Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
118	0.01199	0.3104	b2573	rpoE	-10.72	0.091300	77 -- 87	8 -- 18	RNA polymerase sigma E factor	_____________76__________88\n_____________\|___________\|\n5'-ACA...ACAAA___________UACGG...UGG-3'\n______________AACAGAUGCGU\n______________\|\|\|\|:\|\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	81 -- 87	8 -- 14	-15.0531 kcal/mol	3.12642 kcal/mol	1.20363 kcal/mol	76 88@LB@ \| \|@LB@5'-ACA...ACAAA UACGG...UGG-3'@LB@ AACAGAUGCGU@LB@ \|\|\|\|:\|\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.0531 kcal/mol@LB@Unfolding Energy - mRNA 3.12642 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 77 -- 87@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 8 -- 14@LB@
119	0.01215	0.3104	b3691	dgoT	-8.17	0.239341	58 -- 68	8 -- 21	D-galactonate transporter	_____________57_____________69\n_____________\|______________\|\n5'-GUG...AUGAA______________AGCAG...CCA-3'\n______________GAUAACA___GCGU\n______________\|\|\|\|\|\|\|___\|\|\|:\n______________CUAUUGU___CGCG\n3'-UUU...UACUA_______UUA____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	58 -- 64	15 -- 21	-12.2033 kcal/mol	2.79285 kcal/mol	1.23638 kcal/mol	57 69@LB@ \| \|@LB@5'-GUG...AUGAA AGCAG...CCA-3'@LB@ GAUAACA GCGU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ CUAUUGU CGCG@LB@3'-UUU...UACUA UUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.2033 kcal/mol@LB@Unfolding Energy - mRNA 2.79285 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 58 -- 68@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
124	0.0124	0.3104	b1860	ruvB	-8.20	0.236824	252 -- 265	8 -- 20	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________251____________266\n_____________\|______________\|\n5'-ACG...AAGAU_________C____CAUUC...GUC-3'\n______________GUAGCAGAU_GCGC\n______________:\|\|:\|\|:\|\|_\|\|\|\|\n______________UAUUGUUUA_CGCG\n3'-UUU...ACUAC______________CAGAAAG-5'\n_____________\|______________\|\n_____________21_____________7\n	252 -- 258	14 -- 20	-14.7986 kcal/mol	5.36112 kcal/mol	1.23367 kcal/mol	251 266@LB@ \| \|@LB@5'-ACG...AAGAU C CAUUC...GUC-3'@LB@ GUAGCAGAU GCGC@LB@ :\|\|:\|\|:\|\| \|\|\|\|@LB@ UAUUGUUUA CGCG@LB@3'-UUU...ACUAC CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.20 kcal/mol@LB@Hybridization Energy -14.7986 kcal/mol@LB@Unfolding Energy - mRNA 5.36112 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 252 -- 265@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 14 -- 20@LB@
126	0.01241	0.3104	b4379	yjjW	-11.82	0.058804	207 -- 217	8 -- 18	putative pyruvate formate lyase activating enzyme	_____________206_________218\n_____________\|___________\|\n5'-CGG...UGAAC___________UUUAG...UGC-3'\n______________AGCAGAUGCGC\n______________\|:\|\|:\|\|\|\|\|\|\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	211 -- 217	8 -- 14	-16.9543 kcal/mol	3.92931 kcal/mol	1.20363 kcal/mol	206 218@LB@ \| \|@LB@5'-CGG...UGAAC UUUAG...UGC-3'@LB@ AGCAGAUGCGC@LB@ \|:\|\|:\|\|\|\|\|\|@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -16.9543 kcal/mol@LB@Unfolding Energy - mRNA 3.92931 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 207 -- 217@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 8 -- 14@LB@
132	0.01286	0.3104	b3176	glmM	-8.35	0.224806	246 -- 258	8 -- 20	phosphoglucosamine mutase	_____________245___________259\n_____________\|_____________\|\n5'-GUU...GUCGU____G________CGAUC...CGG-3'\n______________GUAG_GGAUGCGC\n______________:\|\|:_::\|\|\|\|\|\|\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	252 -- 258	8 -- 14	-14.3134 kcal/mol	4.73041 kcal/mol	1.23367 kcal/mol	245 259@LB@ \| \|@LB@5'-GUU...GUCGU G CGAUC...CGG-3'@LB@ GUAG GGAUGCGC@LB@ :\|\|: ::\|\|\|\|\|\|@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -8.35 kcal/mol@LB@Hybridization Energy -14.3134 kcal/mol@LB@Unfolding Energy - mRNA 4.73041 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 8 -- 14@LB@
141	0.01345	0.3104	b3311	rpsQ	-8.13	0.242987	140 -- 150	8 -- 18	30S ribosomal subunit protein S17	_____________139_________151\n_____________\|___________\|\n5'-GGU...GUUGA___________CGCGA...UCU-3'\n______________AGCAAGUGCGU\n______________\|:\|\|\|:\|\|\|\|:\n______________UUGUUUACGCG\n3'-UUU...UACUA___________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	144 -- 150	8 -- 14	-14.6725 kcal/mol	5.33741 kcal/mol	1.20363 kcal/mol	139 151@LB@ \| \|@LB@5'-GGU...GUUGA CGCGA...UCU-3'@LB@ AGCAAGUGCGU@LB@ \|:\|\|\|:\|\|\|\|:@LB@ UUGUUUACGCG@LB@3'-UUU...UACUA CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -8.13 kcal/mol@LB@Hybridization Energy -14.6725 kcal/mol@LB@Unfolding Energy - mRNA 5.33741 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 8 -- 14@LB@
151	0.01442	0.3104	b1395	paaH	-15.43	0.013105	189 -- 216	8 -- 31	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________188__________________________217\n_____________\|____________________________\|\n5'-GGC...GUUCA______AAUA_C________________AAACU...UGU-3'\n______________CGGGGA____G_AUGAUGAUAAAUGUGC\n______________\|:\|\|\|\|____\|_\|\|\|\|\|:\|:\|\|\|\|\|:\|\|\n______________GUCCCU____C_UACUAUUGUUUACGCG\n3'-UUU...CUUAA______A_____________________CAGAAAG-5'\n_____________\|____________________________\|\n_____________32___________________________7\n	210 -- 216	8 -- 14	-28.6523 kcal/mol	5.47369 kcal/mol	7.74551 kcal/mol	188 217@LB@ \| \|@LB@5'-GGC...GUUCA AAUA C AAACU...UGU-3'@LB@ CGGGGA G AUGAUGAUAAAUGUGC@LB@ \|:\|\|\|\| \| \|\|\|\|\|:\|:\|\|\|\|\|:\|\|@LB@ GUCCCU C UACUAUUGUUUACGCG@LB@3'-UUU...CUUAA A CAGAAAG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -28.6523 kcal/mol@LB@Unfolding Energy - mRNA 5.47369 kcal/mol@LB@Unfolding Energy - sRNA 7.74551 kcal/mol@LB@@LB@Position - mRNA 189 -- 216@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 8 -- 14@LB@
163	0.0151	0.3104	b1517	lsrF	-8.60	0.205199	166 -- 179	8 -- 21	putative autoinducer-2 (AI-2) aldolase	_____________165____________180\n_____________\|______________\|\n5'-AAA...AAUAC___UU_U_______AUUAC...AUU-3'\n______________GAU__C_GAUGUGC\n______________\|\|\|__\|_:\|\|\|:\|\|\n______________CUA__G_UUACGCG\n3'-UUU...UACUA___UU_U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	173 -- 179	8 -- 14	-12.6785 kcal/mol	2.84069 kcal/mol	1.23638 kcal/mol	165 180@LB@ \| \|@LB@5'-AAA...AAUAC UU U AUUAC...AUU-3'@LB@ GAU C GAUGUGC@LB@ \|\|\| \| :\|\|\|:\|\|@LB@ CUA G UUACGCG@LB@3'-UUU...UACUA UU U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6785 kcal/mol@LB@Unfolding Energy - mRNA 2.84069 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 166 -- 179@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 8 -- 14@LB@
169	0.01667	0.3104	b3575	yiaK	-9.90	0.125874	198 -- 219	8 -- 29	2 3-diketo-L-gulonate reductase NADH-dependent	_____________197____________________220\n_____________\|______________________\|\n5'-UUU...AGCCU_______AA______UU__A__AGUUA...UCG-3'\n______________GGGAUGA__GUGACA__UG_GC\n______________\|\|\|\|\|\|\|__:\|:\|\|\|__\|\|_\|\|\n______________CCCUACU__UAUUGU__AC_CG\n3'-UUU...UAAGU_______AC______UU__G__CAGAAAG-5'\n_____________\|______________________\|\n_____________30_____________________7\n	198 -- 204	23 -- 29	-23.0827 kcal/mol	5.7681 kcal/mol	7.41331 kcal/mol	197 220@LB@ \| \|@LB@5'-UUU...AGCCU AA UU A AGUUA...UCG-3'@LB@ GGGAUGA GUGACA UG GC@LB@ \|\|\|\|\|\|\| :\|:\|\|\| \|\| \|\|@LB@ CCCUACU UAUUGU AC CG@LB@3'-UUU...UAAGU AC UU G CAGAAAG-5'@LB@ \| \|@LB@ 30 7@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.0827 kcal/mol@LB@Unfolding Energy - mRNA 5.7681 kcal/mol@LB@Unfolding Energy - sRNA 7.41331 kcal/mol@LB@@LB@Position - mRNA 198 -- 219@LB@Position - sRNA 8 -- 29@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
174	0.01734	0.3104	b3470	tusA	-9.03	0.174990	268 -- 281	8 -- 22	mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase	_____________267_____________282\n_____________\|_______________\|\n5'-CAU...ACCGG_______________AAAAC...UGC-3'\n______________UGAUGAU_GGUGCGC\n______________\|\|\|\|:\|:_::\|\|\|\|\|\n______________ACUAUUG_UUACGCG\n3'-UUU...CUACU_______U_______CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	275 -- 281	8 -- 14	-15.1295 kcal/mol	4.85785 kcal/mol	1.23838 kcal/mol	267 282@LB@ \| \|@LB@5'-CAU...ACCGG AAAAC...UGC-3'@LB@ UGAUGAU GGUGCGC@LB@ \|\|\|\|:\|: ::\|\|\|\|\|@LB@ ACUAUUG UUACGCG@LB@3'-UUU...CUACU U CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -15.1295 kcal/mol@LB@Unfolding Energy - mRNA 4.85785 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 268 -- 281@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 8 -- 14@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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service.

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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