Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
54	0.00267	0.1735	b0131	panD	-12.96	0.079905	178 -- 195	5 -- 22	aspartate 1-decarboxylase		_____________177________________196\n_____________\|__________________\|\n5'-AUU...UUAAC____GGGU__________AAGUU...UUG-3'\n______________GACA____AGAAAGGUAG\n______________\|\|\|\|____\|\|\|\|\|:\|:\|\|\n______________CUGU____UCUUUUCGUC\n3'-UUU...UACCC____AGUU__________ACCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	189 -- 195	5 -- 11	-16.4376 kcal/mol	1.9462 kcal/mol	1.53637 kcal/mol	177 196@LB@ \| \|@LB@5'-AUU...UUAAC GGGU AAGUU...UUG-3'@LB@ GACA AGAAAGGUAG@LB@ \|\|\|\| \|\|\|\|\|:\|:\|\|@LB@ CUGU UCUUUUCGUC@LB@3'-UUU...UACCC AGUU ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -12.96 kcal/mol@LB@Hybridization Energy -16.4376 kcal/mol@LB@Unfolding Energy - mRNA 1.9462 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 5 -- 11@LB@
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
167	0.01216	0.2504	b1013	rutR	-12.90	0.082087	181 -- 218	3 -- 35	rut operon transcriptional repressor for	b0796	_____________180________________________________________219\n_____________\|__________________________________________\|\n5'-CAA...GCCAA_______________GAGCGCAUGACG_____C_________AAAAC...AAU-3'\n______________UCUACAAGA_GGGGA____________CAAGG____GCAGUG\n______________\|\|:\|\|\|\|:\|_\|\|\|\|\|____________\|\|\|:\|____\|\|\|\|\|\|\n______________AGGUGUUUU_CCCCU____________GUUUC____CGUCAC\n3'-UUU...ACCCG_________A_____GUA______________UUUU______CG-5'\n_____________\|__________________________________________\|\n_____________36_________________________________________2\n	181 -- 187	29 -- 35	-29.1146 kcal/mol	11.1798 kcal/mol	5.03644 kcal/mol	180 219@LB@ \| \|@LB@5'-CAA...GCCAA GAGCGCAUGACG C AAAAC...AAU-3'@LB@ UCUACAAGA GGGGA CAAGG GCAGUG@LB@ \|\|:\|\|\|\|:\| \|\|\|\|\| \|\|\|:\| \|\|\|\|\|\|@LB@ AGGUGUUUU CCCCU GUUUC CGUCAC@LB@3'-UUU...ACCCG A GUA UUUU CG-5'@LB@ \| \|@LB@ 36 2@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -29.1146 kcal/mol@LB@Unfolding Energy - mRNA 11.1798 kcal/mol@LB@Unfolding Energy - sRNA 5.03644 kcal/mol@LB@@LB@Position - mRNA 181 -- 218@LB@Position - sRNA 3 -- 35@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 29 -- 35@LB@
32	0.001499	0.1635	b0661	miaB	-12.88	0.082685	213 -- 250	6 -- 36	tRNA-i(6)A37 methylthiotransferase		_____________212____________________________________251\n_____________\|______________________________________\|\n5'-CGC...AAAAA_______UU_AAACC_____C_______U___C_____CGAUU...AAC-3'\n______________CUCCAUA__A_____UGGGG_UGUCAGA_GAA_GAGUA\n______________\|\|\|\|\|:\|__\|_____\|\|\|\|\|_::\|\|\|:\|_\|\|\|_:\|\|:\|\n______________GAGGUGU__U_____ACCCC_GUAGUUU_CUU_UUCGU\n3'-UUU...UACCC_______UU___________U_________________CACCG-5'\n_____________\|______________________________________\|\n_____________37_____________________________________5\n	234 -- 240	14 -- 20	-26.1374 kcal/mol	6.57825 kcal/mol	6.67617 kcal/mol	212 251@LB@ \| \|@LB@5'-CGC...AAAAA UU AAACC C U C CGAUU...AAC-3'@LB@ CUCCAUA A UGGGG UGUCAGA GAA GAGUA@LB@ \|\|\|\|\|:\| \| \|\|\|\|\| ::\|\|\|:\| \|\|\| :\|\|:\|@LB@ GAGGUGU U ACCCC GUAGUUU CUU UUCGU@LB@3'-UUU...UACCC UU U CACCG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -26.1374 kcal/mol@LB@Unfolding Energy - mRNA 6.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.67617 kcal/mol@LB@@LB@Position - mRNA 213 -- 250@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 14 -- 20@LB@
138	0.0102	0.2504	b0830	gsiB	-12.88	0.082739	282 -- 298	1 -- 16	glutathione ABC transporter periplasmic binding protein		_____________281_______________299\n_____________\|_________________\|\n5'-GGC...CUGCC_____UGU_________GG-3'\n______________AAAGA___GGUGGUGGC\n______________\|\|\|\|\|___:\|::\|\|\|\|\|\n______________UUUCU___UCGUCACCG\n3'-UUU...UGUAG_____UU__________-5'\n_____________\|________________\|\n_____________17_______________1\n	292 -- 298	1 -- 7	-17.0557 kcal/mol	2.82856 kcal/mol	1.34555 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC UGU GG-3'@LB@ AAAGA GGUGGUGGC@LB@ \|\|\|\|\| :\|::\|\|\|\|\|@LB@ UUUCU UCGUCACCG@LB@3'-UUU...UGUAG UU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -17.0557 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
120	0.00842	0.2462	b1068	yceM	-12.88	0.082928	190 -- 205	9 -- 24	putative oxidoreductase		_____________189______________206\n_____________\|________________\|\n5'-GCG...CAUCU____G_______U___AAAAU...GAG-3'\n______________GGGA_AUUAAAG_GAA\n______________\|\|\|\|_\|\|:\|\|\|\|_:\|\|\n______________CCCU_UAGUUUC_UUU\n3'-UUU...UUUAC____G_______U___CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	195 -- 201	13 -- 19	-15.5519 kcal/mol	2.0153 kcal/mol	0.659805 kcal/mol	189 206@LB@ \| \|@LB@5'-GCG...CAUCU G U AAAAU...GAG-3'@LB@ GGGA AUUAAAG GAA@LB@ \|\|\|\| \|\|:\|\|\|\| :\|\|@LB@ CCCU UAGUUUC UUU@LB@3'-UUU...UUUAC G U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -15.5519 kcal/mol@LB@Unfolding Energy - mRNA 2.0153 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
154	0.01125	0.2504	b3412	bioH	-12.84	0.084220	262 -- 288	1 -- 28	pimeloyl-ACP methyl ester carboxylesterase		_____________261__________________________289\n_____________\|____________________________\|\n5'-GGC...GCACG_________UGAAUGCC___________GUUGC...ACG-3'\n______________GAUGGGGAC________GAAGU_GUGGC\n______________:\|\|\|\|\|\|\|\|________:\|\|\|:_\|\|\|\|\|\n______________UUACCCCUG________UUUCG_CACCG\n3'-UUU...GUGUU_________UAGUUUCU_____U_____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	264 -- 270	20 -- 26	-27.647 kcal/mol	12.2839 kcal/mol	2.519 kcal/mol	261 289@LB@ \| \|@LB@5'-GGC...GCACG UGAAUGCC GUUGC...ACG-3'@LB@ GAUGGGGAC GAAGU GUGGC@LB@ :\|\|\|\|\|\|\|\| :\|\|\|: \|\|\|\|\|@LB@ UUACCCCUG UUUCG CACCG@LB@3'-UUU...GUGUU UAGUUUCU U -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -27.647 kcal/mol@LB@Unfolding Energy - mRNA 12.2839 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 262 -- 288@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 20 -- 26@LB@
30	0.001442	0.1635	b3458	livK	-12.84	0.084462	180 -- 215	6 -- 33	leucine transporter subunit		_____________179___________________________________216\n_____________\|_____________________________________\|\n5'-UGU...AACAU______________UUUUGACU__G___C____U___AAAAC...CGA-3'\n______________CAC_GAAUGGGGAU________AU_AAA_GGAA_GCG\n______________\|\|\|_:\|\|\|\|\|\|\|\|:________\|\|_\|\|\|_\|:\|\|_\|\|:\n______________GUG_UUUACCCCUG________UA_UUU_CUUU_CGU\n3'-UUU...CCGAG___U____________________G________U___CACCG-5'\n_____________\|_____________________________________\|\n_____________34____________________________________5\n	186 -- 192	20 -- 26	-21.4141 kcal/mol	5.49822 kcal/mol	3.07787 kcal/mol	179 216@LB@ \| \|@LB@5'-UGU...AACAU UUUUGACU G C U AAAAC...CGA-3'@LB@ CAC GAAUGGGGAU AU AAA GGAA GCG@LB@ \|\|\| :\|\|\|\|\|\|\|\|: \|\| \|\|\| \|:\|\| \|\|:@LB@ GUG UUUACCCCUG UA UUU CUUU CGU@LB@3'-UUU...CCGAG U G U CACCG-5'@LB@ \| \|@LB@ 34 5@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -21.4141 kcal/mol@LB@Unfolding Energy - mRNA 5.49822 kcal/mol@LB@Unfolding Energy - sRNA 3.07787 kcal/mol@LB@@LB@Position - mRNA 180 -- 215@LB@Position - sRNA 6 -- 33@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 20 -- 26@LB@
77	0.004622	0.2062	b1241	adhE	-12.78	0.086641	182 -- 205	1 -- 21	fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase		_____________181______________________206\n_____________\|________________________\|\n5'-AAU...GUUUA______UC_________UUA____UGUUA...AAA-3'\n______________ACAUUA__AGGAGAGCA___UGGC\n______________\|\|\|\|:\|__\|\|:\|:\|\|\|\|___\|\|\|\|\n______________UGUAGU__UCUUUUCGU___ACCG\n3'-UUU...ACCCC______U__________C______-5'\n_____________\|_______________________\|\n_____________22______________________1\n	192 -- 198	6 -- 12	-20.8292 kcal/mol	6.5343 kcal/mol	1.51103 kcal/mol	181 206@LB@ \| \|@LB@5'-AAU...GUUUA UC UUA UGUUA...AAA-3'@LB@ ACAUUA AGGAGAGCA UGGC@LB@ \|\|\|\|:\| \|\|:\|:\|\|\|\| \|\|\|\|@LB@ UGUAGU UCUUUUCGU ACCG@LB@3'-UUU...ACCCC U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -20.8292 kcal/mol@LB@Unfolding Energy - mRNA 6.5343 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 6 -- 12@LB@
117	0.008014	0.2404	b3052	hldE	-12.77	0.087254	132 -- 161	1 -- 30	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase		_____________131______________________________162\n_____________\|________________________________\|\n5'-GCG...UGGCA_______CUG___G_____AU___________AUUAU...CGC-3'\n______________GAAGUGG____GU_GAAGA__GAAGUA_UGGU\n______________:\|\|:\|\|\|____:\|_:\|\|\|\|__:\|\|\|:\|_\|\|\|:\n______________UUUUACC____UA_UUUCU__UUUCGU_ACCG\n3'-UUU...AGGUG_______CCUG__G_____________C____-5'\n_____________\|_______________________________\|\n_____________31______________________________1\n	132 -- 138	24 -- 30	-21.0542 kcal/mol	5.76621 kcal/mol	2.51911 kcal/mol	131 162@LB@ \| \|@LB@5'-GCG...UGGCA CUG G AU AUUAU...CGC-3'@LB@ GAAGUGG GU GAAGA GAAGUA UGGU@LB@ :\|\|:\|\|\| :\| :\|\|\|\| :\|\|\|:\| \|\|\|:@LB@ UUUUACC UA UUUCU UUUCGU ACCG@LB@3'-UUU...AGGUG CCUG G C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.76621 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 132 -- 161@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 24 -- 30@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