Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
39	0.0008004	0.06626	b1533	eamA	-12.23	0.058236	233 -- 264	16 -- 49	cysteine and O-acetyl-L-serine efflux system		_____________232_________________________________265\n_____________\|___________________________________\|\n5'-GUU...CUACU__UA_____CGUA___G_______A__________UCAUC...UGA-3'\n______________GG__GUGGU____UGG___GGCUA__AUUUUGUGG\n______________\|\|__\|\|\|\|\|____\|\|\|___:\|\|\|\|__\|\|\|\|\|:\|\|\|\n______________CC__CACCA____ACC___UCGAU__UAAAAUACC\n3'-UUU...CGAUU__UC_____AGG____AUG_____CG_________CAAUA...UCG-5'\n_____________\|___________________________________\|\n_____________50__________________________________15\n	258 -- 264	16 -- 22	-27.5137 kcal/mol	10.7081 kcal/mol	4.57266 kcal/mol	232 265@LB@ \| \|@LB@5'-GUU...CUACU UA CGUA G A UCAUC...UGA-3'@LB@ GG GUGGU UGG GGCUA AUUUUGUGG@LB@ \|\| \|\|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CC CACCA ACC UCGAU UAAAAUACC@LB@3'-UUU...CGAUU UC AGG AUG CG CAAUA...UCG-5'@LB@ \| \|@LB@ 50 15@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.5137 kcal/mol@LB@Unfolding Energy - mRNA 10.7081 kcal/mol@LB@Unfolding Energy - sRNA 4.57266 kcal/mol@LB@@LB@Position - mRNA 233 -- 264@LB@Position - sRNA 16 -- 49@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
119	0.005024	0.1407	b2342	fadI	-9.59	0.197573	199 -- 214	6 -- 21	beta-ketoacyl-CoA thiolase anaerobic subunit		_____________198______________215\n_____________\|________________\|\n5'-UCC...GAGUG________CAG_____ACCGC...AUG-3'\n______________UUAUGGGU___GUUUU\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAUACCCA___CAAAA\n3'-UUU...CGUAA________AUA_____AGUCG-5'\n_____________\|________________\|\n_____________22_______________5\n	200 -- 206	14 -- 20	-13.0434 kcal/mol	3.24348 kcal/mol	0.208077 kcal/mol	198 215@LB@ \| \|@LB@5'-UCC...GAGUG CAG ACCGC...AUG-3'@LB@ UUAUGGGU GUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAUACCCA CAAAA@LB@3'-UUU...CGUAA AUA AGUCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0434 kcal/mol@LB@Unfolding Energy - mRNA 3.24348 kcal/mol@LB@Unfolding Energy - sRNA 0.208077 kcal/mol@LB@@LB@Position - mRNA 199 -- 214@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 14 -- 20@LB@
22	0.0002072	0.03165	b2341	fadJ	-8.08	0.343546	182 -- 217	1 -- 44	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase		_____________181__________________________________________218\n_____________\|____________________________________________\|\n5'-CAU...GGCAA__________A________AAUA______AA____ACA______GUUUA...CGG-3'\n______________UGGUUCU_GG___GGC_GG______AUGG___AUG____UCAGC\n______________\|\|\|\|\|\|:_\|\|___:\|\|_:\|______\|\|\|\|___\|\|\|____\|\|\|\|\|\n______________ACCAAGG_CC___UCG_UC______UACC___UAC____AGUCG\n3'-UUU...CCUCC_______A__AUG___A__GUAAAA____CAA___AAAA_____-5'\n_____________\|___________________________________________\|\n_____________45__________________________________________1\n	182 -- 188	38 -- 44	-22.4043 kcal/mol	9.71146 kcal/mol	4.60934 kcal/mol	181 218@LB@ \| \|@LB@5'-CAU...GGCAA A AAUA AA ACA GUUUA...CGG-3'@LB@ UGGUUCU GG GGC GG AUGG AUG UCAGC@LB@ \|\|\|\|\|\|: \|\| :\|\| :\| \|\|\|\| \|\|\| \|\|\|\|\|@LB@ ACCAAGG CC UCG UC UACC UAC AGUCG@LB@3'-UUU...CCUCC A AUG A GUAAAA CAA AAAA -5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -22.4043 kcal/mol@LB@Unfolding Energy - mRNA 9.71146 kcal/mol@LB@Unfolding Energy - sRNA 4.60934 kcal/mol@LB@@LB@Position - mRNA 182 -- 217@LB@Position - sRNA 1 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 38 -- 44@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB		_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
151	0.007423	0.1652	b2895	fldB	-9.53	0.202764	191 -- 224	1 -- 31	flavodoxin 2		_____________190__________________________________225\n_____________\|____________________________________\|\n5'-CGG...CGAGA____UA____AUGAA_______CU_______A____UCCAG...AUA-3'\n______________AGCU__CGUU_____UAUGGGU____UUUUU_CGGU\n______________\|\|\|\|__\|:\|\|_____\|\|\|\|\|\|\|____\|\|\|\|\|_\|:\|:\n______________UCGA__GUAA_____AUACCCA____AAAAA_GUCG\n3'-UUU...CCAUG____UC____A___________AUAC__________-5'\n_____________\|___________________________________\|\n_____________32__________________________________1\n	206 -- 212	14 -- 20	-17.4845 kcal/mol	6.4701 kcal/mol	1.48722 kcal/mol	190 225@LB@ \| \|@LB@5'-CGG...CGAGA UA AUGAA CU A UCCAG...AUA-3'@LB@ AGCU CGUU UAUGGGU UUUUU CGGU@LB@ \|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|:\|:@LB@ UCGA GUAA AUACCCA AAAAA GUCG@LB@3'-UUU...CCAUG UC A AUAC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -17.4845 kcal/mol@LB@Unfolding Energy - mRNA 6.4701 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 191 -- 224@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 14 -- 20@LB@
188	0.01085	0.1919	b1878	flhE	-11.23	0.096033	252 -- 283	16 -- 51	proton seal during flagellar secretion		_____________251__________________________________284\n_____________\|____________________________________\|\n5'-CGU...CCGCC__________A__G___CA____A____GUG_____AAUUA...AUC-3'\n______________GGGGAGG_GG__U_UGG___GGC_AGUA___UA_GG\n______________::\|\|\|\|\|_\|\|__:_\|\|\|___:\|\|_\|\|:\|___\|\|_\|\|\n______________UUCCUCC_CC__G_ACC___UCG_UCGU___AU_CC\n3'-UUU...UCCGA_______A__AA_G___AUG___A____AAA__A__CAAUA...UCG-5'\n_____________\|____________________________________\|\n_____________52___________________________________15\n	252 -- 258	45 -- 51	-25.2373 kcal/mol	9.34808 kcal/mol	4.65624 kcal/mol	251 284@LB@ \| \|@LB@5'-CGU...CCGCC A G CA A GUG AAUUA...AUC-3'@LB@ GGGGAGG GG U UGG GGC AGUA UA GG@LB@ ::\|\|\|\|\| \|\| : \|\|\| :\|\| \|\|:\| \|\| \|\|@LB@ UUCCUCC CC G ACC UCG UCGU AU CC@LB@3'-UUU...UCCGA A AA G AUG A AAA A CAAUA...UCG-5'@LB@ \| \|@LB@ 52 15@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -25.2373 kcal/mol@LB@Unfolding Energy - mRNA 9.34808 kcal/mol@LB@Unfolding Energy - sRNA 4.65624 kcal/mol@LB@@LB@Position - mRNA 252 -- 283@LB@Position - sRNA 16 -- 51@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 45 -- 51@LB@
194	0.01107	0.1919	b3288	fmt	-14.89	0.012048	76 -- 114	11 -- 48	10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase		_____________75_______________________________________115\n_____________\|________________________________________\|\n5'-AUU...AGCAU___A___AUCA___________AAACUG_______A____CUGUC...UGU-3'\n______________GAG_UGG____CCUGGU_CGGC______UUUAUGG_UUAU\n______________\|\|\|_\|\|\|____\|\|\|\|\|\|_\|:\|\|______\|\|\|\|\|\|\|_\|\|\|\|\n______________CUC_ACC____GGACCA_GUCG______AAAUACC_AAUA\n3'-UUU...GAUUC___C___AA________U____AUCGUA_______C____CAAAA...UCG-5'\n_____________\|________________________________________\|\n_____________49_______________________________________10\n	103 -- 109	16 -- 22	-29.2084 kcal/mol	9.72928 kcal/mol	4.59227 kcal/mol	75 115@LB@ \| \|@LB@5'-AUU...AGCAU A AUCA AAACUG A CUGUC...UGU-3'@LB@ GAG UGG CCUGGU CGGC UUUAUGG UUAU@LB@ \|\|\| \|\|\| \|\|\|\|\|\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|@LB@ CUC ACC GGACCA GUCG AAAUACC AAUA@LB@3'-UUU...GAUUC C AA U AUCGUA C CAAAA...UCG-5'@LB@ \| \|@LB@ 49 10@LB@@LB@@LB@Energy -14.89 kcal/mol@LB@Hybridization Energy -29.2084 kcal/mol@LB@Unfolding Energy - mRNA 9.72928 kcal/mol@LB@Unfolding Energy - sRNA 4.59227 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 11 -- 48@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 16 -- 22@LB@
75	0.002192	0.09621	b3950	frwB	-15.16	0.010002	30 -- 54	11 -- 46	putative enzyme IIB component of PTS	b3899	_____________29___________________________________55\n_____________\|____________________________________\|\n5'-GCA...CUGCC_______GAA________A_________________AUCGC...GGG-3'\n______________GGUGGUU________GGC_AGC______UGGGUUAU\n______________\|\|\|\|\|\|\|________:\|\|_\|\|\|______\|\|\|\|\|\|\|\|\n______________CCACCAA________UCG_UCG______ACCCAAUA\n3'-UUU...UUCCU_______GGACCAUG___A___UAAAAU________CAAAA...UCG-5'\n_____________\|____________________________________\|\n_____________47___________________________________10\n	48 -- 54	11 -- 17	-24.5661 kcal/mol	4.81447 kcal/mol	4.59143 kcal/mol	29 55@LB@ \| \|@LB@5'-GCA...CUGCC GAA A AUCGC...GGG-3'@LB@ GGUGGUU GGC AGC UGGGUUAU@LB@ \|\|\|\|\|\|\| :\|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CCACCAA UCG UCG ACCCAAUA@LB@3'-UUU...UUCCU GGACCAUG A UAAAAU CAAAA...UCG-5'@LB@ \| \|@LB@ 47 10@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -24.5661 kcal/mol@LB@Unfolding Energy - mRNA 4.81447 kcal/mol@LB@Unfolding Energy - sRNA 4.59143 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 11 -- 46@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 11 -- 17@LB@
61	0.001594	0.08781	b1905	ftnA	-13.68	0.025904	280 -- 298	27 -- 44	ferritin iron storage protein (cytoplasmic)		_____________279_________________299\n_____________\|___________________\|\n5'-CAU...GCAAA__A_CG_____________UC-3'\n______________UG_G__CCUGGUGCAGCUA\n______________\|\|_\|__\|\|\|\|\|\|:\|\|\|\|\|\|\n______________AC_C__GGACCAUGUCGAU\n3'-UUU...CCUCC____AA_____________CGUAA...UCG-5'\n_____________\|___________________\|\n_____________45__________________26\n	292 -- 298	27 -- 33	-25.294 kcal/mol	7.30746 kcal/mol	4.30747 kcal/mol	279 299@LB@ \| \|@LB@5'-CAU...GCAAA A CG UC-3'@LB@ UG G CCUGGUGCAGCUA@LB@ \|\| \| \|\|\|\|\|\|:\|\|\|\|\|\|@LB@ AC C GGACCAUGUCGAU@LB@3'-UUU...CCUCC AA CGUAA...UCG-5'@LB@ \| \|@LB@ 45 26@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -25.294 kcal/mol@LB@Unfolding Energy - mRNA 7.30746 kcal/mol@LB@Unfolding Energy - sRNA 4.30747 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 27 -- 44@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 27 -- 33@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase		_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 27 -- 33@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:

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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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