Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
67	0.009794	0.4523	b2823	ppdC	-12.40	0.029910	245 -- 275	3 -- 28	putative prepilin peptidase-dependent protein		_____________244_____________________________276\n_____________\|_______________________________\|\n5'-ACG...CCGGA_______UUGGC_____U_____________AUUGU...UCC-3'\n______________GGUAAUG_____GAUGG_GUUGAUGGUGAUG\n______________\|\|\|\|\|\|:_____:\|\|::_\|\|\|:\|\|\|:\|\|\|\|:\n______________CCAUUAU_____UUAUU_CAAUUACUACUAU\n3'-UUU...UACUG_________________U_____________CG-5'\n_____________\|_______________________________\|\n_____________29______________________________2\n	269 -- 275	3 -- 9	-21.5159 kcal/mol	8.35299 kcal/mol	0.766561 kcal/mol	244 276@LB@ \| \|@LB@5'-ACG...CCGGA UUGGC U AUUGU...UCC-3'@LB@ GGUAAUG GAUGG GUUGAUGGUGAUG@LB@ \|\|\|\|\|\|: :\|\|:: \|\|\|:\|\|\|:\|\|\|\|:@LB@ CCAUUAU UUAUU CAAUUACUACUAU@LB@3'-UUU...UACUG U CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -12.40 kcal/mol@LB@Hybridization Energy -21.5159 kcal/mol@LB@Unfolding Energy - mRNA 8.35299 kcal/mol@LB@Unfolding Energy - sRNA 0.766561 kcal/mol@LB@@LB@Position - mRNA 245 -- 275@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 3 -- 9@LB@
116	0.01846	0.5155	b3349	slyD	-11.19	0.055067	245 -- 274	8 -- 47	FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)		_____________244______________________________________275\n_____________\|________________________________________\|\n5'-UGU...CAGGU____A__________________UGUU_____________GUCUC...ACU-3'\n______________ACGU_CAGAA______GACGGUG________GGUUGAUGA\n______________\|\|:\|_\|\|\|\|\|______\|\|\|\|\|\|:________:\|\|\|:\|\|\|\|\n______________UGUA_GUCUU______CUGCCAU________UCAAUUACU\n3'-UUU...UUGUC____A_____UACUUA_______UAUUUAUU_________ACUAUCG-5'\n_____________\|________________________________________\|\n_____________48_______________________________________7\n	268 -- 274	8 -- 14	-23.1983 kcal/mol	5.6913 kcal/mol	6.31565 kcal/mol	244 275@LB@ \| \|@LB@5'-UGU...CAGGU A UGUU GUCUC...ACU-3'@LB@ ACGU CAGAA GACGGUG GGUUGAUGA@LB@ \|\|:\| \|\|\|\|\| \|\|\|\|\|\|: :\|\|\|:\|\|\|\|@LB@ UGUA GUCUU CUGCCAU UCAAUUACU@LB@3'-UUU...UUGUC A UACUUA UAUUUAUU ACUAUCG-5'@LB@ \| \|@LB@ 48 7@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -23.1983 kcal/mol@LB@Unfolding Energy - mRNA 5.6913 kcal/mol@LB@Unfolding Energy - sRNA 6.31565 kcal/mol@LB@@LB@Position - mRNA 245 -- 274@LB@Position - sRNA 8 -- 47@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 8 -- 14@LB@
43	0.004693	0.3568	b1395	paaH	-8.91	0.157263	246 -- 258	49 -- 61	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent		_____________245___________259\n_____________\|_____________\|\n5'-GGC...GCACC_______C_____UUGCU...UGU-3'\n______________AUGGGGG_AGGCA\n______________\|\|:\|\|\|\|_\|::\|\|\n______________UAUCCCC_UUUGU\n3'-UUU...AACUU_______A_____CUGUA...UCG-5'\n_____________\|_____________\|\n_____________62____________48\n	246 -- 252	55 -- 61	-14.1165 kcal/mol	4.46726 kcal/mol	0.738192 kcal/mol	245 259@LB@ \| \|@LB@5'-GGC...GCACC C UUGCU...UGU-3'@LB@ AUGGGGG AGGCA@LB@ \|\|:\|\|\|\| \|::\|\|@LB@ UAUCCCC UUUGU@LB@3'-UUU...AACUU A CUGUA...UCG-5'@LB@ \| \|@LB@ 62 48@LB@@LB@@LB@Energy -8.91 kcal/mol@LB@Hybridization Energy -14.1165 kcal/mol@LB@Unfolding Energy - mRNA 4.46726 kcal/mol@LB@Unfolding Energy - sRNA 0.738192 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 49 -- 61@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 55 -- 61@LB@
65	0.009342	0.4523	b0871	poxB	-9.00	0.151653	248 -- 256	51 -- 59	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding		_____________247_______257\n_____________\|_________\|\n5'-CCG...UCGGC_________ACGCA...GUG-3'\n______________AGGGGUGAA\n______________\|\|\|\|\|\|:\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	250 -- 256	51 -- 57	-12.9194 kcal/mol	3.39064 kcal/mol	0.532875 kcal/mol	247 257@LB@ \| \|@LB@5'-CCG...UCGGC ACGCA...GUG-3'@LB@ AGGGGUGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -12.9194 kcal/mol@LB@Unfolding Energy - mRNA 3.39064 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 248 -- 256@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 51 -- 57@LB@
59	0.008416	0.4523	b0566	envY	-9.46	0.123665	249 -- 263	50 -- 64	porin thermoregulatory transcriptional activator	b1499 b0564 b3515 b4116 b3516	_____________248_____________264\n_____________\|_______________\|\n5'-GGC...AAAAA_______A_______GUCAA...ACU-3'\n______________GAGGUAG_GGUAAGC\n______________\|\|::\|\|\|_\|\|\|\|\|:\|\n______________CUUUAUC_CCAUUUG\n3'-UUU...GCCAA_______C_______UCUGU...UCG-5'\n_____________\|_______________\|\n_____________65______________49\n	257 -- 263	50 -- 56	-15.2892 kcal/mol	5.08919 kcal/mol	0.736811 kcal/mol	248 264@LB@ \| \|@LB@5'-GGC...AAAAA A GUCAA...ACU-3'@LB@ GAGGUAG GGUAAGC@LB@ \|\|::\|\|\| \|\|\|\|\|:\|@LB@ CUUUAUC CCAUUUG@LB@3'-UUU...GCCAA C UCUGU...UCG-5'@LB@ \| \|@LB@ 65 49@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -15.2892 kcal/mol@LB@Unfolding Energy - mRNA 5.08919 kcal/mol@LB@Unfolding Energy - sRNA 0.736811 kcal/mol@LB@@LB@Position - mRNA 249 -- 263@LB@Position - sRNA 50 -- 64@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 50 -- 56@LB@
131	0.02082	0.5217	b2038	rfbC	-12.83	0.023839	249 -- 268	2 -- 18	dTDP-4-deoxyrhamnose-3 5-epimerase		_____________248__________________269\n_____________\|____________________\|\n5'-GGG...AGCCA_____AUU____________AGGUU...CAG-3'\n______________AGAGU___UGGUGAUGAUAG\n______________\|:\|\|\|___\|::\|\|\|\|\|\|\|\|\|\n______________UUUCA___AUUACUACUAUC\n3'-UUU...AUUUA____________________G-5'\n_____________\|____________________\|\n_____________19___________________1\n	262 -- 268	2 -- 8	-17.1909 kcal/mol	4.30321 kcal/mol	0.0608678 kcal/mol	248 269@LB@ \| \|@LB@5'-GGG...AGCCA AUU AGGUU...CAG-3'@LB@ AGAGU UGGUGAUGAUAG@LB@ \|:\|\|\| \|::\|\|\|\|\|\|\|\|\|@LB@ UUUCA AUUACUACUAUC@LB@3'-UUU...AUUUA G-5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -17.1909 kcal/mol@LB@Unfolding Energy - mRNA 4.30321 kcal/mol@LB@Unfolding Energy - sRNA 0.0608678 kcal/mol@LB@@LB@Position - mRNA 249 -- 268@LB@Position - sRNA 2 -- 18@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 2 -- 8@LB@
115	0.01846	0.5155	b4483	tatD	-10.31	0.084235	251 -- 265	1 -- 13	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________250_____________266\n_____________\|_______________\|\n5'-CUG...GACCG________UU_____GUGCG...UCA-3'\n______________UGAUGAUG__GUAGC\n______________\|:\|\|\|\|\|\|__:\|\|\|\|\n______________AUUACUAC__UAUCG\n3'-UUU...UUUCA_______________-5'\n_____________\|______________\|\n_____________14_____________1\n	252 -- 258	6 -- 12	-13.1693 kcal/mol	2.8194 kcal/mol	0.0446954 kcal/mol	250 266@LB@ \| \|@LB@5'-CUG...GACCG UU GUGCG...UCA-3'@LB@ UGAUGAUG GUAGC@LB@ \|:\|\|\|\|\|\| :\|\|\|\|@LB@ AUUACUAC UAUCG@LB@3'-UUU...UUUCA -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -10.31 kcal/mol@LB@Hybridization Energy -13.1693 kcal/mol@LB@Unfolding Energy - mRNA 2.8194 kcal/mol@LB@Unfolding Energy - sRNA 0.0446954 kcal/mol@LB@@LB@Position - mRNA 251 -- 265@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 6 -- 12@LB@
134	0.02184	0.526	b0034	caiF	-11.03	0.059446	251 -- 259	1 -- 9	cai operon transcriptional activator		_____________250_______260\n_____________\|_________\|\n5'-UGA...GAAUG_________UGAAA...AUU-3'\n______________GAUGAUGGC\n______________\|\|\|\|\|\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	253 -- 259	1 -- 7	-13.9707 kcal/mol	2.91573 kcal/mol	0.0200155 kcal/mol	250 260@LB@ \| \|@LB@5'-UGA...GAAUG UGAAA...AUU-3'@LB@ GAUGAUGGC@LB@ \|\|\|\|\|\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -13.9707 kcal/mol@LB@Unfolding Energy - mRNA 2.91573 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 251 -- 259@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 1 -- 7@LB@
38	0.003831	0.3287	b3739	atpI	-13.67	0.015109	253 -- 271	1 -- 16	ATP synthase membrane-bound accessory factor		_____________252_________________272\n_____________\|___________________\|\n5'-GAA...CGUUC_____CUG___________AAGUG...ACC-3'\n______________AGUUA___GUGGUGAUAGC\n______________\|\|\|\|\|___:\|\|:\|\|\|\|\|\|\|\n______________UCAAU___UACUACUAUCG\n3'-UUU...UUAUU___________________-5'\n_____________\|__________________\|\n_____________17_________________1\n	265 -- 271	1 -- 7	-18.239 kcal/mol	4.52285 kcal/mol	0.0492804 kcal/mol	252 272@LB@ \| \|@LB@5'-GAA...CGUUC CUG AAGUG...ACC-3'@LB@ AGUUA GUGGUGAUAGC@LB@ \|\|\|\|\| :\|\|:\|\|\|\|\|\|\|@LB@ UCAAU UACUACUAUCG@LB@3'-UUU...UUAUU -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.67 kcal/mol@LB@Hybridization Energy -18.239 kcal/mol@LB@Unfolding Energy - mRNA 4.52285 kcal/mol@LB@Unfolding Energy - sRNA 0.0492804 kcal/mol@LB@@LB@Position - mRNA 253 -- 271@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 1 -- 7@LB@
52	0.0063	0.3902	b1473	yddG	-8.84	0.162012	257 -- 264	2 -- 9	aromatic amino acid exporter		_____________256______265\n_____________\|________\|\n5'-GCG...AGCAC________GAUUG...CGG-3'\n______________GAUGGUAG\n______________\|\|\|\|:\|\|\|\n______________CUACUAUC\n3'-UUU...AAUUA________G-5'\n_____________\|________\|\n_____________10_______1\n	258 -- 264	2 -- 8	-10.1209 kcal/mol	1.26064 kcal/mol	0.0191352 kcal/mol	256 265@LB@ \| \|@LB@5'-GCG...AGCAC GAUUG...CGG-3'@LB@ GAUGGUAG@LB@ \|\|\|\|:\|\|\|@LB@ CUACUAUC@LB@3'-UUU...AAUUA G-5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.84 kcal/mol@LB@Hybridization Energy -10.1209 kcal/mol@LB@Unfolding Energy - mRNA 1.26064 kcal/mol@LB@Unfolding Energy - sRNA 0.0191352 kcal/mol@LB@@LB@Position - mRNA 257 -- 264@LB@Position - sRNA 2 -- 9@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 2 -- 8@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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