Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
8	1.842e-05	0.007771	b2797	sdaB	-15.07	0.000654	133 -- 147	55 -- 69	L-serine dehydratase 2		_____________132_____________148\n_____________\|_______________\|\n5'-CGA...CUCUC_______________UUUCG...UGA-3'\n______________UGUUCAGCUAAGUCC\n______________\|:\|\|\|\|\|\|:\|\|:\|\|\|\n______________AUAAGUCGGUUUAGG\n3'-AUU...AUUUU_______________CUAAU...AUG-5'\n_____________\|_______________\|\n_____________70______________54\n	141 -- 147	55 -- 61	-22.3059 kcal/mol	1.18067 kcal/mol	6.0797 kcal/mol	132 148@LB@ \| \|@LB@5'-CGA...CUCUC UUUCG...UGA-3'@LB@ UGUUCAGCUAAGUCC@LB@ \|:\|\|\|\|\|\|:\|\|:\|\|\|@LB@ AUAAGUCGGUUUAGG@LB@3'-AUU...AUUUU CUAAU...AUG-5'@LB@ \| \|@LB@ 70 54@LB@@LB@@LB@Energy -15.07 kcal/mol@LB@Hybridization Energy -22.3059 kcal/mol@LB@Unfolding Energy - mRNA 1.18067 kcal/mol@LB@Unfolding Energy - sRNA 6.0797 kcal/mol@LB@@LB@Position - mRNA 133 -- 147@LB@Position - sRNA 55 -- 69@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 55 -- 61@LB@
20	9.41e-05	0.01655	b0721	sdhC	-12.56	0.006704	146 -- 157	4 -- 15	succinate dehydrogenase membrane subunit binds cytochrome b556		_____________145__________158\n_____________\|____________\|\n5'-UCC...AGUUA____________GUAGU...CCG-3'\n______________ACCUCUGUGCCC\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UGGAGACAUGGG\n3'-AUU...UAGAA____________AUG-5'\n_____________\|____________\|\n_____________16___________3\n	151 -- 157	4 -- 10	-23.3451 kcal/mol	4.99288 kcal/mol	5.82084 kcal/mol	145 158@LB@ \| \|@LB@5'-UCC...AGUUA GUAGU...CCG-3'@LB@ ACCUCUGUGCCC@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UGGAGACAUGGG@LB@3'-AUU...UAGAA AUG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -23.3451 kcal/mol@LB@Unfolding Energy - mRNA 4.99288 kcal/mol@LB@Unfolding Energy - sRNA 5.82084 kcal/mol@LB@@LB@Position - mRNA 146 -- 157@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 4 -- 10@LB@
163	0.006545	0.1413	b0532	sfmD	-7.71	0.181786	104 -- 132	48 -- 76	putative outer membrane export usher protein	b3144 b4317 b0940	_____________103____________________________133\n_____________\|______________________________\|\n5'-UCA...GGAAA______________A___UUAA________GUUCA...GCU-3'\n______________GCUGAAAU_UUCAG_CCG____UGAUUAUG\n______________\|\|\|:\|\|\|\|_\|\|\|\|\|_\|\|:____:\|\|\|\|\|:\|\n______________CGAUUUUA_AAGUC_GGU____GCUAAUGC\n3'-AUU...CCCGC________U_________UUAG________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________77_____________________________47\n	126 -- 132	48 -- 54	-23.9612 kcal/mol	8.59534 kcal/mol	7.67378 kcal/mol	103 133@LB@ \| \|@LB@5'-UCA...GGAAA A UUAA GUUCA...GCU-3'@LB@ GCUGAAAU UUCAG CCG UGAUUAUG@LB@ \|\|\|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|\|:\|@LB@ CGAUUUUA AAGUC GGU GCUAAUGC@LB@3'-AUU...CCCGC U UUAG ACUUC...AUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -23.9612 kcal/mol@LB@Unfolding Energy - mRNA 8.59534 kcal/mol@LB@Unfolding Energy - sRNA 7.67378 kcal/mol@LB@@LB@Position - mRNA 104 -- 132@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 48 -- 54@LB@
111	0.003555	0.1127	b2938	speA	-9.18	0.077057	36 -- 48	46 -- 58	biosynthetic arginine decarboxylase PLP-binding		_____________35____________49\n_____________\|_____________\|\n5'-GUU...CUUAC_____________CUUAA...GCA-3'\n______________GUUCGGUUAUGUG\n______________:\|:\|\|:\|\|\|:\|\|\|\n______________UAGGCUAAUGCAC\n3'-AUU...CGGUU_____________UUCAU...AUG-5'\n_____________\|_____________\|\n_____________59____________45\n	42 -- 48	46 -- 52	-14.853 kcal/mol	3.8258 kcal/mol	1.8625 kcal/mol	35 49@LB@ \| \|@LB@5'-GUU...CUUAC CUUAA...GCA-3'@LB@ GUUCGGUUAUGUG@LB@ :\|:\|\|:\|\|\|:\|\|\|@LB@ UAGGCUAAUGCAC@LB@3'-AUU...CGGUU UUCAU...AUG-5'@LB@ \| \|@LB@ 59 45@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -14.853 kcal/mol@LB@Unfolding Energy - mRNA 3.8258 kcal/mol@LB@Unfolding Energy - sRNA 1.8625 kcal/mol@LB@@LB@Position - mRNA 36 -- 48@LB@Position - sRNA 46 -- 58@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 46 -- 52@LB@
173	0.007216	0.1466	b3650	spoT	-5.39	0.520602	11 -- 17	54 -- 60	bifunctional (p)ppGpp synthetase II/ guanosine-3' 5'-bis pyrophosphate 3'-pyrophosphohydrolase		_____________10______18\n_____________\|_______\|\n5'-UAG...GGAAA_______CUGGU...CUC-3'\n______________GGAUCCG\n______________::\|\|\|\|\|\n______________UUUAGGC\n3'-AUU...GUCGG_______UAAUG...AUG-5'\n_____________\|_______\|\n_____________61______53\n	11 -- 17	54 -- 60	-6.87427 kcal/mol	1.21245 kcal/mol	0.286889 kcal/mol	10 18@LB@ \| \|@LB@5'-UAG...GGAAA CUGGU...CUC-3'@LB@ GGAUCCG@LB@ ::\|\|\|\|\|@LB@ UUUAGGC@LB@3'-AUU...GUCGG UAAUG...AUG-5'@LB@ \| \|@LB@ 61 53@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -6.87427 kcal/mol@LB@Unfolding Energy - mRNA 1.21245 kcal/mol@LB@Unfolding Energy - sRNA 0.286889 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 54 -- 60@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 54 -- 60@LB@
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate		_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
12	3.867e-05	0.01134	b0728	sucC	-9.87	0.049323	145 -- 186	43 -- 73	succinyl-CoA synthetase beta subunit		_____________144_________________________________________187\n_____________\|___________________________________________\|\n5'-CGC...GAUAC_____________UACGGUUUAAA____AA_____________GAUGG...AAG-3'\n______________GAAAUAUUCGGUC___________AGAU__CGAUUAC_UGAAG\n______________:\|\|\|\|\|\|\|\|:\|:\|___________\|:\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUUAUAAGUCGG___________UUUA__GCUAAUG_ACUUC\n3'-AUU...GCCGA____________________________G________C_____AUUUU...AUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________42\n	175 -- 181	49 -- 55	-26.5157 kcal/mol	7.48621 kcal/mol	9.17828 kcal/mol	144 187@LB@ \| \|@LB@5'-CGC...GAUAC UACGGUUUAAA AA GAUGG...AAG-3'@LB@ GAAAUAUUCGGUC AGAU CGAUUAC UGAAG@LB@ :\|\|\|\|\|\|\|\|:\|:\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUUAUAAGUCGG UUUA GCUAAUG ACUUC@LB@3'-AUU...GCCGA G C AUUUU...AUG-5'@LB@ \| \|@LB@ 74 42@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -26.5157 kcal/mol@LB@Unfolding Energy - mRNA 7.48621 kcal/mol@LB@Unfolding Energy - sRNA 9.17828 kcal/mol@LB@@LB@Position - mRNA 145 -- 186@LB@Position - sRNA 43 -- 73@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@LB@
65	0.001093	0.05856	b1519	tam	-11.83	0.011992	187 -- 231	1 -- 50	trans-aconitate methyltransferase		_____________186____________________________________________________232\n_____________\|______________________________________________________\|\n5'-UUU...CGCUG_____________AAAU______C_________C__________U___A_____ACUUU...AAU-3'\n______________ACG_GGAGUAAAA____GUCUGA____UGGAAC______CCUCU_UAU_UCUAC\n______________\|\|\|_\|:\|\|\|\|\|\|\|____\|\|\|\|\|\|____\|:\|\|\|\|______\|\|\|\|\|_\|\|:_:\|\|\|\|\n______________UGC_CUUCAUUUU____CAGACU____AUCUUG______GGAGA_AUG_GGAUG\n3'-AUU...GCUAA___A_________C_________UUCU______UAGAAU_____C_________-5'\n_____________\|_____________________________________________________\|\n_____________51____________________________________________________1\n	191 -- 197	39 -- 45	-32.7669 kcal/mol	8.27841 kcal/mol	12.6772 kcal/mol	186 232@LB@ \| \|@LB@5'-UUU...CGCUG AAAU C C U A ACUUU...AAU-3'@LB@ ACG GGAGUAAAA GUCUGA UGGAAC CCUCU UAU UCUAC@LB@ \|\|\| \|:\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|@LB@ UGC CUUCAUUUU CAGACU AUCUUG GGAGA AUG GGAUG@LB@3'-AUU...GCUAA A C UUCU UAGAAU C -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -32.7669 kcal/mol@LB@Unfolding Energy - mRNA 8.27841 kcal/mol@LB@Unfolding Energy - sRNA 12.6772 kcal/mol@LB@@LB@Position - mRNA 187 -- 231@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
140	0.005114	0.1284	b3993	thiE	-7.64	0.188958	243 -- 250	4 -- 11	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)		_____________242______251\n_____________\|________\|\n5'-CAC...CAGGA________GGUGG...UAC-3'\n______________CUGUACCC\n______________\|\|\|\|\|\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	244 -- 250	4 -- 10	-13.9053 kcal/mol	2.83489 kcal/mol	3.45361 kcal/mol	242 251@LB@ \| \|@LB@5'-CAC...CAGGA GGUGG...UAC-3'@LB@ CUGUACCC@LB@ \|\|\|\|\|\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -13.9053 kcal/mol@LB@Unfolding Energy - mRNA 2.83489 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 243 -- 250@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 4 -- 10@LB@
18	6.719e-05	0.01313	b2935	tktA	-10.85	0.025018	263 -- 275	52 -- 64	transketolase 1 thiamine triphosphate-binding		_____________262___________276\n_____________\|_____________\|\n5'-AAG...CAGAA_____________CACCC...UGG-3'\n______________AGCCAAAUCCGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGGUUUAGGCUA\n3'-AUU...AUAAG_____________AUGCA...AUG-5'\n_____________\|_____________\|\n_____________65____________51\n	269 -- 275	52 -- 58	-21.1603 kcal/mol	4.16811 kcal/mol	6.16128 kcal/mol	262 276@LB@ \| \|@LB@5'-AAG...CAGAA CACCC...UGG-3'@LB@ AGCCAAAUCCGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGGUUUAGGCUA@LB@3'-AUU...AUAAG AUGCA...AUG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -21.1603 kcal/mol@LB@Unfolding Energy - mRNA 4.16811 kcal/mol@LB@Unfolding Energy - sRNA 6.16128 kcal/mol@LB@@LB@Position - mRNA 263 -- 275@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 269 -- 275@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)

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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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