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
166	0.01216	0.2504	b4485	ytfR	-12.60	0.094393	18 -- 41	9 -- 34	putative sugar ABC transporter ATPase		_____________17_________________________42\n_____________\|__________________________\|\n5'-CCU...UGAUA________GAA_______________AGAAA...GCC-3'\n______________CCGCAAAA____GA_AUUAGAGAAGA\n______________\|\|:\|\|\|\|\|____\|\|_\|\|:\|:\|\|\|\|:\|\n______________GGUGUUUU____CU_UAGUUUCUUUU\n3'-UUU...CCCGA________ACCC__G___________CGUCACCG-5'\n_____________\|__________________________\|\n_____________35_________________________8\n	35 -- 41	9 -- 15	-17.8797 kcal/mol	1.35017 kcal/mol	3.92941 kcal/mol	17 42@LB@ \| \|@LB@5'-CCU...UGAUA GAA AGAAA...GCC-3'@LB@ CCGCAAAA GA AUUAGAGAAGA@LB@ \|\|:\|\|\|\|\| \|\| \|\|:\|:\|\|\|\|:\|@LB@ GGUGUUUU CU UAGUUUCUUUU@LB@3'-UUU...CCCGA ACCC G CGUCACCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -17.8797 kcal/mol@LB@Unfolding Energy - mRNA 1.35017 kcal/mol@LB@Unfolding Energy - sRNA 3.92941 kcal/mol@LB@@LB@Position - mRNA 18 -- 41@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@LB@
18	0.0007186	0.1243	b3657	yicJ	-19.60	0.001218	184 -- 200	5 -- 21	putative transporter		_____________183_______________201\n_____________\|_________________\|\n5'-CAG...CUAUA_________________AUGAA...UGU-3'\n______________GCAUCAAGGAAAAGCAG\n______________:\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|\n______________UGUAGUUUCUUUUCGUC\n3'-UUU...ACCCC_________________ACCG-5'\n_____________\|_________________\|\n_____________22________________4\n	194 -- 200	5 -- 11	-25.6417 kcal/mol	4.53845 kcal/mol	1.5073 kcal/mol	183 201@LB@ \| \|@LB@5'-CAG...CUAUA AUGAA...UGU-3'@LB@ GCAUCAAGGAAAAGCAG@LB@ :\|\|\|\|\|\|:\|\|\|\|\|\|\|\|\|@LB@ UGUAGUUUCUUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -19.60 kcal/mol@LB@Hybridization Energy -25.6417 kcal/mol@LB@Unfolding Energy - mRNA 4.53845 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 184 -- 200@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
33	0.001538	0.1635	b4141	yjeH	-13.95	0.048780	254 -- 275	1 -- 22	putative transporter		_____________253____________________276\n_____________\|______________________\|\n5'-CAG...CUAUC_______UUAUU_____C____GUGUU...CUG-3'\n______________GACGUCA_____AGGCA_UGGC\n______________\|\|\|:\|\|\|_____\|:\|\|\|_\|\|\|\|\n______________CUGUAGU_____UUCGU_ACCG\n3'-UUU...UACCC_______UUCUU_____C____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	254 -- 260	16 -- 22	-22.2624 kcal/mol	6.77205 kcal/mol	1.54023 kcal/mol	253 276@LB@ \| \|@LB@5'-CAG...CUAUC UUAUU C GUGUU...CUG-3'@LB@ GACGUCA AGGCA UGGC@LB@ \|\|\|:\|\|\| \|:\|\|\| \|\|\|\|@LB@ CUGUAGU UUCGU ACCG@LB@3'-UUU...UACCC UUCUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -22.2624 kcal/mol@LB@Unfolding Energy - mRNA 6.77205 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 16 -- 22@LB@
81	0.004938	0.2139	b0115	aceF	-13.95	0.048783	266 -- 289	7 -- 31	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2		_____________265_________________________290\n_____________\|___________________________\|\n5'-GAU...CUGGU_________C__________UU_____CGAAC...CGC-3'\n______________CAAAGUGGG_GACA___AAG__GAAGC\n______________\|\|\|\|:\|\|\|\|_\|\|\|\|___\|\|\|__:\|\|\|\|\n______________GUUUUACCC_CUGU___UUC__UUUCG\n3'-UUU...GAGGU______________AGU___U______UCACCG-5'\n_____________\|___________________________\|\n_____________32__________________________6\n	268 -- 274	23 -- 29	-21.1287 kcal/mol	4.65658 kcal/mol	2.52208 kcal/mol	265 290@LB@ \| \|@LB@5'-GAU...CUGGU C UU CGAAC...CGC-3'@LB@ CAAAGUGGG GACA AAG GAAGC@LB@ \|\|\|\|:\|\|\|\| \|\|\|\| \|\|\| :\|\|\|\|@LB@ GUUUUACCC CUGU UUC UUUCG@LB@3'-UUU...GAGGU AGU U UCACCG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -21.1287 kcal/mol@LB@Unfolding Energy - mRNA 4.65658 kcal/mol@LB@Unfolding Energy - sRNA 2.52208 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 23 -- 29@LB@
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor		_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@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@
52	0.002562	0.1729	b0881	clpS	-16.21	0.013666	11 -- 25	5 -- 25	regulatory protein for ClpA substrate specificity		_____________10____________________26\n_____________\|_____________________\|\n5'-GCA...UGACA_____________________GUAUG...UCA-3'\n______________GGGGACA______AGGGGCAG\n______________\|\|\|\|\|\|\|______\|:::\|\|\|\|\n______________CCCCUGU______UUUUCGUC\n3'-UUU...UUUUA_______AGUUUC________ACCG-5'\n_____________\|_____________________\|\n_____________26____________________4\n	19 -- 25	5 -- 11	-21.27 kcal/mol	2.56205 kcal/mol	2.50017 kcal/mol	10 26@LB@ \| \|@LB@5'-GCA...UGACA GUAUG...UCA-3'@LB@ GGGGACA AGGGGCAG@LB@ \|\|\|\|\|\|\| \|:::\|\|\|\|@LB@ CCCCUGU UUUUCGUC@LB@3'-UUU...UUUUA AGUUUC ACCG-5'@LB@ \| \|@LB@ 26 4@LB@@LB@@LB@Energy -16.21 kcal/mol@LB@Hybridization Energy -21.27 kcal/mol@LB@Unfolding Energy - mRNA 2.56205 kcal/mol@LB@Unfolding Energy - sRNA 2.50017 kcal/mol@LB@@LB@Position - mRNA 11 -- 25@LB@Position - sRNA 5 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
162	0.012	0.2504	b2079	baeR	-15.58	0.019969	182 -- 201	6 -- 24	response regulator in two-component regulatory system with BaeS		_____________181__________________202\n_____________\|____________________\|\n5'-CAG...GGAAC_____UUA____________UGACC...CGA-3'\n______________GGGAU___CAGAGAGAAGUA\n______________\|\|\|\|:___\|\|:\|\|\|:\|\|\|:\|\n______________CCCUG___GUUUCUUUUCGU\n3'-UUU...UUUAC_____UA_____________CACCG-5'\n_____________\|____________________\|\n_____________25___________________5\n	195 -- 201	6 -- 12	-20.602 kcal/mol	4.32458 kcal/mol	0.702143 kcal/mol	181 202@LB@ \| \|@LB@5'-CAG...GGAAC UUA UGACC...CGA-3'@LB@ GGGAU CAGAGAGAAGUA@LB@ \|\|\|\|: \|\|:\|\|\|:\|\|\|:\|@LB@ CCCUG GUUUCUUUUCGU@LB@3'-UUU...UUUAC UA CACCG-5'@LB@ \| \|@LB@ 25 5@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -20.602 kcal/mol@LB@Unfolding Energy - mRNA 4.32458 kcal/mol@LB@Unfolding Energy - sRNA 0.702143 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 6 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
172	0.01269	0.2504	b0571	cusR	-10.48	0.230388	14 -- 48	1 -- 33	response regulator in two-component regulatory system with CusS	b1969	_____________13___________________________________49\n_____________\|____________________________________\|\n5'-AGC...GGCCA__________CA__A___UAC__________UA___UCAUA...GGC-3'\n______________CACAAAAUGG__GA_GUU___AAGGAGA_CA__GGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|_:\|:___\|\|\|:\|:\|_\|\|__\|\|\|\n______________GUGUUUUACC__CU_UAG___UUCUUUU_GU__CCG\n3'-UUU...CCGAG__________C___G___U_________C__CA___-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	35 -- 41	9 -- 15	-22.821 kcal/mol	9.26274 kcal/mol	3.07861 kcal/mol	13 49@LB@ \| \|@LB@5'-AGC...GGCCA CA A UAC UA UCAUA...GGC-3'@LB@ CACAAAAUGG GA GUU AAGGAGA CA GGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\| :\|: \|\|\|:\|:\| \|\| \|\|\|@LB@ GUGUUUUACC CU UAG UUCUUUU GU CCG@LB@3'-UUU...CCGAG C G U C CA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -22.821 kcal/mol@LB@Unfolding Energy - mRNA 9.26274 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 14 -- 48@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@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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