Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
97	0.01643	0.5385	b2704	srlB	-9.20	0.144516	91 -- 103	75 -- 87	glucitol/sorbitol-specific enzyme IIA component of PTS	_____________90____________104\n_____________\|_____________\|\n5'-GGC...GACAC_________C___GUCCC...CUG-3'\n______________GGUUCGCGU_GGU\n______________:\|\|\|\|:\|\|\|_\|\|:\n______________UCAAGUGCA_CCG\n3'-CGC...CGUUU_________A___AAAUC...AAG-5'\n_____________\|_____________\|\n_____________88____________74\n	93 -- 99	79 -- 85	-16.5171 kcal/mol	6.8003 kcal/mol	0.512669 kcal/mol	90 104@LB@ \| \|@LB@5'-GGC...GACAC C GUCCC...CUG-3'@LB@ GGUUCGCGU GGU@LB@ :\|\|\|\|:\|\|\| \|\|:@LB@ UCAAGUGCA CCG@LB@3'-CGC...CGUUU A AAAUC...AAG-5'@LB@ \| \|@LB@ 88 74@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -16.5171 kcal/mol@LB@Unfolding Energy - mRNA 6.8003 kcal/mol@LB@Unfolding Energy - sRNA 0.512669 kcal/mol@LB@@LB@Position - mRNA 91 -- 103@LB@Position - sRNA 75 -- 87@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 79 -- 85@LB@
102	0.01732	0.5385	b3442	yhhZ	-11.63	0.054951	288 -- 294	75 -- 81	putative Hcp1 family polymorphic toxin protein; putative colicin-like DNase/tRNase activity	_____________287_____295\n_____________\|_______\|\n5'-AUU...GUAAU_______AGAGCG-3'\n______________CGUUGGC\n______________\|\|\|\|\|\|\|\n______________GCAACCG\n3'-CGC...CAAGU_______AAAUC...AAG-5'\n_____________\|_______\|\n_____________82______74\n	288 -- 294	75 -- 81	-12.2648 kcal/mol	0.311297 kcal/mol	0.324493 kcal/mol	287 295@LB@ \| \|@LB@5'-AUU...GUAAU AGAGCG-3'@LB@ CGUUGGC@LB@ \|\|\|\|\|\|\|@LB@ GCAACCG@LB@3'-CGC...CAAGU AAAUC...AAG-5'@LB@ \| \|@LB@ 82 74@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -12.2648 kcal/mol@LB@Unfolding Energy - mRNA 0.311297 kcal/mol@LB@Unfolding Energy - sRNA 0.324493 kcal/mol@LB@@LB@Position - mRNA 288 -- 294@LB@Position - sRNA 75 -- 81@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 75 -- 81@LB@
108	0.0187	0.5385	b1210	hemA	-9.14	0.148366	174 -- 184	75 -- 84	glutamyl tRNA reductase	_____________173_________185\n_____________\|___________\|\n5'-CCU...CCCUA__A________AUUAU...ACA-3'\n______________UC_ACGUUGGU\n______________\|\|_\|\|\|\|\|\|\|:\n______________AG_UGCAACCG\n3'-CGC...UUUCA___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________85__________74\n	178 -- 184	75 -- 81	-12.935 kcal/mol	3.29275 kcal/mol	0.505918 kcal/mol	173 185@LB@ \| \|@LB@5'-CCU...CCCUA A AUUAU...ACA-3'@LB@ UC ACGUUGGU@LB@ \|\| \|\|\|\|\|\|\|:@LB@ AG UGCAACCG@LB@3'-CGC...UUUCA AAAUC...AAG-5'@LB@ \| \|@LB@ 85 74@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.935 kcal/mol@LB@Unfolding Energy - mRNA 3.29275 kcal/mol@LB@Unfolding Energy - sRNA 0.505918 kcal/mol@LB@@LB@Position - mRNA 174 -- 184@LB@Position - sRNA 75 -- 84@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 75 -- 81@LB@
109	0.0187	0.5385	b2616	recN	-10.46	0.088138	200 -- 208	75 -- 83	recombination and repair protein	_____________199_______209\n_____________\|_________\|\n5'-UGA...ACGAC_________ACAAC...CGG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	202 -- 208	75 -- 81	-13.4657 kcal/mol	2.51607 kcal/mol	0.492259 kcal/mol	199 209@LB@ \| \|@LB@5'-UGA...ACGAC ACAAC...CGG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -13.4657 kcal/mol@LB@Unfolding Energy - mRNA 2.51607 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 200 -- 208@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 75 -- 81@LB@
115	0.01932	0.5385	b3475	acpT	-9.48	0.130030	187 -- 194	75 -- 82	4'-phosphopantetheinyl transferase	_____________186______195\n_____________\|________\|\n5'-GGG...AUUAA________CCUGA...GCU-3'\n______________ACGUUGGC\n______________\|\|\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	188 -- 194	75 -- 81	-13.2305 kcal/mol	3.41608 kcal/mol	0.339284 kcal/mol	186 195@LB@ \| \|@LB@5'-GGG...AUUAA CCUGA...GCU-3'@LB@ ACGUUGGC@LB@ \|\|\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2305 kcal/mol@LB@Unfolding Energy - mRNA 3.41608 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 75 -- 81@LB@
127	0.02181	0.5385	b3057	bacA	-7.57	0.267037	62 -- 69	75 -- 82	undecaprenyl pyrophosphate phosphatase	_____________61_______70\n_____________\|________\|\n5'-UUC...GGCGA________GUAAU...UUG-3'\n______________AUGUUGGC\n______________\|:\|\|\|\|\|\|\n______________UGCAACCG\n3'-CGC...UCAAG________AAAUC...AAG-5'\n_____________\|________\|\n_____________83_______74\n	63 -- 69	75 -- 81	-12.0605 kcal/mol	4.15225 kcal/mol	0.339284 kcal/mol	61 70@LB@ \| \|@LB@5'-UUC...GGCGA GUAAU...UUG-3'@LB@ AUGUUGGC@LB@ \|:\|\|\|\|\|\|@LB@ UGCAACCG@LB@3'-CGC...UCAAG AAAUC...AAG-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -12.0605 kcal/mol@LB@Unfolding Energy - mRNA 4.15225 kcal/mol@LB@Unfolding Energy - sRNA 0.339284 kcal/mol@LB@@LB@Position - mRNA 62 -- 69@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 63 -- 69@LB@Position Seed - sRNA 75 -- 81@LB@
139	0.02326	0.5385	b1651	gloA	-10.25	0.095619	225 -- 233	75 -- 83	glyoxalase I Ni-dependent	_____________224_______234\n_____________\|_________\|\n5'-UGG...UGCUG_________GAUUU...AAA-3'\n______________CGCGUUGGC\n______________\|:\|\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	227 -- 233	75 -- 81	-16.4206 kcal/mol	5.67498 kcal/mol	0.492259 kcal/mol	224 234@LB@ \| \|@LB@5'-UGG...UGCUG GAUUU...AAA-3'@LB@ CGCGUUGGC@LB@ \|:\|\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -16.4206 kcal/mol@LB@Unfolding Energy - mRNA 5.67498 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 75 -- 81@LB@
143	0.02402	0.5467	b4029	yjbH	-10.20	0.097639	107 -- 117	75 -- 85	DUF940 family extracellular polysaccharide protein	_____________106_________118\n_____________\|___________\|\n5'-GCG...CAUUA___________CUCGC...AUU-3'\n______________UUUAUGUUGGC\n______________\|\|:\|:\|\|\|\|\|\|\n______________AAGUGCAACCG\n3'-CGC...UUUUC___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________86__________74\n	111 -- 117	75 -- 81	-14.6823 kcal/mol	3.97178 kcal/mol	0.509769 kcal/mol	106 118@LB@ \| \|@LB@5'-GCG...CAUUA CUCGC...AUU-3'@LB@ UUUAUGUUGGC@LB@ \|\|:\|:\|\|\|\|\|\|@LB@ AAGUGCAACCG@LB@3'-CGC...UUUUC AAAUC...AAG-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6823 kcal/mol@LB@Unfolding Energy - mRNA 3.97178 kcal/mol@LB@Unfolding Energy - sRNA 0.509769 kcal/mol@LB@@LB@Position - mRNA 107 -- 117@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 75 -- 81@LB@
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
167	0.02971	0.5559	b3062	ttdB	-9.65	0.121251	224 -- 260	75 -- 106	L-tartrate dehydratase beta subunit	_____________223___________________________________261\n_____________\|_____________________________________\|\n5'-GGA...ACCCC____AAAG___A____________UA_______C___GAUGU...GCG-3'\n______________GAUC____CUG_AGAUCUGCAAGA__UUCGCGU_GGC\n______________\|\|\|\|____\|\|\|_\|\|\|\|\|:\|\|\|\|:\|__\|\|\|:\|\|\|_\|\|\|\n______________CUAG____GAC_UCUAGGCGUUUU__AAGUGCA_CCG\n________3'-CGC___________C____________C________A___AAAUC...AAG-5'\n_____________\|_____________________________________\|\n_____________107___________________________________74\n	250 -- 256	79 -- 85	-36.8095 kcal/mol	15.2774 kcal/mol	11.8787 kcal/mol	223 261@LB@ \| \|@LB@5'-GGA...ACCCC AAAG A UA C GAUGU...GCG-3'@LB@ GAUC CUG AGAUCUGCAAGA UUCGCGU GGC@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\|\|\|\|:\| \|\|\|:\|\|\| \|\|\|@LB@ CUAG GAC UCUAGGCGUUUU AAGUGCA CCG@LB@ 3'-CGC C C A AAAUC...AAG-5'@LB@ \| \|@LB@ 107 74@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -36.8095 kcal/mol@LB@Unfolding Energy - mRNA 15.2774 kcal/mol@LB@Unfolding Energy - sRNA 11.8787 kcal/mol@LB@@LB@Position - mRNA 224 -- 260@LB@Position - sRNA 75 -- 106@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 79 -- 85@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