Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
39	0.0004396	0.03766	b3669	uhpA	-8.50	0.116685	77 -- 96	47 -- 66	response regulator in two-component regulatory system wtih UhpB		_____________76___________________97\n_____________\|____________________\|\n5'-UCA...CGUAA______C_______CG____UUAAC...UUG-3'\n______________UCAGUC_GAUCCGA__AUGU\n______________\|\|\|\|:\|_:\|\|\|\|\|\|__\|:\|\|\n______________AGUCGG_UUAGGCU__UGCA\n3'-AUU...UUAUA______U_______AA____CUUCA...AUG-5'\n_____________\|____________________\|\n_____________67___________________46\n	84 -- 90	53 -- 59	-21.6061 kcal/mol	5.63687 kcal/mol	7.4916 kcal/mol	76 97@LB@ \| \|@LB@5'-UCA...CGUAA C CG UUAAC...UUG-3'@LB@ UCAGUC GAUCCGA AUGU@LB@ \|\|\|\|:\| :\|\|\|\|\|\| \|:\|\|@LB@ AGUCGG UUAGGCU UGCA@LB@3'-AUU...UUAUA U AA CUUCA...AUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -21.6061 kcal/mol@LB@Unfolding Energy - mRNA 5.63687 kcal/mol@LB@Unfolding Energy - sRNA 7.4916 kcal/mol@LB@@LB@Position - mRNA 77 -- 96@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 53 -- 59@LB@
37	0.0003769	0.03584	b1212	prmC	-14.52	0.001141	215 -- 228	43 -- 56	RF-1 and RF-2 N5-glutamine methyltransferase		_____________214____________229\n_____________\|______________\|\n5'-CGU...CAACA______________CAAUA...GCA-3'\n______________CUGGUUACGUGAAG\n______________\|:\|:\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACUUC\n3'-AUU...GUUUA______________AUUUU...AUG-5'\n_____________\|______________\|\n_____________57_____________42\n	222 -- 228	43 -- 49	-20.863 kcal/mol	3.08488 kcal/mol	3.27327 kcal/mol	214 229@LB@ \| \|@LB@5'-CGU...CAACA CAAUA...GCA-3'@LB@ CUGGUUACGUGAAG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACUUC@LB@3'-AUU...GUUUA AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -14.52 kcal/mol@LB@Hybridization Energy -20.863 kcal/mol@LB@Unfolding Energy - mRNA 3.08488 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 43 -- 49@LB@
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate		_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein		_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
143	0.005218	0.1284	b1922	fliA	-8.86	0.094137	133 -- 141	50 -- 58	RNA polymerase sigma 28 (sigma F) factor		_____________132_______142\n_____________\|_________\|\n5'-AGG...UAAUC_________AAAAC...UUC-3'\n______________GUCCGAUUA\n______________:\|\|\|\|\|\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	135 -- 141	50 -- 56	-11.3914 kcal/mol	2.23267 kcal/mol	0.317553 kcal/mol	132 142@LB@ \| \|@LB@5'-AGG...UAAUC AAAAC...UUC-3'@LB@ GUCCGAUUA@LB@ :\|\|\|\|\|\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -11.3914 kcal/mol@LB@Unfolding Energy - mRNA 2.23267 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 133 -- 141@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 50 -- 56@LB@
144	0.005273	0.1288	b1652	rnt	-8.26	0.134019	203 -- 213	48 -- 58	RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair		_____________202_________214\n_____________\|___________\|\n5'-AAG...CAGAU_______A___CUCAA...CCG-3'\n______________GUCCGAU_ACG\n______________:\|\|\|\|\|\|_\|\|\|\n______________UAGGCUA_UGC\n3'-AUU...CGGUU_______A___ACUUC...AUG-5'\n_____________\|___________\|\n_____________59__________47\n	203 -- 209	52 -- 58	-12.2442 kcal/mol	2.4043 kcal/mol	1.55987 kcal/mol	202 214@LB@ \| \|@LB@5'-AAG...CAGAU A CUCAA...CCG-3'@LB@ GUCCGAU ACG@LB@ :\|\|\|\|\|\| \|\|\|@LB@ UAGGCUA UGC@LB@3'-AUU...CGGUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 59 47@LB@@LB@@LB@Energy -8.26 kcal/mol@LB@Hybridization Energy -12.2442 kcal/mol@LB@Unfolding Energy - mRNA 2.4043 kcal/mol@LB@Unfolding Energy - sRNA 1.55987 kcal/mol@LB@@LB@Position - mRNA 203 -- 213@LB@Position - sRNA 48 -- 58@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 52 -- 58@LB@
71	0.001214	0.05856	b1921	fliZ	-11.32	0.017729	260 -- 276	48 -- 65	RpoS antagonist; putative regulator of FliA activity		_____________259________________277\n_____________\|__________________\|\n5'-UGC...AAACA___________C______CGCAU...AUC-3'\n______________CAGCCAGA_CC_AUUGCG\n______________\|\|\|\|\|\|:\|_\|\|_\|\|\|:\|\|\n______________GUCGGUUU_GG_UAAUGC\n3'-AUU...UAUAA________A__C______ACUUC...AUG-5'\n_____________\|__________________\|\n_____________66_________________47\n	261 -- 267	58 -- 64	-20.8295 kcal/mol	2.05358 kcal/mol	7.47467 kcal/mol	259 277@LB@ \| \|@LB@5'-UGC...AAACA C CGCAU...AUC-3'@LB@ CAGCCAGA CC AUUGCG@LB@ \|\|\|\|\|\|:\| \|\| \|\|\|:\|\|@LB@ GUCGGUUU GG UAAUGC@LB@3'-AUU...UAUAA A C ACUUC...AUG-5'@LB@ \| \|@LB@ 66 47@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -20.8295 kcal/mol@LB@Unfolding Energy - mRNA 2.05358 kcal/mol@LB@Unfolding Energy - sRNA 7.47467 kcal/mol@LB@@LB@Position - mRNA 260 -- 276@LB@Position - sRNA 48 -- 65@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 58 -- 64@LB@
51	0.0006491	0.04477	b3224	nanT	-16.25	0.000177	140 -- 151	1 -- 12	sialic acid transporter	b4279	_____________139__________152\n_____________\|____________\|\n5'-CGC...ACGCA____________AAUUU...GUU-3'\n______________UCUGUACCCUAC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACAUGGGAUG\n3'-AUU...AAUGG____________-5'\n_____________\|___________\|\n_____________13__________1\n	145 -- 151	1 -- 7	-21.6524 kcal/mol	1.93745 kcal/mol	3.49051 kcal/mol	139 152@LB@ \| \|@LB@5'-CGC...ACGCA AAUUU...GUU-3'@LB@ UCUGUACCCUAC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACAUGGGAUG@LB@3'-AUU...AAUGG -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -16.25 kcal/mol@LB@Hybridization Energy -21.6524 kcal/mol@LB@Unfolding Energy - mRNA 1.93745 kcal/mol@LB@Unfolding Energy - sRNA 3.49051 kcal/mol@LB@@LB@Position - mRNA 140 -- 151@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding		_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
103	0.003241	0.1101	b0837	yliI	-8.40	0.123505	223 -- 230	4 -- 11	soluble aldose sugar dehydrogenase		_____________222______231\n_____________\|________\|\n5'-GUC...UUUCC________CUUAU...AAC-3'\n______________UUGUGCCC\n______________:\|\|\|:\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	224 -- 230	4 -- 10	-12.324 kcal/mol	0.491988 kcal/mol	3.45361 kcal/mol	222 231@LB@ \| \|@LB@5'-GUC...UUUCC CUUAU...AAC-3'@LB@ UUGUGCCC@LB@ :\|\|\|:\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.324 kcal/mol@LB@Unfolding Energy - mRNA 0.491988 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 223 -- 230@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 4 -- 10@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