Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
141	0.006483	0.1605	b2474	tmcA	-12.94	0.065378	86 -- 105	35 -- 54	elongator methionine tRNA (ac4C34) acetyltransferase	_____________85___________________106\n_____________\|____________________\|\n5'-GAU...AGACA__________U__CAC____CAGCA...UUG-3'\n______________GUUUCACUCA_GG___UUCU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|___\|\|\|:\n______________CAAAGUGAGU_CC___AAGG\n3'-UUU...AGCAA__________C__CUA____UACGA...GCA-5'\n_____________\|____________________\|\n_____________55___________________34\n	89 -- 95	45 -- 51	-18.4772 kcal/mol	3.58569 kcal/mol	1.95269 kcal/mol	85 106@LB@ \| \|@LB@5'-GAU...AGACA U CAC CAGCA...UUG-3'@LB@ GUUUCACUCA GG UUCU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|\|\|:@LB@ CAAAGUGAGU CC AAGG@LB@3'-UUU...AGCAA C CUA UACGA...GCA-5'@LB@ \| \|@LB@ 55 34@LB@@LB@@LB@Energy -12.94 kcal/mol@LB@Hybridization Energy -18.4772 kcal/mol@LB@Unfolding Energy - mRNA 3.58569 kcal/mol@LB@Unfolding Energy - sRNA 1.95269 kcal/mol@LB@@LB@Position - mRNA 86 -- 105@LB@Position - sRNA 35 -- 54@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 45 -- 51@LB@
142	0.006549	0.1605	b3902	rhaD	-9.93	0.251242	192 -- 218	44 -- 69	rhamnulose-1-phosphate aldolase	_____________191_________________________219\n_____________\|___________________________\|\n5'-AGA...CAGGA______AACAUGCAAAACA________UCCUG...UGA-3'\n______________ACACAG_____________UUACUCAG\n______________\|\|\|\|\|\|_____________\|:\|\|\|\|\|\|\n______________UGUGUC_____________AGUGAGUC\n3'-UUU...UGAUG______GUUAAGCAACAA_________CCCUA...GCA-5'\n_____________\|___________________________\|\n_____________70__________________________43\n	212 -- 218	44 -- 50	-16.231 kcal/mol	2.20309 kcal/mol	4.09554 kcal/mol	191 219@LB@ \| \|@LB@5'-AGA...CAGGA AACAUGCAAAACA UCCUG...UGA-3'@LB@ ACACAG UUACUCAG@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UGUGUC AGUGAGUC@LB@3'-UUU...UGAUG GUUAAGCAACAA CCCUA...GCA-5'@LB@ \| \|@LB@ 70 43@LB@@LB@@LB@Energy -9.93 kcal/mol@LB@Hybridization Energy -16.231 kcal/mol@LB@Unfolding Energy - mRNA 2.20309 kcal/mol@LB@Unfolding Energy - sRNA 4.09554 kcal/mol@LB@@LB@Position - mRNA 192 -- 218@LB@Position - sRNA 44 -- 69@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 44 -- 50@LB@
143	0.006558	0.1605	b0161	degP	-10.78	0.178564	159 -- 170	58 -- 69	serine endoprotease (protease Do) membrane-associated	_____________158__________171\n_____________\|____________\|\n5'-AUU...GAAGA____________UGCGU...CGA-3'\n______________ACACAGCAAUUU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UGUGUCGUUAAG\n3'-UUU...UGAUG____________CAACA...GCA-5'\n_____________\|____________\|\n_____________70___________57\n	164 -- 170	58 -- 64	-16.5275 kcal/mol	2.62124 kcal/mol	3.12494 kcal/mol	158 171@LB@ \| \|@LB@5'-AUU...GAAGA UGCGU...CGA-3'@LB@ ACACAGCAAUUU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UGUGUCGUUAAG@LB@3'-UUU...UGAUG CAACA...GCA-5'@LB@ \| \|@LB@ 70 57@LB@@LB@@LB@Energy -10.78 kcal/mol@LB@Hybridization Energy -16.5275 kcal/mol@LB@Unfolding Energy - mRNA 2.62124 kcal/mol@LB@Unfolding Energy - sRNA 3.12494 kcal/mol@LB@@LB@Position - mRNA 159 -- 170@LB@Position - sRNA 58 -- 69@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 58 -- 64@LB@
144	0.006569	0.1605	b2900	yqfB	-12.46	0.083290	200 -- 238	34 -- 70	UPF0267 family protein	_____________199_______________________________________239\n_____________\|_________________________________________\|\n5'-UUC...AGUAC________CAAA__ACA________UUUUUCAAC_______GGAUG...UCA-3'\n______________CAUGCAGC____CG_____UCACUU_________GUUUCCA\n______________\|\|::\|\|\|\|____\|\|_____\|\|\|\|\|:_________:\|\|\|\|\|\|\n______________GUGUGUCG____GC_____AGUGAG_________UAAAGGU\n3'-UUU...CUGAU________UUAA__AACAA______UCCCC___________ACGAA...GCA-5'\n_____________\|_________________________________________\|\n_____________71________________________________________33\n	232 -- 238	34 -- 40	-21.1736 kcal/mol	3.92715 kcal/mol	4.79237 kcal/mol	199 239@LB@ \| \|@LB@5'-UUC...AGUAC CAAA ACA UUUUUCAAC GGAUG...UCA-3'@LB@ CAUGCAGC CG UCACUU GUUUCCA@LB@ \|\|::\|\|\|\| \|\| \|\|\|\|\|: :\|\|\|\|\|\|@LB@ GUGUGUCG GC AGUGAG UAAAGGU@LB@3'-UUU...CUGAU UUAA AACAA UCCCC ACGAA...GCA-5'@LB@ \| \|@LB@ 71 33@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.1736 kcal/mol@LB@Unfolding Energy - mRNA 3.92715 kcal/mol@LB@Unfolding Energy - sRNA 4.79237 kcal/mol@LB@@LB@Position - mRNA 200 -- 238@LB@Position - sRNA 34 -- 70@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 34 -- 40@LB@
145	0.006641	0.1605	b3316	rpsS	-10.41	0.208024	125 -- 141	61 -- 77	30S ribosomal subunit protein S19	_____________124_______________142\n_____________\|_________________\|\n5'-GCG...AAGGU____AG__C________CAAGC...CUU-3'\n______________AAGA__AC_CGCAGCAA\n______________\|\|\|\|__\|\|_\|:\|\|\|\|\|\|\n______________UUCU__UG_GUGUCGUU\n3'-UUU...CCCGU____GA__U________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________78________________60\n	135 -- 141	61 -- 67	-16.0034 kcal/mol	2.33428 kcal/mol	3.25748 kcal/mol	124 142@LB@ \| \|@LB@5'-GCG...AAGGU AG C CAAGC...CUU-3'@LB@ AAGA AC CGCAGCAA@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ UUCU UG GUGUCGUU@LB@3'-UUU...CCCGU GA U AAGCA...GCA-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -16.0034 kcal/mol@LB@Unfolding Energy - mRNA 2.33428 kcal/mol@LB@Unfolding Energy - sRNA 3.25748 kcal/mol@LB@@LB@Position - mRNA 125 -- 141@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 61 -- 67@LB@
146	0.006661	0.1605	b4479	dgoR	-11.67	0.120911	94 -- 106	61 -- 74	D-galactonate catabolism operon transcriptional repressor	_____________93_____________107\n_____________\|______________\|\n5'-UUU...ACAUU______________ACGCG...AAC-3'\n______________AC_ACGCACGGCAA\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\n______________UG_UGUGUGUCGUU\n3'-UUU...GUUUC__A___________AAGCA...GCA-5'\n_____________\|______________\|\n_____________75_____________60\n	100 -- 106	61 -- 67	-16.8512 kcal/mol	1.93692 kcal/mol	3.24589 kcal/mol	93 107@LB@ \| \|@LB@5'-UUU...ACAUU ACGCG...AAC-3'@LB@ AC ACGCACGGCAA@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ UG UGUGUGUCGUU@LB@3'-UUU...GUUUC A AAGCA...GCA-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -16.8512 kcal/mol@LB@Unfolding Energy - mRNA 1.93692 kcal/mol@LB@Unfolding Energy - sRNA 3.24589 kcal/mol@LB@@LB@Position - mRNA 94 -- 106@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 61 -- 67@LB@
147	0.006785	0.1624	b1920	fliY	-15.06	0.020217	159 -- 198	40 -- 75	cystine transporter subunit	_____________158______________________________________199\n_____________\|________________________________________\|\n5'-CCA...ACAAU____C_____U____ACAGACAUAACAA_________U__AUAUG...UGC-3'\n______________GGCU_UACAC_GCAA_____________CAUUCGGGG_GA\n______________\|:\|\|_:\|\|\|\|_\|\|\|\|_____________\|\|:\|\|:\|\|\|_\|\|\n______________CUGA_GUGUG_CGUU_____________GUGAGUCCC_CU\n3'-UUU...CGUUU____U_____U____AAGCAACAAA_______________AAAGG...GCA-5'\n_____________\|________________________________________\|\n_____________76_______________________________________39\n	189 -- 195	42 -- 48	-27.6268 kcal/mol	7.79206 kcal/mol	4.77786 kcal/mol	158 199@LB@ \| \|@LB@5'-CCA...ACAAU C U ACAGACAUAACAA U AUAUG...UGC-3'@LB@ GGCU UACAC GCAA CAUUCGGGG GA@LB@ \|:\|\| :\|\|\|\| \|\|\|\| \|\|:\|\|:\|\|\| \|\|@LB@ CUGA GUGUG CGUU GUGAGUCCC CU@LB@3'-UUU...CGUUU U U AAGCAACAAA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -27.6268 kcal/mol@LB@Unfolding Energy - mRNA 7.79206 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 159 -- 198@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 42 -- 48@LB@
148	0.006951	0.1638	b3995	rsd	-9.56	0.289012	16 -- 28	58 -- 70	stationary phase protein binds sigma 70 RNA polymerase subunit	_____________15____________29\n_____________\|_____________\|\n5'-AAU...UUCGC_____________UCCCU...ACU-3'\n______________CAUAUGGCAAUUC\n______________\|\|:\|::\|\|\|\|\|\|\|\n______________GUGUGUCGUUAAG\n3'-UUU...CUGAU_____________CAACA...GCA-5'\n_____________\|_____________\|\n_____________71____________57\n	22 -- 28	58 -- 64	-15.8606 kcal/mol	3.09015 kcal/mol	3.21169 kcal/mol	15 29@LB@ \| \|@LB@5'-AAU...UUCGC UCCCU...ACU-3'@LB@ CAUAUGGCAAUUC@LB@ \|\|:\|::\|\|\|\|\|\|\|@LB@ GUGUGUCGUUAAG@LB@3'-UUU...CUGAU CAACA...GCA-5'@LB@ \| \|@LB@ 71 57@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -15.8606 kcal/mol@LB@Unfolding Energy - mRNA 3.09015 kcal/mol@LB@Unfolding Energy - sRNA 3.21169 kcal/mol@LB@@LB@Position - mRNA 16 -- 28@LB@Position - sRNA 58 -- 70@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 58 -- 64@LB@
149	0.006962	0.1638	b0935	ssuD	-8.45	0.421381	102 -- 123	48 -- 71	alkanesulfonate monooxygenase FMNH(2)-dependent	_____________101______________________124\n_____________\|________________________\|\n5'-AAA...CAGCA___A_______A____________GAAAA...AAC-3'\n______________GCA_ACGGCAG_UC__UGUUUUAU\n______________:\|\|_\|\|:\|\|\|:_\|\|__\|\|\|\|\|:\|:\n______________UGU_UGUCGUU_AG__ACAAAGUG\n3'-UUU...UCUGA___G_______A__CA________AGUCC...GCA-5'\n_____________\|________________________\|\n_____________72_______________________47\n	117 -- 123	48 -- 54	-17.2917 kcal/mol	5.19453 kcal/mol	3.65243 kcal/mol	101 124@LB@ \| \|@LB@5'-AAA...CAGCA A A GAAAA...AAC-3'@LB@ GCA ACGGCAG UC UGUUUUAU@LB@ :\|\| \|\|:\|\|\|: \|\| \|\|\|\|\|:\|:@LB@ UGU UGUCGUU AG ACAAAGUG@LB@3'-UUU...UCUGA G A CA AGUCC...GCA-5'@LB@ \| \|@LB@ 72 47@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -17.2917 kcal/mol@LB@Unfolding Energy - mRNA 5.19453 kcal/mol@LB@Unfolding Energy - sRNA 3.65243 kcal/mol@LB@@LB@Position - mRNA 102 -- 123@LB@Position - sRNA 48 -- 71@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 48 -- 54@LB@
150	0.006982	0.1638	b3581	sgbH	-9.48	0.297019	138 -- 176	34 -- 74	3-keto-L-gulonate 6-phosphate decarboxylase	_____________137________________________________________177\n_____________\|__________________________________________\|\n5'-UUU...UAUCA__GU_________UC__A___CCG__C_______C_______CGCCC...AAG-3'\n______________AC__UAU_CAGCA__UC_UUG___CA_UUCAGGG___UUUCA\n______________\|\|__:\|:_\|\|\|\|\|__\|\|_\|\|\|___\|\|_:\|\|\|\|\|\|___\|\|:\|\|\n______________UG__GUG_GUCGU__AG_AAC___GU_GAGUCCC___AAGGU\n3'-UUU...GUUUC__AU___U_____UA__C___AAA__________CUA_____ACGAA...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________33\n	164 -- 170	42 -- 48	-24.4875 kcal/mol	10.188 kcal/mol	4.81599 kcal/mol	137 177@LB@ \| \|@LB@5'-UUU...UAUCA GU UC A CCG C C CGCCC...AAG-3'@LB@ AC UAU CAGCA UC UUG CA UUCAGGG UUUCA@LB@ \|\| :\|: \|\|\|\|\| \|\| \|\|\| \|\| :\|\|\|\|\|\| \|\|:\|\|@LB@ UG GUG GUCGU AG AAC GU GAGUCCC AAGGU@LB@3'-UUU...GUUUC AU U UA C AAA CUA ACGAA...GCA-5'@LB@ \| \|@LB@ 75 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -24.4875 kcal/mol@LB@Unfolding Energy - mRNA 10.188 kcal/mol@LB@Unfolding Energy - sRNA 4.81599 kcal/mol@LB@@LB@Position - mRNA 138 -- 176@LB@Position - sRNA 34 -- 74@LB@Position Seed - mRNA 164 -- 170@LB@Position Seed - sRNA 42 -- 48@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