Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
67	0.005347	0.2645	b4278	insG	-9.22	0.173962	151 -- 164	45 -- 58	IS4 transposase	_____________150____________165\n_____________\|______________\|\n5'-GUU...CGAUC_______U______GAAUC...CUC-3'\n______________CAGUGGC_GUGUAA\n______________\|\|\|\|\|\|\|_:\|\|:\|\|\n______________GUCACCG_UACGUU\n3'-UUU...UUUUA_______U______ACCGG...UUG-5'\n_____________\|______________\|\n_____________59_____________44\n	151 -- 157	52 -- 58	-18.8848 kcal/mol	6.17717 kcal/mol	3.48403 kcal/mol	150 165@LB@ \| \|@LB@5'-GUU...CGAUC U GAAUC...CUC-3'@LB@ CAGUGGC GUGUAA@LB@ \|\|\|\|\|\|\| :\|\|:\|\|@LB@ GUCACCG UACGUU@LB@3'-UUU...UUUUA U ACCGG...UUG-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -18.8848 kcal/mol@LB@Unfolding Energy - mRNA 6.17717 kcal/mol@LB@Unfolding Energy - sRNA 3.48403 kcal/mol@LB@@LB@Position - mRNA 151 -- 164@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 52 -- 58@LB@
184	0.02285	0.4143	b4312	fimB	-10.59	0.091292	169 -- 221	1 -- 58	tyrosine recombinase/inversion of on/off regulator of fimA	_____________168________________________________________________________________222\n_____________\|__________________________________________________________________\|\n5'-AUG...ACAGC_____C___UC______UA_____G________________________AGAAUA____UG_____AAAAA...GUA-3'\n______________UAGUG_GCG__UGUAAU____UAA_GGAAAA___________ACGAUGA______AGGC__AUAAC\n______________:\|\|\|\|_\|\|:__\|\|:\|\|\|____:\|\|_:\|\|\|\|\|___________\|\|:\|\|:\|______\|\|\|\|__\|\|\|\|\|\n______________GUCAC_CGU__ACGUUA____GUU_UCUUUU___________UGUUAUU______UCCG__UAUUG\n3'-UUU...UUUUA_________U_______CCGG___G______AUUUUAGACAC_________________UA_____-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	198 -- 204	12 -- 18	-31.4649 kcal/mol	8.72248 kcal/mol	12.1476 kcal/mol	168 222@LB@ \| \|@LB@5'-AUG...ACAGC C UC UA G AGAAUA UG AAAAA...GUA-3'@LB@ UAGUG GCG UGUAAU UAA GGAAAA ACGAUGA AGGC AUAAC@LB@ :\|\|\|\| \|\|: \|\|:\|\|\| :\|\| :\|\|\|\|\| \|\|:\|\|:\| \|\|\|\| \|\|\|\|\|@LB@ GUCAC CGU ACGUUA GUU UCUUUU UGUUAUU UCCG UAUUG@LB@3'-UUU...UUUUA U CCGG G AUUUUAGACAC UA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -31.4649 kcal/mol@LB@Unfolding Energy - mRNA 8.72248 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 169 -- 221@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
71	0.005918	0.2791	b4348	hsdS	-11.53	0.056880	66 -- 85	42 -- 60	specificity determinant for hsdM and hsdR	_____________65___________________86\n_____________\|____________________\|\n5'-CUG...GAUGU_____C_____AA_______GCGAA...UAA-3'\n______________AUUAG_GGCAG__GCGAUGG\n______________\|\|:\|\|_\|\|\|\|:__\|\|:\|\|\|\|\n______________UAGUC_CCGUU__CGUUACC\n3'-UUU...CCUUU_____A_____A________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________61___________________41\n	79 -- 85	42 -- 48	-21.0522 kcal/mol	5.82821 kcal/mol	3.69672 kcal/mol	65 86@LB@ \| \|@LB@5'-CUG...GAUGU C AA GCGAA...UAA-3'@LB@ AUUAG GGCAG GCGAUGG@LB@ \|\|:\|\| \|\|\|\|: \|\|:\|\|\|\|@LB@ UAGUC CCGUU CGUUACC@LB@3'-UUU...CCUUU A A GGGUU...UUG-5'@LB@ \| \|@LB@ 61 41@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -21.0522 kcal/mol@LB@Unfolding Energy - mRNA 5.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.69672 kcal/mol@LB@@LB@Position - mRNA 66 -- 85@LB@Position - sRNA 42 -- 60@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
100	0.009417	0.3118	b4363	yjjB	-11.70	0.052026	267 -- 280	41 -- 54	DUF3815 family inner membrane protein	_____________266____________281\n_____________\|______________\|\n5'-ACU...CGGUC___UU_________GUUCA...GGG-3'\n______________GGC__UGCGAUGGU\n______________\|\|\|__\|\|\|:\|\|\|\|:\n______________CCG__ACGUUACCG\n3'-UUU...AGUCA___UU_________GGUUG...UUG-5'\n_____________\|______________\|\n_____________55_____________40\n	274 -- 280	41 -- 47	-20.909 kcal/mol	5.32115 kcal/mol	3.89026 kcal/mol	266 281@LB@ \| \|@LB@5'-ACU...CGGUC UU GUUCA...GGG-3'@LB@ GGC UGCGAUGGU@LB@ \|\|\| \|\|\|:\|\|\|\|:@LB@ CCG ACGUUACCG@LB@3'-UUU...AGUCA UU GGUUG...UUG-5'@LB@ \| \|@LB@ 55 40@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -20.909 kcal/mol@LB@Unfolding Energy - mRNA 5.32115 kcal/mol@LB@Unfolding Energy - sRNA 3.89026 kcal/mol@LB@@LB@Position - mRNA 267 -- 280@LB@Position - sRNA 41 -- 54@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
88	0.007723	0.2889	b4403	yjtD	-13.82	0.016006	193 -- 211	1 -- 21	putative methyltransferase	_____________192___________________212\n_____________\|_____________________\|\n5'-AUU...GAAGA_________U___________GAUUA...UUG-3'\n______________GUGGCAAUA___GCGUAUAAC\n______________\|\|\|:\|\|\|\|\|___\|\|:\|\|\|\|\|\|\n______________CACUGUUAU___CGUAUAUUG\n3'-UUU...UUAGA_________UUC_________-5'\n_____________\|____________________\|\n_____________22___________________1\n	205 -- 211	1 -- 7	-21.8234 kcal/mol	3.59402 kcal/mol	4.41334 kcal/mol	192 212@LB@ \| \|@LB@5'-AUU...GAAGA U GAUUA...UUG-3'@LB@ GUGGCAAUA GCGUAUAAC@LB@ \|\|\|:\|\|\|\|\| \|\|:\|\|\|\|\|\|@LB@ CACUGUUAU CGUAUAUUG@LB@3'-UUU...UUAGA UUC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -21.8234 kcal/mol@LB@Unfolding Energy - mRNA 3.59402 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 193 -- 211@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 1 -- 7@LB@
26	0.00144	0.1863	b4406	yaeP	-8.75	0.213688	187 -- 204	2 -- 20	UPF0253 family protein	_____________186_________________205\n_____________\|___________________\|\n5'-ACC...AGUGC_____G_____________AAAAA...UGC-3'\n______________UGACA__GAGGGCAUGUGG\n______________\|\|\|\|\|__:\|:\|\|\|\|\|:\|::\n______________ACUGU__UUUCCGUAUAUU\n3'-UUU...UAGAC_____UA____________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	197 -- 203	3 -- 9	-20.0716 kcal/mol	7.09254 kcal/mol	4.22649 kcal/mol	186 205@LB@ \| \|@LB@5'-ACC...AGUGC G AAAAA...UGC-3'@LB@ UGACA GAGGGCAUGUGG@LB@ \|\|\|\|\| :\|:\|\|\|\|\|:\|::@LB@ ACUGU UUUCCGUAUAUU@LB@3'-UUU...UAGAC UA G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -20.0716 kcal/mol@LB@Unfolding Energy - mRNA 7.09254 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 187 -- 204@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
105	0.009758	0.3118	b4478	dgoD	-14.76	0.009064	185 -- 203	43 -- 60	D-galactonate dehydratase	_____________184_________________204\n_____________\|___________________\|\n5'-AAA...GGCGU___G__A____________AAAAU...UGA-3'\n______________AUC_AG_GGCAGUGCAAUG\n______________\|\|\|_\|\|_\|\|\|\|:\|\|\|\|\|\|\|\n______________UAG_UC_CCGUUACGUUAC\n3'-UUU...CCUUU______A____________CGGGU...UUG-5'\n_____________\|___________________\|\n_____________61__________________42\n	197 -- 203	43 -- 49	-22.2033 kcal/mol	3.91427 kcal/mol	3.52557 kcal/mol	184 204@LB@ \| \|@LB@5'-AAA...GGCGU G A AAAAU...UGA-3'@LB@ AUC AG GGCAGUGCAAUG@LB@ \|\|\| \|\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ UAG UC CCGUUACGUUAC@LB@3'-UUU...CCUUU A CGGGU...UUG-5'@LB@ \| \|@LB@ 61 42@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -22.2033 kcal/mol@LB@Unfolding Energy - mRNA 3.91427 kcal/mol@LB@Unfolding Energy - sRNA 3.52557 kcal/mol@LB@@LB@Position - mRNA 185 -- 203@LB@Position - sRNA 43 -- 60@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 43 -- 49@LB@
18	0.0007704	0.1438	b4526	ydaE	-7.35	0.372707	186 -- 222	21 -- 54	conserved protein Rac prophage	_____________185___________________________________223\n_____________\|_____________________________________\|\n5'-ACU...GUAAA_____A__C_____GA____UA____________G__CUUAC...UAU-3'\n______________GGCGG_GU_AUGGU__UGAC__AGAAAAUAAAAU_UG\n______________\|\|\|::_\|:_\|\|\|\|:__::\|\|__\|\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________CCGUU_CG_UACCG__GUUG__UCUUUUAUUUUA_AC\n3'-UUU...AGUCA_____A__U_____G___________________G__ACUGU...UUG-5'\n_____________\|_____________________________________\|\n_____________55____________________________________20\n	212 -- 218	25 -- 31	-28.7009 kcal/mol	12.2907 kcal/mol	9.06413 kcal/mol	185 223@LB@ \| \|@LB@5'-ACU...GUAAA A C GA UA G CUUAC...UAU-3'@LB@ GGCGG GU AUGGU UGAC AGAAAAUAAAAU UG@LB@ \|\|\|:: \|: \|\|\|\|: ::\|\| \|\|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ CCGUU CG UACCG GUUG UCUUUUAUUUUA AC@LB@3'-UUU...AGUCA A U G G ACUGU...UUG-5'@LB@ \| \|@LB@ 55 20@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -28.7009 kcal/mol@LB@Unfolding Energy - mRNA 12.2907 kcal/mol@LB@Unfolding Energy - sRNA 9.06413 kcal/mol@LB@@LB@Position - mRNA 186 -- 222@LB@Position - sRNA 21 -- 54@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 25 -- 31@LB@
95	0.008588	0.304	b4551	yheV	-11.20	0.067476	257 -- 273	47 -- 65	DUF2387 family putative metal-binding protein	_____________256_________________274\n_____________\|___________________\|\n5'-AUC...GCGCA___U_____A_________GGCGC...UUG-3'\n______________GGA___UCA_UGGCGAUGU\n______________\|\|\|___\|\|\|_\|\|\|\|:\|\|\|:\n______________CCU___AGU_ACCGUUACG\n3'-UUU...UACAA___UUU___C_________UUACC...UUG-5'\n_____________\|___________________\|\n_____________66__________________46\n	267 -- 273	47 -- 53	-19.3348 kcal/mol	4.06987 kcal/mol	4.06844 kcal/mol	256 274@LB@ \| \|@LB@5'-AUC...GCGCA U A GGCGC...UUG-3'@LB@ GGA UCA UGGCGAUGU@LB@ \|\|\| \|\|\| \|\|\|\|:\|\|\|:@LB@ CCU AGU ACCGUUACG@LB@3'-UUU...UACAA UUU C UUACC...UUG-5'@LB@ \| \|@LB@ 66 46@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.3348 kcal/mol@LB@Unfolding Energy - mRNA 4.06987 kcal/mol@LB@Unfolding Energy - sRNA 4.06844 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 47 -- 65@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 47 -- 53@LB@
191	0.02382	0.4194	b4567	yjjZ	-11.31	0.063816	288 -- 298	51 -- 61	uncharacterized protein	_____________287_________299\n_____________\|___________\|\n5'-CGG...CGUCA___________GA-3'\n______________GAUCAGUGGCG\n______________:\|\|\|\|\|\|\|\|\|:\n______________UUAGUCACCGU\n3'-UUU...ACCUU___________UACGU...UUG-5'\n_____________\|___________\|\n_____________62__________50\n	292 -- 298	51 -- 57	-17.6489 kcal/mol	3.61415 kcal/mol	2.72961 kcal/mol	287 299@LB@ \| \|@LB@5'-CGG...CGUCA GA-3'@LB@ GAUCAGUGGCG@LB@ :\|\|\|\|\|\|\|\|\|:@LB@ UUAGUCACCGU@LB@3'-UUU...ACCUU UACGU...UUG-5'@LB@ \| \|@LB@ 62 50@LB@@LB@@LB@Energy -11.31 kcal/mol@LB@Hybridization Energy -17.6489 kcal/mol@LB@Unfolding Energy - mRNA 3.61415 kcal/mol@LB@Unfolding Energy - sRNA 2.72961 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 51 -- 61@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 51 -- 57@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