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
116	0.009699	0.2693	b2708	srlQ	-8.08	0.057211	196 -- 214	36 -- 49	D-arabinose 5-phosphate isomerase	_____________195_________________215\n_____________\|___________________\|\n5'-UAC...GGAGA______UGAGU________ACUGA...GCG-3'\n______________GAGCAA_____GAAGCACU\n______________:\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UUCGUU_____CUUCGUGA\n3'-UUU...ACGAA___________________AUUUU...CAA-5'\n_____________\|___________________\|\n_____________50__________________35\n	208 -- 214	36 -- 42	-17.2491 kcal/mol	3.12814 kcal/mol	6.03645 kcal/mol	195 215@LB@ \| \|@LB@5'-UAC...GGAGA UGAGU ACUGA...GCG-3'@LB@ GAGCAA GAAGCACU@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUCGUU CUUCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -17.2491 kcal/mol@LB@Unfolding Energy - mRNA 3.12814 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 36 -- 42@LB@
103	0.00845	0.2642	b0936	ssuA	-4.91	0.333979	11 -- 31	10 -- 40	aliphatic sulfonate ABC transporter periplasmic binding protein	_____________10______________________________32\n_____________\|_______________________________\|\n5'-AGU...UAAGC_______________________________CUGCA...AUC-3'\n______________GCAC_UGAAA________GC_UCAGGAGAUC\n______________\|\|\|\|_\|:\|\|\|________:\|_:\|\|\|\|\|:\|\|\|\n______________CGUG_AUUUU________UG_GGUCCUUUAG\n3'-UUU...UUCUU____A_____UUAAGCAA__U__________ACUAC...CAA-5'\n_____________\|_______________________________\|\n_____________41______________________________9\n	25 -- 31	10 -- 16	-20.0893 kcal/mol	5.95403 kcal/mol	9.22048 kcal/mol	10 32@LB@ \| \|@LB@5'-AGU...UAAGC CUGCA...AUC-3'@LB@ GCAC UGAAA GC UCAGGAGAUC@LB@ \|\|\|\| \|:\|\|\| :\| :\|\|\|\|\|:\|\|\|@LB@ CGUG AUUUU UG GGUCCUUUAG@LB@3'-UUU...UUCUU A UUAAGCAA U ACUAC...CAA-5'@LB@ \| \|@LB@ 41 9@LB@@LB@@LB@Energy -4.91 kcal/mol@LB@Hybridization Energy -20.0893 kcal/mol@LB@Unfolding Energy - mRNA 5.95403 kcal/mol@LB@Unfolding Energy - sRNA 9.22048 kcal/mol@LB@@LB@Position - mRNA 11 -- 31@LB@Position - sRNA 10 -- 40@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 10 -- 16@LB@
20	0.0005034	0.08107	b3962	sthA	-8.00	0.060263	274 -- 291	37 -- 54	pyridine nucleotide transhydrogenase soluble	_____________273________________292\n_____________\|__________________\|\n5'-UAC...GGGCC__G__________U____GCGUC...CAG-3'\n______________UG_UUAAGCAAGG_GCGC\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|:\|\n______________AC_AAUUCGUUCU_CGUG\n3'-UUU...UUUGA__G__________U____AAUUU...CAA-5'\n_____________\|__________________\|\n_____________55_________________36\n	280 -- 286	42 -- 48	-21.3093 kcal/mol	7.14965 kcal/mol	6.1584 kcal/mol	273 292@LB@ \| \|@LB@5'-UAC...GGGCC G U GCGUC...CAG-3'@LB@ UG UUAAGCAAGG GCGC@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\|:\|@LB@ AC AAUUCGUUCU CGUG@LB@3'-UUU...UUUGA G U AAUUU...CAA-5'@LB@ \| \|@LB@ 55 36@LB@@LB@@LB@Energy -8.00 kcal/mol@LB@Hybridization Energy -21.3093 kcal/mol@LB@Unfolding Energy - mRNA 7.14965 kcal/mol@LB@Unfolding Energy - sRNA 6.1584 kcal/mol@LB@@LB@Position - mRNA 274 -- 291@LB@Position - sRNA 37 -- 54@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 42 -- 48@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@LB@
121	0.01057	0.2813	b0452	tesB	-8.75	0.037433	210 -- 223	26 -- 40	acyl-CoA thioesterase 2	_____________209_____________224\n_____________\|_______________\|\n5'-CAA...GUCAG_______________ACUGA...AGG-3'\n______________GCGC_UAAAAAAUUU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|:\n______________CGUG_AUUUUUUAAG\n3'-UUU...UUCUU____A__________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	217 -- 223	26 -- 32	-10.9054 kcal/mol	0.50684 kcal/mol	1.64811 kcal/mol	209 224@LB@ \| \|@LB@5'-CAA...GUCAG ACUGA...AGG-3'@LB@ GCGC UAAAAAAUUU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:@LB@ CGUG AUUUUUUAAG@LB@3'-UUU...UUCUU A CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -10.9054 kcal/mol@LB@Unfolding Energy - mRNA 0.50684 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 210 -- 223@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 26 -- 32@LB@
26	0.0007705	0.09021	b3991	thiG	-9.33	0.025562	246 -- 261	25 -- 41	thiamine biosynthesis ThiGH complex subunit	_____________245_______________262\n_____________\|_________________\|\n5'-GCA...UUACC_____A___________CUUCU...CCG-3'\n______________GGCAC__GGGAAAUUCG\n______________:\|\|\|\|__:::\|\|\|\|\|\|\|\n______________UCGUG__UUUUUUAAGC\n3'-UUU...GUUCU_____AA__________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	255 -- 261	25 -- 31	-14.087 kcal/mol	3.10801 kcal/mol	1.64839 kcal/mol	245 262@LB@ \| \|@LB@5'-GCA...UUACC A CUUCU...CCG-3'@LB@ GGCAC GGGAAAUUCG@LB@ :\|\|\|\| :::\|\|\|\|\|\|\|@LB@ UCGUG UUUUUUAAGC@LB@3'-UUU...GUUCU AA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -14.087 kcal/mol@LB@Unfolding Energy - mRNA 3.10801 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 246 -- 261@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 25 -- 31@LB@
93	0.006966	0.2379	b0436	tig	-6.81	0.123164	173 -- 190	25 -- 42	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________172________________191\n_____________\|__________________\|\n5'-UAC...UGACC_______GU__UUU____AGGUA...UCA-3'\n______________GAGCACU__GA___UUUG\n______________:\|\|\|\|\|\|__:\|___\|\|:\|\n______________UUCGUGA__UU___AAGC\n3'-UUU...CGUUC_______AU__UUU____AAUGU...CAA-5'\n_____________\|__________________\|\n_____________43_________________24\n	173 -- 179	36 -- 42	-10.673 kcal/mol	2.21437 kcal/mol	1.64855 kcal/mol	172 191@LB@ \| \|@LB@5'-UAC...UGACC GU UUU AGGUA...UCA-3'@LB@ GAGCACU GA UUUG@LB@ :\|\|\|\|\|\| :\| \|\|:\|@LB@ UUCGUGA UU AAGC@LB@3'-UUU...CGUUC AU UUU AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -10.673 kcal/mol@LB@Unfolding Energy - mRNA 2.21437 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 173 -- 190@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 36 -- 42@LB@
174	0.01992	0.3669	b1098	tmk	-8.25	0.051647	183 -- 196	29 -- 42	thymidylate kinase	_____________182____________197\n_____________\|______________\|\n5'-UAA...UCUGA______________AAAAA...GCG-3'\n______________AAGUGCUUAAGGAA\n______________\|\|\|::\|\|\|\|\|::\|\|\n______________UUCGUGAAUUUUUU\n3'-UUU...CGUUC______________AAGCA...CAA-5'\n_____________\|______________\|\n_____________43_____________28\n	190 -- 196	29 -- 35	-11.8447 kcal/mol	1.97362 kcal/mol	1.62369 kcal/mol	182 197@LB@ \| \|@LB@5'-UAA...UCUGA AAAAA...GCG-3'@LB@ AAGUGCUUAAGGAA@LB@ \|\|\|::\|\|\|\|\|::\|\|@LB@ UUCGUGAAUUUUUU@LB@3'-UUU...CGUUC AAGCA...CAA-5'@LB@ \| \|@LB@ 43 28@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -11.8447 kcal/mol@LB@Unfolding Energy - mRNA 1.97362 kcal/mol@LB@Unfolding Energy - sRNA 1.62369 kcal/mol@LB@@LB@Position - mRNA 183 -- 196@LB@Position - sRNA 29 -- 42@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
75	0.004391	0.1886	b3708	tnaA	-6.02	0.191179	273 -- 300	28 -- 53	tryptophanase/L-cysteine desulfhydrase PLP-dependent	_____________272_________________________300\n_____________\|___________________________\|\n5'-ACC...CUCGC_____UC__G________A___UU____-3'\n______________GCUUA__GU_AAGAGGCA_UUA__AAAU\n______________\|\|\|\|\|__\|:_\|\|\|\|:\|\|\|_\|\|\|__\|\|\|\|\n______________CGAAU__CG_UUCUUCGU_AAU__UUUA\n3'-UUU...UUGAA_____U____________G___UU____AGCAA...CAA-5'\n_____________\|____________________________\|\n_____________54___________________________27\n	284 -- 290	38 -- 44	-17.9242 kcal/mol	5.66853 kcal/mol	6.23468 kcal/mol	272 300@LB@ \| \|@LB@5'-ACC...CUCGC UC G A UU -3'@LB@ GCUUA GU AAGAGGCA UUA AAAU@LB@ \|\|\|\|\| \|: \|\|\|\|:\|\|\| \|\|\| \|\|\|\|@LB@ CGAAU CG UUCUUCGU AAU UUUA@LB@3'-UUU...UUGAA U G UU AGCAA...CAA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -17.9242 kcal/mol@LB@Unfolding Energy - mRNA 5.66853 kcal/mol@LB@Unfolding Energy - sRNA 6.23468 kcal/mol@LB@@LB@Position - mRNA 273 -- 300@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 38 -- 44@LB@
156	0.01673	0.3455	b0740	tolB	-6.75	0.127692	202 -- 229	33 -- 61	periplasmic protein	_____________201____________________________230\n_____________\|______________________________\|\n5'-UCC...UAUGA______AG__A_________U_________UUUUC...CCG-3'\n______________UGAAGC__GC_UUA__CGAG_AGCAUUUGG\n______________\|\|\|\|:\|__\|\|_\|\|\|__\|:\|\|_\|\|\|\|:\|\|::\n______________ACUUUG__CG_AAU__GUUC_UCGUGAAUU\n3'-UUU...GCCCU______AA______UC____U_________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________62_____________________________32\n	222 -- 228	34 -- 40	-20.0945 kcal/mol	5.97693 kcal/mol	7.37029 kcal/mol	201 230@LB@ \| \|@LB@5'-UCC...UAUGA AG A U UUUUC...CCG-3'@LB@ UGAAGC GC UUA CGAG AGCAUUUGG@LB@ \|\|\|\|:\| \|\| \|\|\| \|:\|\| \|\|\|\|:\|\|::@LB@ ACUUUG CG AAU GUUC UCGUGAAUU@LB@3'-UUU...GCCCU AA UC U UUUUA...CAA-5'@LB@ \| \|@LB@ 62 32@LB@@LB@@LB@Energy -6.75 kcal/mol@LB@Hybridization Energy -20.0945 kcal/mol@LB@Unfolding Energy - mRNA 5.97693 kcal/mol@LB@Unfolding Energy - sRNA 7.37029 kcal/mol@LB@@LB@Position - mRNA 202 -- 229@LB@Position - sRNA 33 -- 61@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 34 -- 40@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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