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
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@
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@
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@
169	0.01937	0.3812	b4557	yidD	-14.07	0.041992	2 -- 13	11 -- 22	membrane protein insertion efficiency factor UPF0161 family inner membrane protein	_____________1______________________14\n_____________\|______________________\|\n__________5'-C____________GUAUCG____UUACA...UCA-3'\n______________UGGGGCAUCCCC_______GUC\n______________\|\|\|\|\|\|\|:\|\|\|\|_______:\|\|\n______________ACCCCGUGGGGG_______UAG\n3'-UUU...UGCGU____________AACGAAG___-5'\n_____________\|_____________________\|\n_____________23____________________11\n	7 -- 13	11 -- 17	-28.608 kcal/mol	8.24927 kcal/mol	10.7363 kcal/mol	1 14@LB@ \| \|@LB@ 5'-C GUAUCG UUACA...UCA-3'@LB@ UGGGGCAUCCCC GUC@LB@ \|\|\|\|\|\|\|:\|\|\|\| :\|\|@LB@ ACCCCGUGGGGG UAG@LB@3'-UUU...UGCGU AACGAAG -5'@LB@ \| \|@LB@ 23 11@LB@@LB@@LB@Energy -14.07 kcal/mol@LB@Hybridization Energy -28.608 kcal/mol@LB@Unfolding Energy - mRNA 8.24927 kcal/mol@LB@Unfolding Energy - sRNA 10.7363 kcal/mol@LB@@LB@Position - mRNA 2 -- 13@LB@Position - sRNA 11 -- 22@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 11 -- 17@LB@
162	0.01805	0.3749	b2499	purM	-13.07	0.067336	182 -- 195	13 -- 27	phosphoribosylaminoimidazole synthetase	_____________181______196\n_____________\|________\|\n__________5'-U________AUGGU...CGC-3'\n______________AUAUUCAG\n______________\|\|\|:\|\|\|\|\n______________UAUGAGUC\n3'-UUU...GUGGU________AGUGU...UAG-5'\n_____________\|________\|\n_____________28_______12\n	3 -- 9	174 -- 180	-7.89877 kcal/mol	1.882 kcal/mol	0.273058 kcal/mol	181 196@LB@ \| \|@LB@ 5'-U AUGGU...CGC-3'@LB@ AUAUUCAG@LB@ \|\|\|:\|\|\|\|@LB@ UAUGAGUC@LB@3'-UUU...GUGGU AGUGU...UAG-5'@LB@ \| \|@LB@ 28 12@LB@@LB@@LB@Energy -13.07 kcal/mol@LB@Hybridization Energy -7.89877 kcal/mol@LB@Unfolding Energy - mRNA 1.882 kcal/mol@LB@Unfolding Energy - sRNA 0.273058 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 13 -- 27@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 174 -- 180@LB@
19	0.001698	0.2633	b2575	trmN	-12.50	0.088044	81 -- 92	14 -- 25	tRNA1(Val) (adenine(37)-N6)-methyltransferase	_____________80___________93\n_____________\|____________\|\n5'-ACC...UACAU__G_________GUAAU...GUA-3'\n______________CC_UGCUUCGUC\n______________\|\|_\|\|\|\|\|\|:\|\|\n______________GG_ACGAAGUAG\n3'-UUU...GUGGG__A_________-5'\n_____________\|___________\|\n_____________26__________14\n	222 -- 228	1 -- 7	-15.2724 kcal/mol	3.783 kcal/mol	1.04836 kcal/mol	80 93@LB@ \| \|@LB@5'-ACC...UACAU G GUAAU...GUA-3'@LB@ CC UGCUUCGUC@LB@ \|\| \|\|\|\|\|\|:\|\|@LB@ GG ACGAAGUAG@LB@3'-UUU...GUGGG A -5'@LB@ \| \|@LB@ 26 14@LB@@LB@@LB@Energy -12.50 kcal/mol@LB@Hybridization Energy -15.2724 kcal/mol@LB@Unfolding Energy - mRNA 3.783 kcal/mol@LB@Unfolding Energy - sRNA 1.04836 kcal/mol@LB@@LB@Position - mRNA 81 -- 92@LB@Position - sRNA 14 -- 25@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 1 -- 7@LB@
80	0.008443	0.3551	b3791	wecE	-14.19	0.039608	22 -- 66	14 -- 64	TDP-4-oxo-6-deoxy-D-glucose transaminase	_____________21______________67\n_____________\|_______________\|\n5'-GAC...ACCGC_______________GGUGA...CCC-3'\n______________GUACU_GGUUAUACA\n______________:\|\|\|\|_:\|\|:\|:\|\|\|\n______________UAUGA_UCAGUGUGU\n3'-UUU...GUGGU_____G_________ACUAC...UAG-5'\n_____________\|_______________\|\n_____________65______________13\n	185 -- 191	167 -- 173	-12.5686 kcal/mol	2.73267 kcal/mol	0.435744 kcal/mol	21 67@LB@ \| \|@LB@5'-GAC...ACCGC GGUGA...CCC-3'@LB@ GUACU GGUUAUACA@LB@ :\|\|\|\| :\|\|:\|:\|\|\|@LB@ UAUGA UCAGUGUGU@LB@3'-UUU...GUGGU G ACUAC...UAG-5'@LB@ \| \|@LB@ 65 13@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -12.5686 kcal/mol@LB@Unfolding Energy - mRNA 2.73267 kcal/mol@LB@Unfolding Energy - sRNA 0.435744 kcal/mol@LB@@LB@Position - mRNA 22 -- 66@LB@Position - sRNA 14 -- 64@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 167 -- 173@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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