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
84	0.01785	0.6177	b4318	fimF	-9.06	0.063721	96 -- 107	44 -- 55	minor component of type 1 fimbriae	b1504 b0943	_____________95___________108\n_____________\|____________\|\n5'-CAU...AAUGG_GA_________AAUGC...UCA-3'\n______________G__GAAGAGGAA\n______________\|__:\|\|\|\|\|\|\|\|\n______________C__UUUCUCCUU\n3'-UUU...CCGGG_AG_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	101 -- 107	44 -- 50	-12.9705 kcal/mol	2.96464 kcal/mol	0.941432 kcal/mol	95 108@LB@ \| \|@LB@5'-CAU...AAUGG GA AAUGC...UCA-3'@LB@ G GAAGAGGAA@LB@ \| :\|\|\|\|\|\|\|\|@LB@ C UUUCUCCUU@LB@3'-UUU...CCGGG AG AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -12.9705 kcal/mol@LB@Unfolding Energy - mRNA 2.96464 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 96 -- 107@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 101 -- 107@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@
167	0.03387	0.6177	b3980	tufB	-7.70	0.119070	183 -- 194	44 -- 55	translation elongation factor EF-Tu 2	b3339	_____________182__________195\n_____________\|____________\|\n5'-UCC...UCCGU___UU_______CAAUC...CUA-3'\n______________GUC__AGAGGGA\n______________\|\|\|__\|\|\|\|\|:\|\n______________CAG__UCUCCUU\n3'-UUU...CCGGG___UU_______AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	188 -- 194	44 -- 50	-14.3886 kcal/mol	5.74361 kcal/mol	0.941432 kcal/mol	182 195@LB@ \| \|@LB@5'-UCC...UCCGU UU CAAUC...CUA-3'@LB@ GUC AGAGGGA@LB@ \|\|\| \|\|\|\|\|:\|@LB@ CAG UCUCCUU@LB@3'-UUU...CCGGG UU AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -7.70 kcal/mol@LB@Hybridization Energy -14.3886 kcal/mol@LB@Unfolding Energy - mRNA 5.74361 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 183 -- 194@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
139	0.02683	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
177	0.03616	0.6177	b1474	fdnG	-8.74	0.074199	188 -- 196	44 -- 52	formate dehydrogenase-N alpha subunit nitrate-inducible	b3894	_____________187_______197\n_____________\|_________\|\n5'-AUU...UGAAA_________AGCAA...CUC-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	190 -- 196	44 -- 50	-11.3772 kcal/mol	1.78024 kcal/mol	0.860683 kcal/mol	187 197@LB@ \| \|@LB@5'-AUU...UGAAA AGCAA...CUC-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -11.3772 kcal/mol@LB@Unfolding Energy - mRNA 1.78024 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
160	0.0322	0.6177	b1550	gnsB	-8.75	0.073686	189 -- 197	44 -- 52	Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)	b4517	_____________188_______198\n_____________\|_________\|\n5'-UGG...GACUA_________AUGAU...UUA-3'\n______________AAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	191 -- 197	44 -- 50	-11.5466 kcal/mol	1.93458 kcal/mol	0.860683 kcal/mol	188 198@LB@ \| \|@LB@5'-UGG...GACUA AUGAU...UUA-3'@LB@ AAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -11.5466 kcal/mol@LB@Unfolding Energy - mRNA 1.93458 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@
168	0.03398	0.6177	b0321	yahG	-8.56	0.080369	183 -- 192	44 -- 53	DUF1116 family protein	b4572	_____________182________193\n_____________\|__________\|\n5'-AUC...AUCUG__________GAAGC...AAC-3'\n______________CAAAGGGGAG\n______________\|\|\|\|\|:\|\|\|:\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	186 -- 192	44 -- 50	-12.9704 kcal/mol	3.47901 kcal/mol	0.927997 kcal/mol	182 193@LB@ \| \|@LB@5'-AUC...AUCUG GAAGC...AAC-3'@LB@ CAAAGGGGAG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -12.9704 kcal/mol@LB@Unfolding Energy - mRNA 3.47901 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 183 -- 192@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 44 -- 50@LB@
1	0	0	b0481	ybaK	-91.37	0.000000	1 -- 79	1 -- 79	Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase		______________1______________________________________________________________________________80\n______________\|______________________________________________________________________________\|\n___________5'-_______________________________________________________________________________AACUC...UCG-3'\n______________AAUGGCCAAUAUCGCUAUUGGCCCGUCAAAGAGGAAUUUCAUUUUUUUAUUAUUAUGCCGUCACUUUAAGCGACGGUGU\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUACCGGUUAUAGCGAUAACCGGGCAGUUUCUCCUUAAAGUAAAAAAAUAAUAAUACGGCAGUGAAAUUCGCUGCCACA\n______3'-UUUUU_______________________________________________________________________________-5'\n_____________\|______________________________________________________________________________\|\n_____________80_____________________________________________________________________________1\n	51 -- 57	23 -- 29	-143.199 kcal/mol	26.5504 kcal/mol	25.2758 kcal/mol	1 80@LB@ \| \|@LB@ 5'- AACUC...UCG-3'@LB@ AAUGGCCAAUAUCGCUAUUGGCCCGUCAAAGAGGAAUUUCAUUUUUUUAUUAUUAUGCCGUCACUUUAAGCGACGGUGU@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUACCGGUUAUAGCGAUAACCGGGCAGUUUCUCCUUAAAGUAAAAAAAUAAUAAUACGGCAGUGAAAUUCGCUGCCACA@LB@ 3'-UUUUU -5'@LB@ \| \|@LB@ 80 1@LB@@LB@@LB@Energy -91.37 kcal/mol@LB@Hybridization Energy -143.199 kcal/mol@LB@Unfolding Energy - mRNA 26.5504 kcal/mol@LB@Unfolding Energy - sRNA 25.2758 kcal/mol@LB@@LB@Position - mRNA 1 -- 79@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 23 -- 29@LB@
2	6.241e-06	0.01004	b1737	chbC	-18.35	0.000789	134 -- 152	38 -- 56	N N'-diacetylchitobiose-specific enzyme IIC component of PTS		_____________133_________________153\n_____________\|___________________\|\n5'-GUU...UUUCC__________UU_______AAAUC...UUC-3'\n______________CGUCAAAGAG__AUUUCAU\n______________\|\|\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________GCAGUUUCUC__UAAAGUA\n3'-UUU...ACCGG__________CU_______AAAAA...ACA-5'\n_____________\|___________________\|\n_____________57__________________37\n	146 -- 152	38 -- 44	-21.3647 kcal/mol	1.83077 kcal/mol	1.17918 kcal/mol	133 153@LB@ \| \|@LB@5'-GUU...UUUCC UU AAAUC...UUC-3'@LB@ CGUCAAAGAG AUUUCAU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCAGUUUCUC UAAAGUA@LB@3'-UUU...ACCGG CU AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -18.35 kcal/mol@LB@Hybridization Energy -21.3647 kcal/mol@LB@Unfolding Energy - mRNA 1.83077 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 134 -- 152@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 38 -- 44@LB@
3	9.453e-06	0.01014	b0681	chiP	-16.40	0.001982	182 -- 193	45 -- 56	chitoporin uptake of chitosugars		_____________181__________194\n_____________\|____________\|\n5'-CUU...UUAUA____________UUAAC...AAG-3'\n______________CGUCAAAGAGGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GCAGUUUCUCCU\n3'-UUU...ACCGG____________UAAAG...ACA-5'\n_____________\|____________\|\n_____________57___________44\n	187 -- 193	45 -- 51	-19.4659 kcal/mol	2.1233 kcal/mol	0.938337 kcal/mol	181 194@LB@ \| \|@LB@5'-CUU...UUAUA UUAAC...AAG-3'@LB@ CGUCAAAGAGGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GCAGUUUCUCCU@LB@3'-UUU...ACCGG UAAAG...ACA-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -19.4659 kcal/mol@LB@Unfolding Energy - mRNA 2.1233 kcal/mol@LB@Unfolding Energy - sRNA 0.938337 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 187 -- 193@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)

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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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