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	Additional homologs
61	0.003184	0.1645	b4112	basS	-6.79	0.124428	7 -- 41	10 -- 54	sensory histidine kinase in two-component regulatory system with BasR		_____________6______________________________________________42\n_____________\|______________________________________________\|\n_____5'-GGUUAA____CA_______C___C_____________GU_____________CUCUA...UAU-3'\n______________UGCU__AAGCAGG_AGU____________CG__GCAUCGGGAAAUU\n______________\|\|\|\|__\|\|\|\|\|:\|_\|\|:____________\|\|__:\|\|:\|:\|\|\|\|\|\|:\n______________ACGA__UUCGUUC_UCG____________GC__UGUGGUCCUUUAG\n3'-UUU...UUUGA____A________U___UGAAUUUUUUAA__AA_____________ACUAC...CAA-5'\n_____________\|______________________________________________\|\n_____________55_____________________________________________9\n	35 -- 41	10 -- 16	-31.3926 kcal/mol	10.7631 kcal/mol	13.8372 kcal/mol	6 42@LB@ \| \|@LB@ 5'-GGUUAA CA C C GU CUCUA...UAU-3'@LB@ UGCU AAGCAGG AGU CG GCAUCGGGAAAUU@LB@ \|\|\|\| \|\|\|\|\|:\| \|\|: \|\| :\|\|:\|:\|\|\|\|\|\|:@LB@ ACGA UUCGUUC UCG GC UGUGGUCCUUUAG@LB@3'-UUU...UUUGA A U UGAAUUUUUUAA AA ACUAC...CAA-5'@LB@ \| \|@LB@ 55 9@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -31.3926 kcal/mol@LB@Unfolding Energy - mRNA 10.7631 kcal/mol@LB@Unfolding Energy - sRNA 13.8372 kcal/mol@LB@@LB@Position - mRNA 7 -- 41@LB@Position - sRNA 10 -- 54@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 10 -- 16@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@
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@
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@
66	0.003432	0.1645	b0882	clpA	-7.45	0.084488	282 -- 290	34 -- 42	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________281_______291\n_____________\|_________\|\n5'-UUU...CCGUC_________UUACU...CGC-3'\n______________GAGCACUUG\n______________:\|\|\|\|\|\|\|:\n______________UUCGUGAAU\n3'-UUU...CGUUC_________UUUUU...CAA-5'\n_____________\|_________\|\n_____________43________33\n	284 -- 290	34 -- 40	-10.5586 kcal/mol	1.49281 kcal/mol	1.61613 kcal/mol	281 291@LB@ \| \|@LB@5'-UUU...CCGUC UUACU...CGC-3'@LB@ GAGCACUUG@LB@ :\|\|\|\|\|\|\|:@LB@ UUCGUGAAU@LB@3'-UUU...CGUUC UUUUU...CAA-5'@LB@ \| \|@LB@ 43 33@LB@@LB@@LB@Energy -7.45 kcal/mol@LB@Hybridization Energy -10.5586 kcal/mol@LB@Unfolding Energy - mRNA 1.49281 kcal/mol@LB@Unfolding Energy - sRNA 1.61613 kcal/mol@LB@@LB@Position - mRNA 282 -- 290@LB@Position - sRNA 34 -- 42@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 34 -- 40@LB@
172	0.01959	0.3668	b0336	codB	-6.02	0.190787	88 -- 108	28 -- 40	cytosine transporter		_____________87____________________109\n_____________\|_____________________\|\n5'-CCA...UUUUU_____CAUUCAUA________AUAUU...UUU-3'\n______________GCACU________UAAAAAAU\n______________\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________CGUGA________AUUUUUUA\n3'-UUU...UUCUU_____________________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________41____________________27\n	102 -- 108	28 -- 34	-8.50412 kcal/mol	0.843154 kcal/mol	1.63611 kcal/mol	87 109@LB@ \| \|@LB@5'-CCA...UUUUU CAUUCAUA AUAUU...UUU-3'@LB@ GCACU UAAAAAAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CGUGA AUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -8.50412 kcal/mol@LB@Unfolding Energy - mRNA 0.843154 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 28 -- 34@LB@
45	0.001912	0.1369	b0080	cra	-5.81	0.213706	183 -- 197	38 -- 52	transcriptional repressor-activator for carbon metabolism		_____________182_____________198\n_____________\|_______________\|\n5'-GGC...UACAU____C__________AUUGU...AAA-3'\n______________UUUA_GCAAGGGGCA\n______________:\|\|\|_\|\|\|\|\|::\|\|\|\n______________GAAU_CGUUCUUCGU\n3'-UUU...UGAAC____U__________GAAUU...CAA-5'\n_____________\|_______________\|\n_____________53______________37\n	191 -- 197	38 -- 44	-16.0644 kcal/mol	4.16124 kcal/mol	6.09169 kcal/mol	182 198@LB@ \| \|@LB@5'-GGC...UACAU C AUUGU...AAA-3'@LB@ UUUA GCAAGGGGCA@LB@ :\|\|\| \|\|\|\|\|::\|\|\|@LB@ GAAU CGUUCUUCGU@LB@3'-UUU...UGAAC U GAAUU...CAA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -5.81 kcal/mol@LB@Hybridization Energy -16.0644 kcal/mol@LB@Unfolding Energy - mRNA 4.16124 kcal/mol@LB@Unfolding Energy - sRNA 6.09169 kcal/mol@LB@@LB@Position - mRNA 183 -- 197@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 38 -- 44@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@
69	0.00357	0.1645	b0571	cusR	-5.90	0.203942	86 -- 99	6 -- 21	response regulator in two-component regulatory system with CusS	b1969	_____________85_______________100\n_____________\|________________\|\n5'-AGC...UUACU_______C________UUUCC...GGC-3'\n______________CGCCAGG___UCUGAU\n______________\|:\|\|\|\|\|___\|\|\|\|\|\|\n______________GUGGUCC___AGACUA\n3'-UUU...GCAAU_______UUU______CACAA-5'\n_____________\|________________\|\n_____________22_______________5\n	86 -- 92	15 -- 21	-18.4182 kcal/mol	4.95815 kcal/mol	7.56001 kcal/mol	85 100@LB@ \| \|@LB@5'-AGC...UUACU C UUUCC...GGC-3'@LB@ CGCCAGG UCUGAU@LB@ \|:\|\|\|\|\| \|\|\|\|\|\|@LB@ GUGGUCC AGACUA@LB@3'-UUU...GCAAU UUU CACAA-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -5.90 kcal/mol@LB@Hybridization Energy -18.4182 kcal/mol@LB@Unfolding Energy - mRNA 4.95815 kcal/mol@LB@Unfolding Energy - sRNA 7.56001 kcal/mol@LB@@LB@Position - mRNA 86 -- 99@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 15 -- 21@LB@
182	0.02157	0.3768	b0887	cydD	-7.84	0.066788	30 -- 38	33 -- 41	glutathione/cysteine ABC transporter export permease/ATPase		_____________29________39\n_____________\|_________\|\n5'-AUU...AUGGC_________UGCGG...UGA-3'\n______________AGCACUUGA\n______________\|\|\|\|\|\|\|:\|\n______________UCGUGAAUU\n3'-UUU...GUUCU_________UUUUA...CAA-5'\n_____________\|_________\|\n_____________42________32\n	32 -- 38	33 -- 39	-10.6359 kcal/mol	1.18174 kcal/mol	1.6188 kcal/mol	29 39@LB@ \| \|@LB@5'-AUU...AUGGC UGCGG...UGA-3'@LB@ AGCACUUGA@LB@ \|\|\|\|\|\|\|:\|@LB@ UCGUGAAUU@LB@3'-UUU...GUUCU UUUUA...CAA-5'@LB@ \| \|@LB@ 42 32@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -10.6359 kcal/mol@LB@Unfolding Energy - mRNA 1.18174 kcal/mol@LB@Unfolding Energy - sRNA 1.6188 kcal/mol@LB@@LB@Position - mRNA 30 -- 38@LB@Position - sRNA 33 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 33 -- 39@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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service.

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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