Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
112	0.009574	0.2693	b2494	bepA	-6.13	0.179960	208 -- 220	29 -- 41	OM protein maintenance and assembly metalloprotease and chaperone periplasmic	_____________207___________221\n_____________\|_____________\|\n5'-UGA...GUUCA____G________AAACC...UGC-3'\n______________GGCA_UUGAAAAA\n______________:\|\|\|_\|\|:\|\|\|\|\|\n______________UCGU_AAUUUUUU\n3'-UUU...GUUCU____G________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	214 -- 220	29 -- 35	-11.3192 kcal/mol	3.5632 kcal/mol	1.62306 kcal/mol	207 221@LB@ \| \|@LB@5'-UGA...GUUCA G AAACC...UGC-3'@LB@ GGCA UUGAAAAA@LB@ :\|\|\| \|\|:\|\|\|\|\|@LB@ UCGU AAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -6.13 kcal/mol@LB@Hybridization Energy -11.3192 kcal/mol@LB@Unfolding Energy - mRNA 3.5632 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 208 -- 220@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 29 -- 35@LB@
119	0.01022	0.2766	b0123	cueO	-7.29	0.093095	47 -- 59	29 -- 41	multicopper oxidase (laccase)	_____________46____________60\n_____________\|_____________\|\n5'-CUG...UACCA__G__________GAUAA...CGU-3'\n______________GG_GCUUAAAGAA\n______________:\|_:\|\|\|\|\|\|:\|\|\n______________UC_UGAAUUUUUU\n3'-UUU...GUUCU__G__________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	53 -- 59	29 -- 35	-11.0144 kcal/mol	2.10364 kcal/mol	1.62306 kcal/mol	46 60@LB@ \| \|@LB@5'-CUG...UACCA G GAUAA...CGU-3'@LB@ GG GCUUAAAGAA@LB@ :\| :\|\|\|\|\|\|:\|\|@LB@ UC UGAAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -11.0144 kcal/mol@LB@Unfolding Energy - mRNA 2.10364 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 47 -- 59@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 29 -- 35@LB@
174	0.01992	0.3669	b1098	tmk	-8.25	0.051647	183 -- 196	29 -- 42	thymidylate kinase	_____________182____________197\n_____________\|______________\|\n5'-UAA...UCUGA______________AAAAA...GCG-3'\n______________AAGUGCUUAAGGAA\n______________\|\|\|::\|\|\|\|\|::\|\|\n______________UUCGUGAAUUUUUU\n3'-UUU...CGUUC______________AAGCA...CAA-5'\n_____________\|______________\|\n_____________43_____________28\n	190 -- 196	29 -- 35	-11.8447 kcal/mol	1.97362 kcal/mol	1.62369 kcal/mol	182 197@LB@ \| \|@LB@5'-UAA...UCUGA AAAAA...GCG-3'@LB@ AAGUGCUUAAGGAA@LB@ \|\|\|::\|\|\|\|\|::\|\|@LB@ UUCGUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -11.8447 kcal/mol@LB@Unfolding Energy - mRNA 1.97362 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 183 -- 196@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
193	0.0233	0.3864	b1563	relE	-9.36	0.025073	16 -- 27	29 -- 40	Qin prophage; toxin of the RelE-RelB toxin-antitoxin system	_____________15___________28\n_____________\|____________\|\n5'-GCG...ACGCC____________AUGGG...UAC-3'\n______________GCGCUUGAAAAA\n______________\|\|:\|\|\|:\|\|\|\|\|\n______________CGUGAAUUUUUU\n3'-UUU...UUCUU____________AAGCA...CAA-5'\n_____________\|____________\|\n_____________41___________28\n	21 -- 27	29 -- 35	-12.3855 kcal/mol	1.40487 kcal/mol	1.62106 kcal/mol	15 28@LB@ \| \|@LB@5'-GCG...ACGCC AUGGG...UAC-3'@LB@ GCGCUUGAAAAA@LB@ \|\|:\|\|\|:\|\|\|\|\|@LB@ CGUGAAUUUUUU@LB@3'-UUU...UUCUU AAGCA...CAA-5'@LB@ \| \|@LB@ 41 28@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -12.3855 kcal/mol@LB@Unfolding Energy - mRNA 1.40487 kcal/mol@LB@Unfolding Energy - sRNA 1.62106 kcal/mol@LB@@LB@Position - mRNA 16 -- 27@LB@Position - sRNA 29 -- 40@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 29 -- 35@LB@
197	0.0237	0.3864	b4001	yjaH	-6.58	0.140477	149 -- 175	29 -- 57	DUF1481 family putative lipoprotein	_____________148____________________________176\n_____________\|______________________________\|\n5'-UGG...CCGGC________CU____________________CGCAG...AUA-3'\n______________AUUUGUUU__GGCA__AGGCACU_GAAAGA\n______________\|:\|\|\|:\|\|__:\|\|\|__\|:\|\|\|\|\|_:\|\|\|:\|\n______________UGAACGAA__UCGU__UUCGUGA_UUUUUU\n3'-UUU...UACUU________U_____UC_______A______AAGCA...CAA-5'\n_____________\|______________________________\|\n_____________58_____________________________28\n	163 -- 169	36 -- 42	-19.7163 kcal/mol	6.91297 kcal/mol	6.22375 kcal/mol	148 176@LB@ \| \|@LB@5'-UGG...CCGGC CU CGCAG...AUA-3'@LB@ AUUUGUUU GGCA AGGCACU GAAAGA@LB@ \|:\|\|\|:\|\| :\|\|\| \|:\|\|\|\|\| :\|\|\|:\|@LB@ UGAACGAA UCGU UUCGUGA UUUUUU@LB@3'-UUU...UACUU U UC A AAGCA...CAA-5'@LB@ \| \|@LB@ 58 28@LB@@LB@@LB@Energy -6.58 kcal/mol@LB@Hybridization Energy -19.7163 kcal/mol@LB@Unfolding Energy - mRNA 6.91297 kcal/mol@LB@Unfolding Energy - sRNA 6.22375 kcal/mol@LB@@LB@Position - mRNA 149 -- 175@LB@Position - sRNA 29 -- 57@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 36 -- 42@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@LB@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter	_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@
186	0.02184	0.3768	b1256	ompW	-5.92	0.201836	13 -- 38	30 -- 57	outer membrane protein W	_____________12___________________________39\n_____________\|____________________________\|\n5'-GAC...UUAAU______GU______A_____________UUGAU...CUG-3'\n______________AUUUGC___AGCGA_AA_UAUUUAAAAA\n______________\|:\|\|\|\|___\|\|\|:\|_\|\|_:\|:\|\|\|\|\|\|\|\n______________UGAACG___UCGUU_UU_GUGAAUUUUU\n3'-UUU...UACUU______AAU_____C__C__________UAAGC...CAA-5'\n_____________\|____________________________\|\n_____________58___________________________29\n	32 -- 38	30 -- 36	-16.1426 kcal/mol	3.99952 kcal/mol	6.22352 kcal/mol	12 39@LB@ \| \|@LB@5'-GAC...UUAAU GU A UUGAU...CUG-3'@LB@ AUUUGC AGCGA AA UAUUUAAAAA@LB@ \|:\|\|\|\| \|\|\|:\| \|\| :\|:\|\|\|\|\|\|\|@LB@ UGAACG UCGUU UU GUGAAUUUUU@LB@3'-UUU...UACUU AAU C C UAAGC...CAA-5'@LB@ \| \|@LB@ 58 29@LB@@LB@@LB@Energy -5.92 kcal/mol@LB@Hybridization Energy -16.1426 kcal/mol@LB@Unfolding Energy - mRNA 3.99952 kcal/mol@LB@Unfolding Energy - sRNA 6.22352 kcal/mol@LB@@LB@Position - mRNA 13 -- 38@LB@Position - sRNA 30 -- 57@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 30 -- 36@LB@
53	0.002646	0.1597	b1704	aroH	-6.03	0.190589	111 -- 120	31 -- 40	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase tryptophan repressible	_____________110________121\n_____________\|__________\|\n5'-CCA...ACCUC__________UCAGC...CCC-3'\n______________GCACUUGAAA\n______________\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUU\n3'-UUU...UUCUU__________UUAAG...CAA-5'\n_____________\|__________\|\n_____________41_________30\n	114 -- 120	31 -- 37	-11.574 kcal/mol	3.92769 kcal/mol	1.61955 kcal/mol	110 121@LB@ \| \|@LB@5'-CCA...ACCUC UCAGC...CCC-3'@LB@ GCACUUGAAA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUU@LB@3'-UUU...UUCUU UUAAG...CAA-5'@LB@ \| \|@LB@ 41 30@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -11.574 kcal/mol@LB@Unfolding Energy - mRNA 3.92769 kcal/mol@LB@Unfolding Energy - sRNA 1.61955 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 31 -- 40@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 31 -- 37@LB@
15	0.0003116	0.06692	b2149	mglA	-7.01	0.109495	281 -- 289	33 -- 41	methyl-galactoside ABC transporter ATPase	_____________280_______290\n_____________\|_________\|\n5'-CGA...GUUAA_________UAACG...AUU-3'\n______________GGCACUUGA\n______________:\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	283 -- 289	33 -- 39	-11.227 kcal/mol	2.59529 kcal/mol	1.6188 kcal/mol	280 290@LB@ \| \|@LB@5'-CGA...GUUAA UAACG...AUU-3'@LB@ GGCACUUGA@LB@ :\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.227 kcal/mol@LB@Unfolding Energy - mRNA 2.59529 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 281 -- 289@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 33 -- 39@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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