n_____________\|___________________\|\n_____________90__________________71\n	213 -- 219	83 -- 89	-21.2611 kcal/mol	3.54366 kcal/mol	7.77515 kcal/mol	212 232@LB@ \| \|@LB@5'-AAG...GACGC A U UUCAU...AGC-3'@LB@ AAUACUG CGCUA UACCA@LB@ \|\|\|\|\|\|\| \|\|\|:\| :\|\|\|\|@LB@ UUAUGAC GCGGU GUGGU@LB@3'-UUU...CGCGC U CCCUU...GUG-5'@LB@ \| \|@LB@ 90 71@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -21.2611 kcal/mol@LB@Unfolding Energy - mRNA 3.54366 kcal/mol@LB@Unfolding Energy - sRNA 7.77515 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 72 -- 89@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 83 -- 89@LB@
196	0.01202	0.2159	b1729	ydjN	-13.87	0.024594	143 -- 155	72 -- 84	putative transporter	_____________142___________156\n_____________\|_____________\|\n5'-CAU...AAUCU_____________UGACU...UGC-3'\n______________UGCGCCAACACUA\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________ACGCGGUUGUGGU\n3'-UUU...UUAUG_____________CCCUU...GUG-5'\n_____________\|_____________\|\n_____________85____________71\n	149 -- 155	72 -- 78	-23.7045 kcal/mol	2.6326 kcal/mol	7.20328 kcal/mol	142 156@LB@ \| \|@LB@5'-CAU...AAUCU UGACU...UGC-3'@LB@ UGCGCCAACACUA@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ ACGCGGUUGUGGU@LB@3'-UUU...UUAUG CCCUU...GUG-5'@LB@ \| \|@LB@ 85 71@LB@@LB@@LB@Energy -13.87 kcal/mol@LB@Hybridization Energy -23.7045 kcal/mol@LB@Unfolding Energy - mRNA 2.6326 kcal/mol@LB@Unfolding Energy - sRNA 7.20328 kcal/mol@LB@@LB@Position - mRNA 143 -- 155@LB@Position - sRNA 72 -- 84@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 72 -- 78@LB@
44	0.002208	0.1727	b1859	znuB	-7.63	0.365449	19 -- 38	72 -- 88	zinc ABC transporter permease	_____________18___________________39\n_____________\|____________________\|\n5'-AUG...AUGAA__________UGAAU_____CAUUU...AUU-3'\n______________GUGCUGUGCC_____CACCA\n______________:\|:\|\|\|:\|\|\|_____\|\|\|\|\|\n______________UAUGACGCGG_____GUGGU\n3'-UUU...GCGCU__________UU________CCCUU...GUG-5'\n_____________\|____________________\|\n_____________89___________________71\n	22 -- 28	79 -- 85	-22.3137 kcal/mol	7.44481 kcal/mol	7.24148 kcal/mol	18 39@LB@ \| \|@LB@5'-AUG...AUGAA UGAAU CAUUU...AUU-3'@LB@ GUGCUGUGCC CACCA@LB@ :\|:\|\|\|:\|\|\| \|\|\|\|\|@LB@ UAUGACGCGG GUGGU@LB@3'-UUU...GCGCU UU CCCUU...GUG-5'@LB@ \| \|@LB@ 89 71@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -22.3137 kcal/mol@LB@Unfolding Energy - mRNA 7.44481 kcal/mol@LB@Unfolding Energy - sRNA 7.24148 kcal/mol@LB@@LB@Position - mRNA 19 -- 38@LB@Position - sRNA 72 -- 88@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 79 -- 85@LB@
57	0.002848	0.1727	b2059	wcaA	-10.75	0.100075	282 -- 295	72 -- 85	putative glycosyl transferase	_____________281____________296\n_____________\|______________\|\n5'-AAC...CGGUU_________G____CAGCA-3'\n______________UUGCGCCAG_ACUA\n______________:\|\|\|\|\|\|\|:_\|\|:\|\n______________GACGCGGUU_UGGU\n3'-UUU...CUUAU_________G____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	284 -- 290	77 -- 83	-19.8604 kcal/mol	1.87274 kcal/mol	7.23443 kcal/mol	281 296@LB@ \| \|@LB@5'-AAC...CGGUU G CAGCA-3'@LB@ UUGCGCCAG ACUA@LB@ :\|\|\|\|\|\|\|: \|\|:\|@LB@ GACGCGGUU UGGU@LB@3'-UUU...CUUAU G CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -19.8604 kcal/mol@LB@Unfolding Energy - mRNA 1.87274 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 77 -- 83@LB@
194	0.01194	0.2159	b3454	livF	-10.01	0.138607	25 -- 47	72 -- 86	branched-chain amino acid ABC transporter ATPase	_____________24______________________48\n_____________\|_______________________\|\n5'-AGA...GCCGA_______AAUCAUCA________CUAUC...UUG-3'\n______________ACUGCGC________CAACACCA\n______________\|\|\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________UGACGCG________GUUGUGGU\n3'-UUU...GCUUA_______________________CCCUU...GUG-5'\n_____________\|_______________________\|\n_____________87______________________71\n	41 -- 47	72 -- 78	-22.1496 kcal/mol	4.90616 kcal/mol	7.23529 kcal/mol	24 48@LB@ \| \|@LB@5'-AGA...GCCGA AAUCAUCA CUAUC...UUG-3'@LB@ ACUGCGC CAACACCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGACGCG GUUGUGGU@LB@3'-UUU...GCUUA CCCUU...GUG-5'@LB@ \| \|@LB@ 87 71@LB@@LB@@LB@Energy -10.01 kcal/mol@LB@Hybridization Energy -22.1496 kcal/mol@LB@Unfolding Energy - mRNA 4.90616 kcal/mol@LB@Unfolding Energy - sRNA 7.23529 kcal/mol@LB@@LB@Position - mRNA 25 -- 47@LB@Position - sRNA 72 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 72 -- 78@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