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	Additional homologs
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@
167	0.01216	0.2504	b1013	rutR	-12.90	0.082087	181 -- 218	3 -- 35	rut operon transcriptional repressor for	b0796	_____________180________________________________________219\n_____________\|__________________________________________\|\n5'-CAA...GCCAA_______________GAGCGCAUGACG_____C_________AAAAC...AAU-3'\n______________UCUACAAGA_GGGGA____________CAAGG____GCAGUG\n______________\|\|:\|\|\|\|:\|_\|\|\|\|\|____________\|\|\|:\|____\|\|\|\|\|\|\n______________AGGUGUUUU_CCCCU____________GUUUC____CGUCAC\n3'-UUU...ACCCG_________A_____GUA______________UUUU______CG-5'\n_____________\|__________________________________________\|\n_____________36_________________________________________2\n	181 -- 187	29 -- 35	-29.1146 kcal/mol	11.1798 kcal/mol	5.03644 kcal/mol	180 219@LB@ \| \|@LB@5'-CAA...GCCAA GAGCGCAUGACG C AAAAC...AAU-3'@LB@ UCUACAAGA GGGGA CAAGG GCAGUG@LB@ \|\|:\|\|\|\|:\| \|\|\|\|\| \|\|\|:\| \|\|\|\|\|\|@LB@ AGGUGUUUU CCCCU GUUUC CGUCAC@LB@3'-UUU...ACCCG A GUA UUUU CG-5'@LB@ \| \|@LB@ 36 2@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -29.1146 kcal/mol@LB@Unfolding Energy - mRNA 11.1798 kcal/mol@LB@Unfolding Energy - sRNA 5.03644 kcal/mol@LB@@LB@Position - mRNA 181 -- 218@LB@Position - sRNA 3 -- 35@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 29 -- 35@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@
83	0.005101	0.2147	b2610	ffh	-14.32	0.040245	57 -- 74	4 -- 21	Signal Recognition Particle (SRP) component with 4.5S RNA (ffs)		_____________56_________________75\n_____________\|__________________\|\n5'-AGG...GAGCA___AG_____________AUAGC...AAG-3'\n______________AUA__AAAGAGAAGCAGU\n______________\|:\|__\|\|\|\|\|:\|\|\|\|\|\|\|\n______________UGU__UUUCUUUUCGUCA\n3'-UUU...ACCCC___AG_____________CCG-5'\n_____________\|__________________\|\n_____________22_________________3\n	68 -- 74	4 -- 10	-18.2522 kcal/mol	2.42435 kcal/mol	1.51 kcal/mol	56 75@LB@ \| \|@LB@5'-AGG...GAGCA AG AUAGC...AAG-3'@LB@ AUA AAAGAGAAGCAGU@LB@ \|:\| \|\|\|\|\|:\|\|\|\|\|\|\|@LB@ UGU UUUCUUUUCGUCA@LB@3'-UUU...ACCCC AG CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -14.32 kcal/mol@LB@Hybridization Energy -18.2522 kcal/mol@LB@Unfolding Energy - mRNA 2.42435 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 57 -- 74@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 4 -- 10@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)		_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
139	0.01022	0.2504	b3163	nlpI	-13.31	0.067339	19 -- 42	4 -- 21	lipoprotein involved in osmotic sensitivity and filamentation		_____________18_______________________43\n_____________\|________________________\|\n5'-AGG...UCUGA___________GCGACU_______CUCAA...CAU-3'\n______________GCAUUAAAGAA______GAGCAGU\n______________:\|\|\|:\|\|\|\|\|\|______:\|\|\|\|\|\|\n______________UGUAGUUUCUU______UUCGUCA\n3'-UUU...ACCCC________________________CCG-5'\n_____________\|________________________\|\n_____________22_______________________3\n	36 -- 42	4 -- 10	-18.4935 kcal/mol	3.67449 kcal/mol	1.51 kcal/mol	18 43@LB@ \| \|@LB@5'-AGG...UCUGA GCGACU CUCAA...CAU-3'@LB@ GCAUUAAAGAA GAGCAGU@LB@ :\|\|\|:\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UGUAGUUUCUU UUCGUCA@LB@3'-UUU...ACCCC CCG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -18.4935 kcal/mol@LB@Unfolding Energy - mRNA 3.67449 kcal/mol@LB@Unfolding Energy - sRNA 1.51 kcal/mol@LB@@LB@Position - mRNA 19 -- 42@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 4 -- 10@LB@
151	0.01116	0.2504	b0903	pflB	-10.70	0.211701	140 -- 166	4 -- 34	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1		_____________139_____________________________167\n_____________\|_______________________________\|\n5'-CAC...GACCA____U______U__________UAC______AAAUA...ACU-3'\n______________CCAU__AAUGG___UGUCGAAG____GCAGU\n______________\|\|\|:__\|\|\|\|\|___::\|\|:\|\|\|____\|\|\|\|\|\n______________GGUG__UUACC___GUAGUUUC____CGUCA\n3'-UUU...CCCGA____UU_____CCU________UUUU_____CCG-5'\n_____________\|_______________________________\|\n_____________35______________________________3\n	152 -- 158	13 -- 19	-21.5315 kcal/mol	6.56187 kcal/mol	4.26884 kcal/mol	139 167@LB@ \| \|@LB@5'-CAC...GACCA U U UAC AAAUA...ACU-3'@LB@ CCAU AAUGG UGUCGAAG GCAGU@LB@ \|\|\|: \|\|\|\|\| ::\|\|:\|\|\| \|\|\|\|\|@LB@ GGUG UUACC GUAGUUUC CGUCA@LB@3'-UUU...CCCGA UU CCU UUUU CCG-5'@LB@ \| \|@LB@ 35 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -21.5315 kcal/mol@LB@Unfolding Energy - mRNA 6.56187 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 140 -- 166@LB@Position - sRNA 4 -- 34@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 13 -- 19@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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