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
111	0.009564	0.2693	b2040	rfbD	-5.00	0.321114	87 -- 99	24 -- 42	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________86__________________100\n_____________\|___________________\|\n5'-GAU...UUUGA___________________AAAAC...CUA-3'\n______________GAGCG______GGAUUCGU\n______________:\|\|\|:______::\|\|\|\|\|\|\n______________UUCGU______UUUAAGCA\n3'-UUU...CGUUC_____GAAUUU________AUGUG...CAA-5'\n_____________\|___________________\|\n_____________43__________________23\n	93 -- 99	24 -- 30	-9.51502 kcal/mol	2.86783 kcal/mol	1.64896 kcal/mol	86 100@LB@ \| \|@LB@5'-GAU...UUUGA AAAAC...CUA-3'@LB@ GAGCG GGAUUCGU@LB@ :\|\|\|: ::\|\|\|\|\|\|@LB@ UUCGU UUUAAGCA@LB@3'-UUU...CGUUC GAAUUU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.00 kcal/mol@LB@Hybridization Energy -9.51502 kcal/mol@LB@Unfolding Energy - mRNA 2.86783 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 87 -- 99@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 24 -- 30@LB@
112	0.009574	0.2693	b2494	bepA	-6.13	0.179960	208 -- 220	29 -- 41	OM protein maintenance and assembly metalloprotease and chaperone periplasmic	_____________207___________221\n_____________\|_____________\|\n5'-UGA...GUUCA____G________AAACC...UGC-3'\n______________GGCA_UUGAAAAA\n______________:\|\|\|_\|\|:\|\|\|\|\|\n______________UCGU_AAUUUUUU\n3'-UUU...GUUCU____G________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	214 -- 220	29 -- 35	-11.3192 kcal/mol	3.5632 kcal/mol	1.62306 kcal/mol	207 221@LB@ \| \|@LB@5'-UGA...GUUCA G AAACC...UGC-3'@LB@ GGCA UUGAAAAA@LB@ :\|\|\| \|\|:\|\|\|\|\|@LB@ UCGU AAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -6.13 kcal/mol@LB@Hybridization Energy -11.3192 kcal/mol@LB@Unfolding Energy - mRNA 3.5632 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 208 -- 220@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 29 -- 35@LB@
113	0.009602	0.2693	b3237	argR	-14.05	0.000763	205 -- 250	27 -- 60	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________204_____________________________________________251\n_____________\|_______________________________________________\|\n5'-ACA...UAUGC______CG____________AGAACUAGUUAA___________C___ACUUA...UGC-3'\n______________GAAGCU__GC_UAAGCAAGA____________AGCAUUUAAAG_AUU\n______________\|\|\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|____________\|\|\|\|:\|\|\|\|\|:_\|\|\|\n______________CUUUGA__CG_AUUCGUUCU____________UCGUGAAUUUU_UAA\n3'-UUU...CCCUA______A___A________________________________U___GCAAU...CAA-5'\n_____________\|_______________________________________________\|\n_____________61______________________________________________26\n	238 -- 244	33 -- 39	-28.1986 kcal/mol	7.87477 kcal/mol	6.27096 kcal/mol	204 251@LB@ \| \|@LB@5'-ACA...UAUGC CG AGAACUAGUUAA C ACUUA...UGC-3'@LB@ GAAGCU GC UAAGCAAGA AGCAUUUAAAG AUU@LB@ \|\|\|:\|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|: \|\|\|@LB@ CUUUGA CG AUUCGUUCU UCGUGAAUUUU UAA@LB@3'-UUU...CCCUA A A U GCAAU...CAA-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -28.1986 kcal/mol@LB@Unfolding Energy - mRNA 7.87477 kcal/mol@LB@Unfolding Energy - sRNA 6.27096 kcal/mol@LB@@LB@Position - mRNA 205 -- 250@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 33 -- 39@LB@
114	0.009652	0.2693	b2614	grpE	-8.47	0.044767	262 -- 275	27 -- 41	heat shock protein	_____________261_____________276\n_____________\|_______________\|\n5'-GAG...GGAUC_____G_________GAGGC...CUG-3'\n______________AGCAC__AAGAGAUU\n______________\|\|\|\|\|__\|\|:\|:\|\|\|\n______________UCGUG__UUUUUUAA\n3'-UUU...GUUCU_____AA________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	269 -- 275	27 -- 33	-11.1078 kcal/mol	0.992631 kcal/mol	1.6427 kcal/mol	261 276@LB@ \| \|@LB@5'-GAG...GGAUC G GAGGC...CUG-3'@LB@ AGCAC AAGAGAUU@LB@ \|\|\|\|\| \|\|:\|:\|\|\|@LB@ UCGUG UUUUUUAA@LB@3'-UUU...GUUCU AA GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -11.1078 kcal/mol@LB@Unfolding Energy - mRNA 0.992631 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 262 -- 275@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 27 -- 33@LB@
115	0.009659	0.2693	b0155	clcA	-5.80	0.214551	108 -- 124	25 -- 40	H(+)/Cl(-) exchange transporter	_____________107_______________125\n_____________\|_________________\|\n5'-AGU...UUUGU__________C___A__CUUUG...UAG-3'\n______________GCAUUUGAAA_AUU_CG\n______________\|\|\|:\|\|:\|\|\|_\|\|\|_\|\|\n______________CGUGAAUUUU_UAA_GC\n3'-UUU...UUCUU__________U______AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	109 -- 115	33 -- 39	-11.0899 kcal/mol	3.63771 kcal/mol	1.64821 kcal/mol	107 125@LB@ \| \|@LB@5'-AGU...UUUGU C A CUUUG...UAG-3'@LB@ GCAUUUGAAA AUU CG@LB@ \|\|\|:\|\|:\|\|\| \|\|\| \|\|@LB@ CGUGAAUUUU UAA GC@LB@3'-UUU...UUCUU U AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -5.80 kcal/mol@LB@Hybridization Energy -11.0899 kcal/mol@LB@Unfolding Energy - mRNA 3.63771 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 108 -- 124@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 33 -- 39@LB@
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@
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@
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@
119	0.01022	0.2766	b0123	cueO	-7.29	0.093095	47 -- 59	29 -- 41	multicopper oxidase (laccase)	_____________46____________60\n_____________\|_____________\|\n5'-CUG...UACCA__G__________GAUAA...CGU-3'\n______________GG_GCUUAAAGAA\n______________:\|_:\|\|\|\|\|\|:\|\|\n______________UC_UGAAUUUUUU\n3'-UUU...GUUCU__G__________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	53 -- 59	29 -- 35	-11.0144 kcal/mol	2.10364 kcal/mol	1.62306 kcal/mol	46 60@LB@ \| \|@LB@5'-CUG...UACCA G GAUAA...CGU-3'@LB@ GG GCUUAAAGAA@LB@ :\| :\|\|\|\|\|\|:\|\|@LB@ UC UGAAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -11.0144 kcal/mol@LB@Unfolding Energy - mRNA 2.10364 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 47 -- 59@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 29 -- 35@LB@
120	0.01039	0.2788	b2314	dedD	-6.27	0.167184	42 -- 54	45 -- 58	membrane-anchored periplasmic protein involved in septation	_____________41_____________55\n_____________\|______________\|\n5'-UUG...AGAAC______________UUUGG...AUU-3'\n______________AAC_UGCUUGAGCA\n______________\|\|\|_\|\|\|\|\|:\|\|\|\|\n______________UUG_ACGAAUUCGU\n3'-UUU...CUACU___A__________UCUUC...CAA-5'\n_____________\|______________\|\n_____________59_____________44\n	47 -- 53	46 -- 52	-15.7533 kcal/mol	3.46622 kcal/mol	6.01947 kcal/mol	41 55@LB@ \| \|@LB@5'-UUG...AGAAC UUUGG...AUU-3'@LB@ AAC UGCUUGAGCA@LB@ \|\|\| \|\|\|\|\|:\|\|\|\|@LB@ UUG ACGAAUUCGU@LB@3'-UUU...CUACU A UCUUC...CAA-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -15.7533 kcal/mol@LB@Unfolding Energy - mRNA 3.46622 kcal/mol@LB@Unfolding Energy - sRNA 6.01947 kcal/mol@LB@@LB@Position - mRNA 42 -- 54@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 46 -- 52@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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