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
60	0.003031	0.1727	b3432	glgB	-10.57	0.108575	114 -- 123	51 -- 60	1 4-alpha-glucan branching enzyme	_____________113________124\n_____________\|__________\|\n5'-CAU...AGAGU__________UCAGG...GAC-3'\n______________GCUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGACGCGGCA\n3'-UUU...AGAAC__________UUUAA...GUG-5'\n_____________\|__________\|\n_____________61_________50\n	117 -- 123	51 -- 57	-20.705 kcal/mol	5.26394 kcal/mol	4.87294 kcal/mol	113 124@LB@ \| \|@LB@5'-CAU...AGAGU UCAGG...GAC-3'@LB@ GCUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGACGCGGCA@LB@3'-UUU...AGAAC UUUAA...GUG-5'@LB@ \| \|@LB@ 61 50@LB@@LB@@LB@Energy -10.57 kcal/mol@LB@Hybridization Energy -20.705 kcal/mol@LB@Unfolding Energy - mRNA 5.26394 kcal/mol@LB@Unfolding Energy - sRNA 4.87294 kcal/mol@LB@@LB@Position - mRNA 114 -- 123@LB@Position - sRNA 51 -- 60@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 51 -- 57@LB@
106	0.005731	0.1855	b0867	amiD	-15.82	0.010089	39 -- 60	64 -- 86	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________38_______________________61\n_____________\|________________________\|\n5'-GAU...AAAGA_______AA_______________GCCUU...CCC-3'\n______________ACUGCGU__AGCAC__GGGAGAUC\n______________\|\|\|\|\|\|:__\|:\|\|\|__\|\|\|\|:\|\|\|\n______________UGACGCG__UUGUG__CCCUUUAG\n3'-UUU...GCUUA_______G______GU________AACCG...GUG-5'\n_____________\|________________________\|\n_____________87_______________________63\n	54 -- 60	64 -- 70	-27.7093 kcal/mol	4.50209 kcal/mol	7.38435 kcal/mol	38 61@LB@ \| \|@LB@5'-GAU...AAAGA AA GCCUU...CCC-3'@LB@ ACUGCGU AGCAC GGGAGAUC@LB@ \|\|\|\|\|\|: \|:\|\|\| \|\|\|\|:\|\|\|@LB@ UGACGCG UUGUG CCCUUUAG@LB@3'-UUU...GCUUA G GU AACCG...GUG-5'@LB@ \| \|@LB@ 87 63@LB@@LB@@LB@Energy -15.82 kcal/mol@LB@Hybridization Energy -27.7093 kcal/mol@LB@Unfolding Energy - mRNA 4.50209 kcal/mol@LB@Unfolding Energy - sRNA 7.38435 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 64 -- 86@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 64 -- 70@LB@
29	0.001588	0.1727	b4371	rsmC	-11.43	0.073969	145 -- 160	74 -- 89	16S rRNA m(2)G1207 methyltransferase SAM-dependent	_____________144______________161\n_____________\|________________\|\n5'-AUC...UCGUC_____C__________AUGGC...UGC-3'\n______________GAUAC_GCGCCAACAU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|:\n______________UUAUG_CGCGGUUGUG\n3'-UUU...CGCGC_____A__________GUCCC...GUG-5'\n_____________\|________________\|\n_____________90_______________73\n	154 -- 160	74 -- 80	-22.1753 kcal/mol	3.46317 kcal/mol	7.27848 kcal/mol	144 161@LB@ \| \|@LB@5'-AUC...UCGUC C AUGGC...UGC-3'@LB@ GAUAC GCGCCAACAU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUAUG CGCGGUUGUG@LB@3'-UUU...CGCGC A GUCCC...GUG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -22.1753 kcal/mol@LB@Unfolding Energy - mRNA 3.46317 kcal/mol@LB@Unfolding Energy - sRNA 7.27848 kcal/mol@LB@@LB@Position - mRNA 145 -- 160@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 74 -- 80@LB@
42	0.002147	0.1727	b0082	rsmH	-13.18	0.033634	23 -- 49	70 -- 94	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________22__________________________50\n_____________\|___________________________\|\n5'-UGG...UAAUC____C_________G____AU______CUGAC...GUC-3'\n______________GCGC_AGUACUGCG_CAAC__GCCGGG\n______________\|\|\|\|_\|:\|\|\|\|\|\|\|_\|\|\|\|__:\|\|:\|\|\n______________CGCG_UUAUGACGC_GUUG__UGGUCC\n3'-UUU...CCCCA____C_________G____________CUUUA...GUG-5'\n_____________\|___________________________\|\n_____________95__________________________69\n	30 -- 36	81 -- 87	-36.7334 kcal/mol	10.4772 kcal/mol	13.036 kcal/mol	22 50@LB@ \| \|@LB@5'-UGG...UAAUC C G AU CUGAC...GUC-3'@LB@ GCGC AGUACUGCG CAAC GCCGGG@LB@ \|\|\|\| \|:\|\|\|\|\|\|\| \|\|\|\| :\|\|:\|\|@LB@ CGCG UUAUGACGC GUUG UGGUCC@LB@3'-UUU...CCCCA C G CUUUA...GUG-5'@LB@ \| \|@LB@ 95 69@LB@@LB@@LB@Energy -13.18 kcal/mol@LB@Hybridization Energy -36.7334 kcal/mol@LB@Unfolding Energy - mRNA 10.4772 kcal/mol@LB@Unfolding Energy - sRNA 13.036 kcal/mol@LB@@LB@Position - mRNA 23 -- 49@LB@Position - sRNA 70 -- 94@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 81 -- 87@LB@
80	0.004451	0.1855	b3578	yiaN	-12.19	0.052777	198 -- 212	52 -- 66	2 3-diketo-L-gulonate TRAP transporter large permease protein	_____________197_____________213\n_____________\|_______________\|\n5'-GGC...GCUUA___A___________AUUUU...UCU-3'\n______________AUC_UGGCUGUGCUG\n______________\|\|\|_\|\|\|\|\|\|:\|\|:\|\n______________UAG_ACCGACGCGGC\n3'-UUU...CCCUU___A___________AUUUA...GUG-5'\n_____________\|_______________\|\n_____________67______________51\n	206 -- 212	52 -- 58	-22.6247 kcal/mol	3.67694 kcal/mol	6.76246 kcal/mol	197 213@LB@ \| \|@LB@5'-GGC...GCUUA A AUUUU...UCU-3'@LB@ AUC UGGCUGUGCUG@LB@ \|\|\| \|\|\|\|\|\|:\|\|:\|@LB@ UAG ACCGACGCGGC@LB@3'-UUU...CCCUU A AUUUA...GUG-5'@LB@ \| \|@LB@ 67 51@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -22.6247 kcal/mol@LB@Unfolding Energy - mRNA 3.67694 kcal/mol@LB@Unfolding Energy - sRNA 6.76246 kcal/mol@LB@@LB@Position - mRNA 198 -- 212@LB@Position - sRNA 52 -- 66@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 52 -- 58@LB@
200	0.01246	0.2193	b0425	panE	-12.07	0.055655	285 -- 293	54 -- 62	2-dehydropantoate reductase NADPH-specific	_____________284_______294\n_____________\|_________\|\n5'-AUC...AGGGC_________GUACCGC-3'\n______________UGGCUGCGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACCGACGCG\n3'-UUU...UUAGA_________GCAUU...GUG-5'\n_____________\|_________\|\n_____________63________53\n	287 -- 293	54 -- 60	-19.0333 kcal/mol	2.09185 kcal/mol	4.8739 kcal/mol	284 294@LB@ \| \|@LB@5'-AUC...AGGGC GUACCGC-3'@LB@ UGGCUGCGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACCGACGCG@LB@3'-UUU...UUAGA GCAUU...GUG-5'@LB@ \| \|@LB@ 63 53@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -19.0333 kcal/mol@LB@Unfolding Energy - mRNA 2.09185 kcal/mol@LB@Unfolding Energy - sRNA 4.8739 kcal/mol@LB@@LB@Position - mRNA 285 -- 293@LB@Position - sRNA 54 -- 62@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 54 -- 60@LB@
185	0.01108	0.2089	b0662	ubiF	-8.33	0.279302	272 -- 292	6 -- 27	2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase	_____________271____________________293\n_____________\|______________________\|\n5'-AAU...GGGCU____________GA___GC___AACGGUGA-3'\n______________GGCACAGCAC_G__UUU__GGU\n______________\|\|\|\|\|\|\|\|\|\|_\|__\|\|\|__\|\|:\n______________CCGUGUCGUG_C__AAA__CCG\n3'-UUU...UGUUC__________A_AA___GU___GCGUG-5'\n_____________\|______________________\|\n_____________28_____________________5\n	275 -- 281	18 -- 24	-24.5826 kcal/mol	6.14687 kcal/mol	10.1088 kcal/mol	271 293@LB@ \| \|@LB@5'-AAU...GGGCU GA GC AACGGUGA-3'@LB@ GGCACAGCAC G UUU GGU@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\| \|\|:@LB@ CCGUGUCGUG C AAA CCG@LB@3'-UUU...UGUUC A AA GU GCGUG-5'@LB@ \| \|@LB@ 28 5@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -24.5826 kcal/mol@LB@Unfolding Energy - mRNA 6.14687 kcal/mol@LB@Unfolding Energy - sRNA 10.1088 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 6 -- 27@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 18 -- 24@LB@
147	0.008705	0.2059	b0071	leuD	-8.42	0.269085	76 -- 114	1 -- 54	3-isopropylmalate dehydratase small subunit	_____________75_____________________________________________________115\n_____________\|______________________________________________________\|\n5'-GCC...AGCAA______C_________A__CCGC_________________________G_____GCAUC...AAG-3'\n______________CCGUAA_UU____UGA_GG____CAGGGGCGCGGC___________GG_CGCAC\n______________\|\|\|\|\|\|_\|\|____\|\|\|_\|:____\|\|:\|\|\|\|:\|:\|\|___________\|\|_\|\|\|\|\|\n______________GGCAUU_AA____ACU_CU____GUUCCCGUGUCG___________CC_GCGUG\n3'-UUU...GACGC______U__UAAU___A__CAAU____________UGACAAAAAGU__G_____-5'\n_____________\|_____________________________________________________\|\n_____________55____________________________________________________1\n	98 -- 104	22 -- 28	-40.9174 kcal/mol	15.4198 kcal/mol	17.077 kcal/mol	75 115@LB@ \| \|@LB@5'-GCC...AGCAA C A CCGC G GCAUC...AAG-3'@LB@ CCGUAA UU UGA GG CAGGGGCGCGGC GG CGCAC@LB@ \|\|\|\|\|\| \|\| \|\|\| \|: \|\|:\|\|\|\|:\|:\|\| \|\| \|\|\|\|\|@LB@ GGCAUU AA ACU CU GUUCCCGUGUCG CC GCGUG@LB@3'-UUU...GACGC U UAAU A CAAU UGACAAAAAGU G -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -40.9174 kcal/mol@LB@Unfolding Energy - mRNA 15.4198 kcal/mol@LB@Unfolding Energy - sRNA 17.077 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 22 -- 28@LB@
173	0.01023	0.2071	b3297	rpsK	-11.54	0.070538	32 -- 43	48 -- 59	30S ribosomal subunit protein S11	_____________31___________44\n_____________\|____________\|\n5'-CGA...GUGAU____________AUCAG...CUA-3'\n______________CUGCGCCGUGAA\n______________\|\|\|\|\|\|\|\|\|:\|\|\n______________GACGCGGCAUUU\n3'-UUU...GAACC____________AAUAA...GUG-5'\n_____________\|____________\|\n_____________60___________47\n	37 -- 43	48 -- 54	-20.6796 kcal/mol	2.9935 kcal/mol	6.14631 kcal/mol	31 44@LB@ \| \|@LB@5'-CGA...GUGAU AUCAG...CUA-3'@LB@ CUGCGCCGUGAA@LB@ \|\|\|\|\|\|\|\|\|:\|\|@LB@ GACGCGGCAUUU@LB@3'-UUU...GAACC AAUAA...GUG-5'@LB@ \| \|@LB@ 60 47@LB@@LB@@LB@Energy -11.54 kcal/mol@LB@Hybridization Energy -20.6796 kcal/mol@LB@Unfolding Energy - mRNA 2.9935 kcal/mol@LB@Unfolding Energy - sRNA 6.14631 kcal/mol@LB@@LB@Position - mRNA 32 -- 43@LB@Position - sRNA 48 -- 59@LB@Position Seed - mRNA 37 -- 43@LB@Position Seed - sRNA 48 -- 54@LB@
33	0.001709	0.1727	b0023	rpsT	-12.95	0.037339	65 -- 78	72 -- 85	30S ribosomal subunit protein S20	_____________64_____________79\n_____________\|______________\|\n5'-UGA...GAAUC________U_____CGUAA...AGA-3'\n______________CUGCGCCA_CACUA\n______________\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________GACGCGGU_GUGGU\n3'-UUU...CUUAU________U_____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	66 -- 72	78 -- 84	-22.3173 kcal/mol	2.13275 kcal/mol	7.23443 kcal/mol	64 79@LB@ \| \|@LB@5'-UGA...GAAUC U CGUAA...AGA-3'@LB@ CUGCGCCA CACUA@LB@ \|\|\|\|\|\|\|\| \|\|\|:\|@LB@ GACGCGGU GUGGU@LB@3'-UUU...CUUAU U CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -22.3173 kcal/mol@LB@Unfolding Energy - mRNA 2.13275 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 65 -- 78@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 78 -- 84@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