Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
105	0.01118	0.3575	b0439	lon	-14.09	0.041610	272 -- 293	1 -- 24	DNA-binding ATP-dependent protease La	_____________271_______294\n_____________\|_________\|\n5'-AUC...CACAU_________CUUAU...GGG-3'\n______________GGUCAUCCC\n______________\|\|\|\|\|\|\|\|\|\n______________CCAGUAGGG\n3'-UUU...UAACG_________UGACG...UAG-5'\n_____________\|_________\|\n_____________25________0\n	277 -- 283	128 -- 134	-16.7868 kcal/mol	1.03204 kcal/mol	4.55487 kcal/mol	271 294@LB@ \| \|@LB@5'-AUC...CACAU CUUAU...GGG-3'@LB@ GGUCAUCCC@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAGUAGGG@LB@3'-UUU...UAACG UGACG...UAG-5'@LB@ \| \|@LB@ 25 0@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -16.7868 kcal/mol@LB@Unfolding Energy - mRNA 1.03204 kcal/mol@LB@Unfolding Energy - sRNA 4.55487 kcal/mol@LB@@LB@Position - mRNA 272 -- 293@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 128 -- 134@LB@
90	0.01008	0.3575	b3994	thiC	-11.53	0.138483	145 -- 158	1 -- 14	phosphomethylpyrimidine synthase	_____________144_________159\n_____________\|___________\|\n5'-AUG...CGUCU___________CGUCG...UUU-3'\n______________CUUGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GAACGAAGUAG\n3'-UUU...UGGGG___________-5'\n_____________\|__________\|\n_____________15_________1\n	152 -- 158	1 -- 7	-17.5294 kcal/mol	1.22878 kcal/mol	1.03329 kcal/mol	144 159@LB@ \| \|@LB@5'-AUG...CGUCU CGUCG...UUU-3'@LB@ CUUGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GAACGAAGUAG@LB@3'-UUU...UGGGG -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -17.5294 kcal/mol@LB@Unfolding Energy - mRNA 1.22878 kcal/mol@LB@Unfolding Energy - sRNA 1.03329 kcal/mol@LB@@LB@Position - mRNA 145 -- 158@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 1 -- 7@LB@
172	0.01969	0.3812	b0213	yafS	-9.47	0.344290	95 -- 113	1 -- 19	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________94________114\n_____________\|_________\|\n5'-UGG...UCAAA_________CUCCU...UCA-3'\n______________CUGUCGUGG\n______________\|\|\|\|\|\|:\|\|\n______________GACAGCGCC\n3'-UUU...GAAGC_________AUUUU...UAG-5'\n_____________\|_________\|\n_____________20________0\n	228 -- 234	50 -- 56	-16.2917 kcal/mol	2.78861 kcal/mol	4.02 kcal/mol	94 114@LB@ \| \|@LB@5'-UGG...UCAAA CUCCU...UCA-3'@LB@ CUGUCGUGG@LB@ \|\|\|\|\|\|:\|\|@LB@ GACAGCGCC@LB@3'-UUU...GAAGC AUUUU...UAG-5'@LB@ \| \|@LB@ 20 0@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -16.2917 kcal/mol@LB@Unfolding Energy - mRNA 2.78861 kcal/mol@LB@Unfolding Energy - sRNA 4.02 kcal/mol@LB@@LB@Position - mRNA 95 -- 113@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 50 -- 56@LB@
200	0.02363	0.3833	b3068	mug	-12.10	0.106144	279 -- 297	1 -- 19	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________278__________________298\n_____________\|____________________\|\n5'-UGG...GGACU___UU_______________CGG-3'\n______________GGU__UCCCUUUGCU_CAUC\n______________\|\|:__:\|\|\|:\|\|\|\|\|_\|\|\|\|\n______________CCG__GGGGGAACGA_GUAG\n3'-UUU...GUACC___U___________A____-5'\n_____________\|___________________\|\n_____________20__________________1\n	287 -- 293	6 -- 12	-22.9494 kcal/mol	3.41941 kcal/mol	8.43224 kcal/mol	278 298@LB@ \| \|@LB@5'-UGG...GGACU UU CGG-3'@LB@ GGU UCCCUUUGCU CAUC@LB@ \|\|: :\|\|\|:\|\|\|\|\| \|\|\|\|@LB@ CCG GGGGGAACGA GUAG@LB@3'-UUU...GUACC U A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -12.10 kcal/mol@LB@Hybridization Energy -22.9494 kcal/mol@LB@Unfolding Energy - mRNA 3.41941 kcal/mol@LB@Unfolding Energy - sRNA 8.43224 kcal/mol@LB@@LB@Position - mRNA 279 -- 297@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 6 -- 12@LB@
195	0.02319	0.3833	b1233	ychJ	-7.86	0.620262	61 -- 80	1 -- 18	UPF0225 family protein	_____________60____________________________________81\n_____________\|_____________________________________\|\n5'-CUU...GCUAC_______________A___CUACU_____________ACGCC...UCA-3'\n______________UGCUCGGUUA_ACAU_GUG_____CAGGC_GGUUAAU\n______________\|:\|\|\|:\|\|:\|_\|\|\|\|_:\|\|_____\|\|\|\|\|_:\|\|:\|\|:\n______________AUGAGUCAGU_UGUA_UAC_____GUCCG_UCAGUUG\n3'-UUU...UGGUU__________G____C_____________U_______AAAGU...UAG-5'\n_____________\|_____________________________________\|\n_____________19____________________________________0\n	139 -- 145	171 -- 177	-29.0991 kcal/mol	9.80481 kcal/mol	8.18679 kcal/mol	60 81@LB@ \| \|@LB@5'-CUU...GCUAC A CUACU ACGCC...UCA-3'@LB@ UGCUCGGUUA ACAU GUG CAGGC GGUUAAU@LB@ \|:\|\|\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\| :\|\|:\|\|:@LB@ AUGAGUCAGU UGUA UAC GUCCG UCAGUUG@LB@3'-UUU...UGGUU G C U AAAGU...UAG-5'@LB@ \| \|@LB@ 19 0@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -29.0991 kcal/mol@LB@Unfolding Energy - mRNA 9.80481 kcal/mol@LB@Unfolding Energy - sRNA 8.18679 kcal/mol@LB@@LB@Position - mRNA 61 -- 80@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 171 -- 177@LB@
21	0.001755	0.2633	b3037	ygiB	-10.05	0.269263	126 -- 141	3 -- 15	DUF1190 family protein	_____________125______________142\n_____________\|________________\|\n5'-AAA...UUCUU_______CUC______AUUUC...UGC-3'\n______________CCCCCUU___GCUUCA\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GGGGGAA___CGAAGU\n3'-UUU...CCCGU________________AG-5'\n_____________\|________________\|\n_____________16_______________2\n	126 -- 132	9 -- 15	-20.0074 kcal/mol	1.89647 kcal/mol	7.00663 kcal/mol	125 142@LB@ \| \|@LB@5'-AAA...UUCUU CUC AUUUC...UGC-3'@LB@ CCCCCUU GCUUCA@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GGGGGAA CGAAGU@LB@3'-UUU...CCCGU AG-5'@LB@ \| \|@LB@ 16 2@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -20.0074 kcal/mol@LB@Unfolding Energy - mRNA 1.89647 kcal/mol@LB@Unfolding Energy - sRNA 7.00663 kcal/mol@LB@@LB@Position - mRNA 126 -- 141@LB@Position - sRNA 3 -- 15@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 9 -- 15@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase	_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 7 -- 13@LB@
42	0.003683	0.2912	b2221	atoD	-14.87	0.028783	141 -- 155	6 -- 19	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit	_____________140_____________156\n_____________\|_______________\|\n5'-UAU...AUUCU_____U_________AUUGC...CCC-3'\n______________GGCAC_CCCCUUGCU\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________CCGUG_GGGGAACGA\n3'-UUU...GUACC_______________AGUAG-5'\n_____________\|_______________\|\n_____________20______________5\n	149 -- 155	6 -- 12	-27.0081 kcal/mol	4.79018 kcal/mol	8.30673 kcal/mol	140 156@LB@ \| \|@LB@5'-UAU...AUUCU U AUUGC...CCC-3'@LB@ GGCAC CCCCUUGCU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCGUG GGGGAACGA@LB@3'-UUU...GUACC AGUAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0081 kcal/mol@LB@Unfolding Energy - mRNA 4.79018 kcal/mol@LB@Unfolding Energy - sRNA 8.30673 kcal/mol@LB@@LB@Position - mRNA 141 -- 155@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@LB@
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone	_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@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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