Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
145	0.01456	0.3231	b1529	marC	-5.50	0.250589	206 -- 227	39 -- 59	UPF0056 family inner membrane protein	_____________205____________________228\n_____________\|______________________\|\n5'-UGG...AUGUU__________A______UU___CUGGG...GCA-3'\n______________AGAUUUGUUU_AAGCAA__GGC\n______________\|:\|:\|\|\|:\|\|_\|\|\|\|\|\|__:\|\|\n______________UUUGAACGAA_UUCGUU__UCG\n3'-UUU...CCUAC_________________CU___UGAAU...CAA-5'\n_____________\|______________________\|\n_____________60_____________________38\n	207 -- 213	52 -- 58	-17.1508 kcal/mol	5.49588 kcal/mol	6.15149 kcal/mol	205 228@LB@ \| \|@LB@5'-UGG...AUGUU A UU CUGGG...GCA-3'@LB@ AGAUUUGUUU AAGCAA GGC@LB@ \|:\|:\|\|\|:\|\| \|\|\|\|\|\| :\|\|@LB@ UUUGAACGAA UUCGUU UCG@LB@3'-UUU...CCUAC CU UGAAU...CAA-5'@LB@ \| \|@LB@ 60 38@LB@@LB@@LB@Energy -5.50 kcal/mol@LB@Hybridization Energy -17.1508 kcal/mol@LB@Unfolding Energy - mRNA 5.49588 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 206 -- 227@LB@Position - sRNA 39 -- 59@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 52 -- 58@LB@
193	0.0233	0.3864	b1563	relE	-9.36	0.025073	16 -- 27	29 -- 40	Qin prophage; toxin of the RelE-RelB toxin-antitoxin system	_____________15___________28\n_____________\|____________\|\n5'-GCG...ACGCC____________AUGGG...UAC-3'\n______________GCGCUUGAAAAA\n______________\|\|:\|\|\|:\|\|\|\|\|\n______________CGUGAAUUUUUU\n3'-UUU...UUCUU____________AAGCA...CAA-5'\n_____________\|____________\|\n_____________41___________28\n	21 -- 27	29 -- 35	-12.3855 kcal/mol	1.40487 kcal/mol	1.62106 kcal/mol	15 28@LB@ \| \|@LB@5'-GCG...ACGCC AUGGG...UAC-3'@LB@ GCGCUUGAAAAA@LB@ \|\|:\|\|\|:\|\|\|\|\|@LB@ CGUGAAUUUUUU@LB@3'-UUU...UUCUU AAGCA...CAA-5'@LB@ \| \|@LB@ 41 28@LB@@LB@@LB@Energy -9.36 kcal/mol@LB@Hybridization Energy -12.3855 kcal/mol@LB@Unfolding Energy - mRNA 1.40487 kcal/mol@LB@Unfolding Energy - sRNA 1.62106 kcal/mol@LB@@LB@Position - mRNA 16 -- 27@LB@Position - sRNA 29 -- 40@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 29 -- 35@LB@
39	0.00159	0.1292	b1637	tyrS	-8.51	0.043578	178 -- 203	5 -- 27	tyrosyl-tRNA synthetase	_____________177________________________204\n_____________\|__________________________\|\n5'-CAU...UGCAG_________A__U_______U_____GCAAG...CGA-3'\n______________UCGUUAUAU_CA_GGAGAUU_UGAUG\n______________\|\|\|\|\|\|:\|:_\|\|_\|\|\|:\|\|:_\|\|\|\|\|\n______________AGCAAUGUG_GU_CCUUUAG_ACUAC\n3'-UUU...UUUUA__________________________ACAA-5'\n_____________\|__________________________\|\n_____________28_________________________4\n	191 -- 197	10 -- 16	-22.7194 kcal/mol	5.60368 kcal/mol	8.60118 kcal/mol	177 204@LB@ \| \|@LB@5'-CAU...UGCAG A U U GCAAG...CGA-3'@LB@ UCGUUAUAU CA GGAGAUU UGAUG@LB@ \|\|\|\|\|\|:\|: \|\| \|\|\|:\|\|: \|\|\|\|\|@LB@ AGCAAUGUG GU CCUUUAG ACUAC@LB@3'-UUU...UUUUA ACAA-5'@LB@ \| \|@LB@ 28 4@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -22.7194 kcal/mol@LB@Unfolding Energy - mRNA 5.60368 kcal/mol@LB@Unfolding Energy - sRNA 8.60118 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 5 -- 27@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 10 -- 16@LB@
21	0.000535	0.08206	b1639	mliC	-10.27	0.013452	27 -- 40	8 -- 21	inhibitor of c-type lysozyme membrane-bound; putative lipoprotein	_____________26_____________41\n_____________\|______________\|\n5'-GCU...GGGAU______________CCUUC...UGG-3'\n______________UACCAGGAAAUCUG\n______________:\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GUGGUCCUUUAGAC\n3'-UUU...GCAAU______________UACACAA-5'\n_____________\|______________\|\n_____________22_____________7\n	32 -- 38	10 -- 16	-22.0821 kcal/mol	4.25106 kcal/mol	7.55865 kcal/mol	26 41@LB@ \| \|@LB@5'-GCU...GGGAU CCUUC...UGG-3'@LB@ UACCAGGAAAUCUG@LB@ :\|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GUGGUCCUUUAGAC@LB@3'-UUU...GCAAU UACACAA-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -22.0821 kcal/mol@LB@Unfolding Energy - mRNA 4.25106 kcal/mol@LB@Unfolding Energy - sRNA 7.55865 kcal/mol@LB@@LB@Position - mRNA 27 -- 40@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 10 -- 16@LB@
88	0.006209	0.2266	b1643	ydhI	-11.55	0.005389	141 -- 153	28 -- 40	DUF1656 family putative inner membrane efflux pump associated protein	_____________140___________154\n_____________\|_____________\|\n5'-UUU...UUUUC_____________AUUUA...GAU-3'\n______________GCACUUAAAGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUUUUA\n3'-UUU...UUCUU_____________AGCAA...CAA-5'\n_____________\|_____________\|\n_____________41____________27\n	144 -- 150	31 -- 37	-15.2864 kcal/mol	2.10141 kcal/mol	1.63611 kcal/mol	140 154@LB@ \| \|@LB@5'-UUU...UUUUC AUUUA...GAU-3'@LB@ GCACUUAAAGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -15.2864 kcal/mol@LB@Unfolding Energy - mRNA 2.10141 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 141 -- 153@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 31 -- 37@LB@
118	0.009927	0.271	b1654	grxD	-11.37	0.006167	180 -- 241	7 -- 60	glutaredoxin-4	_____________179_______________________________________________________________242\n_____________\|_________________________________________________________________\|\n5'-AAA...GUAAA________AGG________CAAUG_____CACUAUCG_______C_A_________AUUG_____AAACC...CUG-3'\n______________GAAGUUUG___AAGCAAGA_____AGCAC________AAAAAAU_C___ACGCCAG_____CUGA\n______________\|\|\|::\|\|\|___\|\|\|\|\|\|\|\|_____\|\|\|\|\|________\|\|\|\|\|\|\|_\|___\|\|:\|\|\|\|_____\|\|\|\|\n______________CUUUGAAC___UUCGUUCU_____UCGUG________UUUUUUA_G___UGUGGUC_____GACU\n3'-UUU...CCCUA________GAA__________________AA_____________A_CAA_______CUUUA____ACACAA-5'\n_____________\|_________________________________________________________________\|\n_____________61________________________________________________________________6\n	227 -- 233	16 -- 22	-34.247 kcal/mol	9.03509 kcal/mol	13.8468 kcal/mol	179 242@LB@ \| \|@LB@5'-AAA...GUAAA AGG CAAUG CACUAUCG C A AUUG AAACC...CUG-3'@LB@ GAAGUUUG AAGCAAGA AGCAC AAAAAAU C ACGCCAG CUGA@LB@ \|\|\|::\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \| \|\|:\|\|\|\| \|\|\|\|@LB@ CUUUGAAC UUCGUUCU UCGUG UUUUUUA G UGUGGUC GACU@LB@3'-UUU...CCCUA GAA AA A CAA CUUUA ACACAA-5'@LB@ \| \|@LB@ 61 6@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -34.247 kcal/mol@LB@Unfolding Energy - mRNA 9.03509 kcal/mol@LB@Unfolding Energy - sRNA 13.8468 kcal/mol@LB@@LB@Position - mRNA 180 -- 241@LB@Position - sRNA 7 -- 60@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 16 -- 22@LB@
155	0.01672	0.3455	b1686	menI	-4.77	0.356790	227 -- 235	36 -- 44	1 4-dihydroxy-2-naphthoyl-CoA hydrolase	_____________226_______236\n_____________\|_________\|\n5'-GGC...ACCCU_________GAAUG...AUG-3'\n______________GGAAGCACU\n______________:\|\|\|\|\|\|\|\|\n______________UCUUCGUGA\n3'-UUU...UUCGU_________AUUUU...CAA-5'\n_____________\|_________\|\n_____________45________35\n	229 -- 235	36 -- 42	-13.4239 kcal/mol	4.1512 kcal/mol	4.5009 kcal/mol	226 236@LB@ \| \|@LB@5'-GGC...ACCCU GAAUG...AUG-3'@LB@ GGAAGCACU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUUCGUGA@LB@3'-UUU...UUCGU AUUUU...CAA-5'@LB@ \| \|@LB@ 45 35@LB@@LB@@LB@Energy -4.77 kcal/mol@LB@Hybridization Energy -13.4239 kcal/mol@LB@Unfolding Energy - mRNA 4.1512 kcal/mol@LB@Unfolding Energy - sRNA 4.5009 kcal/mol@LB@@LB@Position - mRNA 227 -- 235@LB@Position - sRNA 36 -- 44@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 36 -- 42@LB@
53	0.002646	0.1597	b1704	aroH	-6.03	0.190589	111 -- 120	31 -- 40	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase tryptophan repressible	_____________110________121\n_____________\|__________\|\n5'-CCA...ACCUC__________UCAGC...CCC-3'\n______________GCACUUGAAA\n______________\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUU\n3'-UUU...UUCUU__________UUAAG...CAA-5'\n_____________\|__________\|\n_____________41_________30\n	114 -- 120	31 -- 37	-11.574 kcal/mol	3.92769 kcal/mol	1.61955 kcal/mol	110 121@LB@ \| \|@LB@5'-CCA...ACCUC UCAGC...CCC-3'@LB@ GCACUUGAAA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUU@LB@3'-UUU...UUCUU UUAAG...CAA-5'@LB@ \| \|@LB@ 41 30@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -11.574 kcal/mol@LB@Unfolding Energy - mRNA 3.92769 kcal/mol@LB@Unfolding Energy - sRNA 1.61955 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 31 -- 40@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 31 -- 37@LB@
117	0.009786	0.2694	b1706	ydiU	-6.16	0.177349	6 -- 27	36 -- 55	UPF0061 family protein	_____________5______________________28\n_____________\|______________________\|\n______5'-UGCAA____AUCAUU____________GAUAC...AUA-3'\n______________UUGC______GCGGGAGGCAUU\n______________\|\|\|\|______\|\|::\|\|:\|\|\|:\|\n______________AACG______CGUUCUUCGUGA\n3'-UUU...CUUUG____AAUU______________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	21 -- 27	36 -- 42	-19.2761 kcal/mol	6.93839 kcal/mol	6.17795 kcal/mol	5 28@LB@ \| \|@LB@ 5'-UGCAA AUCAUU GAUAC...AUA-3'@LB@ UUGC GCGGGAGGCAUU@LB@ \|\|\|\| \|\|::\|\|:\|\|\|:\|@LB@ AACG CGUUCUUCGUGA@LB@3'-UUU...CUUUG AAUU AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.16 kcal/mol@LB@Hybridization Energy -19.2761 kcal/mol@LB@Unfolding Energy - mRNA 6.93839 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 36 -- 42@LB@
90	0.006331	0.2266	b1710	btuE	-7.57	0.078405	256 -- 270	25 -- 39	glutathione peroxidase	_____________255_____________271\n_____________\|_______________\|\n5'-GCA...GACCA____G__________CCGGU...UCG-3'\n______________CGCU_GAGAAGUUCG\n______________\|:\|\|_:\|:\|\|:\|\|\|\|\n______________GUGA_UUUUUUAAGC\n3'-UUU...UCUUC____A__________AAUGU...CAA-5'\n_____________\|_______________\|\n_____________40______________24\n	264 -- 270	25 -- 31	-13.949 kcal/mol	4.72897 kcal/mol	1.64678 kcal/mol	255 271@LB@ \| \|@LB@5'-GCA...GACCA G CCGGU...UCG-3'@LB@ CGCU GAGAAGUUCG@LB@ \|:\|\| :\|:\|\|:\|\|\|\|@LB@ GUGA UUUUUUAAGC@LB@3'-UUU...UCUUC A AAUGU...CAA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -7.57 kcal/mol@LB@Hybridization Energy -13.949 kcal/mol@LB@Unfolding Energy - mRNA 4.72897 kcal/mol@LB@Unfolding Energy - sRNA 1.64678 kcal/mol@LB@@LB@Position - mRNA 256 -- 270@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 25 -- 31@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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