Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
195	0.02349	0.3864	b3982	nusG	-7.66	0.074558	21 -- 55	24 -- 55	transcription termination factor	_____________20__________________________________56\n_____________\|___________________________________\|\n5'-GAC...UACCG______UU__CCGU_______GUACC_____C___AAGGU...ACA-3'\n______________UUGCUU__GC____GAAGCGC_____GAAGU_CGU\n______________\|\|\|\|\|\|__\|\|____\|\|\|\|\|:\|_____:\|\|:\|_\|\|\|\n______________AACGAA__CG____CUUCGUG_____UUUUA_GCA\n3'-UUU...CUUUG______UU__UU_________AAUU______A___AUGUG...CAA-5'\n_____________\|___________________________________\|\n_____________56__________________________________23\n	35 -- 41	37 -- 43	-23.8738 kcal/mol	9.94572 kcal/mol	6.27216 kcal/mol	20 56@LB@ \| \|@LB@5'-GAC...UACCG UU CCGU GUACC C AAGGU...ACA-3'@LB@ UUGCUU GC GAAGCGC GAAGU CGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\|\|:\| :\|\|:\| \|\|\|@LB@ AACGAA CG CUUCGUG UUUUA GCA@LB@3'-UUU...CUUUG UU UU AAUU A AUGUG...CAA-5'@LB@ \| \|@LB@ 56 23@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -23.8738 kcal/mol@LB@Unfolding Energy - mRNA 9.94572 kcal/mol@LB@Unfolding Energy - sRNA 6.27216 kcal/mol@LB@@LB@Position - mRNA 21 -- 55@LB@Position - sRNA 24 -- 55@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 37 -- 43@LB@
9	7.531e-05	0.02695	b0491	fetB	-11.86	0.004271	187 -- 209	25 -- 47	iron export ABC transporter permease; peroxide resistance protein	_____________186_____________________210\n_____________\|_______________________\|\n5'-GCC...GAAAU___________GCUAU___C___CAUAA...AGA-3'\n______________GCAGGAAGCAC_____GAA_UCG\n______________\|\|\|:\|\|\|\|\|\|\|_____:\|\|_\|\|\|\n______________CGUUCUUCGUG_____UUU_AGC\n3'-UUU...GAAUU___________AAUUU___A___AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	191 -- 197	37 -- 43	-22.8314 kcal/mol	4.71887 kcal/mol	6.25056 kcal/mol	186 210@LB@ \| \|@LB@5'-GCC...GAAAU GCUAU C CAUAA...AGA-3'@LB@ GCAGGAAGCAC GAA UCG@LB@ \|\|\|:\|\|\|\|\|\|\| :\|\| \|\|\|@LB@ CGUUCUUCGUG UUU AGC@LB@3'-UUU...GAAUU AAUUU A AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -22.8314 kcal/mol@LB@Unfolding Energy - mRNA 4.71887 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 187 -- 209@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 37 -- 43@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@LB@
33	0.001071	0.1045	b2058	wcaB	-10.41	0.012241	46 -- 64	25 -- 42	putative acyl transferase	_____________45__________________65\n_____________\|___________________\|\n5'-ACC...ACCGC______AA___C_______ACCGC...AGA-3'\n______________AAGCAC__AGA_AAAUUCG\n______________\|\|\|\|\|\|__\|:\|_\|\|\|\|\|\|\|\n______________UUCGUG__UUU_UUUAAGC\n3'-UUU...CGUUC______AA___________AAUGU...CAA-5'\n_____________\|___________________\|\n_____________43__________________24\n	58 -- 64	25 -- 31	-12.8013 kcal/mol	0.745291 kcal/mol	1.64855 kcal/mol	45 65@LB@ \| \|@LB@5'-ACC...ACCGC AA C ACCGC...AGA-3'@LB@ AAGCAC AGA AAAUUCG@LB@ \|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ UUCGUG UUU UUUAAGC@LB@3'-UUU...CGUUC AA AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -12.8013 kcal/mol@LB@Unfolding Energy - mRNA 0.745291 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 46 -- 64@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 25 -- 31@LB@
36	0.001384	0.121	b2573	rpoE	-5.96	0.197133	163 -- 178	25 -- 41	RNA polymerase sigma E factor	_____________162_______________179\n_____________\|_________________\|\n5'-ACA...UCGAU_____GU__________GUUUG...UGG-3'\n______________AGCGC___GGAAAUUUG\n______________\|\|\|:\|___::\|\|\|\|\|:\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	172 -- 178	25 -- 31	-12.5895 kcal/mol	4.97735 kcal/mol	1.64839 kcal/mol	162 179@LB@ \| \|@LB@5'-ACA...UCGAU GU GUUUG...UGG-3'@LB@ AGCGC GGAAAUUUG@LB@ \|\|\|:\| ::\|\|\|\|\|:\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -5.96 kcal/mol@LB@Hybridization Energy -12.5895 kcal/mol@LB@Unfolding Energy - mRNA 4.97735 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 163 -- 178@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 25 -- 31@LB@
37	0.00139	0.121	b2222	atoA	-4.53	0.397320	265 -- 276	25 -- 38	acetyl-CoA:acetoacetyl-CoA transferase beta subunit	_____________264____________277\n_____________\|______________\|\n5'-CGC...CGUUA______________GUUUA...AUU-3'\n______________ACUUAGGGA__UCG\n______________\|\|\|\|\|:::\|__\|\|\|\n______________UGAAUUUUU__AGC\n3'-UUU...CUUCG_________UA___AAUGU...CAA-5'\n_____________\|______________\|\n_____________39_____________24\n	266 -- 272	31 -- 37	-7.73128 kcal/mol	1.76584 kcal/mol	1.4343 kcal/mol	264 277@LB@ \| \|@LB@5'-CGC...CGUUA GUUUA...AUU-3'@LB@ ACUUAGGGA UCG@LB@ \|\|\|\|\|:::\| \|\|\|@LB@ UGAAUUUUU AGC@LB@3'-UUU...CUUCG UA AAUGU...CAA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -4.53 kcal/mol@LB@Hybridization Energy -7.73128 kcal/mol@LB@Unfolding Energy - mRNA 1.76584 kcal/mol@LB@Unfolding Energy - sRNA 1.4343 kcal/mol@LB@@LB@Position - mRNA 265 -- 276@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 31 -- 37@LB@
42	0.001686	0.1293	b2733	mutS	-6.21	0.172669	203 -- 222	25 -- 42	methyl-directed mismatch repair protein	_____________202__________________223\n_____________\|____________________\|\n5'-GAU...CCCAU______AA_________U__ACGCC...UGG-3'\n______________GAGUGC__UAGAAAAUU_CG\n______________:\|\|::\|__\|\|:\|\|\|\|\|\|_\|\|\n______________UUCGUG__AUUUUUUAA_GC\n3'-UUU...CGUUC______A_____________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________43___________________24\n	213 -- 219	27 -- 33	-10.4027 kcal/mol	2.54535 kcal/mol	1.64855 kcal/mol	202 223@LB@ \| \|@LB@5'-GAU...CCCAU AA U ACGCC...UGG-3'@LB@ GAGUGC UAGAAAAUU CG@LB@ :\|\|::\| \|\|:\|\|\|\|\|\| \|\|@LB@ UUCGUG AUUUUUUAA GC@LB@3'-UUU...CGUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.21 kcal/mol@LB@Hybridization Energy -10.4027 kcal/mol@LB@Unfolding Energy - mRNA 2.54535 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 203 -- 222@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 27 -- 33@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone	_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@LB@
60	0.00317	0.1645	b0466	ybaM	-6.37	0.157728	143 -- 158	25 -- 40	DUF2496 family protein	_____________142_______________159\n_____________\|_________________\|\n5'-GCA...GCCAU_____GG__________AAAAC...CGC-3'\n______________GCGCU__AAAAAAU_CG\n______________\|\|:\|\|__\|\|\|\|\|\|\|_\|\|\n______________CGUGA__UUUUUUA_GC\n3'-UUU...UUCUU_____A________A__AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	150 -- 156	28 -- 34	-11.3444 kcal/mol	3.32327 kcal/mol	1.64821 kcal/mol	142 159@LB@ \| \|@LB@5'-GCA...GCCAU GG AAAAC...CGC-3'@LB@ GCGCU AAAAAAU CG@LB@ \|\|:\|\| \|\|\|\|\|\|\| \|\|@LB@ CGUGA UUUUUUA GC@LB@3'-UUU...UUCUU A A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -11.3444 kcal/mol@LB@Unfolding Energy - mRNA 3.32327 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 143 -- 158@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 28 -- 34@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