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
146	0.01469	0.3231	b0026	ileS	-7.82	0.067581	147 -- 206	2 -- 59	isoleucyl-tRNA synthetase	_____________146_____________________________________________________________207\n_____________\|_______________________________________________________________\|\n5'-AUG...UAACA____CG________CU_UUAU___AUCAAACC_____A__GA______A___________A__GACUA...CUG-3'\n______________AAAC__GCUUAAGC__G____GUA________GAAAU_CG____ACCG__GAAUCUGAUG_GU\n______________\|\|\|\|__\|\|\|\|\|\|\|\|__\|____\|:\|________:\|\|\|\|_\|\|____\|\|\|:__:\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUG__CGAAUUCG__C____CGU________UUUUA_GC____UGGU__UUUAGACUAC_CA\n3'-UUU...CCUAC____AA________UU_UU_____GAAUU________A__AAUG____CC__________A__A-5'\n_____________\|_______________________________________________________________\|\n_____________60______________________________________________________________1\n	197 -- 203	5 -- 11	-33.6314 kcal/mol	11.9684 kcal/mol	13.8468 kcal/mol	146 207@LB@ \| \|@LB@5'-AUG...UAACA CG CU UUAU AUCAAACC A GA A A GACUA...CUG-3'@LB@ AAAC GCUUAAGC G GUA GAAAU CG ACCG GAAUCUGAUG GU@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \| \|:\| :\|\|\|\| \|\| \|\|\|: :\|\|\|\|\|\|\|\|\| \|\|@LB@ UUUG CGAAUUCG C CGU UUUUA GC UGGU UUUAGACUAC CA@LB@3'-UUU...CCUAC AA UU UU GAAUU A AAUG CC A A-5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -7.82 kcal/mol@LB@Hybridization Energy -33.6314 kcal/mol@LB@Unfolding Energy - mRNA 11.9684 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 147 -- 206@LB@Position - sRNA 2 -- 59@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 5 -- 11@LB@
185	0.02171	0.3768	b0059	rapA	-7.86	0.065955	35 -- 74	2 -- 42	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________34___________________________________________75\n_____________\|____________________________________________\|\n5'-GCU...AUUUU_____AAAA__________CCAG______U___________C__GACGA...UUU-3'\n______________GAGCA____AAAGAGUUCG____AUACCA_____UUUGAUG_GU\n______________:\|\|\|\|____\|\|\|:\|:\|\|\|\|____\|:\|\|\|\|_____\|:\|\|\|\|\|_\|\|\n______________UUCGU____UUUUUUAAGC____UGUGGU_____AGACUAC_CA\n3'-UUU...CGUUC_____GAA___________AA________CCUUU_______A__A-5'\n_____________\|____________________________________________\|\n_____________43___________________________________________1\n	47 -- 53	25 -- 31	-26.2778 kcal/mol	9.20057 kcal/mol	9.22149 kcal/mol	34 75@LB@ \| \|@LB@5'-GCU...AUUUU AAAA CCAG U C GACGA...UUU-3'@LB@ GAGCA AAAGAGUUCG AUACCA UUUGAUG GU@LB@ :\|\|\|\| \|\|\|:\|:\|\|\|\| \|:\|\|\|\| \|:\|\|\|\|\| \|\|@LB@ UUCGU UUUUUUAAGC UGUGGU AGACUAC CA@LB@3'-UUU...CGUUC GAA AA CCUUU A A-5'@LB@ \| \|@LB@ 43 1@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -26.2778 kcal/mol@LB@Unfolding Energy - mRNA 9.20057 kcal/mol@LB@Unfolding Energy - sRNA 9.22149 kcal/mol@LB@@LB@Position - mRNA 35 -- 74@LB@Position - sRNA 2 -- 42@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 25 -- 31@LB@
45	0.001912	0.1369	b0080	cra	-5.81	0.213706	183 -- 197	38 -- 52	transcriptional repressor-activator for carbon metabolism	_____________182_____________198\n_____________\|_______________\|\n5'-GGC...UACAU____C__________AUUGU...AAA-3'\n______________UUUA_GCAAGGGGCA\n______________:\|\|\|_\|\|\|\|\|::\|\|\|\n______________GAAU_CGUUCUUCGU\n3'-UUU...UGAAC____U__________GAAUU...CAA-5'\n_____________\|_______________\|\n_____________53______________37\n	191 -- 197	38 -- 44	-16.0644 kcal/mol	4.16124 kcal/mol	6.09169 kcal/mol	182 198@LB@ \| \|@LB@5'-GGC...UACAU C AUUGU...AAA-3'@LB@ UUUA GCAAGGGGCA@LB@ :\|\|\| \|\|\|\|\|::\|\|\|@LB@ GAAU CGUUCUUCGU@LB@3'-UUU...UGAAC U GAAUU...CAA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -5.81 kcal/mol@LB@Hybridization Energy -16.0644 kcal/mol@LB@Unfolding Energy - mRNA 4.16124 kcal/mol@LB@Unfolding Energy - sRNA 6.09169 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 38 -- 44@LB@
147	0.01475	0.3231	b0084	ftsI	-4.75	0.360226	157 -- 172	24 -- 39	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3	_____________156_______________173\n_____________\|_________________\|\n5'-GUU...UCCGU___A________A____AGUGC...UGG-3'\n______________CAC__AGAAAAU_UCGU\n______________\|\|\|__\|:\|\|\|\|\|_\|\|\|\|\n______________GUG__UUUUUUA_AGCA\n3'-UUU...UCUUC___AA____________AUGUG...CAA-5'\n_____________\|_________________\|\n_____________40________________23\n	161 -- 167	28 -- 34	-7.76704 kcal/mol	1.36905 kcal/mol	1.64726 kcal/mol	156 173@LB@ \| \|@LB@5'-GUU...UCCGU A A AGUGC...UGG-3'@LB@ CAC AGAAAAU UCGU@LB@ \|\|\| \|:\|\|\|\|\| \|\|\|\|@LB@ GUG UUUUUUA AGCA@LB@3'-UUU...UCUUC AA AUGUG...CAA-5'@LB@ \| \|@LB@ 40 23@LB@@LB@@LB@Energy -4.75 kcal/mol@LB@Hybridization Energy -7.76704 kcal/mol@LB@Unfolding Energy - mRNA 1.36905 kcal/mol@LB@Unfolding Energy - sRNA 1.64726 kcal/mol@LB@@LB@Position - mRNA 157 -- 172@LB@Position - sRNA 24 -- 39@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 28 -- 34@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@
136	0.01308	0.3087	b0131	panD	-6.12	0.181240	260 -- 282	17 -- 40	aspartate 1-decarboxylase	_____________259______________________283\n_____________\|________________________\|\n5'-AUU...GACCU_____AU_________________UUGAC...UUG-3'\n______________GCACU__GAAGGUUC_UUGCGCCA\n______________\|\|\|\|\|__:\|\|::\|\|\|_\|\|:\|:\|\|\|\n______________CGUGA__UUUUUAAG_AAUGUGGU\n3'-UUU...UUCUU_____AU________C________CCUUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________16\n	268 -- 274	26 -- 32	-23.1255 kcal/mol	7.80932 kcal/mol	9.19627 kcal/mol	259 283@LB@ \| \|@LB@5'-AUU...GACCU AU UUGAC...UUG-3'@LB@ GCACU GAAGGUUC UUGCGCCA@LB@ \|\|\|\|\| :\|\|::\|\|\| \|\|:\|:\|\|\|@LB@ CGUGA UUUUUAAG AAUGUGGU@LB@3'-UUU...UUCUU AU C CCUUU...CAA-5'@LB@ \| \|@LB@ 41 16@LB@@LB@@LB@Energy -6.12 kcal/mol@LB@Hybridization Energy -23.1255 kcal/mol@LB@Unfolding Energy - mRNA 7.80932 kcal/mol@LB@Unfolding Energy - sRNA 9.19627 kcal/mol@LB@@LB@Position - mRNA 260 -- 282@LB@Position - sRNA 17 -- 40@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 26 -- 32@LB@
70	0.003574	0.1645	b0145	dksA	-6.64	0.135564	191 -- 197	39 -- 45	transcriptional regulator of rRNA transcription; DnaK suppressor protein	_____________190_____198\n_____________\|_______\|\n5'-AAU...UUAAG_______AACAU...AUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	191 -- 197	39 -- 45	-7.63285 kcal/mol	0.475666 kcal/mol	0.514773 kcal/mol	190 198@LB@ \| \|@LB@5'-AAU...UUAAG AACAU...AUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -7.63285 kcal/mol@LB@Unfolding Energy - mRNA 0.475666 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 191 -- 197@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
115	0.009659	0.2693	b0155	clcA	-5.80	0.214551	108 -- 124	25 -- 40	H(+)/Cl(-) exchange transporter	_____________107_______________125\n_____________\|_________________\|\n5'-AGU...UUUGU__________C___A__CUUUG...UAG-3'\n______________GCAUUUGAAA_AUU_CG\n______________\|\|\|:\|\|:\|\|\|_\|\|\|_\|\|\n______________CGUGAAUUUU_UAA_GC\n3'-UUU...UUCUU__________U______AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	109 -- 115	33 -- 39	-11.0899 kcal/mol	3.63771 kcal/mol	1.64821 kcal/mol	107 125@LB@ \| \|@LB@5'-AGU...UUUGU C A CUUUG...UAG-3'@LB@ GCAUUUGAAA AUU CG@LB@ \|\|\|:\|\|:\|\|\| \|\|\| \|\|@LB@ CGUGAAUUUU UAA GC@LB@3'-UUU...UUCUU U AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -5.80 kcal/mol@LB@Hybridization Energy -11.0899 kcal/mol@LB@Unfolding Energy - mRNA 3.63771 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 108 -- 124@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 33 -- 39@LB@
40	0.001639	0.1292	b0156	erpA	-9.82	0.018424	105 -- 133	14 -- 48	iron-sulfur cluster insertion protein	_____________104_________________________________134\n_____________\|___________________________________\|\n5'-UAG...CAGCC________________________AA_________UAUUA...UAC-3'\n______________AGCGAGAA_UACUUGAA_____CG__AUACCAGGG\n______________\|\|\|:\|\|\|\|_:\|\|\|\|:\|\|_____\|\|__\|:\|\|\|\|\|\|:\n______________UCGUUCUU_GUGAAUUU_____GC__UGUGGUCCU\n3'-UUU...CGAAU________C________UUUAA__AA_________UUAGA...CAA-5'\n_____________\|___________________________________\|\n_____________49__________________________________13\n	127 -- 133	14 -- 20	-29.1703 kcal/mol	5.55319 kcal/mol	13.801 kcal/mol	104 134@LB@ \| \|@LB@5'-UAG...CAGCC AA UAUUA...UAC-3'@LB@ AGCGAGAA UACUUGAA CG AUACCAGGG@LB@ \|\|\|:\|\|\|\| :\|\|\|\|:\|\| \|\| \|:\|\|\|\|\|\|:@LB@ UCGUUCUU GUGAAUUU GC UGUGGUCCU@LB@3'-UUU...CGAAU C UUUAA AA UUAGA...CAA-5'@LB@ \| \|@LB@ 49 13@LB@@LB@@LB@Energy -9.82 kcal/mol@LB@Hybridization Energy -29.1703 kcal/mol@LB@Unfolding Energy - mRNA 5.55319 kcal/mol@LB@Unfolding Energy - sRNA 13.801 kcal/mol@LB@@LB@Position - mRNA 105 -- 133@LB@Position - sRNA 14 -- 48@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 14 -- 20@LB@
31	0.0009469	0.09599	b0166	dapD	-11.60	0.005180	96 -- 124	11 -- 40	2 3 4 5-tetrahydropyridine-2-carboxylate N-succinyltransferase	_____________95_____________________________125\n_____________\|______________________________\|\n5'-UUG...GGCGU________UAACGA_______G________GCAUC...AGG-3'\n______________GCGCUUAA_______GUUGCA_CAGGAAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|:\|\|_\|\|\|\|\|\|:\|\n______________CGUGAAUU_______CAAUGU_GUCCUUUA\n3'-UUU...UUCUU________UUUUAAG______G________GACUA...CAA-5'\n_____________\|______________________________\|\n_____________41_____________________________10\n	97 -- 103	33 -- 39	-29.7713 kcal/mol	8.96001 kcal/mol	9.20882 kcal/mol	95 125@LB@ \| \|@LB@5'-UUG...GGCGU UAACGA G GCAUC...AGG-3'@LB@ GCGCUUAA GUUGCA CAGGAAGU@LB@ \|\|:\|\|\|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ CGUGAAUU CAAUGU GUCCUUUA@LB@3'-UUU...UUCUU UUUUAAG G GACUA...CAA-5'@LB@ \| \|@LB@ 41 10@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -29.7713 kcal/mol@LB@Unfolding Energy - mRNA 8.96001 kcal/mol@LB@Unfolding Energy - sRNA 9.20882 kcal/mol@LB@@LB@Position - mRNA 96 -- 124@LB@Position - sRNA 11 -- 40@LB@Position Seed - mRNA 97 -- 103@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)

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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