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
69	0.003755	0.191	b0889	lrp	-14.02	0.046951	165 -- 212	1 -- 32	leucine-responsive global transcriptional regulator	_____________164______________________________________________213\n_____________\|________________________________________________\|\n5'-GUG...GUCAG______GUA____AGGAAUA________CAAUAAUAAU_____AUA__AAGAA...AGC-3'\n______________ACAGGA___GGGA_______CAGAGAGA__________GGUAG___GC\n______________\|\|\|::\|___\|\|\|\|_______\|\|:\|\|\|:\|__________:\|:\|\|___\|\|\n______________UGUUUU___CCCU_______GUUUCUUU__________UCGUC___CG\n3'-UUU...CGAGG______AC_____GUA___________________________AC___-5'\n_____________\|_______________________________________________\|\n_____________33______________________________________________1\n	186 -- 192	10 -- 16	-19.2298 kcal/mol	2.66644 kcal/mol	2.53929 kcal/mol	164 213@LB@ \| \|@LB@5'-GUG...GUCAG GUA AGGAAUA CAAUAAUAAU AUA AAGAA...AGC-3'@LB@ ACAGGA GGGA CAGAGAGA GGUAG GC@LB@ \|\|\|::\| \|\|\|\| \|\|:\|\|\|:\| :\|:\|\| \|\|@LB@ UGUUUU CCCU GUUUCUUU UCGUC CG@LB@3'-UUU...CGAGG AC GUA AC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.02 kcal/mol@LB@Hybridization Energy -19.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.66644 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 165 -- 212@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 10 -- 16@LB@
70	0.003861	0.1936	b3559	glyS	-15.28	0.023738	120 -- 130	1 -- 11	glycine tRNA synthetase beta subunit	_____________119_________131\n_____________\|___________\|\n5'-CGC...UGACC___________AGAAG...CGG-3'\n______________AAAGCAGUGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	124 -- 130	1 -- 7	-20.0617 kcal/mol	3.50787 kcal/mol	1.27751 kcal/mol	119 131@LB@ \| \|@LB@5'-CGC...UGACC AGAAG...CGG-3'@LB@ AAAGCAGUGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -20.0617 kcal/mol@LB@Unfolding Energy - mRNA 3.50787 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 120 -- 130@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 1 -- 7@LB@
71	0.003993	0.1953	b2347	yfdC	-11.68	0.141997	251 -- 269	1 -- 17	putative inner membrane protein	_____________250__________________270\n_____________\|____________________\|\n5'-GCA...GAGAG_______AAA______C___AAAAA...UCC-3'\n______________CGAAGAA___GAGC_G_GGC\n______________\|:\|\|\|\|\|___:\|\|\|_\|_\|\|\|\n______________GUUUCUU___UUCG_C_CCG\n3'-UUU...CUGUA______________U_A___-5'\n_____________\|___________________\|\n_____________18__________________1\n	251 -- 257	11 -- 17	-16.1242 kcal/mol	3.00377 kcal/mol	1.43853 kcal/mol	250 270@LB@ \| \|@LB@5'-GCA...GAGAG AAA C AAAAA...UCC-3'@LB@ CGAAGAA GAGC G GGC@LB@ \|:\|\|\|\|\| :\|\|\| \| \|\|\|@LB@ GUUUCUU UUCG C CCG@LB@3'-UUU...CUGUA U A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -16.1242 kcal/mol@LB@Unfolding Energy - mRNA 3.00377 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 11 -- 17@LB@
74	0.004177	0.1979	b2155	cirA	-15.75	0.017995	130 -- 157	1 -- 33	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter	_____________129________________________________158\n_____________\|__________________________________\|\n5'-GGA...CCGUA_________________________U_____A__GAUAA...UGG-3'\n______________CGCAA___GGGGACGU_GAAGAAGA___GUG_GC\n______________\|:\|\|\|___\|\|\|\|\|\|:\|_:\|\|\|\|\|:\|___\|\|\|_\|\|\n______________GUGUU___CCCCUGUA_UUUCUUUU___CAC_CG\n3'-UUU...CCGAG_____UUA________G________CGU______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	144 -- 150	9 -- 15	-28.6012 kcal/mol	9.77062 kcal/mol	3.07861 kcal/mol	129 158@LB@ \| \|@LB@5'-GGA...CCGUA U A GAUAA...UGG-3'@LB@ CGCAA GGGGACGU GAAGAAGA GUG GC@LB@ \|:\|\|\| \|\|\|\|\|\|:\| :\|\|\|\|\|:\| \|\|\| \|\|@LB@ GUGUU CCCCUGUA UUUCUUUU CAC CG@LB@3'-UUU...CCGAG UUA G CGU -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -28.6012 kcal/mol@LB@Unfolding Energy - mRNA 9.77062 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 130 -- 157@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 9 -- 15@LB@
75	0.00423	0.1979	b1917	yecC	-10.99	0.188691	288 -- 298	1 -- 11	putative ABC transporter ATPase	_____________287_________299\n_____________\|___________\|\n5'-CUG...CUGGC___________AA-3'\n______________GAAGUGGUGGC\n______________:\|\|\|::\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	292 -- 298	1 -- 7	-16.6045 kcal/mol	4.33348 kcal/mol	1.27751 kcal/mol	287 299@LB@ \| \|@LB@5'-CUG...CUGGC AA-3'@LB@ GAAGUGGUGGC@LB@ :\|\|\|::\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.6045 kcal/mol@LB@Unfolding Energy - mRNA 4.33348 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
77	0.004622	0.2062	b1241	adhE	-12.78	0.086641	182 -- 205	1 -- 21	fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase	_____________181______________________206\n_____________\|________________________\|\n5'-AAU...GUUUA______UC_________UUA____UGUUA...AAA-3'\n______________ACAUUA__AGGAGAGCA___UGGC\n______________\|\|\|\|:\|__\|\|:\|:\|\|\|\|___\|\|\|\|\n______________UGUAGU__UCUUUUCGU___ACCG\n3'-UUU...ACCCC______U__________C______-5'\n_____________\|_______________________\|\n_____________22______________________1\n	192 -- 198	6 -- 12	-20.8292 kcal/mol	6.5343 kcal/mol	1.51103 kcal/mol	181 206@LB@ \| \|@LB@5'-AAU...GUUUA UC UUA UGUUA...AAA-3'@LB@ ACAUUA AGGAGAGCA UGGC@LB@ \|\|\|\|:\| \|\|:\|:\|\|\|\| \|\|\|\|@LB@ UGUAGU UCUUUUCGU ACCG@LB@3'-UUU...ACCCC U C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -20.8292 kcal/mol@LB@Unfolding Energy - mRNA 6.5343 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 182 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 6 -- 12@LB@
78	0.004634	0.2062	b1601	tqsA	-18.27	0.003423	191 -- 205	1 -- 25	pheromone AI-2 transporter	_____________190_______________________206\n_____________\|_________________________\|\n5'-AUU...AAAAC_________________________AAAGC...UCA-3'\n______________GGGGACA_________AGCA_UGGC\n______________\|\|\|\|\|\|\|_________\|\|\|\|_\|\|\|\|\n______________CCCCUGU_________UCGU_ACCG\n3'-UUU...UUUUA_______AGUUUCUUU____C____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	191 -- 197	19 -- 25	-23.2822 kcal/mol	2.49324 kcal/mol	2.51748 kcal/mol	190 206@LB@ \| \|@LB@5'-AUU...AAAAC AAAGC...UCA-3'@LB@ GGGGACA AGCA UGGC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ CCCCUGU UCGU ACCG@LB@3'-UUU...UUUUA AGUUUCUUU C -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -23.2822 kcal/mol@LB@Unfolding Energy - mRNA 2.49324 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 19 -- 25@LB@
79	0.004643	0.2062	b2264	menD	-12.62	0.093644	52 -- 86	1 -- 30	2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase; SEPHCHC synthase	_____________51_____________________________________87\n_____________\|______________________________________\|\n5'-CGU...GAGCA_______CAGGAAAUC____A_____C___________UGCGU...GUU-3'\n______________AGAGUGG_________GACA_CAAAG___GGCAG_GGC\n______________\|:\|:\|\|\|_________\|\|\|\|_\|\|\|\|\|___:\|\|\|\|_\|\|\|\n______________UUUUACC_________CUGU_GUUUC___UCGUC_CCG\n3'-UUU...AGGUG_______C____________A_____UUU_____A___-5'\n_____________\|_____________________________________\|\n_____________31____________________________________1\n	52 -- 58	24 -- 30	-24.8101 kcal/mol	9.6737 kcal/mol	2.51911 kcal/mol	51 87@LB@ \| \|@LB@5'-CGU...GAGCA CAGGAAAUC A C UGCGU...GUU-3'@LB@ AGAGUGG GACA CAAAG GGCAG GGC@LB@ \|:\|:\|\|\| \|\|\|\| \|\|\|\|\| :\|\|\|\| \|\|\|@LB@ UUUUACC CUGU GUUUC UCGUC CCG@LB@3'-UUU...AGGUG C A UUU A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -24.8101 kcal/mol@LB@Unfolding Energy - mRNA 9.6737 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 52 -- 86@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 24 -- 30@LB@
82	0.005087	0.2147	b2741	rpoS	-15.46	0.021295	2 -- 28	1 -- 25	RNA polymerase sigma S (sigma 38) factor	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C___A___ACAA____UU___________AAAAA...AGG-3'\n______________GGG_ACA____GAAG__AAGGCGG_GGC\n______________\|\|\|_\|\|\|____:\|\|\|__\|\|:\|\|:\|_\|\|\|\n______________CCC_UGU____UUUC__UUUCGUC_CCG\n3'-UUU...UUUUA___C___AG______U________A___-5'\n_____________\|___________________________\|\n_____________26__________________________1\n	19 -- 25	5 -- 11	-23.9329 kcal/mol	5.95047 kcal/mol	2.51748 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C A ACAA UU AAAAA...AGG-3'@LB@ GGG ACA GAAG AAGGCGG GGC@LB@ \|\|\| \|\|\| :\|\|\| \|\|:\|\|:\| \|\|\|@LB@ CCC UGU UUUC UUUCGUC CCG@LB@3'-UUU...UUUUA C AG U A -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -23.9329 kcal/mol@LB@Unfolding Energy - mRNA 5.95047 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
86	0.005461	0.2147	b0002	thrA	-11.41	0.159352	219 -- 235	1 -- 25	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________218_________________________236\n_____________\|___________________________\|\n5'-CCA...AGUUC__C__U_____________________AAAUG...UGG-3'\n______________GG_GG_ACAU__________CAGUGGC\n______________\|\|_\|\|_\|\|\|\|__________\|\|\|\|\|\|\|\n______________CC_CC_UGUA__________GUCACCG\n3'-UUU...UUUUA__________GUUUCUUUUC_______-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	229 -- 235	1 -- 7	-18.4664 kcal/mol	4.54068 kcal/mol	2.51748 kcal/mol	218 236@LB@ \| \|@LB@5'-CCA...AGUUC C U AAAUG...UGG-3'@LB@ GG GG ACAU CAGUGGC@LB@ \|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CC CC UGUA GUCACCG@LB@3'-UUU...UUUUA GUUUCUUUUC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -18.4664 kcal/mol@LB@Unfolding Energy - mRNA 4.54068 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@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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