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	Additional homologs
170	0.01004	0.2071	b3887	dtd	-7.24	0.420466	57 -- 66	52 -- 62	D-tyr-tRNA(Tyr) deacylase		_____________56__________67\n_____________\|___________\|\n5'-GGA...AUUUA___________GCGGU...UCG-3'\n______________UGG_UGUGCUG\n______________\|\|\|_\|\|:\|\|:\|\n______________ACC_ACGCGGC\n3'-UUU...UUAGA___G_______AUUUA...GUG-5'\n_____________\|___________\|\n_____________63__________51\n	60 -- 66	52 -- 58	-13.8062 kcal/mol	1.68508 kcal/mol	4.8804 kcal/mol	56 67@LB@ \| \|@LB@5'-GGA...AUUUA GCGGU...UCG-3'@LB@ UGG UGUGCUG@LB@ \|\|\| \|\|:\|\|:\|@LB@ ACC ACGCGGC@LB@3'-UUU...UUAGA G AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -7.24 kcal/mol@LB@Hybridization Energy -13.8062 kcal/mol@LB@Unfolding Energy - mRNA 1.68508 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 57 -- 66@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 52 -- 58@LB@
180	0.01069	0.2089	b4529	ydbJ	-7.20	0.426635	222 -- 243	41 -- 61	DUF333 family putative lipoprotein		_____________221____________________244\n_____________\|______________________\|\n5'-GCA...GGGUA__G_______C_UU________CGGCG...GUU-3'\n______________GG_UGUGCCG_U__AUUGUUGU\n______________\|\|_\|\|:\|\|\|\|_\|__\|\|\|:\|\|:\|\n______________CC_ACGCGGC_A__UAAUAAUA\n3'-UUU...UAGAA__G_________UU________CUACU...GUG-5'\n_____________\|______________________\|\n_____________62_____________________40\n	225 -- 231	52 -- 58	-21.8046 kcal/mol	7.13894 kcal/mol	7.46625 kcal/mol	221 244@LB@ \| \|@LB@5'-GCA...GGGUA G C UU CGGCG...GUU-3'@LB@ GG UGUGCCG U AUUGUUGU@LB@ \|\| \|\|:\|\|\|\| \| \|\|\|:\|\|:\|@LB@ CC ACGCGGC A UAAUAAUA@LB@3'-UUU...UAGAA G UU CUACU...GUG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -21.8046 kcal/mol@LB@Unfolding Energy - mRNA 7.13894 kcal/mol@LB@Unfolding Energy - sRNA 7.46625 kcal/mol@LB@@LB@Position - mRNA 222 -- 243@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 52 -- 58@LB@
161	0.009429	0.2062	b1372	stfR	-7.17	0.431291	283 -- 297	69 -- 83	Rac prophage; putative tail fiber protein	b1547	_____________282_____________298\n_____________\|_______________\|\n5'-CAC...AAAAC__AA________C__UGG-3'\n______________GU__CAGCACCA_GG\n______________\|:__\|\|:\|\|\|\|\|_\|\|\n______________CG__GUUGUGGU_CC\n3'-UUU...UAUGA__CG________C__UUUAG...GUG-5'\n_____________\|_______________\|\n_____________84______________68\n	288 -- 294	72 -- 78	-17.3245 kcal/mol	2.81769 kcal/mol	7.33837 kcal/mol	282 298@LB@ \| \|@LB@5'-CAC...AAAAC AA C UGG-3'@LB@ GU CAGCACCA GG@LB@ \|: \|\|:\|\|\|\|\| \|\|@LB@ CG GUUGUGGU CC@LB@3'-UUU...UAUGA CG C UUUAG...GUG-5'@LB@ \| \|@LB@ 84 68@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -17.3245 kcal/mol@LB@Unfolding Energy - mRNA 2.81769 kcal/mol@LB@Unfolding Energy - sRNA 7.33837 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 69 -- 83@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 72 -- 78@LB@
70	0.003478	0.1727	b1919	dcyD	-7.16	0.432573	249 -- 279	53 -- 83	D-cysteine desulfhydrase PLP-dependent		_____________248_______________________________280\n_____________\|_________________________________\|\n5'-CUG...UCGGC____________CUC___U________C_____UUUCU...GGG-3'\n______________GCGCCAACGCCG___GAA_AUCU__GC_GCGCU\n______________\|\|\|\|\|\|\|\|:\|\|:___\|\|\|_\|\|\|\|__\|\|_\|\|\|\|:\n______________CGCGGUUGUGGU___CUU_UAGA__CG_CGCGG\n3'-UUU...UAUGA____________CC_________AC__A_____CAUUU...GUG-5'\n_____________\|_________________________________\|\n_____________84________________________________52\n	252 -- 258	74 -- 80	-36.5845 kcal/mol	12.956 kcal/mol	16.4685 kcal/mol	248 280@LB@ \| \|@LB@5'-CUG...UCGGC CUC U C UUUCU...GGG-3'@LB@ GCGCCAACGCCG GAA AUCU GC GCGCU@LB@ \|\|\|\|\|\|\|\|:\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|:@LB@ CGCGGUUGUGGU CUU UAGA CG CGCGG@LB@3'-UUU...UAUGA CC AC A CAUUU...GUG-5'@LB@ \| \|@LB@ 84 52@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -36.5845 kcal/mol@LB@Unfolding Energy - mRNA 12.956 kcal/mol@LB@Unfolding Energy - sRNA 16.4685 kcal/mol@LB@@LB@Position - mRNA 249 -- 279@LB@Position - sRNA 53 -- 83@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 74 -- 80@LB@
152	0.009044	0.2059	b1448	mnaT	-7.00	0.457084	229 -- 266	50 -- 86	methionine N-acyltransferase; L-amino acid N-acyltransferase		_____________228____________________________________267\n_____________\|______________________________________\|\n5'-CGC...AGCCG_________C_____C________AUAACCA_______UUGUA...CGG-3'\n______________ACUGUGCUG_CAUUG_GGAAAUUU_______CGCCGUG\n______________\|\|\|\|:\|\|::_\|\|:::_\|\|\|\|\|\|:\|_______\|\|\|\|\|\|:\n______________UGACGCGGU_GUGGU_CCUUUAGA_______GCGGCAU\n3'-UUU...GCUUA_________U_____C________ACCGAC________UUAAU...GUG-5'\n_____________\|______________________________________\|\n_____________87_____________________________________49\n	260 -- 266	50 -- 56	-33.8437 kcal/mol	9.99136 kcal/mol	16.8518 kcal/mol	228 267@LB@ \| \|@LB@5'-CGC...AGCCG C C AUAACCA UUGUA...CGG-3'@LB@ ACUGUGCUG CAUUG GGAAAUUU CGCCGUG@LB@ \|\|\|\|:\|\|:: \|\|::: \|\|\|\|\|\|:\| \|\|\|\|\|\|:@LB@ UGACGCGGU GUGGU CCUUUAGA GCGGCAU@LB@3'-UUU...GCUUA U C ACCGAC UUAAU...GUG-5'@LB@ \| \|@LB@ 87 49@LB@@LB@@LB@Energy -7.00 kcal/mol@LB@Hybridization Energy -33.8437 kcal/mol@LB@Unfolding Energy - mRNA 9.99136 kcal/mol@LB@Unfolding Energy - sRNA 16.8518 kcal/mol@LB@@LB@Position - mRNA 229 -- 266@LB@Position - sRNA 50 -- 86@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 50 -- 56@LB@
132	0.007501	0.1993	b1947	fliO	-6.89	0.474041	212 -- 250	53 -- 93	flagellar biosynthesis protein		_____________211_____________________________________________251\n_____________\|_______________________________________________\|\n5'-AUG...AACCA______________AAUCUUCC_______UU________________ACUGC...UCG-3'\n______________CGC___UACUGUGC________GCGCCGG_____UCU__GCUGCGCC\n______________\|\|\|___\|\|\|\|\|:\|\|________:\|:\|\|:\|_____\|\|\|__\|\|\|\|\|\|\|\|\n______________GCG___AUGACGCG________UGUGGUC_____AGA__CGACGCGG\n3'-UUU...CCCAC___CUU________GU_____________CCUUU___AC________CAUUU...GUG-5'\n_____________\|_______________________________________________\|\n_____________94______________________________________________52\n	244 -- 250	53 -- 59	-40.0502 kcal/mol	16.0889 kcal/mol	17.0683 kcal/mol	211 251@LB@ \| \|@LB@5'-AUG...AACCA AAUCUUCC UU ACUGC...UCG-3'@LB@ CGC UACUGUGC GCGCCGG UCU GCUGCGCC@LB@ \|\|\| \|\|\|\|\|:\|\| :\|:\|\|:\| \|\|\| \|\|\|\|\|\|\|\|@LB@ GCG AUGACGCG UGUGGUC AGA CGACGCGG@LB@3'-UUU...CCCAC CUU GU CCUUU AC CAUUU...GUG-5'@LB@ \| \|@LB@ 94 52@LB@@LB@@LB@Energy -6.89 kcal/mol@LB@Hybridization Energy -40.0502 kcal/mol@LB@Unfolding Energy - mRNA 16.0889 kcal/mol@LB@Unfolding Energy - sRNA 17.0683 kcal/mol@LB@@LB@Position - mRNA 212 -- 250@LB@Position - sRNA 53 -- 93@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 53 -- 59@LB@
61	0.003042	0.1727	b0104	guaC	-6.79	0.490983	117 -- 124	52 -- 59	GMP reductase		_____________116______125\n_____________\|________\|\n5'-AUG...CAGUC________CAUUG...GUC-3'\n______________UUGCGCCG\n______________:\|\|\|\|\|\|\|\n______________GACGCGGC\n3'-UUU...GAACC________AUUUA...GUG-5'\n_____________\|________\|\n_____________60_______51\n	118 -- 124	52 -- 58	-14.4979 kcal/mol	2.89251 kcal/mol	4.81798 kcal/mol	116 125@LB@ \| \|@LB@5'-AUG...CAGUC CAUUG...GUC-3'@LB@ UUGCGCCG@LB@ :\|\|\|\|\|\|\|@LB@ GACGCGGC@LB@3'-UUU...GAACC AUUUA...GUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -14.4979 kcal/mol@LB@Unfolding Energy - mRNA 2.89251 kcal/mol@LB@Unfolding Energy - sRNA 4.81798 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 52 -- 58@LB@
76	0.003978	0.182	b0336	codB	-6.71	0.504284	39 -- 48	1 -- 11	cytosine transporter		_____________38__________49\n_____________\|___________\|\n5'-CCA...UCUUA___________CCACU...UUU-3'\n______________UCAGGCC_UAC\n______________\|\|\|\|\|\|\|_:\|\|\n______________AGUCCGG_GUG\n3'-UUU...CAAAA_______C___-5'\n_____________\|__________\|\n_____________12_________1\n	39 -- 45	5 -- 11	-14.8291 kcal/mol	2.46298 kcal/mol	5.60325 kcal/mol	38 49@LB@ \| \|@LB@5'-CCA...UCUUA CCACU...UUU-3'@LB@ UCAGGCC UAC@LB@ \|\|\|\|\|\|\| :\|\|@LB@ AGUCCGG GUG@LB@3'-UUU...CAAAA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -6.71 kcal/mol@LB@Hybridization Energy -14.8291 kcal/mol@LB@Unfolding Energy - mRNA 2.46298 kcal/mol@LB@Unfolding Energy - sRNA 5.60325 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 5 -- 11@LB@
167	0.009922	0.2071	b0367	tauC	-5.98	0.628340	152 -- 162	85 -- 95	taurine ABC transporter permease		_____________151_________163\n_____________\|___________\|\n5'-AUA...CGCCA___________GUUUU...UUU-3'\n______________UGCGCGAAUAU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________ACGCGCUUAUG\n3'-UUU...GCCCC___________ACGCG...GUG-5'\n_____________\|___________\|\n_____________96__________84\n	154 -- 160	87 -- 93	-16.0697 kcal/mol	4.17782 kcal/mol	5.90856 kcal/mol	151 163@LB@ \| \|@LB@5'-AUA...CGCCA GUUUU...UUU-3'@LB@ UGCGCGAAUAU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ ACGCGCUUAUG@LB@3'-UUU...GCCCC ACGCG...GUG-5'@LB@ \| \|@LB@ 96 84@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -16.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.17782 kcal/mol@LB@Unfolding Energy - sRNA 5.90856 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 85 -- 95@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 87 -- 93@LB@
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase		_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@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)

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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

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