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
181	0.0215	0.3768	b3843	ubiD	-7.81	0.067872	2 -- 28	14 -- 40	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C_______CAGUACA___AA_________UUGCA...UGG-3'\n______________GCGCUUG________GU__AUACCAGGA\n______________\|\|:\|\|\|:________\|\|__\|:\|\|\|\|\|\|\|\n______________CGUGAAU________CA__UGUGGUCCU\n3'-UUU...UUCUU_______UUUUUAAG__A__________UUAGA...CAA-5'\n_____________\|____________________________\|\n_____________41___________________________13\n	22 -- 28	14 -- 20	-21.9915 kcal/mol	4.97788 kcal/mol	9.20436 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C CAGUACA AA UUGCA...UGG-3'@LB@ GCGCUUG GU AUACCAGGA@LB@ \|\|:\|\|\|: \|\| \|:\|\|\|\|\|\|\|@LB@ CGUGAAU CA UGUGGUCCU@LB@3'-UUU...UUCUU UUUUUAAG A UUAGA...CAA-5'@LB@ \| \|@LB@ 41 13@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -21.9915 kcal/mol@LB@Unfolding Energy - mRNA 4.97788 kcal/mol@LB@Unfolding Energy - sRNA 9.20436 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 14 -- 40@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 14 -- 20@LB@
157	0.01701	0.3489	b3856	mobB	-4.94	0.329991	189 -- 197	52 -- 60	molybdopterin-guanine dinucleotide biosynthesis protein B	_____________188_______198\n_____________\|_________\|\n5'-GUG...CCAGA_________CCGAU...CCA-3'\n______________GGAGCUUGC\n______________\|:\|:\|\|\|\|\|\n______________CUUUGAACG\n3'-UUU...CCCUA_________AAUUC...CAA-5'\n_____________\|_________\|\n_____________61________51\n	191 -- 197	52 -- 58	-10.6989 kcal/mol	2.59286 kcal/mol	3.16562 kcal/mol	188 198@LB@ \| \|@LB@5'-GUG...CCAGA CCGAU...CCA-3'@LB@ GGAGCUUGC@LB@ \|:\|:\|\|\|\|\|@LB@ CUUUGAACG@LB@3'-UUU...CCCUA AAUUC...CAA-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -4.94 kcal/mol@LB@Hybridization Energy -10.6989 kcal/mol@LB@Unfolding Energy - mRNA 2.59286 kcal/mol@LB@Unfolding Energy - sRNA 3.16562 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@LB@
158	0.01725	0.3504	b3857	mobA	-11.09	0.007545	184 -- 212	5 -- 35	molybdopterin-guanine dinucleotide synthase	_____________183_____________________________213\n_____________\|_______________________________\|\n5'-UCC...CACAA_______GG___________U__________ACGAC...AAC-3'\n______________UAAAAGA__CG__AUAUCGG_GAAUCUGAUG\n______________\|\|\|\|\|:\|__\|\|__\|:\|:\|:\|_:\|\|\|\|\|\|\|\|\|\n______________AUUUUUU__GC__UGUGGUC_UUUAGACUAC\n3'-UUU...CGUGA_______AA__AA_______C__________ACAA-5'\n_____________\|_______________________________\|\n_____________36______________________________4\n	184 -- 190	29 -- 35	-25.0811 kcal/mol	5.24608 kcal/mol	8.74745 kcal/mol	183 213@LB@ \| \|@LB@5'-UCC...CACAA GG U ACGAC...AAC-3'@LB@ UAAAAGA CG AUAUCGG GAAUCUGAUG@LB@ \|\|\|\|\|:\| \|\| \|:\|:\|:\| :\|\|\|\|\|\|\|\|\|@LB@ AUUUUUU GC UGUGGUC UUUAGACUAC@LB@3'-UUU...CGUGA AA AA C ACAA-5'@LB@ \| \|@LB@ 36 4@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -25.0811 kcal/mol@LB@Unfolding Energy - mRNA 5.24608 kcal/mol@LB@Unfolding Energy - sRNA 8.74745 kcal/mol@LB@@LB@Position - mRNA 184 -- 212@LB@Position - sRNA 5 -- 35@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 29 -- 35@LB@
78	0.004685	0.1935	b3905	rhaS	-7.96	0.061746	70 -- 86	26 -- 40	transcriptional activator of rhaBAD and rhaT	_____________69________________87\n_____________\|_________________\|\n5'-UGG...UCACC______CCU________ACGCU...AUG-3'\n______________GCAUUU___GAAAAUUC\n______________\|\|\|:\|\|___:\|\|\|\|\|\|\|\n______________CGUGAA___UUUUUAAG\n3'-UUU...UUCUU______U__________CAAUG...CAA-5'\n_____________\|_________________\|\n_____________41________________25\n	80 -- 86	26 -- 32	-11.6625 kcal/mol	2.05222 kcal/mol	1.64811 kcal/mol	69 87@LB@ \| \|@LB@5'-UGG...UCACC CCU ACGCU...AUG-3'@LB@ GCAUUU GAAAAUUC@LB@ \|\|\|:\|\| :\|\|\|\|\|\|\|@LB@ CGUGAA UUUUUAAG@LB@3'-UUU...UUCUU U CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -11.6625 kcal/mol@LB@Unfolding Energy - mRNA 2.05222 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 70 -- 86@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 26 -- 32@LB@
101	0.007657	0.2442	b3928	zapB	-6.83	0.122013	220 -- 239	38 -- 54	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________219__________________240\n_____________\|____________________\|\n5'-UUU...AGAAG________AAACU_______AAAGU...AAG-3'\n______________UGUUUGAG_____GGAAGCA\n______________\|\|:\|\|:\|\|_____:\|\|\|\|\|\|\n______________ACGAAUUC_____UCUUCGU\n3'-UUU...UUUGA________GU__________GAAUU...CAA-5'\n_____________\|____________________\|\n_____________55___________________37\n	233 -- 239	38 -- 44	-16.6983 kcal/mol	3.7204 kcal/mol	6.15149 kcal/mol	219 240@LB@ \| \|@LB@5'-UUU...AGAAG AAACU AAAGU...AAG-3'@LB@ UGUUUGAG GGAAGCA@LB@ \|\|:\|\|:\|\| :\|\|\|\|\|\|@LB@ ACGAAUUC UCUUCGU@LB@3'-UUU...UUUGA GU GAAUU...CAA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -16.6983 kcal/mol@LB@Unfolding Energy - mRNA 3.7204 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 220 -- 239@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 38 -- 44@LB@
198	0.02375	0.3864	b3946	fsaB	-8.18	0.053967	105 -- 117	26 -- 40	fructose-6-phosphate aldolase 2	_____________104_____________118\n_____________\|_______________\|\n5'-UGG...AUCAU_______________CGUAA...CUG-3'\n______________GCAC__GAAGAAUUC\n______________\|\|\|\|__:\|\|:\|\|\|\|\|\n______________CGUG__UUUUUUAAG\n3'-UUU...UUCUU____AA_________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	111 -- 117	26 -- 32	-11.851 kcal/mol	2.02524 kcal/mol	1.64811 kcal/mol	104 118@LB@ \| \|@LB@5'-UGG...AUCAU CGUAA...CUG-3'@LB@ GCAC GAAGAAUUC@LB@ \|\|\|\| :\|\|:\|\|\|\|\|@LB@ CGUG UUUUUUAAG@LB@3'-UUU...UUCUU AA CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.18 kcal/mol@LB@Hybridization Energy -11.851 kcal/mol@LB@Unfolding Energy - mRNA 2.02524 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 105 -- 117@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 26 -- 32@LB@
20	0.0005034	0.08107	b3962	sthA	-8.00	0.060263	274 -- 291	37 -- 54	pyridine nucleotide transhydrogenase soluble	_____________273________________292\n_____________\|__________________\|\n5'-UAC...GGGCC__G__________U____GCGUC...CAG-3'\n______________UG_UUAAGCAAGG_GCGC\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|:\|\n______________AC_AAUUCGUUCU_CGUG\n3'-UUU...UUUGA__G__________U____AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	280 -- 286	42 -- 48	-21.3093 kcal/mol	7.14965 kcal/mol	6.1584 kcal/mol	273 292@LB@ \| \|@LB@5'-UAC...GGGCC G U GCGUC...CAG-3'@LB@ UG UUAAGCAAGG GCGC@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\|:\|@LB@ AC AAUUCGUUCU CGUG@LB@3'-UUU...UUUGA G U AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -8.00 kcal/mol@LB@Hybridization Energy -21.3093 kcal/mol@LB@Unfolding Energy - mRNA 7.14965 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 274 -- 291@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 42 -- 48@LB@
195	0.02349	0.3864	b3982	nusG	-7.66	0.074558	21 -- 55	24 -- 55	transcription termination factor	_____________20__________________________________56\n_____________\|___________________________________\|\n5'-GAC...UACCG______UU__CCGU_______GUACC_____C___AAGGU...ACA-3'\n______________UUGCUU__GC____GAAGCGC_____GAAGU_CGU\n______________\|\|\|\|\|\|__\|\|____\|\|\|\|\|:\|_____:\|\|:\|_\|\|\|\n______________AACGAA__CG____CUUCGUG_____UUUUA_GCA\n3'-UUU...CUUUG______UU__UU_________AAUU______A___AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________56__________________________________23\n	35 -- 41	37 -- 43	-23.8738 kcal/mol	9.94572 kcal/mol	6.27216 kcal/mol	20 56@LB@ \| \|@LB@5'-GAC...UACCG UU CCGU GUACC C AAGGU...ACA-3'@LB@ UUGCUU GC GAAGCGC GAAGU CGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|:\| :\|\|:\| \|\|\|@LB@ AACGAA CG CUUCGUG UUUUA GCA@LB@3'-UUU...CUUUG UU UU AAUU A AUGUG...CAA-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -23.8738 kcal/mol@LB@Unfolding Energy - mRNA 9.94572 kcal/mol@LB@Unfolding Energy - sRNA 6.27216 kcal/mol@LB@@LB@Position - mRNA 21 -- 55@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 37 -- 43@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@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@

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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