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
190	0.03948	0.6177	b2914	rpiA	-5.25	0.339968	76 -- 83	45 -- 52	ribose 5-phosphate isomerase constitutive		_____________75_______84\n_____________\|________\|\n5'-GAA...GGGCG________UGCCU...CAC-3'\n______________AAAGGGGA\n______________\|\|\|\|:\|\|\|\n______________UUUCUCCU\n3'-UUU...GGCAG________UAAAG...ACA-5'\n_____________\|________\|\n_____________53_______44\n	77 -- 83	45 -- 51	-8.77639 kcal/mol	2.67801 kcal/mol	0.850469 kcal/mol	75 84@LB@ \| \|@LB@5'-GAA...GGGCG UGCCU...CAC-3'@LB@ AAAGGGGA@LB@ \|\|\|\|:\|\|\|@LB@ UUUCUCCU@LB@3'-UUU...GGCAG UAAAG...ACA-5'@LB@ \| \|@LB@ 53 44@LB@@LB@@LB@Energy -5.25 kcal/mol@LB@Hybridization Energy -8.77639 kcal/mol@LB@Unfolding Energy - mRNA 2.67801 kcal/mol@LB@Unfolding Energy - sRNA 0.850469 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 45 -- 52@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 45 -- 51@LB@
57	0.01201	0.6177	b2959	yggL	-9.33	0.056423	82 -- 92	47 -- 57	DUF469 family protein		_____________81__________93\n_____________\|___________\|\n5'-GUA...AAAAC___________CAAUG...CAU-3'\n______________CUGUCAGAGAG\n______________\|:\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	86 -- 92	47 -- 53	-15.1623 kcal/mol	3.10124 kcal/mol	2.73556 kcal/mol	81 93@LB@ \| \|@LB@5'-GUA...AAAAC CAAUG...CAU-3'@LB@ CUGUCAGAGAG@LB@ \|:\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -15.1623 kcal/mol@LB@Unfolding Energy - mRNA 3.10124 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 82 -- 92@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 47 -- 53@LB@
105	0.0216	0.6177	b2962	yggX	-9.20	0.059738	186 -- 194	45 -- 53	oxidative damage protective factor for iron-sulfur proteins		_____________185_______195\n_____________\|_________\|\n5'-UCA...GUCGA_________UGAUU...AGA-3'\n______________UAAAGAGGA\n______________:\|\|\|\|\|\|\|\|\n______________GUUUCUCCU\n3'-UUU...GGGCA_________UAAAG...ACA-5'\n_____________\|_________\|\n_____________54________44\n	188 -- 194	45 -- 51	-10.7665 kcal/mol	0.645872 kcal/mol	0.917553 kcal/mol	185 195@LB@ \| \|@LB@5'-UCA...GUCGA UGAUU...AGA-3'@LB@ UAAAGAGGA@LB@ :\|\|\|\|\|\|\|\|@LB@ GUUUCUCCU@LB@3'-UUU...GGGCA UAAAG...ACA-5'@LB@ \| \|@LB@ 54 44@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -10.7665 kcal/mol@LB@Unfolding Energy - mRNA 0.645872 kcal/mol@LB@Unfolding Energy - sRNA 0.917553 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 45 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 45 -- 51@LB@
74	0.01569	0.6177	b3012	dkgA	-8.72	0.074604	189 -- 197	44 -- 52	2 5-diketo-D-gluconate reductase A		_____________188_______198\n_____________\|_________\|\n5'-CUG...AUAUA_________CGUAU...CCA-3'\n______________AAGGAGGAA\n______________\|\|:\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.1725 kcal/mol	1.58724 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-CUG...AUAUA CGUAU...CCA-3'@LB@ AAGGAGGAA@LB@ \|\|:\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.1725 kcal/mol@LB@Unfolding Energy - mRNA 1.58724 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 44 -- 50@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB		_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@LB@
151	0.03043	0.6177	b3081	fadH	-8.56	0.080347	290 -- 297	43 -- 50	2 4-dienoyl-CoA reductase NADH and FMN-linked		_____________289______298\n_____________\|________\|\n5'-UGG...GGGCU________ACC-3'\n______________GGAGGAAU\n______________:\|\|\|\|\|\|\|\n______________UCUCCUUA\n3'-UUU...CAGUU________AAGUA...ACA-5'\n_____________\|________\|\n_____________51_______42\n	291 -- 297	43 -- 49	-10.5858 kcal/mol	1.17616 kcal/mol	0.845564 kcal/mol	289 298@LB@ \| \|@LB@5'-UGG...GGGCU ACC-3'@LB@ GGAGGAAU@LB@ :\|\|\|\|\|\|\|@LB@ UCUCCUUA@LB@3'-UUU...CAGUU AAGUA...ACA-5'@LB@ \| \|@LB@ 51 42@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -10.5858 kcal/mol@LB@Unfolding Energy - mRNA 1.17616 kcal/mol@LB@Unfolding Energy - sRNA 0.845564 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 43 -- 50@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
97	0.01904	0.6177	b3102	yqjG	-9.04	0.064335	159 -- 168	44 -- 53	putative S-transferase		_____________158________169\n_____________\|__________\|\n5'-GCA...AAAAA__________GCUCC...GGC-3'\n______________CGAGGAGGAA\n______________\|:\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-13.5343 kcal/mol	3.56251 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-GCA...AAAAA GCUCC...GGC-3'@LB@ CGAGGAGGAA@LB@ \|:\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.5343 kcal/mol@LB@Unfolding Energy - mRNA 3.56251 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
15	0.003313	0.593	b3133	agaV	-12.53	0.012445	185 -- 194	44 -- 53	N-acetylgalactosamine-specific enzyme IIB component of PTS		_____________184________195\n_____________\|__________\|\n5'-UCA...CAAAA__________CACGC...UAG-3'\n______________CAAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-14.1596 kcal/mol	0.702602 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UCA...CAAAA CACGC...UAG-3'@LB@ CAAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.1596 kcal/mol@LB@Unfolding Energy - mRNA 0.702602 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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@
63	0.01324	0.6177	b3140	agaD	-9.33	0.056359	182 -- 192	45 -- 55	N-acetylgalactosamine-specific enzyme IID component of PTS		_____________181_________193\n_____________\|___________\|\n5'-GCG...AAAAU_AA________CUACA...GUU-3'\n______________G__GAAGAGGA\n______________\|__:\|\|\|\|\|\|\|\n______________C__UUUCUCCU\n3'-UUU...CCGGG_AG________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	186 -- 192	45 -- 51	-11.186 kcal/mol	0.927202 kcal/mol	0.930875 kcal/mol	181 193@LB@ \| \|@LB@5'-GCG...AAAAU AA CUACA...GUU-3'@LB@ G GAAGAGGA@LB@ \| :\|\|\|\|\|\|\|@LB@ C UUUCUCCU@LB@3'-UUU...CCGGG AG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -11.186 kcal/mol@LB@Unfolding Energy - mRNA 0.927202 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 182 -- 192@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 45 -- 51@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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