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
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin	_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@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@
94	0.006975	0.2379	b1284	yciT	-8.66	0.039674	34 -- 64	15 -- 42	global regulator of transcription; DeoR family	_____________33_______________________________65\n_____________\|________________________________\|\n5'-GCA...AUCUC___A________GCA___C_____________UUGCU...CCA-3'\n______________GAG_UACUUAAA___GAA_UC_UUGCGCCAGG\n______________:\|\|_:\|\|\|\|\|\|\|___:\|\|_\|\|_\|\|:\|:\|\|\|\|\|\n______________UUC_GUGAAUUU___UUU_AG_AAUGUGGUCC\n3'-UUU...CGUUC__________________A__C__________UUUAG...CAA-5'\n_____________\|________________________________\|\n_____________43_______________________________14\n	58 -- 64	15 -- 21	-23.4161 kcal/mol	5.55126 kcal/mol	9.20431 kcal/mol	33 65@LB@ \| \|@LB@5'-GCA...AUCUC A GCA C UUGCU...CCA-3'@LB@ GAG UACUUAAA GAA UC UUGCGCCAGG@LB@ :\|\| :\|\|\|\|\|\|\| :\|\| \|\| \|\|:\|:\|\|\|\|\|@LB@ UUC GUGAAUUU UUU AG AAUGUGGUCC@LB@3'-UUU...CGUUC A C UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -23.4161 kcal/mol@LB@Unfolding Energy - mRNA 5.55126 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 34 -- 64@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
189	0.02233	0.3796	b3417	malP	-8.63	0.040366	227 -- 245	35 -- 53	maltodextrin phosphorylase	_____________226_________________246\n_____________\|___________________\|\n5'-ACA...GAUAA__AAUUU____________UCACG...GCC-3'\n______________GC_____CAGGAAGCGCUU\n______________\|\|_____\|\|:\|\|\|\|\|:\|\|\|\n______________CG_____GUUCUUCGUGAA\n3'-UUU...UUGAA__AAUUC____________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	239 -- 245	35 -- 41	-18.4249 kcal/mol	3.68713 kcal/mol	6.10399 kcal/mol	226 246@LB@ \| \|@LB@5'-ACA...GAUAA AAUUU UCACG...GCC-3'@LB@ GC CAGGAAGCGCUU@LB@ \|\| \|\|:\|\|\|\|\|:\|\|\|@LB@ CG GUUCUUCGUGAA@LB@3'-UUU...UUGAA AAUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -18.4249 kcal/mol@LB@Unfolding Energy - mRNA 3.68713 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 227 -- 245@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 35 -- 41@LB@
74	0.004124	0.1795	b2599	pheA	-8.54	0.042758	34 -- 48	29 -- 42	chorismate mutase and prephenate dehydratase P-protein	_____________33______________49\n_____________\|_______________\|\n5'-UGA...UACUA___U___________ACAAA...UCG-3'\n______________AAG_CACUUAAGGAA\n______________\|\|\|_\|\|\|\|\|\|\|::\|\|\n______________UUC_GUGAAUUUUUU\n3'-UUU...CGUUC_______________AAGCA...CAA-5'\n_____________\|_______________\|\n_____________43______________28\n	42 -- 48	29 -- 35	-11.0993 kcal/mol	0.931405 kcal/mol	1.62369 kcal/mol	33 49@LB@ \| \|@LB@5'-UGA...UACUA U ACAAA...UCG-3'@LB@ AAG CACUUAAGGAA@LB@ \|\|\| \|\|\|\|\|\|\|::\|\|@LB@ UUC GUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -11.0993 kcal/mol@LB@Unfolding Energy - mRNA 0.931405 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 34 -- 48@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 29 -- 35@LB@
187	0.02188	0.3768	b3065	rpsU	-8.54	0.042773	188 -- 200	37 -- 49	30S ribosomal subunit protein S21	_____________187___________201\n_____________\|_____________\|\n5'-GAC...AUCAA_____________AUGCC...GUC-3'\n______________AGGUGAGAGGCAC\n______________\|:\|::\|\|\|:\|\|\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	194 -- 200	37 -- 43	-18.635 kcal/mol	4.05763 kcal/mol	6.03369 kcal/mol	187 201@LB@ \| \|@LB@5'-GAC...AUCAA AUGCC...GUC-3'@LB@ AGGUGAGAGGCAC@LB@ \|:\|::\|\|\|:\|\|\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -18.635 kcal/mol@LB@Unfolding Energy - mRNA 4.05763 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 188 -- 200@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 37 -- 43@LB@
95	0.007016	0.2379	b0464	acrR	-8.52	0.043413	219 -- 228	37 -- 46	transcriptional repressor	_____________218________229\n_____________\|__________\|\n5'-AAG...CCAAA__________AAGAA...CGC-3'\n______________CAAGAAGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	222 -- 228	37 -- 43	-15.2794 kcal/mol	1.54243 kcal/mol	5.21654 kcal/mol	218 229@LB@ \| \|@LB@5'-AAG...CCAAA AAGAA...CGC-3'@LB@ CAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -15.2794 kcal/mol@LB@Unfolding Energy - mRNA 1.54243 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 37 -- 43@LB@
39	0.00159	0.1292	b1637	tyrS	-8.51	0.043578	178 -- 203	5 -- 27	tyrosyl-tRNA synthetase	_____________177________________________204\n_____________\|__________________________\|\n5'-CAU...UGCAG_________A__U_______U_____GCAAG...CGA-3'\n______________UCGUUAUAU_CA_GGAGAUU_UGAUG\n______________\|\|\|\|\|\|:\|:_\|\|_\|\|\|:\|\|:_\|\|\|\|\|\n______________AGCAAUGUG_GU_CCUUUAG_ACUAC\n3'-UUU...UUUUA__________________________ACAA-5'\n_____________\|__________________________\|\n_____________28_________________________4\n	191 -- 197	10 -- 16	-22.7194 kcal/mol	5.60368 kcal/mol	8.60118 kcal/mol	177 204@LB@ \| \|@LB@5'-CAU...UGCAG A U U GCAAG...CGA-3'@LB@ UCGUUAUAU CA GGAGAUU UGAUG@LB@ \|\|\|\|\|\|:\|: \|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ AGCAAUGUG GU CCUUUAG ACUAC@LB@3'-UUU...UUUUA ACAA-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -22.7194 kcal/mol@LB@Unfolding Energy - mRNA 5.60368 kcal/mol@LB@Unfolding Energy - sRNA 8.60118 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
159	0.01739	0.3504	b2426	ucpA	-8.50	0.043854	215 -- 229	36 -- 49	furfural resistance protein putative short-chain oxidoreductase	_____________214_____________230\n_____________\|_______________\|\n5'-GUG...CUCAC________C______GAUUA...UAA-3'\n______________GGGCAAGA_AGCACU\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	216 -- 222	42 -- 48	-19.0239 kcal/mol	4.4828 kcal/mol	6.03645 kcal/mol	214 230@LB@ \| \|@LB@5'-GUG...CUCAC C GAUUA...UAA-3'@LB@ GGGCAAGA AGCACU@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -19.0239 kcal/mol@LB@Unfolding Energy - mRNA 4.4828 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 215 -- 229@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 42 -- 48@LB@
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@

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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