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
179	0.02223	0.4143	b2167	fruA	-7.15	0.399094	192 -- 200	5 -- 13	fused fructose-specific PTS enzymes: IIBcomponent/IIC components		_____________191_______201\n_____________\|_________\|\n5'-CGC...GCAGG_________AUGAA...AAA-3'\n______________AGAGGCAUA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCCGUAU\n3'-UUU...UGUUA_________AUUG-5'\n_____________\|_________\|\n_____________14________4\n	194 -- 200	5 -- 11	-11.8443 kcal/mol	1.8873 kcal/mol	2.80332 kcal/mol	191 201@LB@ \| \|@LB@5'-CGC...GCAGG AUGAA...AAA-3'@LB@ AGAGGCAUA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCCGUAU@LB@3'-UUU...UGUUA AUUG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -7.15 kcal/mol@LB@Hybridization Energy -11.8443 kcal/mol@LB@Unfolding Energy - mRNA 1.8873 kcal/mol@LB@Unfolding Energy - sRNA 2.80332 kcal/mol@LB@@LB@Position - mRNA 192 -- 200@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
123	0.01273	0.3462	b1817	manX	-9.41	0.160028	181 -- 191	9 -- 19	fused mannose-specific PTS enzymes: IIA component/IIB component		_____________180_________192\n_____________\|___________\|\n5'-UUA...UUAAC___________AGGUA...GGA-3'\n______________GAUAAUAAAGG\n______________\|\|:\|\|\|\|\|\|\|\|\n______________CUGUUAUUUCC\n3'-UUU...AGACA___________GUAUAUUG-5'\n_____________\|___________\|\n_____________20__________8\n	185 -- 191	9 -- 15	-11.4394 kcal/mol	1.08042 kcal/mol	0.949641 kcal/mol	180 192@LB@ \| \|@LB@5'-UUA...UUAAC AGGUA...GGA-3'@LB@ GAUAAUAAAGG@LB@ \|\|:\|\|\|\|\|\|\|\|@LB@ CUGUUAUUUCC@LB@3'-UUU...AGACA GUAUAUUG-5'@LB@ \| \|@LB@ 20 8@LB@@LB@@LB@Energy -9.41 kcal/mol@LB@Hybridization Energy -11.4394 kcal/mol@LB@Unfolding Energy - mRNA 1.08042 kcal/mol@LB@Unfolding Energy - sRNA 0.949641 kcal/mol@LB@@LB@Position - mRNA 181 -- 191@LB@Position - sRNA 9 -- 19@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 9 -- 15@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@
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@
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@
90	0.007755	0.2889	b1852	zwf	-12.23	0.039232	191 -- 223	38 -- 65	glucose-6-phosphate 1-dehydrogenase		_____________190_______________________________224\n_____________\|_________________________________\|\n5'-UCA...CUUAA_______G_CA_______AAC____ACA_____GGCCU...UGG-3'\n______________GGAGAAU_A__UGGCGGU___GCAA___GCCCA\n______________\|\|\|:\|\|\|_\|__\|\|\|\|::\|___\|\|\|\|___\|\|\|\|\|\n______________CCUUUUA_U__ACCGUUA___CGUU___CGGGU\n3'-UUU...UACAA_______G_C_______________AC______UGUCU...UUG-5'\n_____________\|_________________________________\|\n_____________66________________________________37\n	202 -- 208	49 -- 55	-27.1425 kcal/mol	8.24293 kcal/mol	6.67322 kcal/mol	190 224@LB@ \| \|@LB@5'-UCA...CUUAA G CA AAC ACA GGCCU...UGG-3'@LB@ GGAGAAU A UGGCGGU GCAA GCCCA@LB@ \|\|\|:\|\|\| \| \|\|\|\|::\| \|\|\|\| \|\|\|\|\|@LB@ CCUUUUA U ACCGUUA CGUU CGGGU@LB@3'-UUU...UACAA G C AC UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.1425 kcal/mol@LB@Unfolding Energy - mRNA 8.24293 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 191 -- 223@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 49 -- 55@LB@
69	0.005697	0.2777	b0829	gsiA	-9.42	0.158982	246 -- 287	28 -- 64	glutathione ABC transporter ATPase		_____________245__________________________________________288\n_____________\|____________________________________________\|\n5'-CGG...CGGUU_______UGAAUAUU__CUUU_________A_____________GCUGC...GCA-3'\n______________GAAAAUC________GC____AUGCA__GG_CCAGCAGAAAAUA\n______________\|\|\|\|\|\|\|________\|\|____\|\|\|\|\|__\|\|_\|\|\|:\|\|\|\|\|\|\|\|\|\n______________CUUUUAG________CG____UACGU__CC_GGUUGUCUUUUAU\n3'-UUU...ACAAC_______UCAC______U________UA__G_____________UUUAG...UUG-5'\n_____________\|____________________________________________\|\n_____________65___________________________________________27\n	246 -- 252	58 -- 64	-27.8415 kcal/mol	7.44564 kcal/mol	10.972 kcal/mol	245 288@LB@ \| \|@LB@5'-CGG...CGGUU UGAAUAUU CUUU A GCUGC...GCA-3'@LB@ GAAAAUC GC AUGCA GG CCAGCAGAAAAUA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\| \|\| \|\|\|:\|\|\|\|\|\|\|\|\|@LB@ CUUUUAG CG UACGU CC GGUUGUCUUUUAU@LB@3'-UUU...ACAAC UCAC U UA G UUUAG...UUG-5'@LB@ \| \|@LB@ 65 27@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -27.8415 kcal/mol@LB@Unfolding Energy - mRNA 7.44564 kcal/mol@LB@Unfolding Energy - sRNA 10.972 kcal/mol@LB@@LB@Position - mRNA 246 -- 287@LB@Position - sRNA 28 -- 64@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 58 -- 64@LB@
79	0.006804	0.2822	b2947	gshB	-11.48	0.058268	213 -- 229	39 -- 54	glutathione synthetase		_____________212_______________230\n_____________\|_________________\|\n5'-UGC...AGCUC____UC_______A___CAUCG...ACG-3'\n______________GGCA__GUGAUGG_CCC\n______________\|\|\|\|__\|::\|\|\|\|_\|\|\|\n______________CCGU__CGUUACC_GGG\n3'-UUU...AGUCA____UA___________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________55________________38\n	219 -- 225	42 -- 48	-21.2333 kcal/mol	4.99211 kcal/mol	4.76022 kcal/mol	212 230@LB@ \| \|@LB@5'-UGC...AGCUC UC A CAUCG...ACG-3'@LB@ GGCA GUGAUGG CCC@LB@ \|\|\|\| \|::\|\|\|\| \|\|\|@LB@ CCGU CGUUACC GGG@LB@3'-UUU...AGUCA UA UUGUC...UUG-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -21.2333 kcal/mol@LB@Unfolding Energy - mRNA 4.99211 kcal/mol@LB@Unfolding Energy - sRNA 4.76022 kcal/mol@LB@@LB@Position - mRNA 213 -- 229@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 42 -- 48@LB@
10	0.0004066	0.1262	b3429	glgA	-9.74	0.137242	173 -- 185	51 -- 64	glycogen synthase		_____________172____________186\n_____________\|______________\|\n5'-GUA...GCUAC______________UAAAC...ACG-3'\n______________GGAAGUUAG_GGCA\n______________\|:\|\|:\|:\|\|_\|\|\|\|\n______________CUUUUAGUC_CCGU\n3'-UUU...ACAAC_________A____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	175 -- 181	56 -- 62	-15.3924 kcal/mol	2.76007 kcal/mol	2.8882 kcal/mol	172 186@LB@ \| \|@LB@5'-GUA...GCUAC UAAAC...ACG-3'@LB@ GGAAGUUAG GGCA@LB@ \|:\|\|:\|:\|\| \|\|\|\|@LB@ CUUUUAGUC CCGU@LB@3'-UUU...ACAAC A UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -15.3924 kcal/mol@LB@Unfolding Energy - mRNA 2.76007 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 173 -- 185@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 56 -- 62@LB@
51	0.003814	0.237	b3888	yiiD	-11.06	0.072417	149 -- 179	39 -- 72	GNAT family putative N-acetyltransferase		_____________148_________________________________180\n_____________\|___________________________________\|\n5'-UUU...UGCGG_____CA__U______C___U______________CGUGA...AUC-3'\n______________AUAUG__GG___AUCG_UGG_CAAUG__AUGGCCC\n______________\|\|\|\|\|__\|\|___\|\|\|:_\|\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UAUAC__CC___UAGU_ACC_GUUAC__UACCGGG\n3'-UUU...AAAAA_____AA__UUU____C_________GU_______UUGUC...UUG-5'\n_____________\|___________________________________\|\n_____________73__________________________________38\n	173 -- 179	39 -- 45	-28.8621 kcal/mol	10.5098 kcal/mol	7.29447 kcal/mol	148 180@LB@ \| \|@LB@5'-UUU...UGCGG CA U C U CGUGA...AUC-3'@LB@ AUAUG GG AUCG UGG CAAUG AUGGCCC@LB@ \|\|\|\|\| \|\| \|\|\|: \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UAUAC CC UAGU ACC GUUAC UACCGGG@LB@3'-UUU...AAAAA AA UUU C GU UUGUC...UUG-5'@LB@ \| \|@LB@ 73 38@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -28.8621 kcal/mol@LB@Unfolding Energy - mRNA 10.5098 kcal/mol@LB@Unfolding Energy - sRNA 7.29447 kcal/mol@LB@@LB@Position - mRNA 149 -- 179@LB@Position - sRNA 39 -- 72@LB@Position Seed - mRNA 173 -- 179@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)

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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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