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
101	0.007657	0.2442	b3928	zapB	-6.83	0.122013	220 -- 239	38 -- 54	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________219__________________240\n_____________\|____________________\|\n5'-UUU...AGAAG________AAACU_______AAAGU...AAG-3'\n______________UGUUUGAG_____GGAAGCA\n______________\|\|:\|\|:\|\|_____:\|\|\|\|\|\|\n______________ACGAAUUC_____UCUUCGU\n3'-UUU...UUUGA________GU__________GAAUU...CAA-5'\n_____________\|____________________\|\n_____________55___________________37\n	233 -- 239	38 -- 44	-16.6983 kcal/mol	3.7204 kcal/mol	6.15149 kcal/mol	219 240@LB@ \| \|@LB@5'-UUU...AGAAG AAACU AAAGU...AAG-3'@LB@ UGUUUGAG GGAAGCA@LB@ \|\|:\|\|:\|\| :\|\|\|\|\|\|@LB@ ACGAAUUC UCUUCGU@LB@3'-UUU...UUUGA GU GAAUU...CAA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -16.6983 kcal/mol@LB@Unfolding Energy - mRNA 3.7204 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 220 -- 239@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 38 -- 44@LB@
105	0.008762	0.2688	b2735	ygbI	-7.10	0.103888	185 -- 196	38 -- 49	DeoR family putative transcriptional regulator	_____________184__________197\n_____________\|____________\|\n5'-UUC...GGACA___G________AAAGU...AUA-3'\n______________AAG_AAGGAGCA\n______________\|\|\|_\|\|\|:\|\|\|\|\n______________UUC_UUCUUCGU\n3'-UUU...ACGAA___G________GAAUU...CAA-5'\n_____________\|____________\|\n_____________50___________37\n	190 -- 196	38 -- 44	-14.2659 kcal/mol	1.1364 kcal/mol	6.02696 kcal/mol	184 197@LB@ \| \|@LB@5'-UUC...GGACA G AAAGU...AUA-3'@LB@ AAG AAGGAGCA@LB@ \|\|\| \|\|\|:\|\|\|\|@LB@ UUC UUCUUCGU@LB@3'-UUU...ACGAA G GAAUU...CAA-5'@LB@ \| \|@LB@ 50 37@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -14.2659 kcal/mol@LB@Unfolding Energy - mRNA 1.1364 kcal/mol@LB@Unfolding Energy - sRNA 6.02696 kcal/mol@LB@@LB@Position - mRNA 185 -- 196@LB@Position - sRNA 38 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 38 -- 44@LB@
133	0.0127	0.3077	b2452	eutH	-4.80	0.352106	186 -- 194	38 -- 46	ethanolamine transporter	_____________185_______195\n_____________\|_________\|\n5'-UUG...ACUAA_________AAGGC...UCC-3'\n______________CAGGGAGUA\n______________\|\|:\|:\|\|:\|\n______________GUUCUUCGU\n3'-UUU...AAUUC_________GAAUU...CAA-5'\n_____________\|_________\|\n_____________47________37\n	188 -- 194	38 -- 44	-8.62764 kcal/mol	1.2009 kcal/mol	2.62609 kcal/mol	185 195@LB@ \| \|@LB@5'-UUG...ACUAA AAGGC...UCC-3'@LB@ CAGGGAGUA@LB@ \|\|:\|:\|\|:\|@LB@ GUUCUUCGU@LB@3'-UUU...AAUUC GAAUU...CAA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -4.80 kcal/mol@LB@Hybridization Energy -8.62764 kcal/mol@LB@Unfolding Energy - mRNA 1.2009 kcal/mol@LB@Unfolding Energy - sRNA 2.62609 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 38 -- 44@LB@
13	0.0002543	0.06302	b3583	sgbE	-8.82	0.035786	171 -- 191	39 -- 61	L-ribulose-5-phosphate 4-epimerase	_____________170_____________________192\n_____________\|_______________________\|\n5'-CAA...UGGAU__________GUAU_________UGGAU...ACG-3'\n______________UGAAGC__GC____GCAGGAGGC\n______________\|\|\|\|:\|__\|\|____\|\|\|:\|\|:\|\|\n______________ACUUUG__CG____CGUUCUUCG\n3'-UUU...GCCCU______AA__AAUU_________UGAAU...CAA-5'\n_____________\|_______________________\|\n_____________62______________________38\n	185 -- 191	39 -- 45	-21.2799 kcal/mol	5.20492 kcal/mol	7.25518 kcal/mol	170 192@LB@ \| \|@LB@5'-CAA...UGGAU GUAU UGGAU...ACG-3'@LB@ UGAAGC GC GCAGGAGGC@LB@ \|\|\|\|:\| \|\| \|\|\|:\|\|:\|\|@LB@ ACUUUG CG CGUUCUUCG@LB@3'-UUU...GCCCU AA AAUU UGAAU...CAA-5'@LB@ \| \|@LB@ 62 38@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -21.2799 kcal/mol@LB@Unfolding Energy - mRNA 5.20492 kcal/mol@LB@Unfolding Energy - sRNA 7.25518 kcal/mol@LB@@LB@Position - mRNA 171 -- 191@LB@Position - sRNA 39 -- 61@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 39 -- 45@LB@
18	0.0004863	0.08107	b2217	rcsB	-10.91	0.008593	172 -- 193	39 -- 59	response regulator in two-component regulatory system with RcsC and YojN	_____________171____________________194\n_____________\|______________________\|\n5'-AAC...GUCAA_________GU_______U___CUAUU...GCG-3'\n______________GAGCUUGCU__AGCAAGG_AGC\n______________:\|:\|\|\|\|\|\|__\|\|\|\|\|\|:_\|\|\|\n______________UUUGAACGA__UCGUUCU_UCG\n3'-UUU...CCUAC_________AU___________UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	183 -- 189	42 -- 48	-25.4912 kcal/mol	8.43277 kcal/mol	6.15149 kcal/mol	171 194@LB@ \| \|@LB@5'-AAC...GUCAA GU U CUAUU...GCG-3'@LB@ GAGCUUGCU AGCAAGG AGC@LB@ :\|:\|\|\|\|\|\| \|\|\|\|\|\|: \|\|\|@LB@ UUUGAACGA UCGUUCU UCG@LB@3'-UUU...CCUAC AU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -25.4912 kcal/mol@LB@Unfolding Energy - mRNA 8.43277 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 42 -- 48@LB@
70	0.003574	0.1645	b0145	dksA	-6.64	0.135564	191 -- 197	39 -- 45	transcriptional regulator of rRNA transcription; DnaK suppressor protein	_____________190_____198\n_____________\|_______\|\n5'-AAU...UUAAG_______AACAU...AUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	191 -- 197	39 -- 45	-7.63285 kcal/mol	0.475666 kcal/mol	0.514773 kcal/mol	190 198@LB@ \| \|@LB@5'-AAU...UUAAG AACAU...AUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -7.63285 kcal/mol@LB@Unfolding Energy - mRNA 0.475666 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 191 -- 197@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@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@
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@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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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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