Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
121	0.006643	0.1913	b1813	nudL	-11.92	0.059353	114 -- 132	70 -- 86	putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase		_____________113_________________133\n_____________\|___________________\|\n5'-CCU...GUGGA____U________G_____AAGAA...CUG-3'\n______________AUUG_CGCCGAUA_CCAGG\n______________\|:\|\|_\|\|\|\|:\|:\|_\|\|\|\|\|\n______________UGAC_GCGGUUGU_GGUCC\n3'-UUU...GCUUA___________________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	120 -- 126	75 -- 81	-24.7024 kcal/mol	5.50013 kcal/mol	7.27772 kcal/mol	113 133@LB@ \| \|@LB@5'-CCU...GUGGA U G AAGAA...CUG-3'@LB@ AUUG CGCCGAUA CCAGG@LB@ \|:\|\| \|\|\|\|:\|:\| \|\|\|\|\|@LB@ UGAC GCGGUUGU GGUCC@LB@3'-UUU...GCUUA CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -24.7024 kcal/mol@LB@Unfolding Energy - mRNA 5.50013 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 114 -- 132@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 75 -- 81@LB@
14	0.0004762	0.1198	b2286	nuoC	-13.55	0.028468	156 -- 179	68 -- 87	NADH:ubiquinone oxidoreductase fused CD subunit		_____________155______________________180\n_____________\|________________________\|\n5'-AGG...AAGCU_____________GUCA___C___CCAUU...CCU-3'\n______________UACUGCGCCGACA____CCA_GGA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|____\|\|\|_\|\|\|\n______________AUGACGCGGUUGU____GGU_CCU\n3'-UUU...CGCUU____________________C___UUAGA...GUG-5'\n_____________\|________________________\|\n_____________88_______________________67\n	162 -- 168	75 -- 81	-29.2495 kcal/mol	8.32219 kcal/mol	7.38006 kcal/mol	155 180@LB@ \| \|@LB@5'-AGG...AAGCU GUCA C CCAUU...CCU-3'@LB@ UACUGCGCCGACA CCA GGA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ AUGACGCGGUUGU GGU CCU@LB@3'-UUU...CGCUU C UUAGA...GUG-5'@LB@ \| \|@LB@ 88 67@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -29.2495 kcal/mol@LB@Unfolding Energy - mRNA 8.32219 kcal/mol@LB@Unfolding Energy - sRNA 7.38006 kcal/mol@LB@@LB@Position - mRNA 156 -- 179@LB@Position - sRNA 68 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 75 -- 81@LB@
18	0.001002	0.1727	b2284	nuoF	-9.91	0.144715	4 -- 28	1 -- 36	NADH:ubiquinone oxidoreductase chain F		_____________3____________________________________29\n_____________\|____________________________________\|\n________5'-AAC______C________________________G____UCGAG...ACG-3'\n______________GGUUAU_AGGGUAU___________UCAGGC_GCGC\n______________:\|\|\|\|:_\|\|\|\|:\|:___________\|\|\|\|\|\|_\|\|:\|\n______________UCAAUG_UCCCGUG___________AGUCCG_CGUG\n3'-UUU...ACUAC______U_______UCGUGACAAAA______G____-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	11 -- 17	23 -- 29	-32.4986 kcal/mol	7.53826 kcal/mol	15.052 kcal/mol	3 29@LB@ \| \|@LB@ 5'-AAC C G UCGAG...ACG-3'@LB@ GGUUAU AGGGUAU UCAGGC GCGC@LB@ :\|\|\|\|: \|\|\|\|:\|: \|\|\|\|\|\| \|\|:\|@LB@ UCAAUG UCCCGUG AGUCCG CGUG@LB@3'-UUU...ACUAC U UCGUGACAAAA G -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -32.4986 kcal/mol@LB@Unfolding Energy - mRNA 7.53826 kcal/mol@LB@Unfolding Energy - sRNA 15.052 kcal/mol@LB@@LB@Position - mRNA 4 -- 28@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 23 -- 29@LB@
8	0.000265	0.1166	b1244	oppB	-12.83	0.039495	280 -- 295	70 -- 84	oligopeptide ABC transporter permease		_____________279______________296\n_____________\|________________\|\n5'-UCC...UAUGA______UC________AAGCC-3'\n______________UGCGCC__GCGCCGGG\n______________\|\|\|\|\|\|__:\|:\|\|:\|\|\n______________ACGCGG__UGUGGUCC\n3'-UUU...UUAUG______U_________CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	289 -- 295	70 -- 76	-25.4509 kcal/mol	5.37602 kcal/mol	7.24859 kcal/mol	279 296@LB@ \| \|@LB@5'-UCC...UAUGA UC AAGCC-3'@LB@ UGCGCC GCGCCGGG@LB@ \|\|\|\|\|\| :\|:\|\|:\|\|@LB@ ACGCGG UGUGGUCC@LB@3'-UUU...UUAUG U CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -25.4509 kcal/mol@LB@Unfolding Energy - mRNA 5.37602 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 280 -- 295@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 70 -- 76@LB@
63	0.003148	0.1727	b0131	panD	-12.33	0.049519	276 -- 291	70 -- 84	aspartate 1-decarboxylase		_____________275______________292\n_____________\|________________\|\n5'-AUU...GUUCU_______UUG______AUUUU...UUG-3'\n______________UGCGCCA___ACCAGG\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________ACGCGGU___UGGUCC\n3'-UUU...UUAUG_______UG_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	276 -- 282	78 -- 84	-24.0598 kcal/mol	4.4848 kcal/mol	7.24859 kcal/mol	275 292@LB@ \| \|@LB@5'-AUU...GUUCU UUG AUUUU...UUG-3'@LB@ UGCGCCA ACCAGG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACGCGGU UGGUCC@LB@3'-UUU...UUAUG UG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -24.0598 kcal/mol@LB@Unfolding Energy - mRNA 4.4848 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 276 -- 291@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 78 -- 84@LB@
200	0.01246	0.2193	b0425	panE	-12.07	0.055655	285 -- 293	54 -- 62	2-dehydropantoate reductase NADPH-specific		_____________284_______294\n_____________\|_________\|\n5'-AUC...AGGGC_________GUACCGC-3'\n______________UGGCUGCGC\n______________\|\|\|\|\|\|\|\|\|\n______________ACCGACGCG\n3'-UUU...UUAGA_________GCAUU...GUG-5'\n_____________\|_________\|\n_____________63________53\n	287 -- 293	54 -- 60	-19.0333 kcal/mol	2.09185 kcal/mol	4.8739 kcal/mol	284 294@LB@ \| \|@LB@5'-AUC...AGGGC GUACCGC-3'@LB@ UGGCUGCGC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACCGACGCG@LB@3'-UUU...UUAGA GCAUU...GUG-5'@LB@ \| \|@LB@ 63 53@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -19.0333 kcal/mol@LB@Unfolding Energy - mRNA 2.09185 kcal/mol@LB@Unfolding Energy - sRNA 4.8739 kcal/mol@LB@@LB@Position - mRNA 285 -- 293@LB@Position - sRNA 54 -- 62@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 54 -- 60@LB@
78	0.004296	0.1855	b3258	panF	-10.37	0.118507	142 -- 153	52 -- 62	pantothenate:sodium symporter		_____________141__________154\n_____________\|____________\|\n5'-GGC...UUUAU___A________GGCGA...UUA-3'\n______________UGG_CUGUGCUG\n______________\|\|\|_\|\|\|:\|\|:\|\n______________ACC_GACGCGGC\n3'-UUU...UUAGA____________AUUUA...GUG-5'\n_____________\|____________\|\n_____________63___________51\n	147 -- 153	52 -- 58	-17.1407 kcal/mol	1.89201 kcal/mol	4.8804 kcal/mol	141 154@LB@ \| \|@LB@5'-GGC...UUUAU A GGCGA...UUA-3'@LB@ UGG CUGUGCUG@LB@ \|\|\| \|\|\|:\|\|:\|@LB@ ACC GACGCGGC@LB@3'-UUU...UUAGA AUUUA...GUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -17.1407 kcal/mol@LB@Unfolding Energy - mRNA 1.89201 kcal/mol@LB@Unfolding Energy - sRNA 4.8804 kcal/mol@LB@@LB@Position - mRNA 142 -- 153@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 52 -- 58@LB@
115	0.006085	0.1855	b3030	parE	-11.34	0.077071	10 -- 31	65 -- 86	DNA topoisomerase IV subunit B		_____________9______________________32\n_____________\|______________________\|\n5'-UUU...AUCUG_____UG_____GAC_______GAAGU...ACC-3'\n______________GCUGC__CAACA___GGGAGAU\n______________:\|\|\|\|__\|\|\|\|\|___\|\|\|\|:\|\|\n______________UGACG__GUUGU___CCCUUUA\n3'-UUU...GCUUA_____CG_____GGU_______GAACC...GUG-5'\n_____________\|______________________\|\n_____________87_____________________64\n	25 -- 31	65 -- 71	-24.4704 kcal/mol	5.74549 kcal/mol	7.38332 kcal/mol	9 32@LB@ \| \|@LB@5'-UUU...AUCUG UG GAC GAAGU...ACC-3'@LB@ GCUGC CAACA GGGAGAU@LB@ :\|\|\|\| \|\|\|\|\| \|\|\|\|:\|\|@LB@ UGACG GUUGU CCCUUUA@LB@3'-UUU...GCUUA CG GGU GAACC...GUG-5'@LB@ \| \|@LB@ 87 64@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -24.4704 kcal/mol@LB@Unfolding Energy - mRNA 5.74549 kcal/mol@LB@Unfolding Energy - sRNA 7.38332 kcal/mol@LB@@LB@Position - mRNA 10 -- 31@LB@Position - sRNA 65 -- 86@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 65 -- 71@LB@
130	0.007275	0.1966	b1638	pdxH	-11.04	0.087983	237 -- 249	47 -- 59	pyridoxine 5'-phosphate oxidase		_____________236___________250\n_____________\|_____________\|\n5'-UCU...CGCAU_____________ACACC...CCC-3'\n______________CUGCGCCGUGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________GACGCGGCAUUUA\n3'-UUU...GAACC_____________AUAAU...GUG-5'\n_____________\|_____________\|\n_____________60____________46\n	243 -- 249	47 -- 53	-22.1181 kcal/mol	4.88729 kcal/mol	6.18672 kcal/mol	236 250@LB@ \| \|@LB@5'-UCU...CGCAU ACACC...CCC-3'@LB@ CUGCGCCGUGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ GACGCGGCAUUUA@LB@3'-UUU...GAACC AUAAU...GUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -11.04 kcal/mol@LB@Hybridization Energy -22.1181 kcal/mol@LB@Unfolding Energy - mRNA 4.88729 kcal/mol@LB@Unfolding Energy - sRNA 6.18672 kcal/mol@LB@@LB@Position - mRNA 237 -- 249@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
108	0.005783	0.1855	b3951	pflD	-15.90	0.009733	233 -- 258	63 -- 86	putative glycine radical domain-containing pyruvate formate-lyase	b0823	_____________232________________________259\n_____________\|__________________________\|\n5'-GAU...ACUGC_____UU_________C_U_______CGCUG...AAA-3'\n______________ACUGU__GCCAAUACC_G_GAAAUCU\n______________\|\|\|\|:__\|\|\|\|\|:\|\|\|_\|_\|\|\|\|\|\|\|\n______________UGACG__CGGUUGUGG_C_CUUUAGA\n3'-UUU...GCUUA________________U_C_______ACCGA...GUG-5'\n_____________\|__________________________\|\n_____________87_________________________62\n	252 -- 258	63 -- 69	-27.9307 kcal/mol	4.64309 kcal/mol	7.38602 kcal/mol	232 259@LB@ \| \|@LB@5'-GAU...ACUGC UU C U CGCUG...AAA-3'@LB@ ACUGU GCCAAUACC G GAAAUCU@LB@ \|\|\|\|: \|\|\|\|\|:\|\|\| \| \|\|\|\|\|\|\|@LB@ UGACG CGGUUGUGG C CUUUAGA@LB@3'-UUU...GCUUA U C ACCGA...GUG-5'@LB@ \| \|@LB@ 87 62@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -27.9307 kcal/mol@LB@Unfolding Energy - mRNA 4.64309 kcal/mol@LB@Unfolding Energy - sRNA 7.38602 kcal/mol@LB@@LB@Position - mRNA 233 -- 258@LB@Position - sRNA 63 -- 86@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 63 -- 69@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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