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
129	0.009293	0.2491	b0428	cyoE	-12.51	0.098557	18 -- 26	1 -- 9	protoheme IX farnesyltransferase	_____________17________27\n_____________\|_________\|\n5'-GGA...GCAAU_________ACAGG...GCA-3'\n______________GGCAGUGGU\n______________:\|\|\|\|\|\|\|:\n______________UCGUCACCG\n3'-UUU...UCUUU_________-5'\n_____________\|________\|\n_____________10_______1\n	20 -- 26	1 -- 7	-15.8954 kcal/mol	2.13019 kcal/mol	1.2588 kcal/mol	17 27@LB@ \| \|@LB@5'-GGA...GCAAU ACAGG...GCA-3'@LB@ GGCAGUGGU@LB@ :\|\|\|\|\|\|\|:@LB@ UCGUCACCG@LB@3'-UUU...UCUUU -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -12.51 kcal/mol@LB@Hybridization Energy -15.8954 kcal/mol@LB@Unfolding Energy - mRNA 2.13019 kcal/mol@LB@Unfolding Energy - sRNA 1.2588 kcal/mol@LB@@LB@Position - mRNA 18 -- 26@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.005693	0.2147	b2099	yegU	-12.49	0.099484	183 -- 197	7 -- 22	ADP-ribosylglycohydrolase family protein	_____________182______________198\n_____________\|________________\|\n5'-GUG...GCGUU________________UAAAU...CAC-3'\n______________GACA_CAAGGGGAAGU\n______________\|\|\|\|_\|\|\|:\|::\|\|\|:\n______________CUGU_GUUUCUUUUCG\n3'-UUU...UACCC____A___________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	191 -- 197	7 -- 13	-15.6094 kcal/mol	2.53245 kcal/mol	0.590875 kcal/mol	182 198@LB@ \| \|@LB@5'-GUG...GCGUU UAAAU...CAC-3'@LB@ GACA CAAGGGGAAGU@LB@ \|\|\|\| \|\|\|:\|::\|\|\|:@LB@ CUGU GUUUCUUUUCG@LB@3'-UUU...UACCC A UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -12.49 kcal/mol@LB@Hybridization Energy -15.6094 kcal/mol@LB@Unfolding Energy - mRNA 2.53245 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 7 -- 13@LB@
159	0.01174	0.2504	b3886	yihY	-12.46	0.100688	17 -- 39	6 -- 26	BrkB family putative transporter inner membrane protein	_____________16______________________40\n_____________\|_______________________\|\n5'-UAU...AGAUC________CG____CCU______CGAAU...CAA-3'\n______________UGGGGAUG__CAAA___GAAGCA\n______________\|\|\|\|\|\|::__\|\|\|\|___:\|\|\|\|\|\n______________ACCCCUGU__GUUU___UUUCGU\n3'-UUU...GUUUU________A_____CU_______CACCG-5'\n_____________\|_______________________\|\n_____________27______________________5\n	18 -- 24	19 -- 25	-18.1196 kcal/mol	4.95346 kcal/mol	0.706421 kcal/mol	16 40@LB@ \| \|@LB@5'-UAU...AGAUC CG CCU CGAAU...CAA-3'@LB@ UGGGGAUG CAAA GAAGCA@LB@ \|\|\|\|\|\|:: \|\|\|\| :\|\|\|\|\|@LB@ ACCCCUGU GUUU UUUCGU@LB@3'-UUU...GUUUU A CU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -18.1196 kcal/mol@LB@Unfolding Energy - mRNA 4.95346 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 17 -- 39@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 19 -- 25@LB@
191	0.01405	0.2529	b3532	bcsB	-12.45	0.101006	205 -- 235	1 -- 16	regulator of cellulose synthase cyclic di-GMP binding	_____________204_____________________________236\n_____________\|_______________________________\|\n5'-AAG...GAUGA________CUAUUCUGGAUUUGU________UAUGG...UCA-3'\n______________AAAGAAAA_______________GCAGUGGC\n______________\|\|\|\|\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UUUCUUUU_______________CGUCACCG\n3'-UUU...UGUAG_______________________________-5'\n_____________\|______________________________\|\n_____________17_____________________________1\n	229 -- 235	1 -- 7	-19.2133 kcal/mol	5.41496 kcal/mol	1.34555 kcal/mol	204 236@LB@ \| \|@LB@5'-AAG...GAUGA CUAUUCUGGAUUUGU UAUGG...UCA-3'@LB@ AAAGAAAA GCAGUGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUCUUUU CGUCACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.2133 kcal/mol@LB@Unfolding Energy - mRNA 5.41496 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 205 -- 235@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
173	0.01269	0.2504	b4172	hfq	-12.44	0.101529	181 -- 205	1 -- 21	global sRNA chaperone; HF-I host factor for RNA phage Q beta replication	_____________180_______________________206\n_____________\|_________________________\|\n5'-GAA...AAUAA____A__________AG__AA____UAAGG...AAG-3'\n______________GCAU_UAAGGAAAAG__AG__UGGC\n______________:\|\|\|_:\|\|:\|\|\|\|\|\|__\|\|__\|\|\|\|\n______________UGUA_GUUUCUUUUC__UC__ACCG\n3'-UUU...ACCCC_______________G_________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	189 -- 195	8 -- 14	-17.6301 kcal/mol	3.67752 kcal/mol	1.51103 kcal/mol	180 206@LB@ \| \|@LB@5'-GAA...AAUAA A AG AA UAAGG...AAG-3'@LB@ GCAU UAAGGAAAAG AG UGGC@LB@ :\|\|\| :\|\|:\|\|\|\|\|\| \|\| \|\|\|\|@LB@ UGUA GUUUCUUUUC UC ACCG@LB@3'-UUU...ACCCC G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.6301 kcal/mol@LB@Unfolding Energy - mRNA 3.67752 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 181 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 8 -- 14@LB@
42	0.002133	0.1648	b0968	yccX	-12.44	0.101807	184 -- 198	5 -- 23	weak acylphosphatase	_____________183_________________199\n_____________\|___________________\|\n5'-GGC...AUUAA___________________CAAUG...CCG-3'\n______________GGAUA____AGGAGAGCAG\n______________\|\|\|:\|____\|\|:\|:\|\|\|\|\|\n______________CCUGU____UCUUUUCGUC\n3'-UUU...UUACC_____AGUU__________ACCG-5'\n_____________\|___________________\|\n_____________24__________________4\n	192 -- 198	5 -- 11	-17.1825 kcal/mol	3.17176 kcal/mol	1.57523 kcal/mol	183 199@LB@ \| \|@LB@5'-GGC...AUUAA CAAUG...CCG-3'@LB@ GGAUA AGGAGAGCAG@LB@ \|\|\|:\| \|\|:\|:\|\|\|\|\|@LB@ CCUGU UCUUUUCGUC@LB@3'-UUU...UUACC AGUU ACCG-5'@LB@ \| \|@LB@ 24 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.1825 kcal/mol@LB@Unfolding Energy - mRNA 3.17176 kcal/mol@LB@Unfolding Energy - sRNA 1.57523 kcal/mol@LB@@LB@Position - mRNA 184 -- 198@LB@Position - sRNA 5 -- 23@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
116	0.007938	0.2401	b0008	talB	-12.38	0.104625	254 -- 276	7 -- 26	transaldolase B	_____________253_____________________277\n_____________\|_______________________\|\n5'-AGG...GACAC___________C__CAAU_____UGUAU...CAA-3'\n______________UGGGGACAUCG_GG____GAAGC\n______________\|\|\|\|\|\|\|\|\|\|:_:\|____:\|\|\|\|\n______________ACCCCUGUAGU_UC____UUUCG\n3'-UUU...GUUUU___________U__U________UCACCG-5'\n_____________\|_______________________\|\n_____________27______________________6\n	258 -- 264	16 -- 22	-23.5048 kcal/mol	10.4229 kcal/mol	0.706388 kcal/mol	253 277@LB@ \| \|@LB@5'-AGG...GACAC C CAAU UGUAU...CAA-3'@LB@ UGGGGACAUCG GG GAAGC@LB@ \|\|\|\|\|\|\|\|\|\|: :\| :\|\|\|\|@LB@ ACCCCUGUAGU UC UUUCG@LB@3'-UUU...GUUUU U U UCACCG-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -23.5048 kcal/mol@LB@Unfolding Energy - mRNA 10.4229 kcal/mol@LB@Unfolding Energy - sRNA 0.706388 kcal/mol@LB@@LB@Position - mRNA 254 -- 276@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
196	0.01416	0.2529	b0870	ltaE	-12.27	0.109556	23 -- 39	7 -- 23	L-allo-threonine aldolase PLP-dependent	_____________22________________40\n_____________\|_________________\|\n5'-GUC...GUGGU__U__C___________UAGCC...ACC-3'\n______________GG_CG_CAAAGAAGAGU\n______________\|\|_\|:_\|\|\|\|\|\|\|:\|\|:\n______________CC_GU_GUUUCUUUUCG\n3'-UUU...UUACC__U__A___________UCACCG-5'\n_____________\|_________________\|\n_____________24________________6\n	33 -- 39	7 -- 13	-15.8177 kcal/mol	2.94498 kcal/mol	0.599063 kcal/mol	22 40@LB@ \| \|@LB@5'-GUC...GUGGU U C UAGCC...ACC-3'@LB@ GG CG CAAAGAAGAGU@LB@ \|\| \|: \|\|\|\|\|\|\|:\|\|:@LB@ CC GU GUUUCUUUUCG@LB@3'-UUU...UUACC U A UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -15.8177 kcal/mol@LB@Unfolding Energy - mRNA 2.94498 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 23 -- 39@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 7 -- 13@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9	_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@LB@
23	0.0008148	0.1243	b2573	rpoE	-12.22	0.112158	248 -- 284	1 -- 24	RNA polymerase sigma E factor	_____________247___________________________________285\n_____________\|_____________________________________\|\n5'-ACA...CAGAA____G______AAGCCUUUAACUUACU_______C__UAUCA...UGG-3'\n______________GGGA_AUCAGA________________GGUAGUG_GC\n______________\|\|\|\|_\|\|\|\|:\|________________:\|:\|\|\|\|_\|\|\n______________CCCU_UAGUUU________________UCGUCAC_CG\n3'-UUU...UUUAC____G______CUUU______________________-5'\n_____________\|____________________________________\|\n_____________25___________________________________1\n	275 -- 281	3 -- 9	-22.4239 kcal/mol	7.75978 kcal/mol	2.44282 kcal/mol	247 285@LB@ \| \|@LB@5'-ACA...CAGAA G AAGCCUUUAACUUACU C UAUCA...UGG-3'@LB@ GGGA AUCAGA GGUAGUG GC@LB@ \|\|\|\| \|\|\|\|:\| :\|:\|\|\|\| \|\|@LB@ CCCU UAGUUU UCGUCAC CG@LB@3'-UUU...UUUAC G CUUU -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.4239 kcal/mol@LB@Unfolding Energy - mRNA 7.75978 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 248 -- 284@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@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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