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
114	0.009652	0.2693	b2614	grpE	-8.47	0.044767	262 -- 275	27 -- 41	heat shock protein	_____________261_____________276\n_____________\|_______________\|\n5'-GAG...GGAUC_____G_________GAGGC...CUG-3'\n______________AGCAC__AAGAGAUU\n______________\|\|\|\|\|__\|\|:\|:\|\|\|\n______________UCGUG__UUUUUUAA\n3'-UUU...GUUCU_____AA________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	269 -- 275	27 -- 33	-11.1078 kcal/mol	0.992631 kcal/mol	1.6427 kcal/mol	261 276@LB@ \| \|@LB@5'-GAG...GGAUC G GAGGC...CUG-3'@LB@ AGCAC AAGAGAUU@LB@ \|\|\|\|\| \|\|:\|:\|\|\|@LB@ UCGUG UUUUUUAA@LB@3'-UUU...GUUCU AA GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.1078 kcal/mol@LB@Unfolding Energy - mRNA 0.992631 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 262 -- 275@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@LB@
150	0.01547	0.3321	b3736	atpF	-5.86	0.208717	262 -- 272	37 -- 47	F0 sector of membrane-bound ATP synthase subunit b	_____________261_________273\n_____________\|___________\|\n5'-AUU...GUUCU___U_______GUAUG...UCG-3'\n______________GCA_GAAGUAC\n______________\|\|\|_\|\|\|\|:\|\|\n______________CGU_CUUCGUG\n3'-UUU...GAAUU___U_______AAUUU...CAA-5'\n_____________\|___________\|\n_____________48__________36\n	266 -- 272	37 -- 43	-12.6044 kcal/mol	1.50868 kcal/mol	5.23944 kcal/mol	261 273@LB@ \| \|@LB@5'-AUU...GUUCU U GUAUG...UCG-3'@LB@ GCA GAAGUAC@LB@ \|\|\| \|\|\|\|:\|\|@LB@ CGU CUUCGUG@LB@3'-UUU...GAAUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 48 36@LB@@LB@@LB@Energy -5.86 kcal/mol@LB@Hybridization Energy -12.6044 kcal/mol@LB@Unfolding Energy - mRNA 1.50868 kcal/mol@LB@Unfolding Energy - sRNA 5.23944 kcal/mol@LB@@LB@Position - mRNA 262 -- 272@LB@Position - sRNA 37 -- 47@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 37 -- 43@LB@
177	0.02045	0.3721	b3148	yraN	-6.85	0.120614	263 -- 276	37 -- 54	UPF0102 family protein	_____________262________________277\n_____________\|__________________\|\n5'-GGU...GGCGA__________________AAGCG...GCA-3'\n______________UGC____GUGGGAAGCAC\n______________\|\|\|____\|:::\|\|\|\|\|\|\|\n______________ACG____CGUUCUUCGUG\n3'-UUU...UUUGA___AAUU___________AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	270 -- 276	37 -- 43	-17.1481 kcal/mol	4.14332 kcal/mol	6.1584 kcal/mol	262 277@LB@ \| \|@LB@5'-GGU...GGCGA AAGCG...GCA-3'@LB@ UGC GUGGGAAGCAC@LB@ \|\|\| \|:::\|\|\|\|\|\|\|@LB@ ACG CGUUCUUCGUG@LB@3'-UUU...UUUGA AAUU AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -17.1481 kcal/mol@LB@Unfolding Energy - mRNA 4.14332 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 263 -- 276@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 37 -- 43@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@
138	0.01322	0.3087	b1523	yneG	-4.22	0.452951	267 -- 281	24 -- 41	DUF4186 family protein	_____________266________________282\n_____________\|__________________\|\n5'-AUG...GUCUG_____________G____CAGUA...AAG-3'\n______________GGCA__UGAAAGA__CGU\n______________:\|\|\|__\|:\|\|\|:\|__\|\|\|\n______________UCGU__AUUUUUU__GCA\n3'-UUU...GUUCU____GA_______AA___AUGUG...CAA-5'\n_____________\|__________________\|\n_____________42_________________23\n	271 -- 277	29 -- 35	-8.58312 kcal/mol	2.71204 kcal/mol	1.64881 kcal/mol	266 282@LB@ \| \|@LB@5'-AUG...GUCUG G CAGUA...AAG-3'@LB@ GGCA UGAAAGA CGU@LB@ :\|\|\| \|:\|\|\|:\| \|\|\|@LB@ UCGU AUUUUUU GCA@LB@3'-UUU...GUUCU GA AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -4.22 kcal/mol@LB@Hybridization Energy -8.58312 kcal/mol@LB@Unfolding Energy - mRNA 2.71204 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 267 -- 281@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 29 -- 35@LB@
22	0.0006536	0.09021	b1245	oppC	-8.46	0.045181	270 -- 288	37 -- 58	oligopeptide ABC transporter permease	_____________269____________________289\n_____________\|______________________\|\n5'-GGU...GGCGC_________________C____GUCGA...UUA-3'\n______________AGCUUGU___GGCAGGA_GCAC\n______________\|:\|\|\|\|:___:\|\|\|:\|\|_\|\|\|\|\n______________UUGAACG___UCGUUCU_CGUG\n3'-UUU...CUACU_______AAU_______U____AAUUU...CAA-5'\n_____________\|______________________\|\n_____________59_____________________36\n	277 -- 283	42 -- 48	-22.602 kcal/mol	7.90039 kcal/mol	6.24354 kcal/mol	269 289@LB@ \| \|@LB@5'-GGU...GGCGC C GUCGA...UUA-3'@LB@ AGCUUGU GGCAGGA GCAC@LB@ \|:\|\|\|\|: :\|\|\|:\|\| \|\|\|\|@LB@ UUGAACG UCGUUCU CGUG@LB@3'-UUU...CUACU AAU U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -8.46 kcal/mol@LB@Hybridization Energy -22.602 kcal/mol@LB@Unfolding Energy - mRNA 7.90039 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 270 -- 288@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
75	0.004391	0.1886	b3708	tnaA	-6.02	0.191179	273 -- 300	28 -- 53	tryptophanase/L-cysteine desulfhydrase PLP-dependent	_____________272_________________________300\n_____________\|___________________________\|\n5'-ACC...CUCGC_____UC__G________A___UU____-3'\n______________GCUUA__GU_AAGAGGCA_UUA__AAAU\n______________\|\|\|\|\|__\|:_\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|\n______________CGAAU__CG_UUCUUCGU_AAU__UUUA\n3'-UUU...UUGAA_____U____________G___UU____AGCAA...CAA-5'\n_____________\|____________________________\|\n_____________54___________________________27\n	284 -- 290	38 -- 44	-17.9242 kcal/mol	5.66853 kcal/mol	6.23468 kcal/mol	272 300@LB@ \| \|@LB@5'-ACC...CUCGC UC G A UU -3'@LB@ GCUUA GU AAGAGGCA UUA AAAU@LB@ \|\|\|\|\| \|: \|\|\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ CGAAU CG UUCUUCGU AAU UUUA@LB@3'-UUU...UUGAA U G UU AGCAA...CAA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -17.9242 kcal/mol@LB@Unfolding Energy - mRNA 5.66853 kcal/mol@LB@Unfolding Energy - sRNA 6.23468 kcal/mol@LB@@LB@Position - mRNA 273 -- 300@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
20	0.0005034	0.08107	b3962	sthA	-8.00	0.060263	274 -- 291	37 -- 54	pyridine nucleotide transhydrogenase soluble	_____________273________________292\n_____________\|__________________\|\n5'-UAC...GGGCC__G__________U____GCGUC...CAG-3'\n______________UG_UUAAGCAAGG_GCGC\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|:\|\n______________AC_AAUUCGUUCU_CGUG\n3'-UUU...UUUGA__G__________U____AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	280 -- 286	42 -- 48	-21.3093 kcal/mol	7.14965 kcal/mol	6.1584 kcal/mol	273 292@LB@ \| \|@LB@5'-UAC...GGGCC G U GCGUC...CAG-3'@LB@ UG UUAAGCAAGG GCGC@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\|:\|@LB@ AC AAUUCGUUCU CGUG@LB@3'-UUU...UUUGA G U AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -8.00 kcal/mol@LB@Hybridization Energy -21.3093 kcal/mol@LB@Unfolding Energy - mRNA 7.14965 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 274 -- 291@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 42 -- 48@LB@
134	0.01281	0.308	b3316	rpsS	-8.71	0.038435	274 -- 288	39 -- 53	30S ribosomal subunit protein S19	_____________273______________289\n_____________\|________________\|\n5'-GCG...GGAAA__G____A________CCCUG...CUU-3'\n______________GC__GAG_CAAGAAGC\n______________\|\|__:\|\|_\|\|\|\|\|\|\|\|\n______________CG__UUC_GUUCUUCG\n3'-UUU...UUGAA__AA____________UGAAU...CAA-5'\n_____________\|________________\|\n_____________54_______________38\n	282 -- 288	39 -- 45	-16.1876 kcal/mol	1.46049 kcal/mol	6.01745 kcal/mol	273 289@LB@ \| \|@LB@5'-GCG...GGAAA G A CCCUG...CUU-3'@LB@ GC GAG CAAGAAGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|\|@LB@ CG UUC GUUCUUCG@LB@3'-UUU...UUGAA AA UGAAU...CAA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -16.1876 kcal/mol@LB@Unfolding Energy - mRNA 1.46049 kcal/mol@LB@Unfolding Energy - sRNA 6.01745 kcal/mol@LB@@LB@Position - mRNA 274 -- 288@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 39 -- 45@LB@
135	0.01294	0.3087	b3785	wzzE	-4.46	0.409883	275 -- 291	39 -- 56	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein	_____________274_________________292\n_____________\|___________________\|\n5'-GCU...CGUAC___________U_______UAUGG...UUA-3'\n______________CUUGU__GGGC_GGGAAGC\n______________\|\|\|\|:__::\|\|_::\|\|\|\|\|\n______________GAACG__UUCG_UUCUUCG\n3'-UUU...ACUUU_____AA____________UGAAU...CAA-5'\n_____________\|___________________\|\n_____________57__________________38\n	285 -- 291	39 -- 45	-16.5835 kcal/mol	6.01236 kcal/mol	6.11167 kcal/mol	274 292@LB@ \| \|@LB@5'-GCU...CGUAC U UAUGG...UUA-3'@LB@ CUUGU GGGC GGGAAGC@LB@ \|\|\|\|: ::\|\| ::\|\|\|\|\|@LB@ GAACG UUCG UUCUUCG@LB@3'-UUU...ACUUU AA UGAAU...CAA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -4.46 kcal/mol@LB@Hybridization Energy -16.5835 kcal/mol@LB@Unfolding Energy - mRNA 6.01236 kcal/mol@LB@Unfolding Energy - sRNA 6.11167 kcal/mol@LB@@LB@Position - mRNA 275 -- 291@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 39 -- 45@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

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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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