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
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring	_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@LB@
30	0.001906	0.2094	b0616	citE	-12.56	0.043465	103 -- 116	8 -- 21	citrate lyase citryl-ACP lyase (beta) subunit	_____________102____________117\n_____________\|______________\|\n5'-CAA...AUGUC_________G____ACUGG...UCU-3'\n______________GAUGACAAA_GCGC\n______________\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CUAUUGUUU_CGCG\n3'-UUU...UACUA_________A____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	105 -- 111	13 -- 19	-17.9482 kcal/mol	4.14919 kcal/mol	1.23638 kcal/mol	102 117@LB@ \| \|@LB@5'-CAA...AUGUC G ACUGG...UCU-3'@LB@ GAUGACAAA GCGC@LB@ \|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -17.9482 kcal/mol@LB@Unfolding Energy - mRNA 4.14919 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 103 -- 116@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 13 -- 19@LB@
60	0.00555	0.3084	b2062	wza	-10.85	0.086669	18 -- 25	4 -- 11	colanic acid export protein; outer membrane auxillary lipoprotein	_____________17_______26\n_____________\|________\|\n5'-AAA...CGGUA________GGAUG...GCA-3'\n______________GCGUGUCU\n______________\|\|\|:\|\|\|\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	19 -- 25	4 -- 10	-13.9362 kcal/mol	1.92535 kcal/mol	1.15639 kcal/mol	17 26@LB@ \| \|@LB@5'-AAA...CGGUA GGAUG...GCA-3'@LB@ GCGUGUCU@LB@ \|\|\|:\|\|\|\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -13.9362 kcal/mol@LB@Unfolding Energy - mRNA 1.92535 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 18 -- 25@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 4 -- 10@LB@
29	0.001844	0.2094	b2047	wcaJ	-13.26	0.032615	200 -- 222	7 -- 21	colanic biosynthesis UDP-glucose lipid carrier transferase	_____________199_____________________223\n_____________\|_______________________\|\n5'-GCA...ACAAC__________CUAAAAAA_____AGCGA...UAU-3'\n______________GAUGACAAAU________GCGCG\n______________\|\|\|:\|\|\|\|\|\|________\|\|\|\|\|\n______________CUAUUGUUUA________CGCGC\n3'-UUU...UACUA_______________________AGAAAG-5'\n_____________\|_______________________\|\n_____________22______________________6\n	203 -- 209	12 -- 18	-17.5174 kcal/mol	3.01646 kcal/mol	1.24179 kcal/mol	199 223@LB@ \| \|@LB@5'-GCA...ACAAC CUAAAAAA AGCGA...UAU-3'@LB@ GAUGACAAAU GCGCG@LB@ \|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUUUA CGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -17.5174 kcal/mol@LB@Unfolding Energy - mRNA 3.01646 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 200 -- 222@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 12 -- 18@LB@
51	0.004574	0.3024	b3529	yhjK	-9.99	0.121635	195 -- 213	1 -- 18	cyclic-di-GMP phosphodiesterase	_____________194_________________214\n_____________\|___________________\|\n5'-AGC...GGGGA_____UU_______AAG__GCUCG...AUC-3'\n______________GACAA__UGCGCGU___UC\n______________:\|\|\|\|__\|\|\|\|\|\|\|___\|\|\n______________UUGUU__ACGCGCA___AG\n3'-UUU...UACUA_____U________GAA__-5'\n_____________\|__________________\|\n_____________19_________________1\n	202 -- 208	6 -- 12	-16.8324 kcal/mol	5.6017 kcal/mol	1.24077 kcal/mol	194 214@LB@ \| \|@LB@5'-AGC...GGGGA UU AAG GCUCG...AUC-3'@LB@ GACAA UGCGCGU UC@LB@ :\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ UUGUU ACGCGCA AG@LB@3'-UUU...UACUA U GAA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -16.8324 kcal/mol@LB@Unfolding Energy - mRNA 5.6017 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 195 -- 213@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@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@
152	0.01445	0.3104	b0385	yaiC	-12.21	0.050169	39 -- 67	12 -- 42	diguanylate cyclase cellulose regualtor	_____________38_______________________________68\n_____________\|________________________________\|\n5'-CAA...CAACA_______________U______C_________UUAUG...CCG-3'\n______________AUCUCUGAA___AGG_GAUGAU_GUAAUAAGU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|_\|\|\|\|\|\|_:\|\|\|:\|\|:\|\n______________UAGAGACUU___UCC_CUACUA_UAUUGUUUA\n3'-UUU...UAAAG_________AAG__________C_________CGCGC...AAG-5'\n_____________\|________________________________\|\n_____________43_______________________________11\n	40 -- 46	35 -- 41	-28.8147 kcal/mol	7.19368 kcal/mol	9.40905 kcal/mol	38 68@LB@ \| \|@LB@5'-CAA...CAACA U C UUAUG...CCG-3'@LB@ AUCUCUGAA AGG GAUGAU GUAAUAAGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\| :\|\|\|:\|\|:\|@LB@ UAGAGACUU UCC CUACUA UAUUGUUUA@LB@3'-UUU...UAAAG AAG C CGCGC...AAG-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -28.8147 kcal/mol@LB@Unfolding Energy - mRNA 7.19368 kcal/mol@LB@Unfolding Energy - sRNA 9.40905 kcal/mol@LB@@LB@Position - mRNA 39 -- 67@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 35 -- 41@LB@
20	0.0008552	0.1448	b4137	cutA	-9.23	0.162618	220 -- 236	1 -- 16	divalent-cation tolerance protein copper sensitivity	_____________219_______________237\n_____________\|_________________\|\n5'-CAA...AAGUU_____AC_______G__GUGGU...CGG-3'\n______________CGAAU__CGCGUCU_UC\n______________\|:\|\|\|__\|\|\|\|\|\|\|_\|\|\n______________GUUUA__GCGCAGA_AG\n3'-UUU...CUAUU_____C________A__-5'\n_____________\|________________\|\n_____________17_______________1\n	227 -- 233	4 -- 10	-14.9299 kcal/mol	4.46216 kcal/mol	1.23857 kcal/mol	219 237@LB@ \| \|@LB@5'-CAA...AAGUU AC G GUGGU...CGG-3'@LB@ CGAAU CGCGUCU UC@LB@ \|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUUUA GCGCAGA AG@LB@3'-UUU...CUAUU C A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -14.9299 kcal/mol@LB@Unfolding Energy - mRNA 4.46216 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 220 -- 236@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@LB@
49	0.004401	0.299	b0093	ftsQ	-10.19	0.112476	259 -- 274	4 -- 20	divisome assembly protein membrane anchored protein involved in growth of wall at septum	_____________258_______________275\n_____________\|_________________\|\n5'-GCU...CCGCA________A________GGCGG...CCG-3'\n______________AUAAUGGA__CGCGUCU\n______________\|\|\|\|:::\|__\|\|\|\|\|\|\|\n______________UAUUGUUU__GCGCAGA\n3'-UUU...ACUAC________AC_______AAG-5'\n_____________\|_________________\|\n_____________21________________3\n	268 -- 274	4 -- 10	-13.8485 kcal/mol	2.40331 kcal/mol	1.25368 kcal/mol	258 275@LB@ \| \|@LB@5'-GCU...CCGCA A GGCGG...CCG-3'@LB@ AUAAUGGA CGCGUCU@LB@ \|\|\|\|:::\| \|\|\|\|\|\|\|@LB@ UAUUGUUU GCGCAGA@LB@3'-UUU...ACUAC AC AAG-5'@LB@ \| \|@LB@ 21 3@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -13.8485 kcal/mol@LB@Unfolding Energy - mRNA 2.40331 kcal/mol@LB@Unfolding Energy - sRNA 1.25368 kcal/mol@LB@@LB@Position - mRNA 259 -- 274@LB@Position - sRNA 4 -- 20@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 4 -- 10@LB@
114	0.01161	0.3104	b3392	hofP	-8.60	0.204995	138 -- 147	1 -- 11	DNA catabolic protein	_____________137_________148\n_____________\|___________\|\n5'-ACU...CGUGA___________GUUAA...GCG-3'\n______________GC_CGUUUUUC\n______________\|\|_\|\|\|:\|\|\|\|\n______________CG_GCAGAAAG\n3'-UUU...GUUUA__C________-5'\n_____________\|__________\|\n_____________12_________1\n	141 -- 147	1 -- 7	-12.6405 kcal/mol	2.86562 kcal/mol	1.17076 kcal/mol	137 148@LB@ \| \|@LB@5'-ACU...CGUGA GUUAA...GCG-3'@LB@ GC CGUUUUUC@LB@ \|\| \|\|\|:\|\|\|\|@LB@ CG GCAGAAAG@LB@3'-UUU...GUUUA C -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.6405 kcal/mol@LB@Unfolding Energy - mRNA 2.86562 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 138 -- 147@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 1 -- 7@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching