Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
78	0.004685	0.1935	b3905	rhaS	-7.96	0.061746	70 -- 86	26 -- 40	transcriptional activator of rhaBAD and rhaT	_____________69________________87\n_____________\|_________________\|\n5'-UGG...UCACC______CCU________ACGCU...AUG-3'\n______________GCAUUU___GAAAAUUC\n______________\|\|\|:\|\|___:\|\|\|\|\|\|\|\n______________CGUGAA___UUUUUAAG\n3'-UUU...UUCUU______U__________CAAUG...CAA-5'\n_____________\|_________________\|\n_____________41________________25\n	80 -- 86	26 -- 32	-11.6625 kcal/mol	2.05222 kcal/mol	1.64811 kcal/mol	69 87@LB@ \| \|@LB@5'-UGG...UCACC CCU ACGCU...AUG-3'@LB@ GCAUUU GAAAAUUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -11.6625 kcal/mol@LB@Unfolding Energy - mRNA 2.05222 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 70 -- 86@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 26 -- 32@LB@
70	0.003574	0.1645	b0145	dksA	-6.64	0.135564	191 -- 197	39 -- 45	transcriptional regulator of rRNA transcription; DnaK suppressor protein	_____________190_____198\n_____________\|_______\|\n5'-AAU...UUAAG_______AACAU...AUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	191 -- 197	39 -- 45	-7.63285 kcal/mol	0.475666 kcal/mol	0.514773 kcal/mol	190 198@LB@ \| \|@LB@5'-AAU...UUAAG AACAU...AUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -7.63285 kcal/mol@LB@Unfolding Energy - mRNA 0.475666 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 191 -- 197@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
95	0.007016	0.2379	b0464	acrR	-8.52	0.043413	219 -- 228	37 -- 46	transcriptional repressor	_____________218________229\n_____________\|__________\|\n5'-AAG...CCAAA__________AAGAA...CGC-3'\n______________CAAGAAGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	222 -- 228	37 -- 43	-15.2794 kcal/mol	1.54243 kcal/mol	5.21654 kcal/mol	218 229@LB@ \| \|@LB@5'-AAG...CCAAA AAGAA...CGC-3'@LB@ CAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -15.2794 kcal/mol@LB@Unfolding Energy - mRNA 1.54243 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 37 -- 43@LB@
4	1.769e-05	0.01424	b2105	rcnR	-7.88	0.065143	12 -- 26	36 -- 49	transcriptional repressor of rcnA	_____________11______________27\n_____________\|_______________\|\n5'-UGA...GCACC________U______GGGGA...ACG-3'\n______________AAGUAAGA_GGCGCU\n______________\|\|\|:\|\|\|\|_:\|\|:\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	13 -- 19	42 -- 48	-15.6635 kcal/mol	1.75127 kcal/mol	6.03645 kcal/mol	11 27@LB@ \| \|@LB@5'-UGA...GCACC U GGGGA...ACG-3'@LB@ AAGUAAGA GGCGCU@LB@ \|\|\|:\|\|\|\| :\|\|:\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -15.6635 kcal/mol@LB@Unfolding Energy - mRNA 1.75127 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 12 -- 26@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 42 -- 48@LB@
45	0.001912	0.1369	b0080	cra	-5.81	0.213706	183 -- 197	38 -- 52	transcriptional repressor-activator for carbon metabolism	_____________182_____________198\n_____________\|_______________\|\n5'-GGC...UACAU____C__________AUUGU...AAA-3'\n______________UUUA_GCAAGGGGCA\n______________:\|\|\|_\|\|\|\|\|::\|\|\|\n______________GAAU_CGUUCUUCGU\n3'-UUU...UGAAC____U__________GAAUU...CAA-5'\n_____________\|_______________\|\n_____________53______________37\n	191 -- 197	38 -- 44	-16.0644 kcal/mol	4.16124 kcal/mol	6.09169 kcal/mol	182 198@LB@ \| \|@LB@5'-GGC...UACAU C AUUGU...AAA-3'@LB@ UUUA GCAAGGGGCA@LB@ :\|\|\| \|\|\|\|\|::\|\|\|@LB@ GAAU CGUUCUUCGU@LB@3'-UUU...UGAAC U GAAUU...CAA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -5.81 kcal/mol@LB@Hybridization Energy -16.0644 kcal/mol@LB@Unfolding Energy - mRNA 4.16124 kcal/mol@LB@Unfolding Energy - sRNA 6.09169 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 38 -- 44@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@LB@
64	0.003339	0.1645	b3166	truB	-7.27	0.093914	187 -- 199	36 -- 48	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________186___________200\n_____________\|_____________\|\n5'-GGC...ACGAC_________G___AAUGA...AAC-3'\n______________AGCAAGGAG_ACU\n______________\|\|\|\|\|\|:\|\|_\|\|\|\n______________UCGUUCUUC_UGA\n3'-UUU...CGAAU_________G___AUUUU...CAA-5'\n_____________\|_____________\|\n_____________49____________35\n	189 -- 195	40 -- 46	-16.8762 kcal/mol	3.76451 kcal/mol	5.83861 kcal/mol	186 200@LB@ \| \|@LB@5'-GGC...ACGAC G AAUGA...AAC-3'@LB@ AGCAAGGAG ACU@LB@ \|\|\|\|\|\|:\|\| \|\|\|@LB@ UCGUUCUUC UGA@LB@3'-UUU...CGAAU G AUUUU...CAA-5'@LB@ \| \|@LB@ 49 35@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -16.8762 kcal/mol@LB@Unfolding Energy - mRNA 3.76451 kcal/mol@LB@Unfolding Energy - sRNA 5.83861 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 36 -- 48@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
10	0.0001005	0.03239	b1260	trpA	-10.26	0.013526	184 -- 203	5 -- 22	tryptophan synthase alpha subunit	_____________183__________________204\n_____________\|____________________\|\n5'-GCC...UGAAA____GAG_____________GAACG...CAU-3'\n______________GCAC___GGGAAAUCUGAUG\n______________:\|\|\|___:\|\|\|\|\|\|\|\|\|\|\|\|\n______________UGUG___UCCUUUAGACUAC\n3'-UUU...AGCAA____G_______________ACAA-5'\n_____________\|____________________\|\n_____________23___________________4\n	192 -- 198	10 -- 16	-23.1901 kcal/mol	5.35202 kcal/mol	7.57357 kcal/mol	183 204@LB@ \| \|@LB@5'-GCC...UGAAA GAG GAACG...CAU-3'@LB@ GCAC GGGAAAUCUGAUG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UGUG UCCUUUAGACUAC@LB@3'-UUU...AGCAA G ACAA-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -23.1901 kcal/mol@LB@Unfolding Energy - mRNA 5.35202 kcal/mol@LB@Unfolding Energy - sRNA 7.57357 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
75	0.004391	0.1886	b3708	tnaA	-6.02	0.191179	273 -- 300	28 -- 53	tryptophanase/L-cysteine desulfhydrase PLP-dependent	_____________272_________________________300\n_____________\|___________________________\|\n5'-ACC...CUCGC_____UC__G________A___UU____-3'\n______________GCUUA__GU_AAGAGGCA_UUA__AAAU\n______________\|\|\|\|\|__\|:_\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|\n______________CGAAU__CG_UUCUUCGU_AAU__UUUA\n3'-UUU...UUGAA_____U____________G___UU____AGCAA...CAA-5'\n_____________\|____________________________\|\n_____________54___________________________27\n	284 -- 290	38 -- 44	-17.9242 kcal/mol	5.66853 kcal/mol	6.23468 kcal/mol	272 300@LB@ \| \|@LB@5'-ACC...CUCGC UC G A UU -3'@LB@ GCUUA GU AAGAGGCA UUA AAAU@LB@ \|\|\|\|\| \|: \|\|\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ CGAAU CG UUCUUCGU AAU UUUA@LB@3'-UUU...UUGAA U G UU AGCAA...CAA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -17.9242 kcal/mol@LB@Unfolding Energy - mRNA 5.66853 kcal/mol@LB@Unfolding Energy - sRNA 6.23468 kcal/mol@LB@@LB@Position - mRNA 273 -- 300@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@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