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
63	0.003148	0.1727	b0131	panD	-12.33	0.049519	276 -- 291	70 -- 84	aspartate 1-decarboxylase		_____________275______________292\n_____________\|________________\|\n5'-AUU...GUUCU_______UUG______AUUUU...UUG-3'\n______________UGCGCCA___ACCAGG\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________ACGCGGU___UGGUCC\n3'-UUU...UUAUG_______UG_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	276 -- 282	78 -- 84	-24.0598 kcal/mol	4.4848 kcal/mol	7.24859 kcal/mol	275 292@LB@ \| \|@LB@5'-AUU...GUUCU UUG AUUUU...UUG-3'@LB@ UGCGCCA ACCAGG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACGCGGU UGGUCC@LB@3'-UUU...UUAUG UG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -24.0598 kcal/mol@LB@Unfolding Energy - mRNA 4.4848 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 276 -- 291@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 78 -- 84@LB@
83	0.004611	0.1855	b1593	ynfK	-13.15	0.034145	276 -- 295	66 -- 83	putative dethiobiotin synthetase		_____________275__________________296\n_____________\|____________________\|\n5'-CAC...UACAA________CUC_________AACGG-3'\n______________GCGUUAGC___CCAGGGAAA\n______________\|\|\|::\|:\|___\|\|\|\|\|\|\|\|\|\n______________CGCGGUUG___GGUCCCUUU\n3'-UUU...UAUGA________U___________AGAAC...GUG-5'\n_____________\|____________________\|\n_____________84___________________65\n	289 -- 295	66 -- 72	-26.3491 kcal/mol	5.84339 kcal/mol	7.35847 kcal/mol	275 296@LB@ \| \|@LB@5'-CAC...UACAA CUC AACGG-3'@LB@ GCGUUAGC CCAGGGAAA@LB@ \|\|\|::\|:\| \|\|\|\|\|\|\|\|\|@LB@ CGCGGUUG GGUCCCUUU@LB@3'-UUU...UAUGA U AGAAC...GUG-5'@LB@ \| \|@LB@ 84 65@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -26.3491 kcal/mol@LB@Unfolding Energy - mRNA 5.84339 kcal/mol@LB@Unfolding Energy - sRNA 7.35847 kcal/mol@LB@@LB@Position - mRNA 276 -- 295@LB@Position - sRNA 66 -- 83@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 66 -- 72@LB@
86	0.004777	0.1855	b3157	yhbT	-11.83	0.061936	277 -- 294	70 -- 85	SCP-2 sterol transfer family protein		_____________276________________295\n_____________\|__________________\|\n5'-CUG...GCCAU________AA________UUCUUG-3'\n______________UUGCGCUA__ACGCCAGG\n______________:\|\|\|\|\|:\|__\|\|:\|\|\|\|\|\n______________GACGCGGU__UGUGGUCC\n3'-UUU...CUUAU__________________CUUUA...GUG-5'\n_____________\|__________________\|\n_____________86_________________69\n	288 -- 294	70 -- 76	-24.8001 kcal/mol	5.69349 kcal/mol	7.27689 kcal/mol	276 295@LB@ \| \|@LB@5'-CUG...GCCAU AA UUCUUG-3'@LB@ UUGCGCUA ACGCCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|\|@LB@ GACGCGGU UGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -24.8001 kcal/mol@LB@Unfolding Energy - mRNA 5.69349 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 277 -- 294@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 70 -- 76@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator		_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 25 -- 31@LB@
8	0.000265	0.1166	b1244	oppB	-12.83	0.039495	280 -- 295	70 -- 84	oligopeptide ABC transporter permease		_____________279______________296\n_____________\|________________\|\n5'-UCC...UAUGA______UC________AAGCC-3'\n______________UGCGCC__GCGCCGGG\n______________\|\|\|\|\|\|__:\|:\|\|:\|\|\n______________ACGCGG__UGUGGUCC\n3'-UUU...UUAUG______U_________CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	289 -- 295	70 -- 76	-25.4509 kcal/mol	5.37602 kcal/mol	7.24859 kcal/mol	279 296@LB@ \| \|@LB@5'-UCC...UAUGA UC AAGCC-3'@LB@ UGCGCC GCGCCGGG@LB@ \|\|\|\|\|\| :\|:\|\|:\|\|@LB@ ACGCGG UGUGGUCC@LB@3'-UUU...UUAUG U CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -25.4509 kcal/mol@LB@Unfolding Energy - mRNA 5.37602 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
104	0.005642	0.1855	b1476	fdnI	-8.74	0.236866	280 -- 291	51 -- 62	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible		_____________279__________292\n_____________\|____________\|\n5'-CGU...CUUCC____G_______CCGGG...UUU-3'\n______________UGGU_GCGCUGU\n______________\|\|\|:_\|\|\|\|:\|\|\n______________ACCG_CGCGGCA\n3'-UUU...UUAGA____A_______UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	285 -- 291	51 -- 57	-16.7644 kcal/mol	3.14516 kcal/mol	4.8826 kcal/mol	279 292@LB@ \| \|@LB@5'-CGU...CUUCC G CCGGG...UUU-3'@LB@ UGGU GCGCUGU@LB@ \|\|\|: \|\|\|\|:\|\|@LB@ ACCG CGCGGCA@LB@3'-UUU...UUAGA A UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -16.7644 kcal/mol@LB@Unfolding Energy - mRNA 3.14516 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 280 -- 291@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
57	0.002848	0.1727	b2059	wcaA	-10.75	0.100075	282 -- 295	72 -- 85	putative glycosyl transferase		_____________281____________296\n_____________\|______________\|\n5'-AAC...CGGUU_________G____CAGCA-3'\n______________UUGCGCCAG_ACUA\n______________:\|\|\|\|\|\|\|:_\|\|:\|\n______________GACGCGGUU_UGGU\n3'-UUU...CUUAU_________G____CCCUU...GUG-5'\n_____________\|______________\|\n_____________86_____________71\n	284 -- 290	77 -- 83	-19.8604 kcal/mol	1.87274 kcal/mol	7.23443 kcal/mol	281 296@LB@ \| \|@LB@5'-AAC...CGGUU G CAGCA-3'@LB@ UUGCGCCAG ACUA@LB@ :\|\|\|\|\|\|\|: \|\|:\|@LB@ GACGCGGUU UGGU@LB@3'-UUU...CUUAU G CCCUU...GUG-5'@LB@ \| \|@LB@ 86 71@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -19.8604 kcal/mol@LB@Unfolding Energy - mRNA 1.87274 kcal/mol@LB@Unfolding Energy - sRNA 7.23443 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 72 -- 85@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 77 -- 83@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@
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@
135	0.007679	0.1993	b0096	lpxC	-11.14	0.084212	289 -- 298	76 -- 85	UDP-3-O-acyl N-acetylglucosamine deacetylase		_____________288________299\n_____________\|__________\|\n5'-GAA...ACGCC__________CA-3'\n______________CUGCGCCGGC\n______________\|\|\|\|\|\|\|::\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	292 -- 298	76 -- 82	-18.1767 kcal/mol	1.93848 kcal/mol	5.09564 kcal/mol	288 299@LB@ \| \|@LB@5'-GAA...ACGCC CA-3'@LB@ CUGCGCCGGC@LB@ \|\|\|\|\|\|\|::\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -11.14 kcal/mol@LB@Hybridization Energy -18.1767 kcal/mol@LB@Unfolding Energy - mRNA 1.93848 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 289 -- 298@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 76 -- 82@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

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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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