Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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	Additional homologs
143	0.02405	0.526	b3292	zntR	-11.17	0.055543	275 -- 285	1 -- 12	zntA gene transcriptional activator		_____________274__________286\n_____________\|____________\|\n5'-UGA...CAGCA____________AUGAA...CUG-3'\n______________GAUGAUGG_AGC\n______________:\|\|\|\|\|\|:_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	276 -- 282	5 -- 11	-12.3439 kcal/mol	1.13072 kcal/mol	0.0394463 kcal/mol	274 286@LB@ \| \|@LB@5'-UGA...CAGCA AUGAA...CUG-3'@LB@ GAUGAUGG AGC@LB@ :\|\|\|\|\|\|: \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -12.3439 kcal/mol@LB@Unfolding Energy - mRNA 1.13072 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 275 -- 285@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 5 -- 11@LB@
198	0.03373	0.5555	b3915	fieF	-7.92	0.235762	278 -- 297	1 -- 19	ferrous iron and zinc transporter		_____________277__________________298\n_____________\|____________________\|\n5'-AAA...CUGAU____A__UU__C________AUA-3'\n______________UAAA_UU__UG_AUGGUGGU\n______________\|\|\|\|_\|\|__\|\|_\|\|\|:\|:\|:\n______________AUUU_AA__AC_UACUAUCG\n3'-UUU...UAUUU____C__UU___________-5'\n_____________\|___________________\|\n_____________20__________________1\n	291 -- 297	1 -- 7	-10.0103 kcal/mol	2.02347 kcal/mol	0.0638423 kcal/mol	277 298@LB@ \| \|@LB@5'-AAA...CUGAU A UU C AUA-3'@LB@ UAAA UU UG AUGGUGGU@LB@ \|\|\|\| \|\| \|\| \|\|\|:\|:\|:@LB@ AUUU AA AC UACUAUCG@LB@3'-UUU...UAUUU C UU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -10.0103 kcal/mol@LB@Unfolding Energy - mRNA 2.02347 kcal/mol@LB@Unfolding Energy - sRNA 0.0638423 kcal/mol@LB@@LB@Position - mRNA 278 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 1 -- 7@LB@
125	0.01993	0.5155	b2347	yfdC	-8.10	0.220050	281 -- 291	15 -- 25	putative inner membrane protein		_____________280_________292\n_____________\|___________\|\n5'-GCA...AUAGA___________ACCGA...UCC-3'\n______________AAUAGAUGAAG\n______________\|\|\|\|:\|\|:\|\|\|\n______________UUAUUUAUUUC\n3'-UUU...UGCCA___________AAUUA...UCG-5'\n_____________\|___________\|\n_____________26__________14\n	285 -- 291	15 -- 21	-8.49349 kcal/mol	0.301625 kcal/mol	0.0943905 kcal/mol	280 292@LB@ \| \|@LB@5'-GCA...AUAGA ACCGA...UCC-3'@LB@ AAUAGAUGAAG@LB@ \|\|\|\|:\|\|:\|\|\|@LB@ UUAUUUAUUUC@LB@3'-UUU...UGCCA AAUUA...UCG-5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -8.49349 kcal/mol@LB@Unfolding Energy - mRNA 0.301625 kcal/mol@LB@Unfolding Energy - sRNA 0.0943905 kcal/mol@LB@@LB@Position - mRNA 281 -- 291@LB@Position - sRNA 15 -- 25@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 15 -- 21@LB@
107	0.01649	0.5059	b0830	gsiB	-12.67	0.025954	282 -- 298	1 -- 18	glutathione ABC transporter periplasmic binding protein		_____________281________________299\n_____________\|__________________\|\n5'-GGC...CUGCC____AU____________GG-3'\n______________AAAG___GUGGUGGUGGC\n______________\|\|\|\|___:\|\|:\|\|:\|:\|\|\n______________UUUC___UACUACUAUCG\n3'-UUU...AUUUA____AAU___________-5'\n_____________\|_________________\|\n_____________19________________1\n	292 -- 298	1 -- 7	-15.5562 kcal/mol	2.82856 kcal/mol	0.0611543 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC AU GG-3'@LB@ AAAG GUGGUGGUGGC@LB@ \|\|\|\| :\|\|:\|\|:\|:\|\|@LB@ UUUC UACUACUAUCG@LB@3'-UUU...AUUUA AAU -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -15.5562 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
193	0.03268	0.5507	b2513	yfgM	-8.78	0.166450	282 -- 288	52 -- 58	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________281_____289\n_____________\|_______\|\n5'-GGC...CUGUU_______UUUUG...UUG-3'\n______________GGGGUGA\n______________\|\|\|\|\|:\|\n______________CCCCAUU\n3'-UUU...UUUAU_______UGUCU...UCG-5'\n_____________\|_______\|\n_____________59______51\n	282 -- 288	52 -- 58	-10.2706 kcal/mol	1.44003 kcal/mol	0.0533 kcal/mol	281 289@LB@ \| \|@LB@5'-GGC...CUGUU UUUUG...UUG-3'@LB@ GGGGUGA@LB@ \|\|\|\|\|:\|@LB@ CCCCAUU@LB@3'-UUU...UUUAU UGUCU...UCG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -10.2706 kcal/mol@LB@Unfolding Energy - mRNA 1.44003 kcal/mol@LB@Unfolding Energy - sRNA 0.0533 kcal/mol@LB@@LB@Position - mRNA 282 -- 288@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 52 -- 58@LB@
171	0.02792	0.531	b2754	ygbF	-9.28	0.134010	284 -- 290	53 -- 59	CRISPR adaptation ssRNA endonuclease		_____________283_____291\n_____________\|_______\|\n5'-UGG...CGUGC_______UAUGU...GUG-3'\n______________AGGGGUA\n______________\|\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	284 -- 290	53 -- 59	-11.8962 kcal/mol	2.55869 kcal/mol	0.0564539 kcal/mol	283 291@LB@ \| \|@LB@5'-UGG...CGUGC UAUGU...GUG-3'@LB@ AGGGGUA@LB@ \|\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.28 kcal/mol@LB@Hybridization Energy -11.8962 kcal/mol@LB@Unfolding Energy - mRNA 2.55869 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 284 -- 290@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 53 -- 59@LB@
22	0.001016	0.1516	b0734	cydB	-13.57	0.015928	285 -- 300	49 -- 64	cytochrome d terminal oxidase subunit II		_____________284_____________300\n_____________\|_______________\|\n5'-CGA...GUUUC__C_____________-3'\n______________GA_AUGGGGGUGGGCA\n______________\|\|_\|\|:\|\|\|\|\|:::\|\|\n______________CU_UAUCCCCAUUUGU\n3'-UUU...GCCAA__U_____________CUGUA...UCG-5'\n_____________\|________________\|\n_____________65_______________48\n	294 -- 300	49 -- 55	-19.142 kcal/mol	4.83222 kcal/mol	0.738518 kcal/mol	284 300@LB@ \| \|@LB@5'-CGA...GUUUC C -3'@LB@ GA AUGGGGGUGGGCA@LB@ \|\| \|\|:\|\|\|\|\|:::\|\|@LB@ CU UAUCCCCAUUUGU@LB@3'-UUU...GCCAA U CUGUA...UCG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.142 kcal/mol@LB@Unfolding Energy - mRNA 4.83222 kcal/mol@LB@Unfolding Energy - sRNA 0.738518 kcal/mol@LB@@LB@Position - mRNA 285 -- 300@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 49 -- 55@LB@
176	0.02871	0.5353	b0518	fdrA	-11.39	0.049925	288 -- 297	6 -- 15	putative NAD(P)-binding acyl-CoA synthetase	b0320	_____________287________298\n_____________\|__________\|\n5'-CGC...AAAAU__________UUU-3'\n______________GUUGAUGAUG\n______________\|\|\|:\|\|\|\|\|\|\n______________CAAUUACUAC\n3'-UUU...UAUUU__________UAUCG-5'\n_____________\|__________\|\n_____________16_________5\n	291 -- 297	6 -- 12	-11.8608 kcal/mol	0.426728 kcal/mol	0.0442104 kcal/mol	287 298@LB@ \| \|@LB@5'-CGC...AAAAU UUU-3'@LB@ GUUGAUGAUG@LB@ \|\|\|:\|\|\|\|\|\|@LB@ CAAUUACUAC@LB@3'-UUU...UAUUU UAUCG-5'@LB@ \| \|@LB@ 16 5@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -11.8608 kcal/mol@LB@Unfolding Energy - mRNA 0.426728 kcal/mol@LB@Unfolding Energy - sRNA 0.0442104 kcal/mol@LB@@LB@Position - mRNA 288 -- 297@LB@Position - sRNA 6 -- 15@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 6 -- 12@LB@
183	0.03025	0.5427	b0999	cbpM	-7.72	0.255487	289 -- 296	53 -- 60	modulator of CbpA co-chaperone		_____________288______297\n_____________\|________\|\n5'-AUC...CGGUU________GUUG-3'\n______________UGGGGGUG\n______________\|:\|\|\|\|\|:\n______________AUCCCCAU\n3'-UUU...ACUUU________UUGUC...UCG-5'\n_____________\|________\|\n_____________61_______52\n	290 -- 296	53 -- 59	-12.779 kcal/mol	4.99203 kcal/mol	0.0710089 kcal/mol	288 297@LB@ \| \|@LB@5'-AUC...CGGUU GUUG-3'@LB@ UGGGGGUG@LB@ \|:\|\|\|\|\|:@LB@ AUCCCCAU@LB@3'-UUU...ACUUU UUGUC...UCG-5'@LB@ \| \|@LB@ 61 52@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -12.779 kcal/mol@LB@Unfolding Energy - mRNA 4.99203 kcal/mol@LB@Unfolding Energy - sRNA 0.0710089 kcal/mol@LB@@LB@Position - mRNA 289 -- 296@LB@Position - sRNA 53 -- 60@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 53 -- 59@LB@
85	0.01268	0.4896	b1827	kdgR	-11.91	0.038409	291 -- 299	56 -- 64	KDG regulon transcriptional repressor		_____________290_______300\n_____________\|_________\|\n5'-GCC...AGCGC_________A-3'\n______________GAAAUAGGG\n______________\|\|\|\|\|\|\|\|\|\n______________CUUUAUCCC\n3'-UUU...GCCAA_________CAUUU...UCG-5'\n_____________\|_________\|\n_____________65________55\n	293 -- 299	56 -- 62	-12.6296 kcal/mol	0.690209 kcal/mol	0.02823 kcal/mol	290 300@LB@ \| \|@LB@5'-GCC...AGCGC A-3'@LB@ GAAAUAGGG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CUUUAUCCC@LB@3'-UUU...GCCAA CAUUU...UCG-5'@LB@ \| \|@LB@ 65 55@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -12.6296 kcal/mol@LB@Unfolding Energy - mRNA 0.690209 kcal/mol@LB@Unfolding Energy - sRNA 0.02823 kcal/mol@LB@@LB@Position - mRNA 291 -- 299@LB@Position - sRNA 56 -- 64@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 56 -- 62@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