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
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@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease	_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
28	0.001577	0.1727	b0598	cstA	-11.00	0.089647	31 -- 48	28 -- 45	carbon starvation protein involved in peptide utilization; APC peptide transporter family protein	_____________30__________________49\n_____________\|___________________\|\n5'-GUA...ACAGA___________A_______AAAAC...ACG-3'\n______________AUUA_GAUGAG_UUGCAGG\n______________\|\|\|\|_\|\|\|\|\|\|_\|\|:\|\|:\|\n______________UAAU_CUACUC_AAUGUUC\n3'-UUU...UUUAA____A______________CCGUG...GUG-5'\n_____________\|___________________\|\n_____________46__________________27\n	42 -- 48	28 -- 34	-16.2081 kcal/mol	3.25033 kcal/mol	1.95571 kcal/mol	30 49@LB@ \| \|@LB@5'-GUA...ACAGA A AAAAC...ACG-3'@LB@ AUUA GAUGAG UUGCAGG@LB@ \|\|\|\| \|\|\|\|\|\| \|\|:\|\|:\|@LB@ UAAU CUACUC AAUGUUC@LB@3'-UUU...UUUAA A CCGUG...GUG-5'@LB@ \| \|@LB@ 46 27@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -16.2081 kcal/mol@LB@Unfolding Energy - mRNA 3.25033 kcal/mol@LB@Unfolding Energy - sRNA 1.95571 kcal/mol@LB@@LB@Position - mRNA 31 -- 48@LB@Position - sRNA 28 -- 45@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 28 -- 34@LB@
38	0.002093	0.1727	b1174	minE	-11.55	0.070176	37 -- 55	69 -- 87	cell division topological specificity factor	_____________36___________________56\n_____________\|____________________\|\n5'-AAC...AGUAU_________UCUA_______UGAAC...AUG-3'\n______________UGC_GCGCC____ACCAGGG\n______________\|:\|_\|\|\|\|\|____\|\|\|\|\|\|\|\n______________AUG_CGCGG____UGGUCCC\n3'-UUU...CGCUU___A_____UUG________UUUAG...GUG-5'\n_____________\|____________________\|\n_____________88___________________68\n	49 -- 55	69 -- 75	-25.7186 kcal/mol	6.79304 kcal/mol	7.3743 kcal/mol	36 56@LB@ \| \|@LB@5'-AAC...AGUAU UCUA UGAAC...AUG-3'@LB@ UGC GCGCC ACCAGGG@LB@ \|:\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ AUG CGCGG UGGUCCC@LB@3'-UUU...CGCUU A UUG UUUAG...GUG-5'@LB@ \| \|@LB@ 88 68@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -25.7186 kcal/mol@LB@Unfolding Energy - mRNA 6.79304 kcal/mol@LB@Unfolding Energy - sRNA 7.3743 kcal/mol@LB@@LB@Position - mRNA 37 -- 55@LB@Position - sRNA 69 -- 87@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 69 -- 75@LB@
39	0.002105	0.1727	b3249	mreD	-13.67	0.026871	102 -- 115	74 -- 87	cell wall structural complex MreBCD transmembrane component MreD	_____________101____________116\n_____________\|______________\|\n5'-CCU...GCGCC______________AGCCU...UUU-3'\n______________UGCUGCGCCGACAC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\|\n______________AUGACGCGGUUGUG\n3'-UUU...CGCUU______________GUCCC...GUG-5'\n_____________\|______________\|\n_____________88_____________73\n	109 -- 115	74 -- 80	-25.8251 kcal/mol	5.39353 kcal/mol	6.75739 kcal/mol	101 116@LB@ \| \|@LB@5'-CCU...GCGCC AGCCU...UUU-3'@LB@ UGCUGCGCCGACAC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|\|@LB@ AUGACGCGGUUGUG@LB@3'-UUU...CGCUU GUCCC...GUG-5'@LB@ \| \|@LB@ 88 73@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -25.8251 kcal/mol@LB@Unfolding Energy - mRNA 5.39353 kcal/mol@LB@Unfolding Energy - sRNA 6.75739 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 74 -- 87@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 74 -- 80@LB@
139	0.008022	0.2031	b0311	betA	-9.91	0.144745	36 -- 54	64 -- 80	choline dehydrogenase a flavoprotein	_____________35__________________55\n_____________\|___________________\|\n5'-CGU...CUGGA________U____C_____CCCGG...AAG-3'\n______________UCAACACC_GGGG_GAAUC\n______________:\|\|\|\|\|\|\|_:\|\|\|_:\|\|\|\|\n______________GGUUGUGG_UCCC_UUUAG\n3'-UUU...GACGC___________________AACCG...GUG-5'\n_____________\|___________________\|\n_____________81__________________63\n	37 -- 43	73 -- 79	-20.9821 kcal/mol	4.03056 kcal/mol	7.04361 kcal/mol	35 55@LB@ \| \|@LB@5'-CGU...CUGGA U C CCCGG...AAG-3'@LB@ UCAACACC GGGG GAAUC@LB@ :\|\|\|\|\|\|\| :\|\|\| :\|\|\|\|@LB@ GGUUGUGG UCCC UUUAG@LB@3'-UUU...GACGC AACCG...GUG-5'@LB@ \| \|@LB@ 81 63@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -20.9821 kcal/mol@LB@Unfolding Energy - mRNA 4.03056 kcal/mol@LB@Unfolding Energy - sRNA 7.04361 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 64 -- 80@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 73 -- 79@LB@
182	0.01083	0.2089	b0314	betT	-9.44	0.176432	217 -- 228	66 -- 77	choline transporter of high affinity	_____________216__________229\n_____________\|____________\|\n5'-UUC...UUCAC___G________AGGAC...UCC-3'\n______________ACA_CAGGGAAA\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________UGU_GUCCCUUU\n3'-UUU...GCGGU___G________AGAAC...GUG-5'\n_____________\|____________\|\n_____________78___________65\n	222 -- 228	66 -- 72	-15.8835 kcal/mol	1.82432 kcal/mol	4.61119 kcal/mol	216 229@LB@ \| \|@LB@5'-UUC...UUCAC G AGGAC...UCC-3'@LB@ ACA CAGGGAAA@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ UGU GUCCCUUU@LB@3'-UUU...GCGGU G AGAAC...GUG-5'@LB@ \| \|@LB@ 78 65@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -15.8835 kcal/mol@LB@Unfolding Energy - mRNA 1.82432 kcal/mol@LB@Unfolding Energy - sRNA 4.61119 kcal/mol@LB@@LB@Position - mRNA 217 -- 228@LB@Position - sRNA 66 -- 77@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 66 -- 72@LB@
181	0.0108	0.2089	b1683	sufB	-11.33	0.077347	153 -- 175	52 -- 74	component of SufBCD Fe-S cluster assembly scaffold	_____________152_______________________176\n_____________\|_________________________\|\n5'-GUU...AAAGC____AAU___UG__________G__AAAGC...AGC-3'\n______________CCAG___GAA____UGGCUGUG_CG\n______________\|\|\|\|___\|\|\|____\|\|\|\|\|\|:\|_\|\|\n______________GGUC___CUU____ACCGACGC_GC\n3'-UUU...GUUGU____C_____UAGA________G__AUUUA...GUG-5'\n_____________\|_________________________\|\n_____________75________________________51\n	166 -- 172	55 -- 61	-23.8546 kcal/mol	3.76094 kcal/mol	8.7601 kcal/mol	152 176@LB@ \| \|@LB@5'-GUU...AAAGC AAU UG G AAAGC...AGC-3'@LB@ CCAG GAA UGGCUGUG CG@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:\| \|\|@LB@ GGUC CUU ACCGACGC GC@LB@3'-UUU...GUUGU C UAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -23.8546 kcal/mol@LB@Unfolding Energy - mRNA 3.76094 kcal/mol@LB@Unfolding Energy - sRNA 8.7601 kcal/mol@LB@@LB@Position - mRNA 153 -- 175@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 55 -- 61@LB@
153	0.009069	0.2059	b3529	yhjK	-8.15	0.299018	186 -- 212	47 -- 74	cyclic-di-GMP phosphodiesterase	_____________185__________________________213\n_____________\|____________________________\|\n5'-AGC...GAUUU_________GACAAU_____________CGCUC...AUC-3'\n______________CCGGGGGGA______UUGCG_CGUAAGU\n______________\|\|:\|\|\|::\|______:\|\|\|\|_\|\|\|\|\|:\|\n______________GGUCCCUUU______GACGC_GCAUUUA\n3'-UUU...GUUGU_________AGAACC_____G_______AUAAU...GUG-5'\n_____________\|____________________________\|\n_____________75___________________________46\n	187 -- 193	67 -- 73	-27.1977 kcal/mol	10.2409 kcal/mol	8.80319 kcal/mol	185 213@LB@ \| \|@LB@5'-AGC...GAUUU GACAAU CGCUC...AUC-3'@LB@ CCGGGGGGA UUGCG CGUAAGU@LB@ \|\|:\|\|\|::\| :\|\|\|\| \|\|\|\|\|:\|@LB@ GGUCCCUUU GACGC GCAUUUA@LB@3'-UUU...GUUGU AGAACC G AUAAU...GUG-5'@LB@ \| \|@LB@ 75 46@LB@@LB@@LB@Energy -8.15 kcal/mol@LB@Hybridization Energy -27.1977 kcal/mol@LB@Unfolding Energy - mRNA 10.2409 kcal/mol@LB@Unfolding Energy - sRNA 8.80319 kcal/mol@LB@@LB@Position - mRNA 186 -- 212@LB@Position - sRNA 47 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 67 -- 73@LB@
64	0.003238	0.1727	b2578	eamB	-8.70	0.240388	240 -- 262	70 -- 85	cysteine and O-acetylserine exporter	_____________239_____________________263\n_____________\|_______________________\|\n5'-GUC...ACACC___AUUAC____AU_________ACCGA...CGC-3'\n______________CUG_____CGCU__GACGCCAGG\n______________\|\|\|_____\|\|\|:__:\|\|:\|\|\|\|\|\n______________GAC_____GCGG__UUGUGGUCC\n3'-UUU...CUUAU_______________________CUUUA...GUG-5'\n_____________\|_______________________\|\n_____________86______________________69\n	256 -- 262	70 -- 76	-20.6717 kcal/mol	4.69447 kcal/mol	7.27689 kcal/mol	239 263@LB@ \| \|@LB@5'-GUC...ACACC AUUAC AU ACCGA...CGC-3'@LB@ CUG CGCU GACGCCAGG@LB@ \|\|\| \|\|\|: :\|\|:\|\|\|\|\|@LB@ GAC GCGG UUGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -20.6717 kcal/mol@LB@Unfolding Energy - mRNA 4.69447 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 70 -- 76@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