Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
60	0.004583	0.2539	b0674	asnB	-9.07	0.186262	281 -- 298	39 -- 51	asparagine synthetase B		_____________280________________299\n_____________\|__________________\|\n5'-ACA...CGCCU______UCAUC_______GG-3'\n______________GAUGCG_____GUGGCCC\n______________:\|\|\|\|:_____:\|\|\|\|\|\|\n______________UUACGU_____UACCGGG\n3'-UUU...CACCG__________________UUGUC...UUG-5'\n_____________\|__________________\|\n_____________52_________________38\n	292 -- 298	39 -- 45	-18.7239 kcal/mol	4.90882 kcal/mol	4.74571 kcal/mol	280 299@LB@ \| \|@LB@5'-ACA...CGCCU UCAUC GG-3'@LB@ GAUGCG GUGGCCC@LB@ :\|\|\|\|: :\|\|\|\|\|\|@LB@ UUACGU UACCGGG@LB@3'-UUU...CACCG UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -18.7239 kcal/mol@LB@Unfolding Energy - mRNA 4.90882 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 281 -- 298@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
119	0.01177	0.3326	b4262	lptG	-9.06	0.186805	47 -- 70	7 -- 29	lipopolysaccharide export ABC permease		_____________46_______________________71\n_____________\|________________________\|\n5'-CCA...CUCCC_______GAAC_____________AGCUG...UCA-3'\n______________UGAAAUC____GGCGGUAAAGGUA\n______________\|:\|\|\|\|\|____\|:\|::\|\|\|\|\|\|:\|\n______________AUUUUAG____CUGUUAUUUCCGU\n3'-UUU...CUUUU_______ACA______________AUAUUG-5'\n_____________\|________________________\|\n_____________30_______________________6\n	64 -- 70	7 -- 13	-21.2282 kcal/mol	7.28231 kcal/mol	4.88318 kcal/mol	46 71@LB@ \| \|@LB@5'-CCA...CUCCC GAAC AGCUG...UCA-3'@LB@ UGAAAUC GGCGGUAAAGGUA@LB@ \|:\|\|\|\|\| \|:\|::\|\|\|\|\|\|:\|@LB@ AUUUUAG CUGUUAUUUCCGU@LB@3'-UUU...CUUUU ACA AUAUUG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -21.2282 kcal/mol@LB@Unfolding Energy - mRNA 7.28231 kcal/mol@LB@Unfolding Energy - sRNA 4.88318 kcal/mol@LB@@LB@Position - mRNA 47 -- 70@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 7 -- 13@LB@
80	0.006956	0.2822	b1914	uvrY	-9.02	0.189987	260 -- 281	5 -- 24	response regulator in two-component regulatory system with BarA		_____________259____________________282\n_____________\|______________________\|\n5'-UUC...CGCAU____GAA____UA_________AAAGU...CAU-3'\n______________UCUG___GAUA__AAGGGUAUA\n______________\|\|\|\|___\|\|:\|__\|\|:\|\|:\|\|\|\n______________AGAC___CUGU__UUUCCGUAU\n3'-UUU...AUUUU____A______UA_________AUUG-5'\n_____________\|______________________\|\n_____________25_____________________4\n	275 -- 281	5 -- 11	-15.9126 kcal/mol	2.27135 kcal/mol	4.61703 kcal/mol	259 282@LB@ \| \|@LB@5'-UUC...CGCAU GAA UA AAAGU...CAU-3'@LB@ UCUG GAUA AAGGGUAUA@LB@ \|\|\|\| \|\|:\| \|\|:\|\|:\|\|\|@LB@ AGAC CUGU UUUCCGUAU@LB@3'-UUU...AUUUU A UA AUUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -15.9126 kcal/mol@LB@Unfolding Energy - mRNA 2.27135 kcal/mol@LB@Unfolding Energy - sRNA 4.61703 kcal/mol@LB@@LB@Position - mRNA 260 -- 281@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 5 -- 11@LB@
30	0.001842	0.2065	b3574	yiaJ	-8.97	0.194276	228 -- 279	20 -- 64	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon		_____________227_____________________________________________________280\n_____________\|_______________________________________________________\|\n5'-CCC...AAAAA_____CG__A___________GAAAAAGAGC______C______CC_________UUCGC...UUG-3'\n______________GAGAA__AG_UGGC___GCAG__________GUCCAG_CGGAAG__AGAGUCUGU\n______________\|\|:\|\|__\|\|_\|\|\|\|___\|\|\|:__________\|:\|\|\|:_\|:\|\|\|:__\|:\|:\|\|\|\|\|\n______________CUUUU__UC_ACCG___CGUU__________CGGGUU_GUCUUU__UUUUAGACA\n3'-UUU...ACAAC_____AG_______UUA____AC_____________________UA_________CUGUU...UUG-5'\n_____________\|_______________________________________________________\|\n_____________65______________________________________________________19\n	273 -- 279	20 -- 26	-33.3994 kcal/mol	13.3805 kcal/mol	11.0456 kcal/mol	227 280@LB@ \| \|@LB@5'-CCC...AAAAA CG A GAAAAAGAGC C CC UUCGC...UUG-3'@LB@ GAGAA AG UGGC GCAG GUCCAG CGGAAG AGAGUCUGU@LB@ \|\|:\|\| \|\| \|\|\|\| \|\|\|: \|:\|\|\|: \|:\|\|\|: \|:\|:\|\|\|\|\|@LB@ CUUUU UC ACCG CGUU CGGGUU GUCUUU UUUUAGACA@LB@3'-UUU...ACAAC AG UUA AC UA CUGUU...UUG-5'@LB@ \| \|@LB@ 65 19@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -33.3994 kcal/mol@LB@Unfolding Energy - mRNA 13.3805 kcal/mol@LB@Unfolding Energy - sRNA 11.0456 kcal/mol@LB@@LB@Position - mRNA 228 -- 279@LB@Position - sRNA 20 -- 64@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 20 -- 26@LB@
33	0.002101	0.2088	b1300	puuC	-8.92	0.198515	81 -- 101	2 -- 20	gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase	b0312	_____________80____________________102\n_____________\|_____________________\|\n5'-GGC...CGGCU___AG_______U________AGAAU...AAA-3'\n______________UGA__GAUGAAG_GUAUAUAA\n______________\|\|\|__:\|\|:\|\|\|_\|:\|\|\|\|\|\|\n______________ACU__UUAUUUC_CGUAUAUU\n3'-UUU...UAGAC___G_________________G-5'\n_____________\|_____________________\|\n_____________21____________________1\n	94 -- 100	3 -- 9	-14.4968 kcal/mol	1.34672 kcal/mol	4.22649 kcal/mol	80 102@LB@ \| \|@LB@5'-GGC...CGGCU AG U AGAAU...AAA-3'@LB@ UGA GAUGAAG GUAUAUAA@LB@ \|\|\| :\|\|:\|\|\| \|:\|\|\|\|\|\|@LB@ ACU UUAUUUC CGUAUAUU@LB@3'-UUU...UAGAC G G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -14.4968 kcal/mol@LB@Unfolding Energy - mRNA 1.34672 kcal/mol@LB@Unfolding Energy - sRNA 4.22649 kcal/mol@LB@@LB@Position - mRNA 81 -- 101@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 3 -- 9@LB@
199	0.02539	0.4256	b2094	gatA	-8.91	0.199733	27 -- 47	1 -- 21	galactitol-specific enzyme IIA component of PTS		_____________26_____________________48\n_____________\|______________________\|\n5'-UUA...UGAUG____AUCU______________AUCCC...AUG-3'\n______________GUGA____UGAAGGCGUG_GAC\n______________\|\|\|\|____\|:\|\|\|\|\|:\|:_:\|\|\n______________CACU____AUUUCCGUAU_UUG\n3'-UUU...UUAGA____GUU___________A___-5'\n_____________\|_____________________\|\n_____________22____________________1\n	38 -- 44	5 -- 11	-17.7737 kcal/mol	4.45083 kcal/mol	4.41334 kcal/mol	26 48@LB@ \| \|@LB@5'-UUA...UGAUG AUCU AUCCC...AUG-3'@LB@ GUGA UGAAGGCGUG GAC@LB@ \|\|\|\| \|:\|\|\|\|\|:\|: :\|\|@LB@ CACU AUUUCCGUAU UUG@LB@3'-UUU...UUAGA GUU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -17.7737 kcal/mol@LB@Unfolding Energy - mRNA 4.45083 kcal/mol@LB@Unfolding Energy - sRNA 4.41334 kcal/mol@LB@@LB@Position - mRNA 27 -- 47@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
29	0.001819	0.2065	b3648	gmk	-8.89	0.201842	236 -- 243	51 -- 58	guanylate kinase		_____________235______244\n_____________\|________\|\n5'-GUG...GCCCC________CGGGU...CCC-3'\n______________CAGUGGCG\n______________\|\|\|\|\|\|\|:\n______________GUCACCGU\n3'-UUU...UUUUA________UACGU...UUG-5'\n_____________\|________\|\n_____________59_______50\n	237 -- 243	51 -- 57	-13.8917 kcal/mol	2.3096 kcal/mol	2.69685 kcal/mol	235 244@LB@ \| \|@LB@5'-GUG...GCCCC CGGGU...CCC-3'@LB@ CAGUGGCG@LB@ \|\|\|\|\|\|\|:@LB@ GUCACCGU@LB@3'-UUU...UUUUA UACGU...UUG-5'@LB@ \| \|@LB@ 59 50@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -13.8917 kcal/mol@LB@Unfolding Energy - mRNA 2.3096 kcal/mol@LB@Unfolding Energy - sRNA 2.69685 kcal/mol@LB@@LB@Position - mRNA 236 -- 243@LB@Position - sRNA 51 -- 58@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 51 -- 57@LB@
92	0.007983	0.2918	b2513	yfgM	-8.87	0.203113	70 -- 109	9 -- 65	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________69___________________________________________________________110\n_____________\|____________________________________________________________\|\n5'-GGC...UGCUG__U_____UGA_____________C___A_______________________________AUUUG...UUG-3'\n______________GG_GAGUC___AGUGGC____UAA_GGC_CAGCAG________________UAGUGAAGG\n______________\|\|_:\|:\|\|___\|\|\|\|\|\|____:\|\|_\|\|\|_\|\|:\|\|\|________________:\|:\|:\|\|\|\|\n______________CC_UUUAG___UCACCG____GUU_CCG_GUUGUC________________GUUAUUUCC\n3'-UUU...UACAA__U______________UUAC___A___G______UUUUAUUUUAGACACU_________GUAUAUUG-5'\n_____________\|____________________________________________________________\|\n_____________66___________________________________________________________8\n	103 -- 109	9 -- 15	-31.9345 kcal/mol	11.9273 kcal/mol	11.1365 kcal/mol	69 110@LB@ \| \|@LB@5'-GGC...UGCUG U UGA C A AUUUG...UUG-3'@LB@ GG GAGUC AGUGGC UAA GGC CAGCAG UAGUGAAGG@LB@ \|\| :\|:\|\| \|\|\|\|\|\| :\|\| \|\|\| \|\|:\|\|\| :\|:\|:\|\|\|\|@LB@ CC UUUAG UCACCG GUU CCG GUUGUC GUUAUUUCC@LB@3'-UUU...UACAA U UUAC A G UUUUAUUUUAGACACU GUAUAUUG-5'@LB@ \| \|@LB@ 66 8@LB@@LB@@LB@Energy -8.87 kcal/mol@LB@Hybridization Energy -31.9345 kcal/mol@LB@Unfolding Energy - mRNA 11.9273 kcal/mol@LB@Unfolding Energy - sRNA 11.1365 kcal/mol@LB@@LB@Position - mRNA 70 -- 109@LB@Position - sRNA 9 -- 65@LB@Position Seed - mRNA 103 -- 109@LB@Position Seed - sRNA 9 -- 15@LB@
169	0.02007	0.3993	b1680	sufS	-8.85	0.205059	78 -- 94	33 -- 48	cysteine desulfurase stimulated by SufE; selenocysteine lyase PLP-dependent		_____________77________________95\n_____________\|_________________\|\n5'-AAA...AAUCA____GAU__________UGAUC...CGC-3'\n______________GCAG___GCCCAGCAGA\n______________\|\|\|:___\|\|\|\|\|:\|\|\|\|\n______________CGUU___CGGGUUGUCU\n3'-UUU...CGUUA____AC___________UUUAU...UUG-5'\n_____________\|_________________\|\n_____________49________________32\n	85 -- 91	36 -- 42	-22.7432 kcal/mol	5.30025 kcal/mol	8.59426 kcal/mol	77 95@LB@ \| \|@LB@5'-AAA...AAUCA GAU UGAUC...CGC-3'@LB@ GCAG GCCCAGCAGA@LB@ \|\|\|: \|\|\|\|\|:\|\|\|\|@LB@ CGUU CGGGUUGUCU@LB@3'-UUU...CGUUA AC UUUAU...UUG-5'@LB@ \| \|@LB@ 49 32@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -22.7432 kcal/mol@LB@Unfolding Energy - mRNA 5.30025 kcal/mol@LB@Unfolding Energy - sRNA 8.59426 kcal/mol@LB@@LB@Position - mRNA 78 -- 94@LB@Position - sRNA 33 -- 48@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 36 -- 42@LB@
38	0.00253	0.2088	b3789	rffH	-8.84	0.205897	98 -- 106	51 -- 59	glucose-1-phosphate thymidylyltransferase		_____________97________107\n_____________\|_________\|\n5'-GGC...ACGGU_________UCUGG...UGA-3'\n______________UCAGUGGUA\n______________\|\|\|\|\|\|\|:\|\n______________AGUCACCGU\n3'-UUU...CUUUU_________UACGU...UUG-5'\n_____________\|_________\|\n_____________60________50\n	100 -- 106	51 -- 57	-13.9039 kcal/mol	2.34576 kcal/mol	2.71896 kcal/mol	97 107@LB@ \| \|@LB@5'-GGC...ACGGU UCUGG...UGA-3'@LB@ UCAGUGGUA@LB@ \|\|\|\|\|\|\|:\|@LB@ AGUCACCGU@LB@3'-UUU...CUUUU UACGU...UUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -13.9039 kcal/mol@LB@Unfolding Energy - mRNA 2.34576 kcal/mol@LB@Unfolding Energy - sRNA 2.71896 kcal/mol@LB@@LB@Position - mRNA 98 -- 106@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 51 -- 57@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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