Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
99	0.01653	0.5385	b0004	thrC	-7.16	0.308279	183 -- 210	49 -- 64	L-threonine synthase	_____________182__________________________211\n_____________\|____________________________\|\n5'-CGC...GCGCA_____AC___AAAACUAAAU________ACAAU...ACG-3'\n______________CGAGU__UGG__________GAAACUCU\n______________\|\|\|\|\|__\|\|:__________\|\|\|\|\|\|\|\|\n______________GCUCA__ACU__________CUUUGAGA\n3'-CGC...AAUAA____________________________GCUUU...AAG-5'\n_____________\|____________________________\|\n_____________65___________________________48\n	204 -- 210	49 -- 55	-14.0058 kcal/mol	2.63666 kcal/mol	4.20534 kcal/mol	182 211@LB@ \| \|@LB@5'-CGC...GCGCA AC AAAACUAAAU ACAAU...ACG-3'@LB@ CGAGU UGG GAAACUCU@LB@ \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|@LB@ GCUCA ACU CUUUGAGA@LB@3'-CGC...AAUAA GCUUU...AAG-5'@LB@ \| \|@LB@ 65 48@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -14.0058 kcal/mol@LB@Unfolding Energy - mRNA 2.63666 kcal/mol@LB@Unfolding Energy - sRNA 4.20534 kcal/mol@LB@@LB@Position - mRNA 183 -- 210@LB@Position - sRNA 49 -- 64@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 49 -- 55@LB@
149	0.0249	0.5467	b0737	tolQ	-11.44	0.059241	123 -- 143	57 -- 77	membrane spanning protein in TolA-TolQ-TolR complex	_____________122___________________144\n_____________\|_____________________\|\n5'-GCA...GCAGA____C__________C_____CCCAC...CCA-3'\n______________GGUU_UGGUUGUUUG_GUUGA\n______________\|\|:\|_\|:\|\|\|:\|\|:\|_\|\|\|\|\|\n______________CCGA_AUCAAUAAGC_CAACU\n3'-CGC...UGCAA____A__________U_____CUUUG...AAG-5'\n_____________\|_____________________\|\n_____________78____________________56\n	130 -- 136	64 -- 70	-20.7122 kcal/mol	8.05008 kcal/mol	1.21841 kcal/mol	122 144@LB@ \| \|@LB@5'-GCA...GCAGA C C CCCAC...CCA-3'@LB@ GGUU UGGUUGUUUG GUUGA@LB@ \|\|:\| \|:\|\|\|:\|\|:\| \|\|\|\|\|@LB@ CCGA AUCAAUAAGC CAACU@LB@3'-CGC...UGCAA A U CUUUG...AAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.7122 kcal/mol@LB@Unfolding Energy - mRNA 8.05008 kcal/mol@LB@Unfolding Energy - sRNA 1.21841 kcal/mol@LB@@LB@Position - mRNA 123 -- 143@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 64 -- 70@LB@
33	0.006009	0.5385	b1264	trpE	-12.63	0.036478	39 -- 48	79 -- 88	component I of anthranilate synthase	_____________38_________49\n_____________\|__________\|\n5'-UGU...UACGC__________AAAAA...CGG-3'\n______________AAGUUCACGU\n______________\|\|\|\|\|\|\|\|\|\|\n______________UUCAAGUGCA\n3'-CGC...GCGUU__________ACCGA...AAG-5'\n_____________\|__________\|\n_____________89_________78\n	42 -- 48	79 -- 85	-13.8612 kcal/mol	0.721964 kcal/mol	0.505265 kcal/mol	38 49@LB@ \| \|@LB@5'-UGU...UACGC AAAAA...CGG-3'@LB@ AAGUUCACGU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UUCAAGUGCA@LB@3'-CGC...GCGUU ACCGA...AAG-5'@LB@ \| \|@LB@ 89 78@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8612 kcal/mol@LB@Unfolding Energy - mRNA 0.721964 kcal/mol@LB@Unfolding Energy - sRNA 0.505265 kcal/mol@LB@@LB@Position - mRNA 39 -- 48@LB@Position - sRNA 79 -- 88@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 79 -- 85@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@LB@
167	0.02971	0.5559	b3062	ttdB	-9.65	0.121251	224 -- 260	75 -- 106	L-tartrate dehydratase beta subunit	_____________223___________________________________261\n_____________\|_____________________________________\|\n5'-GGA...ACCCC____AAAG___A____________UA_______C___GAUGU...GCG-3'\n______________GAUC____CUG_AGAUCUGCAAGA__UUCGCGU_GGC\n______________\|\|\|\|____\|\|\|_\|\|\|\|\|:\|\|\|\|:\|__\|\|\|:\|\|\|_\|\|\|\n______________CUAG____GAC_UCUAGGCGUUUU__AAGUGCA_CCG\n________3'-CGC___________C____________C________A___AAAUC...AAG-5'\n_____________\|_____________________________________\|\n_____________107___________________________________74\n	250 -- 256	79 -- 85	-36.8095 kcal/mol	15.2774 kcal/mol	11.8787 kcal/mol	223 261@LB@ \| \|@LB@5'-GGA...ACCCC AAAG A UA C GAUGU...GCG-3'@LB@ GAUC CUG AGAUCUGCAAGA UUCGCGU GGC@LB@ \|\|\|\| \|\|\| \|\|\|\|\|:\|\|\|\|:\| \|\|\|:\|\|\| \|\|\|@LB@ CUAG GAC UCUAGGCGUUUU AAGUGCA CCG@LB@ 3'-CGC C C A AAAUC...AAG-5'@LB@ \| \|@LB@ 107 74@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -36.8095 kcal/mol@LB@Unfolding Energy - mRNA 15.2774 kcal/mol@LB@Unfolding Energy - sRNA 11.8787 kcal/mol@LB@@LB@Position - mRNA 224 -- 260@LB@Position - sRNA 75 -- 106@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 79 -- 85@LB@
111	0.01894	0.5385	b2600	tyrA	-7.88	0.238290	191 -- 206	74 -- 89	fused chorismate mutase T/prephenate dehydrogenase	_____________190______________207\n_____________\|________________\|\n5'-UCG...CUUAA_________UA_____GCUGA...UGG-3'\n______________GAGGUUUAU__UGGUU\n______________:\|:\|\|\|:\|:__\|\|\|:\|\n______________UUUCAAGUG__ACCGA\n3'-CGC...GGCGU_________CA_____AAUCA...AAG-5'\n_____________\|________________\|\n_____________90_______________73\n	193 -- 199	81 -- 87	-12.4695 kcal/mol	4.06959 kcal/mol	0.517373 kcal/mol	190 207@LB@ \| \|@LB@5'-UCG...CUUAA UA GCUGA...UGG-3'@LB@ GAGGUUUAU UGGUU@LB@ :\|:\|\|\|:\|: \|\|\|:\|@LB@ UUUCAAGUG ACCGA@LB@3'-CGC...GGCGU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.4695 kcal/mol@LB@Unfolding Energy - mRNA 4.06959 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 191 -- 206@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 81 -- 87@LB@
71	0.01305	0.5385	b3843	ubiD	-10.23	0.096580	123 -- 132	80 -- 89	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________122________133\n_____________\|__________\|\n5'-CGC...CCGUC__________CUAAU...UGG-3'\n______________AGAGUUCACG\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUCAAGUGC\n3'-CGC...GGCGU__________AACCG...AAG-5'\n_____________\|__________\|\n_____________90_________79\n	126 -- 132	80 -- 86	-13.04 kcal/mol	2.30553 kcal/mol	0.506316 kcal/mol	122 133@LB@ \| \|@LB@5'-CGC...CCGUC CUAAU...UGG-3'@LB@ AGAGUUCACG@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUCAAGUGC@LB@3'-CGC...GGCGU AACCG...AAG-5'@LB@ \| \|@LB@ 90 79@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 2.30553 kcal/mol@LB@Unfolding Energy - sRNA 0.506316 kcal/mol@LB@@LB@Position - mRNA 123 -- 132@LB@Position - sRNA 80 -- 89@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 80 -- 86@LB@
154	0.02609	0.5541	b4195	ulaC	-15.85	0.009707	6 -- 31	56 -- 80	L-ascorbate-specific enzyme IIA component of PTS	_____________5__________________________32\n_____________\|__________________________\|\n______5'-GCGCG______GAGUACAAAAG_________UGGCG...UGG-3'\n______________GUUGGC___________CGAGUUGAG\n______________\|\|\|\|\|\|___________\|\|\|\|\|\|\|\|\|\n______________CAACCG___________GCUCAACUC\n3'-CGC...AAGUG______AAAUCAAUAA__________UUUGA...AAG-5'\n_____________\|__________________________\|\n_____________81_________________________55\n	25 -- 31	56 -- 62	-23.4839 kcal/mol	5.91355 kcal/mol	1.71557 kcal/mol	5 32@LB@ \| \|@LB@ 5'-GCGCG GAGUACAAAAG UGGCG...UGG-3'@LB@ GUUGGC CGAGUUGAG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CAACCG GCUCAACUC@LB@3'-CGC...AAGUG AAAUCAAUAA UUUGA...AAG-5'@LB@ \| \|@LB@ 81 55@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -23.4839 kcal/mol@LB@Unfolding Energy - mRNA 5.91355 kcal/mol@LB@Unfolding Energy - sRNA 1.71557 kcal/mol@LB@@LB@Position - mRNA 6 -- 31@LB@Position - sRNA 56 -- 80@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 56 -- 62@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@LB@
171	0.03054	0.5559	b0045	yaaU	-10.82	0.076059	142 -- 153	73 -- 84	putative MFS sugar transporter; membrane protein	_____________141__________154\n_____________\|____________\|\n5'-AAG...ACGGC_G__________GAUAC...UAC-3'\n______________U_AUGUUGGUUU\n______________\|_\|:\|\|\|\|\|:\|\|\n______________A_UGCAACCGAA\n3'-CGC...UUUCA_G__________AUCAA...AAG-5'\n_____________\|____________\|\n_____________85___________72\n	147 -- 153	73 -- 79	-12.9415 kcal/mol	1.60777 kcal/mol	0.508835 kcal/mol	141 154@LB@ \| \|@LB@5'-AAG...ACGGC G GAUAC...UAC-3'@LB@ U AUGUUGGUUU@LB@ \| \|:\|\|\|\|\|:\|\|@LB@ A UGCAACCGAA@LB@3'-CGC...UUUCA G AUCAA...AAG-5'@LB@ \| \|@LB@ 85 72@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -12.9415 kcal/mol@LB@Unfolding Energy - mRNA 1.60777 kcal/mol@LB@Unfolding Energy - sRNA 0.508835 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 73 -- 84@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 73 -- 79@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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