Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring		_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@LB@
93	0.009444	0.3104	b3822	recQ	-7.42	0.310549	176 -- 212	9 -- 45	ATP-dependent DNA helicase		_____________175____________________________________213\n_____________\|______________________________________\|\n5'-CGC...CUGUU________A__CAA__________AU______CAG___GAAGU...UUA-3'\n______________UUUAUUUC_GG___UC_GGGGUGA__GUGGCG___GCG\n______________\|\|:\|\|:\|\|_\|:___\|\|_\|\|\|:\|\|\|__:\|::\|:___\|\|\|\n______________AAGUAGAG_CU___AG_CCCUACU__UAUUGU___CGC\n3'-UUU...UUUUA________A__UA___U_______AC______UUA___GCAGAAAG-5'\n_____________\|______________________________________\|\n_____________46_____________________________________8\n	192 -- 198	23 -- 29	-25.6556 kcal/mol	8.78202 kcal/mol	9.45193 kcal/mol	175 213@LB@ \| \|@LB@5'-CGC...CUGUU A CAA AU CAG GAAGU...UUA-3'@LB@ UUUAUUUC GG UC GGGGUGA GUGGCG GCG@LB@ \|\|:\|\|:\|\| \|: \|\| \|\|\|:\|\|\| :\|::\|: \|\|\|@LB@ AAGUAGAG CU AG CCCUACU UAUUGU CGC@LB@3'-UUU...UUUUA A UA U AC UUA GCAGAAAG-5'@LB@ \| \|@LB@ 46 8@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -25.6556 kcal/mol@LB@Unfolding Energy - mRNA 8.78202 kcal/mol@LB@Unfolding Energy - sRNA 9.45193 kcal/mol@LB@@LB@Position - mRNA 176 -- 212@LB@Position - sRNA 9 -- 45@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 23 -- 29@LB@
185	0.01831	0.3104	b3164	pnp	-7.42	0.310961	131 -- 137	8 -- 14	polynucleotide phosphorylase/polyadenylase		_____________130_____138\n_____________\|_______\|\n5'-AGC...GCGAG_______AGAAG...UUA-3'\n______________GAUGCGC\n______________:\|\|\|\|\|\|\n______________UUACGCG\n3'-UUU...AUUGU_______CAGAAAG-5'\n_____________\|_______\|\n_____________15______7\n	131 -- 137	8 -- 14	-10.1419 kcal/mol	2.24272 kcal/mol	0.481462 kcal/mol	130 138@LB@ \| \|@LB@5'-AGC...GCGAG AGAAG...UUA-3'@LB@ GAUGCGC@LB@ :\|\|\|\|\|\|@LB@ UUACGCG@LB@3'-UUU...AUUGU CAGAAAG-5'@LB@ \| \|@LB@ 15 7@LB@@LB@@LB@Energy -7.42 kcal/mol@LB@Hybridization Energy -10.1419 kcal/mol@LB@Unfolding Energy - mRNA 2.24272 kcal/mol@LB@Unfolding Energy - sRNA 0.481462 kcal/mol@LB@@LB@Position - mRNA 131 -- 137@LB@Position - sRNA 8 -- 14@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 8 -- 14@LB@
146	0.01406	0.3104	b3831	udp	-7.35	0.318150	153 -- 161	1 -- 9	uridine phosphorylase		_____________152_______162\n_____________\|_________\|\n5'-AUC...GUAAA_________UGCUU...AGA-3'\n______________GUGUCUUUU\n______________\|:\|\|\|\|\|\|:\n______________CGCAGAAAG\n3'-UUU...UUACG_________-5'\n_____________\|________\|\n_____________10_______1\n	155 -- 161	1 -- 7	-10.4616 kcal/mol	1.99462 kcal/mol	1.11751 kcal/mol	152 162@LB@ \| \|@LB@5'-AUC...GUAAA UGCUU...AGA-3'@LB@ GUGUCUUUU@LB@ \|:\|\|\|\|\|\|:@LB@ CGCAGAAAG@LB@3'-UUU...UUACG -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -10.4616 kcal/mol@LB@Unfolding Energy - mRNA 1.99462 kcal/mol@LB@Unfolding Energy - sRNA 1.11751 kcal/mol@LB@@LB@Position - mRNA 153 -- 161@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 155 -- 161@LB@Position Seed - sRNA 1 -- 7@LB@
183	0.01807	0.3104	b1508	hipB	-7.23	0.331427	238 -- 247	10 -- 19	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________237________248\n_____________\|__________\|\n5'-AUG...GCAAU__________AAUGA...AAA-3'\n______________UGGCGAAUGC\n______________\|::\|:\|\|\|\|\|\n______________AUUGUUUACG\n3'-UUU...CUACU__________CGCAG...AAG-5'\n_____________\|__________\|\n_____________20_________9\n	241 -- 247	10 -- 16	-11.7956 kcal/mol	3.36082 kcal/mol	1.20833 kcal/mol	237 248@LB@ \| \|@LB@5'-AUG...GCAAU AAUGA...AAA-3'@LB@ UGGCGAAUGC@LB@ \|::\|:\|\|\|\|\|@LB@ AUUGUUUACG@LB@3'-UUU...CUACU CGCAG...AAG-5'@LB@ \| \|@LB@ 20 9@LB@@LB@@LB@Energy -7.23 kcal/mol@LB@Hybridization Energy -11.7956 kcal/mol@LB@Unfolding Energy - mRNA 3.36082 kcal/mol@LB@Unfolding Energy - sRNA 1.20833 kcal/mol@LB@@LB@Position - mRNA 238 -- 247@LB@Position - sRNA 10 -- 19@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 10 -- 16@LB@
149	0.01422	0.3104	b0415	ribE	-7.20	0.333957	258 -- 265	4 -- 11	riboflavin synthase beta chain		_____________257______266\n_____________\|________\|\n5'-CGG...CCAUC________CAACA...GUG-3'\n______________GCGCGUUU\n______________\|\|\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	259 -- 265	4 -- 10	-13.1965 kcal/mol	4.83677 kcal/mol	1.15639 kcal/mol	257 266@LB@ \| \|@LB@5'-CGG...CCAUC CAACA...GUG-3'@LB@ GCGCGUUU@LB@ \|\|\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.20 kcal/mol@LB@Hybridization Energy -13.1965 kcal/mol@LB@Unfolding Energy - mRNA 4.83677 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 258 -- 265@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 4 -- 10@LB@
128	0.01258	0.3104	b0677	nagA	-7.18	0.336330	272 -- 297	1 -- 22	N-acetylglucosamine-6-phosphate deacetylase		_____________271________________________298\n_____________\|__________________________\|\n5'-AAC...AUCGC_______CU___UAAAA______G__CGG-3'\n______________UGAUGGC__GAU_____GCGUCU_UC\n______________\|\|\|\|::\|__:\|\|_____\|\|\|\|\|\|_\|\|\n______________ACUAUUG__UUA_____CGCAGA_AG\n3'-UUU...CUACU_______U____CG_________A__-5'\n_____________\|_________________________\|\n_____________23________________________1\n	272 -- 278	16 -- 22	-15.3811 kcal/mol	6.93964 kcal/mol	1.25963 kcal/mol	271 298@LB@ \| \|@LB@5'-AAC...AUCGC CU UAAAA G CGG-3'@LB@ UGAUGGC GAU GCGUCU UC@LB@ \|\|\|\|::\| :\|\| \|\|\|\|\|\| \|\|@LB@ ACUAUUG UUA CGCAGA AG@LB@3'-UUU...CUACU U CG A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -7.18 kcal/mol@LB@Hybridization Energy -15.3811 kcal/mol@LB@Unfolding Energy - mRNA 6.93964 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 272 -- 297@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 16 -- 22@LB@
130	0.01263	0.3104	b1952	dsrB	-7.17	0.338083	230 -- 240	7 -- 18	uncharacterized protein		_____________229__________241\n_____________\|____________\|\n5'-CGU...GUCAA____________GUCCG...ACC-3'\n______________AACGGAUG_GCG\n______________\|\|\|::\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	231 -- 237	11 -- 17	-11.9456 kcal/mol	3.57064 kcal/mol	1.20891 kcal/mol	229 241@LB@ \| \|@LB@5'-CGU...GUCAA GUCCG...ACC-3'@LB@ AACGGAUG GCG@LB@ \|\|\|::\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -11.9456 kcal/mol@LB@Unfolding Energy - mRNA 3.57064 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 11 -- 17@LB@
107	0.01107	0.3104	b0723	sdhA	-7.08	0.348281	169 -- 200	7 -- 42	succinate dehydrogenase flavoprotein subunit		_____________168__________________________________201\n_____________\|____________________________________\|\n5'-GGU...ACGUG____A________UU_______UG____________AUGAA...GUG-3'\n______________AUUU_UGGAUUCG___GUGGUG_____GGGUGUGUG\n______________\|\|:\|_\|\|:\|\|\|\|:___:\|\|:\|\|_____:::\|\|:\|:\|\n______________UAGA_ACUUAAGU___UACUAC_____UUUACGCGC\n3'-UUU...UAAAG____G________CCC______UAUUG_________AGAAAG-5'\n_____________\|____________________________________\|\n_____________43___________________________________6\n	194 -- 200	7 -- 13	-22.2639 kcal/mol	5.75915 kcal/mol	9.42962 kcal/mol	168 201@LB@ \| \|@LB@5'-GGU...ACGUG A UU UG AUGAA...GUG-3'@LB@ AUUU UGGAUUCG GUGGUG GGGUGUGUG@LB@ \|\|:\| \|\|:\|\|\|\|: :\|\|:\|\| :::\|\|:\|:\|@LB@ UAGA ACUUAAGU UACUAC UUUACGCGC@LB@3'-UUU...UAAAG G CCC UAUUG AGAAAG-5'@LB@ \| \|@LB@ 43 6@LB@@LB@@LB@Energy -7.08 kcal/mol@LB@Hybridization Energy -22.2639 kcal/mol@LB@Unfolding Energy - mRNA 5.75915 kcal/mol@LB@Unfolding Energy - sRNA 9.42962 kcal/mol@LB@@LB@Position - mRNA 169 -- 200@LB@Position - sRNA 7 -- 42@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 7 -- 13@LB@
66	0.006019	0.3087	b0223	yafJ	-7.05	0.351504	68 -- 78	1 -- 10	type 2 glutamine amidotransferase family protein		_____________67__________79\n_____________\|___________\|\n5'-GCG...GCUGA________A__AUGCC...AAG-3'\n______________CGCGUCUU_UC\n______________\|\|\|\|\|\|\|\|_\|\|\n______________GCGCAGAA_AG\n3'-UUU...UUUAC___________-5'\n_____________\|__________\|\n_____________11_________1\n	69 -- 75	3 -- 9	-12.9748 kcal/mol	4.76165 kcal/mol	1.16635 kcal/mol	67 79@LB@ \| \|@LB@5'-GCG...GCUGA A AUGCC...AAG-3'@LB@ CGCGUCUU UC@LB@ \|\|\|\|\|\|\|\| \|\|@LB@ GCGCAGAA AG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -7.05 kcal/mol@LB@Hybridization Energy -12.9748 kcal/mol@LB@Unfolding Energy - mRNA 4.76165 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 68 -- 78@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 69 -- 75@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)

Job resubmission

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usability assessment

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service.

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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