Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
50	0.002349	0.1648	b2040	rfbD	-20.63	0.000491	127 -- 157	3 -- 32	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________126______________________________158\n_____________\|________________________________\|\n5'-GAU...CCAAU__________UU____AUGU____________CCUAU...CUA-3'\n______________ACAAAAUGGG__GAUA_____GAAAAGUGGUG\n______________\|\|\|\|\|\|\|\|\|\|__\|\|:\|_____\|\|\|\|\|\|::\|\|\|\n______________UGUUUUACCC__CUGU_____CUUUUCGUCAC\n3'-UUU...CGAGG________________AGUUU___________CG-5'\n_____________\|________________________________\|\n_____________33_______________________________2\n	151 -- 157	3 -- 9	-27.2371 kcal/mol	4.0691 kcal/mol	2.53925 kcal/mol	126 158@LB@ \| \|@LB@5'-GAU...CCAAU UU AUGU CCUAU...CUA-3'@LB@ ACAAAAUGGG GAUA GAAAAGUGGUG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|::\|\|\|@LB@ UGUUUUACCC CUGU CUUUUCGUCAC@LB@3'-UUU...CGAGG AGUUU CG-5'@LB@ \| \|@LB@ 33 2@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -27.2371 kcal/mol@LB@Unfolding Energy - mRNA 4.0691 kcal/mol@LB@Unfolding Energy - sRNA 2.53925 kcal/mol@LB@@LB@Position - mRNA 127 -- 157@LB@Position - sRNA 3 -- 32@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 3 -- 9@LB@
58	0.00302	0.1789	b0556	rzpD	-16.79	0.009474	64 -- 103	3 -- 36	DLP12 prophage; putative murein endopeptidase	_____________63_________________________________________104\n_____________\|__________________________________________\|\n5'-CGC...CGCUU___________AAACCA___C___________C_____U___AUCAG...ACA-3'\n______________CUUCGCAAAAU______GGG_GAUAUCAAAGG___GCA_GUG\n______________\|\|:\|:\|\|\|\|\|\|______\|\|\|_\|\|:\|\|\|\|\|\|\|:___\|\|\|_\|\|\|\n______________GAGGUGUUUUA______CCC_CUGUAGUUUCU___CGU_CAC\n3'-UUU...UACCC________________________________UUU_______CG-5'\n_____________\|__________________________________________\|\n_____________37_________________________________________2\n	89 -- 95	12 -- 18	-34.1904 kcal/mol	10.724 kcal/mol	6.67685 kcal/mol	63 104@LB@ \| \|@LB@5'-CGC...CGCUU AAACCA C C U AUCAG...ACA-3'@LB@ CUUCGCAAAAU GGG GAUAUCAAAGG GCA GUG@LB@ \|\|:\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\|\|\|\|\|: \|\|\| \|\|\|@LB@ GAGGUGUUUUA CCC CUGUAGUUUCU CGU CAC@LB@3'-UUU...UACCC UUU CG-5'@LB@ \| \|@LB@ 37 2@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -34.1904 kcal/mol@LB@Unfolding Energy - mRNA 10.724 kcal/mol@LB@Unfolding Energy - sRNA 6.67685 kcal/mol@LB@@LB@Position - mRNA 64 -- 103@LB@Position - sRNA 3 -- 36@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 12 -- 18@LB@
101	0.006298	0.2188	b3549	tag	-14.94	0.028658	147 -- 165	3 -- 21	3-methyl-adenine DNA glycosylase I constitutive	_____________146__________________166\n_____________\|____________________\|\n5'-GCA...CCGAU_________________C__AAAUU...AAA-3'\n______________GCGUC_AAGAAAAGCGG_UG\n______________:\|:\|\|_\|\|\|\|\|\|\|\|\|:\|_\|\|\n______________UGUAG_UUCUUUUCGUC_AC\n3'-UUU...ACCCC_____U______________CG-5'\n_____________\|____________________\|\n_____________22___________________2\n	156 -- 162	5 -- 11	-20.7072 kcal/mol	4.25403 kcal/mol	1.5107 kcal/mol	146 166@LB@ \| \|@LB@5'-GCA...CCGAU C AAAUU...AAA-3'@LB@ GCGUC AAGAAAAGCGG UG@LB@ :\|:\|\| \|\|\|\|\|\|\|\|\|:\| \|\|@LB@ UGUAG UUCUUUUCGUC AC@LB@3'-UUU...ACCCC U CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.7072 kcal/mol@LB@Unfolding Energy - mRNA 4.25403 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 147 -- 165@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 5 -- 11@LB@
110	0.007401	0.2348	b0784	moaD	-14.78	0.031320	178 -- 203	3 -- 25	molybdopterin synthase small subunit	_____________177________________________204\n_____________\|__________________________\|\n5'-GCA...AAGUC___U___U______U________A__AUUAA...AGC-3'\n______________GGG_GAC_UUAAGG_GGAAGCGG_UG\n______________\|\|\|_\|\|\|_\|:\|\|:\|_::\|\|\|\|:\|_\|\|\n______________CCC_CUG_AGUUUC_UUUUCGUC_AC\n3'-UUU...UUUUA_______U__________________CG-5'\n_____________\|__________________________\|\n_____________26_________________________2\n	194 -- 200	5 -- 11	-23.9822 kcal/mol	6.68375 kcal/mol	2.5166 kcal/mol	177 204@LB@ \| \|@LB@5'-GCA...AAGUC U U U A AUUAA...AGC-3'@LB@ GGG GAC UUAAGG GGAAGCGG UG@LB@ \|\|\| \|\|\| \|:\|\|:\| ::\|\|\|\|:\| \|\|@LB@ CCC CUG AGUUUC UUUUCGUC AC@LB@3'-UUU...UUUUA U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.9822 kcal/mol@LB@Unfolding Energy - mRNA 6.68375 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
132	0.00937	0.2491	b1120	cobB	-12.17	0.114836	175 -- 191	3 -- 18	deacetylase of acs and cheY chemotaxis regulator	_____________174_______________192\n_____________\|_________________\|\n5'-CGC...UUUUU_______U_________CCGGA...AUC-3'\n______________UCAGAGA_AAAGUGGUG\n______________\|\|\|:\|\|\|_\|\|\|\|::\|\|\|\n______________AGUUUCU_UUUCGUCAC\n3'-UUU...CCUGU_________________CG-5'\n_____________\|_________________\|\n_____________19________________2\n	185 -- 191	3 -- 9	-17.0979 kcal/mol	3.47557 kcal/mol	1.45388 kcal/mol	174 192@LB@ \| \|@LB@5'-CGC...UUUUU U CCGGA...AUC-3'@LB@ UCAGAGA AAAGUGGUG@LB@ \|\|\|:\|\|\| \|\|\|\|::\|\|\|@LB@ AGUUUCU UUUCGUCAC@LB@3'-UUU...CCUGU CG-5'@LB@ \| \|@LB@ 19 2@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -17.0979 kcal/mol@LB@Unfolding Energy - mRNA 3.47557 kcal/mol@LB@Unfolding Energy - sRNA 1.45388 kcal/mol@LB@@LB@Position - mRNA 175 -- 191@LB@Position - sRNA 3 -- 18@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 3 -- 9@LB@
150	0.01097	0.2504	b1878	flhE	-16.24	0.013409	257 -- 279	3 -- 25	proton seal during flagellar secretion	_____________256_____________________280\n_____________\|_______________________\|\n5'-CGU...GGGGA________G_C___C________UAGGA...AUC-3'\n______________GGGGAUGU_G_AGG_AAGUAGUG\n______________\|\|\|\|\|::\|_:_\|\|:_\|\|\|:\|\|\|\|\n______________CCCCUGUA_U_UCU_UUCGUCAC\n3'-UUU...UUUUA________G_U___U________CG-5'\n_____________\|_______________________\|\n_____________26______________________2\n	273 -- 279	3 -- 9	-26.0465 kcal/mol	7.2914 kcal/mol	2.5166 kcal/mol	256 280@LB@ \| \|@LB@5'-CGU...GGGGA G C C UAGGA...AUC-3'@LB@ GGGGAUGU G AGG AAGUAGUG@LB@ \|\|\|\|\|::\| : \|\|: \|\|\|:\|\|\|\|@LB@ CCCCUGUA U UCU UUCGUCAC@LB@3'-UUU...UUUUA G U U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -16.24 kcal/mol@LB@Hybridization Energy -26.0465 kcal/mol@LB@Unfolding Energy - mRNA 7.2914 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 257 -- 279@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 3 -- 9@LB@
169	0.01228	0.2504	b3386	rpe	-13.36	0.065831	171 -- 203	3 -- 33	D-ribulose-5-phosphate 3-epimerase	_____________170_______________________________204\n_____________\|_________________________________\|\n5'-CGC...UCACC_______AAAUAAUUC______________A__AAACA...UGC-3'\n______________CGCGAAA_________UCAAGGAGAAGCGG_UG\n______________\|:\|:\|\|\|_________\|\|\|\|:\|\|:\|\|\|\|:\|_\|\|\n______________GUGUUUU_________AGUUUCUUUUCGUC_AC\n3'-UUU...CCGAG_______ACCCCUGU__________________CG-5'\n_____________\|_________________________________\|\n_____________34________________________________2\n	194 -- 200	5 -- 11	-23.2607 kcal/mol	6.82691 kcal/mol	3.0786 kcal/mol	170 204@LB@ \| \|@LB@5'-CGC...UCACC AAAUAAUUC A AAACA...UGC-3'@LB@ CGCGAAA UCAAGGAGAAGCGG UG@LB@ \|:\|:\|\|\| \|\|\|\|:\|\|:\|\|\|\|:\| \|\|@LB@ GUGUUUU AGUUUCUUUUCGUC AC@LB@3'-UUU...CCGAG ACCCCUGU CG-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -23.2607 kcal/mol@LB@Unfolding Energy - mRNA 6.82691 kcal/mol@LB@Unfolding Energy - sRNA 3.0786 kcal/mol@LB@@LB@Position - mRNA 171 -- 203@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
182	0.01317	0.2504	b2101	yegW	-15.40	0.022099	126 -- 162	3 -- 28	putative DNA-binding transcriptional regulator	_____________125______________________________________163\n_____________\|________________________________________\|\n5'-CGG...UCGUU_________________AACGCCUUAAAUAA_________AUAUA...AAA-3'\n______________GAUGGG___AUUAAAGA______________GAAGCAGUG\n______________:\|\|\|\|\|___\|\|:\|\|\|\|\|______________:\|\|\|\|\|\|\|\|\n______________UUACCC___UAGUUUCU______________UUUCGUCAC\n3'-UUU...GUGUU______CUG_______________________________CG-5'\n_____________\|________________________________________\|\n_____________29_______________________________________2\n	156 -- 162	3 -- 9	-24.3736 kcal/mol	6.45453 kcal/mol	2.51813 kcal/mol	125 163@LB@ \| \|@LB@5'-CGG...UCGUU AACGCCUUAAAUAA AUAUA...AAA-3'@LB@ GAUGGG AUUAAAGA GAAGCAGUG@LB@ :\|\|\|\|\| \|\|:\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUACCC UAGUUUCU UUUCGUCAC@LB@3'-UUU...GUGUU CUG CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -24.3736 kcal/mol@LB@Unfolding Energy - mRNA 6.45453 kcal/mol@LB@Unfolding Energy - sRNA 2.51813 kcal/mol@LB@@LB@Position - mRNA 126 -- 162@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 3 -- 9@LB@
47	0.002271	0.1648	b3169	nusA	-13.61	0.058009	55 -- 79	4 -- 28	transcription termination/antitermination L factor	_____________54__________________________80\n_____________\|___________________________\|\n5'-UUG...UCGUA_____CA________UC__________AGACG...CAG-3'\n______________AAUGG__GGGCGUUA____AAAGCGGU\n______________\|\|\|\|\|__\|\|:\|:\|:\|____\|\|\|\|\|:\|\|\n______________UUACC__CCUGUAGU____UUUCGUCA\n3'-UUU...GUGUU_______________UUCU________CCG-5'\n_____________\|___________________________\|\n_____________29__________________________3\n	73 -- 79	4 -- 10	-21.8237 kcal/mol	5.69952 kcal/mol	2.51457 kcal/mol	54 80@LB@ \| \|@LB@5'-UUG...UCGUA CA UC AGACG...CAG-3'@LB@ AAUGG GGGCGUUA AAAGCGGU@LB@ \|\|\|\|\| \|\|:\|:\|:\| \|\|\|\|\|:\|\|@LB@ UUACC CCUGUAGU UUUCGUCA@LB@3'-UUU...GUGUU UUCU CCG-5'@LB@ \| \|@LB@ 29 3@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -21.8237 kcal/mol@LB@Unfolding Energy - mRNA 5.69952 kcal/mol@LB@Unfolding Energy - sRNA 2.51457 kcal/mol@LB@@LB@Position - mRNA 55 -- 79@LB@Position - sRNA 4 -- 28@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter	_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@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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