Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
132	0.01159	0.2883	bsu33140	yvqJ	-14.19	0.043338	185 -- 204	31 -- 52	MFS transporter	_____________184____________________205\n_____________\|______________________\|\n5'-GAC...GGCAA____GG___C_________U__UGAAU...UUA-3'\n______________CGGG____G_UCUGAUGGA_GG\n______________\|\|\|:____\|_\|\|\|\|\|\|:\|\|_\|\|\n______________GCCU____C_AGACUAUCU_CC\n3'-UUU...AAAAA____AGAA_U_________C__CAACC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________30\n	195 -- 201	34 -- 40	-19.4408 kcal/mol	4.27934 kcal/mol	0.976414 kcal/mol	184 205@LB@ \| \|@LB@5'-GAC...GGCAA GG C U UGAAU...UUA-3'@LB@ CGGG G UCUGAUGGA GG@LB@ \|\|\|: \| \|\|\|\|\|\|:\|\| \|\|@LB@ GCCU C AGACUAUCU CC@LB@3'-UUU...AAAAA AGAA U C CAACC...AUA-5'@LB@ \| \|@LB@ 53 30@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -19.4408 kcal/mol@LB@Unfolding Energy - mRNA 4.27934 kcal/mol@LB@Unfolding Energy - sRNA 0.976414 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 31 -- 52@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
144	0.01244	0.2883	bsu15720	def	-10.99	0.152648	175 -- 193	31 -- 50	peptide deformylase	_____________174___________________194\n_____________\|_____________________\|\n5'-GCG...UGUAA_____CAC_____________UAACA...AUG-3'\n______________GAUCU___GUCU__UGGAGGG\n______________\|\|\|\|\|___:\|\|\|__\|:\|\|\|\|\|\n______________CUAGA___UAGA__AUCUCCC\n3'-UUU...AAAGC_____AC_____CU_______CAACC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________30\n	187 -- 193	31 -- 37	-18.0798 kcal/mol	6.12249 kcal/mol	0.970579 kcal/mol	174 194@LB@ \| \|@LB@5'-GCG...UGUAA CAC UAACA...AUG-3'@LB@ GAUCU GUCU UGGAGGG@LB@ \|\|\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ CUAGA UAGA AUCUCCC@LB@3'-UUU...AAAGC AC CU CAACC...AUA-5'@LB@ \| \|@LB@ 51 30@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -18.0798 kcal/mol@LB@Unfolding Energy - mRNA 6.12249 kcal/mol@LB@Unfolding Energy - sRNA 0.970579 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 31 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
154	0.01388	0.2994	bsu23480	dacF	-14.01	0.046761	175 -- 192	31 -- 51	D-alanyl-D-alanine carboxypeptidase DacF	_____________174___________________193\n_____________\|_____________________\|\n5'-UGG...AAAAA_____A___A___________CUUUU...UUG-3'\n______________GGAUU_UGA____AUGGAGGG\n______________\|\|\|\|:_\|\|\|____\|\|:\|\|\|\|\|\n______________CCUAG_ACU____UAUCUCCC\n3'-UUU...AAAAG_____A___AGAC________CAACC...AUA-5'\n_____________\|_____________________\|\n_____________52____________________30\n	186 -- 192	31 -- 37	-18.482 kcal/mol	3.50235 kcal/mol	0.970589 kcal/mol	174 193@LB@ \| \|@LB@5'-UGG...AAAAA A A CUUUU...UUG-3'@LB@ GGAUU UGA AUGGAGGG@LB@ \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|@LB@ CCUAG ACU UAUCUCCC@LB@3'-UUU...AAAAG A AGAC CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -18.482 kcal/mol@LB@Unfolding Energy - mRNA 3.50235 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 175 -- 192@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 31 -- 37@LB@
174	0.01668	0.3152	bsu22210	yprB	-13.05	0.069799	168 -- 191	31 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'	_____________167______________________192\n_____________\|________________________\|\n5'-AUU...AGCUG_______AAAU___GUAA______AGGCC...AUG-3'\n______________UUGGAUC____GUC____GGAGGG\n______________\|:\|\|\|\|\|____:\|\|____:\|\|\|\|\|\n______________AGCCUAG____UAG____UCUCCC\n3'-UUU...AAAAA_______AAC____ACUA______CAACC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________30\n	168 -- 174	47 -- 53	-20.3327 kcal/mol	6.30079 kcal/mol	0.981784 kcal/mol	167 192@LB@ \| \|@LB@5'-AUU...AGCUG AAAU GUAA AGGCC...AUG-3'@LB@ UUGGAUC GUC GGAGGG@LB@ \|:\|\|\|\|\| :\|\| :\|\|\|\|\|@LB@ AGCCUAG UAG UCUCCC@LB@3'-UUU...AAAAA AAC ACUA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -20.3327 kcal/mol@LB@Unfolding Energy - mRNA 6.30079 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 47 -- 53@LB@
176	0.01673	0.3152	bsu08790	thiC	-9.56	0.245346	273 -- 280	31 -- 38	phosphomethylpyrimidine synthase	_____________272______281\n_____________\|________\|\n5'-GGC...UAUAC________UUCUU...AAG-3'\n______________GUGGAGGG\n______________:\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	274 -- 280	31 -- 37	-12.4867 kcal/mol	2.26991 kcal/mol	0.65488 kcal/mol	272 281@LB@ \| \|@LB@5'-GGC...UAUAC UUCUU...AAG-3'@LB@ GUGGAGGG@LB@ :\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -12.4867 kcal/mol@LB@Unfolding Energy - mRNA 2.26991 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 273 -- 280@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 31 -- 37@LB@
177	0.01681	0.3152	bsu00910	ispF	-14.14	0.044127	219 -- 247	31 -- 51	2-D-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________218____________________________248\n_____________\|______________________________\|\n5'-UCG...GACAA__________G__CAUCAAUUA________CCGUC...UUG-3'\n______________GGAUU_UGAU_UG_________GUGGAGGG\n______________\|\|\|\|:_\|\|\|\|_\|\|_________:\|:\|\|\|\|\|\n______________CCUAG_ACUA_AC_________UAUCUCCC\n3'-UUU...AAAAG_____A____G___________________CAACC...AUA-5'\n_____________\|______________________________\|\n_____________52_____________________________30\n	241 -- 247	31 -- 37	-21.3343 kcal/mol	6.22033 kcal/mol	0.970589 kcal/mol	218 248@LB@ \| \|@LB@5'-UCG...GACAA G CAUCAAUUA CCGUC...UUG-3'@LB@ GGAUU UGAU UG GUGGAGGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|:\|\|\|\|\|@LB@ CCUAG ACUA AC UAUCUCCC@LB@3'-UUU...AAAAG A G CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -21.3343 kcal/mol@LB@Unfolding Energy - mRNA 6.22033 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 219 -- 247@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 31 -- 37@LB@
183	0.01776	0.3237	bsu08550	sspK	-13.38	0.060997	172 -- 193	31 -- 48	small acid-soluble spore protein K	_____________171____________________194\n_____________\|______________________\|\n5'-UUU...CAACU_________C__ACC_______AUAUG...ACG-3'\n______________UUUUGAUCU_GA___UAGGGGG\n______________\|:\|\|\|\|\|\|\|_\|\|___\|\|\|:\|\|\|\n______________AGAACUAGA_CU___AUCUCCC\n3'-UUU...AGCCU______________________CAACC...AUA-5'\n_____________\|______________________\|\n_____________49_____________________30\n	187 -- 193	31 -- 37	-20.1262 kcal/mol	5.7766 kcal/mol	0.970395 kcal/mol	171 194@LB@ \| \|@LB@5'-UUU...CAACU C ACC AUAUG...ACG-3'@LB@ UUUUGAUCU GA UAGGGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ AGAACUAGA CU AUCUCCC@LB@3'-UUU...AGCCU CAACC...AUA-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -20.1262 kcal/mol@LB@Unfolding Energy - mRNA 5.7766 kcal/mol@LB@Unfolding Energy - sRNA 0.970395 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
32	0.001154	0.119	bsu32820	fadE	-9.01	0.290043	236 -- 252	32 -- 52	acyl-CoA dehydrogenase	_____________235____________________253\n_____________\|______________________\|\n5'-AUU...GGCGG________UA____________AUGUC...AGC-3'\n______________CGGAUUUU__AUC_____GAGG\n______________\|\|\|\|\|:\|\|__\|\|\|_____\|\|\|\|\n______________GCCUAGAA__UAG_____CUCC\n3'-UUU...AAAAA________C____ACUAU____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	237 -- 243	45 -- 51	-13.909 kcal/mol	3.91995 kcal/mol	0.976384 kcal/mol	235 253@LB@ \| \|@LB@5'-AUU...GGCGG UA AUGUC...AGC-3'@LB@ CGGAUUUU AUC GAGG@LB@ \|\|\|\|\|:\|\| \|\|\| \|\|\|\|@LB@ GCCUAGAA UAG CUCC@LB@3'-UUU...AAAAA C ACUAU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -13.909 kcal/mol@LB@Unfolding Energy - mRNA 3.91995 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 236 -- 252@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 45 -- 51@LB@
42	0.001862	0.1479	bsu40320	argI	-8.56	0.330283	1 -- 17	32 -- 48	arginase	______________1_________________18\n______________\|_________________\|\n___________5'-_____C_______CC___AGCAG...UGA-3'\n______________UCUUG_AUUUGAU___GG\n______________\|\|\|\|\|_\|\|:\|\|\|\|___\|\|\n______________AGAAC_UAGACUA___CC\n3'-UUU...AGCCU_____________UCU__CCAAC...AUA-5'\n_____________\|__________________\|\n_____________49_________________31\n	7 -- 13	37 -- 43	-12.1859 kcal/mol	2.6521 kcal/mol	0.970016 kcal/mol	1 18@LB@ \| \|@LB@ 5'- C CC AGCAG...UGA-3'@LB@ UCUUG AUUUGAU GG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|@LB@ AGAAC UAGACUA CC@LB@3'-UUU...AGCCU UCU CCAAC...AUA-5'@LB@ \| \|@LB@ 49 31@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.1859 kcal/mol@LB@Unfolding Energy - mRNA 2.6521 kcal/mol@LB@Unfolding Energy - sRNA 0.970016 kcal/mol@LB@@LB@Position - mRNA 1 -- 17@LB@Position - sRNA 32 -- 48@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 37 -- 43@LB@
43	0.00194	0.1492	bsu01370	adk	-12.74	0.079154	128 -- 149	32 -- 52	adenylate kinase	_____________127____________________150\n_____________\|______________________\|\n5'-UUU...UACCG_______A___AAAAC______AAAUG...AUA-3'\n______________UGGAUUU_UGA_____UAGAGG\n______________:\|\|\|\|:\|_\|\|\|_____\|\|\|\|\|\|\n______________GCCUAGA_ACU_____AUCUCC\n3'-UUU...AAAAA___________AGACU______CCAAC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________31\n	128 -- 134	46 -- 52	-16.4639 kcal/mol	2.75066 kcal/mol	0.976384 kcal/mol	127 150@LB@ \| \|@LB@5'-UUU...UACCG A AAAAC AAAUG...AUA-3'@LB@ UGGAUUU UGA UAGAGG@LB@ :\|\|\|\|:\| \|\|\| \|\|\|\|\|\|@LB@ GCCUAGA ACU AUCUCC@LB@3'-UUU...AAAAA AGACU CCAAC...AUA-5'@LB@ \| \|@LB@ 53 31@LB@@LB@@LB@Energy -12.74 kcal/mol@LB@Hybridization Energy -16.4639 kcal/mol@LB@Unfolding Energy - mRNA 2.75066 kcal/mol@LB@Unfolding Energy - sRNA 0.976384 kcal/mol@LB@@LB@Position - mRNA 128 -- 149@LB@Position - sRNA 32 -- 52@LB@Position Seed - mRNA 128 -- 134@LB@Position Seed - sRNA 46 -- 52@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