Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
86	0.01794	0.6177	b3260	dusB	-7.53	0.128932	119 -- 138	38 -- 55	tRNA-dihydrouridine synthase B		_____________118__________________139\n_____________\|____________________\|\n5'-ACU...GAUUG_______UUU__CC______CUCGU...GAG-3'\n______________GUCAAAG___GG__UUUCAU\n______________\|\|\|\|\|\|\|___\|\|__\|\|\|\|\|\|\n______________CAGUUUC___CC__AAAGUA\n3'-UUU...CCGGG_______U____UU______AAAAA...ACA-5'\n_____________\|____________________\|\n_____________56___________________37\n	119 -- 125	49 -- 55	-13.3869 kcal/mol	4.6894 kcal/mol	1.17036 kcal/mol	118 139@LB@ \| \|@LB@5'-ACU...GAUUG UUU CC CUCGU...GAG-3'@LB@ GUCAAAG GG UUUCAU@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ CAGUUUC CC AAAGUA@LB@3'-UUU...CCGGG U UU AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.53 kcal/mol@LB@Hybridization Energy -13.3869 kcal/mol@LB@Unfolding Energy - mRNA 4.6894 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 119 -- 138@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 49 -- 55@LB@
196	0.04084	0.6177	b3137	kbaY	-7.51	0.129887	187 -- 200	37 -- 51	tagatose 6-phosphate aldolase 1 kbaY subunit	b2096	_____________186_____________201\n_____________\|_______________\|\n5'-CAC...GGCAU_______UCG_____AUGAG...CGA-3'\n______________AAGAGGA____CAUU\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________UUCUCCU____GUAA\n3'-UUU...GCAGU_______UAAA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________52______________36\n	187 -- 193	45 -- 51	-11.4071 kcal/mol	2.82588 kcal/mol	1.07049 kcal/mol	186 201@LB@ \| \|@LB@5'-CAC...GGCAU UCG AUGAG...CGA-3'@LB@ AAGAGGA CAUU@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ UUCUCCU GUAA@LB@3'-UUU...GCAGU UAAA AAAAA...ACA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -11.4071 kcal/mol@LB@Unfolding Energy - mRNA 2.82588 kcal/mol@LB@Unfolding Energy - sRNA 1.07049 kcal/mol@LB@@LB@Position - mRNA 187 -- 200@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
171	0.0346	0.6177	b1865	nudB	-7.50	0.130652	189 -- 196	46 -- 53	dihydroneopterin triphosphate pyrophosphatase		_____________188______197\n_____________\|________\|\n5'-UGA...GUCAA________CAGCG...CCG-3'\n______________CGAAGAGG\n______________\|:\|\|\|\|\|\|\n______________GUUUCUCC\n3'-UUU...GGGCA________UUAAA...ACA-5'\n_____________\|________\|\n_____________54_______45\n	190 -- 196	46 -- 52	-10.7995 kcal/mol	2.39118 kcal/mol	0.910679 kcal/mol	188 197@LB@ \| \|@LB@5'-UGA...GUCAA CAGCG...CCG-3'@LB@ CGAAGAGG@LB@ \|:\|\|\|\|\|\|@LB@ GUUUCUCC@LB@3'-UUU...GGGCA UUAAA...ACA-5'@LB@ \| \|@LB@ 54 45@LB@@LB@@LB@Energy -7.50 kcal/mol@LB@Hybridization Energy -10.7995 kcal/mol@LB@Unfolding Energy - mRNA 2.39118 kcal/mol@LB@Unfolding Energy - sRNA 0.910679 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 46 -- 53@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 46 -- 52@LB@
22	0.004195	0.5992	b3715	yieH	-7.44	0.134211	287 -- 299	41 -- 55	phosphoenolpyruvate and 6-phosphogluconate phosphatase		_____________286_____________300\n_____________\|_______________\|\n5'-CUG...ACGAU___UC__________G-3'\n______________GUU____AGGAAUUU\n______________\|\|:____\|\|\|\|\|\|\|\|\n______________CAG____UCCUUAAA\n3'-UUU...CCGGG___UUUC________GUAAA...ACA-5'\n_____________\|_______________\|\n_____________56______________40\n	293 -- 299	41 -- 47	-8.9861 kcal/mol	0.60049 kcal/mol	0.947844 kcal/mol	286 300@LB@ \| \|@LB@5'-CUG...ACGAU UC G-3'@LB@ GUU AGGAAUUU@LB@ \|\|: \|\|\|\|\|\|\|\|@LB@ CAG UCCUUAAA@LB@3'-UUU...CCGGG UUUC GUAAA...ACA-5'@LB@ \| \|@LB@ 56 40@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -8.9861 kcal/mol@LB@Unfolding Energy - mRNA 0.60049 kcal/mol@LB@Unfolding Energy - sRNA 0.947844 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 41 -- 55@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 41 -- 47@LB@
124	0.02431	0.6177	b2044	wcaL	-7.42	0.135034	145 -- 156	45 -- 56	putative glycosyl transferase		_____________144__________157\n_____________\|____________\|\n5'-GGG...GUGAG_______C____AUGCA...AGA-3'\n______________CGUCAGA_AGGA\n______________\|\|\|\|\|:\|_\|\|\|\|\n______________GCAGUUU_UCCU\n3'-UUU...ACCGG_______C____UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	145 -- 151	50 -- 56	-12.5799 kcal/mol	4.21745 kcal/mol	0.938337 kcal/mol	144 157@LB@ \| \|@LB@5'-GGG...GUGAG C AUGCA...AGA-3'@LB@ CGUCAGA AGGA@LB@ \|\|\|\|\|:\| \|\|\|\|@LB@ GCAGUUU UCCU@LB@3'-UUU...ACCGG C UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -12.5799 kcal/mol@LB@Unfolding Energy - mRNA 4.21745 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 145 -- 156@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
101	0.01972	0.6177	b3636	rpmG	-7.41	0.136064	187 -- 193	44 -- 50	50S ribosomal subunit protein L33		_____________186_____194\n_____________\|_______\|\n5'-CAC...UACUU_______AUAAA...AAC-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	187 -- 193	44 -- 50	-8.97978 kcal/mol	0.747566 kcal/mol	0.825028 kcal/mol	186 194@LB@ \| \|@LB@5'-CAC...UACUU AUAAA...AAC-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -7.41 kcal/mol@LB@Hybridization Energy -8.97978 kcal/mol@LB@Unfolding Energy - mRNA 0.747566 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
181	0.03769	0.6177	b0912	ihfB	-7.34	0.140491	192 -- 199	43 -- 50	integration host factor (IHF) DNA-binding protein beta subunit		_____________191______200\n_____________\|________\|\n5'-ACG...GAACC________CAUGA...UGG-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	193 -- 199	43 -- 49	-10.3812 kcal/mol	2.20002 kcal/mol	0.845564 kcal/mol	191 200@LB@ \| \|@LB@5'-ACG...GAACC CAUGA...UGG-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -7.34 kcal/mol@LB@Hybridization Energy -10.3812 kcal/mol@LB@Unfolding Energy - mRNA 2.20002 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 192 -- 199@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 43 -- 49@LB@
106	0.02162	0.6177	b1831	proQ	-7.28	0.143813	159 -- 202	38 -- 75	RNA chaperone putative ProP translation regulator		_____________158_____________________________________________203\n_____________\|_______________________________________________\|\n5'-UUA...UUCAU___UG______U________A____CGUUGU__UC___A________GGAAA...CGC-3'\n______________GCC_____CGC_UGUUGGCU_CGUC______AA__AGG_AAUUUCAU\n______________\|\|\|_____\|\|\|_\|:\|\|\|\|\|:_\|\|\|\|______\|\|__\|\|\|_\|\|\|\|\|\|\|\|\n______________CGG_____GCG_AUAACCGG_GCAG______UU__UCC_UUAAAGUA\n3'-UUU...UUUAC___UUAUA_________________________UC____________AAAAA...ACA-5'\n_____________\|_______________________________________________\|\n_____________76______________________________________________37\n	196 -- 202	38 -- 44	-31.8607 kcal/mol	10.974 kcal/mol	13.6034 kcal/mol	158 203@LB@ \| \|@LB@5'-UUA...UUCAU UG U A CGUUGU UC A GGAAA...CGC-3'@LB@ GCC CGC UGUUGGCU CGUC AA AGG AAUUUCAU@LB@ \|\|\| \|\|\| \|:\|\|\|\|\|: \|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ CGG GCG AUAACCGG GCAG UU UCC UUAAAGUA@LB@3'-UUU...UUUAC UUAUA UC AAAAA...ACA-5'@LB@ \| \|@LB@ 76 37@LB@@LB@@LB@Energy -7.28 kcal/mol@LB@Hybridization Energy -31.8607 kcal/mol@LB@Unfolding Energy - mRNA 10.974 kcal/mol@LB@Unfolding Energy - sRNA 13.6034 kcal/mol@LB@@LB@Position - mRNA 159 -- 202@LB@Position - sRNA 38 -- 75@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
54	0.01118	0.6177	b0127	yadG	-7.27	0.144346	282 -- 299	40 -- 55	putative ABC transporter ATPase		_____________281________________300\n_____________\|__________________\|\n5'-UGU...UGCAG_______C___U______U-3'\n______________GUCGAAG_GGG_GAUUUU\n______________\|\|\|:\|\|\|_:\|\|_:\|\|\|\|:\n______________CAGUUUC_UCC_UUAAAG\n3'-UUU...CCGGG__________________UAAAA...ACA-5'\n_____________\|__________________\|\n_____________56_________________39\n	282 -- 288	49 -- 55	-13.6497 kcal/mol	5.35692 kcal/mol	1.01784 kcal/mol	281 300@LB@ \| \|@LB@5'-UGU...UGCAG C U U-3'@LB@ GUCGAAG GGG GAUUUU@LB@ \|\|\|:\|\|\| :\|\| :\|\|\|\|:@LB@ CAGUUUC UCC UUAAAG@LB@3'-UUU...CCGGG UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -13.6497 kcal/mol@LB@Unfolding Energy - mRNA 5.35692 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 282 -- 299@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 49 -- 55@LB@
154	0.03071	0.6177	b0368	tauD	-7.18	0.150437	69 -- 85	40 -- 55	taurine dioxygenase 2-oxoglutarate-dependent		_____________68________________86\n_____________\|_________________\|\n5'-GUG...GUUCA_____C___U_______UCGCA...AAC-3'\n______________GUCAG_GGG_GAAUUUC\n______________\|\|\|\|:_\|:\|_\|\|\|\|\|\|\|\n______________CAGUU_CUC_CUUAAAG\n3'-UUU...CCGGG_____U___________UAAAA...ACA-5'\n_____________\|_________________\|\n_____________56________________39\n	79 -- 85	40 -- 46	-16.0696 kcal/mol	7.86965 kcal/mol	1.01784 kcal/mol	68 86@LB@ \| \|@LB@5'-GUG...GUUCA C U UCGCA...AAC-3'@LB@ GUCAG GGG GAAUUUC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|\|@LB@ CAGUU CUC CUUAAAG@LB@3'-UUU...CCGGG U UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -16.0696 kcal/mol@LB@Unfolding Energy - mRNA 7.86965 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 40 -- 46@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)

Job resubmission

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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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