Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
14	0.0004057	0.09812	b0886	cydC	-15.95	0.010534	194 -- 211	2 -- 21	glutathione/cysteine ABC transporter export permease/ATPase		_____________193__________________212\n_____________\|____________________\|\n5'-GCG...GAGGA___U________________GCUAC...UCG-3'\n______________GAU__UAAAUGCGCG_CUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUA__GUUUACGCGC_GAAA\n3'-UUU...UACUA___UU__________A____G-5'\n_____________\|____________________\|\n_____________22___________________1\n	201 -- 207	7 -- 13	-19.6155 kcal/mol	2.41081 kcal/mol	1.25756 kcal/mol	193 212@LB@ \| \|@LB@5'-GCG...GAGGA U GCUAC...UCG-3'@LB@ GAU UAAAUGCGCG CUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUA GUUUACGCGC GAAA@LB@3'-UUU...UACUA UU A G-5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -19.6155 kcal/mol@LB@Unfolding Energy - mRNA 2.41081 kcal/mol@LB@Unfolding Energy - sRNA 1.25756 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 2 -- 21@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
76	0.007084	0.3087	b4214	cysQ	-5.34	0.578728	11 -- 17	26 -- 32	3'(2') 5'-bisphosphate nucleotidase		_____________10______18\n_____________\|_______\|\n5'-AAC...AAUCA_______CAUCC...ACA-3'\n______________UCAGGGA\n______________\|\|\|\|\|\|\|\n______________AGUCCCU\n3'-UUU...ACUUA_______ACUAC...AAG-5'\n_____________\|_______\|\n_____________33______25\n	11 -- 17	26 -- 32	-11.6237 kcal/mol	0.931861 kcal/mol	5.35475 kcal/mol	10 18@LB@ \| \|@LB@5'-AAC...AAUCA CAUCC...ACA-3'@LB@ UCAGGGA@LB@ \|\|\|\|\|\|\|@LB@ AGUCCCU@LB@3'-UUU...ACUUA ACUAC...AAG-5'@LB@ \| \|@LB@ 33 25@LB@@LB@@LB@Energy -5.34 kcal/mol@LB@Hybridization Energy -11.6237 kcal/mol@LB@Unfolding Energy - mRNA 0.931861 kcal/mol@LB@Unfolding Energy - sRNA 5.35475 kcal/mol@LB@@LB@Position - mRNA 11 -- 17@LB@Position - sRNA 26 -- 32@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 26 -- 32@LB@
82	0.007621	0.3104	b3388	damX	-7.48	0.304490	3 -- 13	8 -- 18	cell division protein that binds to the septal ring		_____________2___________14\n_____________\|___________\|\n_________5'-GG__G________UUAAU...AAC-3'\n______________GA_AGAUGCGC\n______________:\|_\|:\|\|\|\|\|\|\n______________UU_UUUACGCG\n3'-UUU...UACUA__G________CAGAAAG-5'\n_____________\|___________\|\n_____________19__________7\n	7 -- 13	8 -- 14	-13.7317 kcal/mol	5.04786 kcal/mol	1.20363 kcal/mol	2 14@LB@ \| \|@LB@ 5'-GG G UUAAU...AAC-3'@LB@ GA AGAUGCGC@LB@ :\| \|:\|\|\|\|\|\|@LB@ UU UUUACGCG@LB@3'-UUU...UACUA G CAGAAAG-5'@LB@ \| \|@LB@ 19 7@LB@@LB@@LB@Energy -7.48 kcal/mol@LB@Hybridization Energy -13.7317 kcal/mol@LB@Unfolding Energy - mRNA 5.04786 kcal/mol@LB@Unfolding Energy - sRNA 1.20363 kcal/mol@LB@@LB@Position - mRNA 3 -- 13@LB@Position - sRNA 8 -- 18@LB@Position Seed - mRNA 7 -- 13@LB@Position Seed - sRNA 8 -- 14@LB@
119	0.01215	0.3104	b3691	dgoT	-8.17	0.239341	58 -- 68	8 -- 21	D-galactonate transporter		_____________57_____________69\n_____________\|______________\|\n5'-GUG...AUGAA______________AGCAG...CCA-3'\n______________GAUAACA___GCGU\n______________\|\|\|\|\|\|\|___\|\|\|:\n______________CUAUUGU___CGCG\n3'-UUU...UACUA_______UUA____CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	58 -- 64	15 -- 21	-12.2033 kcal/mol	2.79285 kcal/mol	1.23638 kcal/mol	57 69@LB@ \| \|@LB@5'-GUG...AUGAA AGCAG...CCA-3'@LB@ GAUAACA GCGU@LB@ \|\|\|\|\|\|\| \|\|\|:@LB@ CUAUUGU CGCG@LB@3'-UUU...UACUA UUA CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -12.2033 kcal/mol@LB@Unfolding Energy - mRNA 2.79285 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 58 -- 68@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
173	0.0173	0.3104	b0145	dksA	-10.49	0.099910	175 -- 187	5 -- 21	transcriptional regulator of rRNA transcription; DnaK suppressor protein		_____________174_______________188\n_____________\|_________________\|\n5'-AAU...GGAUC_________________AAGGA...AUG-3'\n______________GAUA____GUGCGUGUU\n______________\|\|\|\|____:\|\|\|\|:\|\|:\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	181 -- 187	5 -- 11	-14.603 kcal/mol	2.85898 kcal/mol	1.24955 kcal/mol	174 188@LB@ \| \|@LB@5'-AAU...GGAUC AAGGA...AUG-3'@LB@ GAUA GUGCGUGUU@LB@ \|\|\|\| :\|\|\|\|:\|\|:@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -14.603 kcal/mol@LB@Unfolding Energy - mRNA 2.85898 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 175 -- 187@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 5 -- 11@LB@
40	0.002726	0.2279	b1799	dmlR	-13.48	0.029707	223 -- 239	2 -- 20	transcriptional activator of dmlA	b3060	_____________222_________________240\n_____________\|___________________\|\n5'-CGC...GCUGA_____U_____________AUGCU...CGG-3'\n______________AUGAU___UGCGCGUCUUU\n______________\|\|:\|:___\|\|\|\|\|\|\|\|\|\|\|\n______________UAUUG___ACGCGCAGAAA\n3'-UUU...ACUAC_____UUU___________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	233 -- 239	2 -- 8	-19.9945 kcal/mol	5.2543 kcal/mol	1.25604 kcal/mol	222 240@LB@ \| \|@LB@5'-CGC...GCUGA U AUGCU...CGG-3'@LB@ AUGAU UGCGCGUCUUU@LB@ \|\|:\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ UAUUG ACGCGCAGAAA@LB@3'-UUU...ACUAC UUU G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.9945 kcal/mol@LB@Unfolding Energy - mRNA 5.2543 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 223 -- 239@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 2 -- 8@LB@
130	0.01263	0.3104	b1952	dsrB	-7.17	0.338083	230 -- 240	7 -- 18	uncharacterized protein		_____________229__________241\n_____________\|____________\|\n5'-CGU...GUCAA____________GUCCG...ACC-3'\n______________AACGGAUG_GCG\n______________\|\|\|::\|\|\|_\|\|\|\n______________UUGUUUAC_CGC\n3'-UUU...UACUA________G___AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	231 -- 237	11 -- 17	-11.9456 kcal/mol	3.57064 kcal/mol	1.20891 kcal/mol	229 241@LB@ \| \|@LB@5'-CGU...GUCAA GUCCG...ACC-3'@LB@ AACGGAUG GCG@LB@ \|\|\|::\|\|\| \|\|\|@LB@ UUGUUUAC CGC@LB@3'-UUU...UACUA G AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -7.17 kcal/mol@LB@Hybridization Energy -11.9456 kcal/mol@LB@Unfolding Energy - mRNA 3.57064 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 230 -- 240@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 11 -- 17@LB@
15	0.000461	0.102	b2140	dusC	-12.07	0.053129	194 -- 211	3 -- 22	tRNA-dihydrouridine synthase C		_____________193__________________212\n_____________\|____________________\|\n5'-AAU...GCGGG_________________G__ACUGG...UUG-3'\n______________UGAUGAU__AUGCGUGU_UU\n______________\|\|\|\|:\|:__\|\|\|\|\|:\|\|_\|\|\n______________ACUAUUG__UACGCGCA_AA\n3'-UUU...CUACU_______UU________G__AG-5'\n_____________\|____________________\|\n_____________23___________________2\n	202 -- 208	6 -- 12	-18.0697 kcal/mol	4.73944 kcal/mol	1.259 kcal/mol	193 212@LB@ \| \|@LB@5'-AAU...GCGGG G ACUGG...UUG-3'@LB@ UGAUGAU AUGCGUGU UU@LB@ \|\|\|\|:\|: \|\|\|\|\|:\|\| \|\|@LB@ ACUAUUG UACGCGCA AA@LB@3'-UUU...CUACU UU G AG-5'@LB@ \| \|@LB@ 23 2@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -18.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.73944 kcal/mol@LB@Unfolding Energy - sRNA 1.259 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 3 -- 22@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
121	0.01226	0.3104	b3209	elbB	-12.57	0.043302	225 -- 240	4 -- 18	isoprenoid biosynthesis protein with amidotransferase-like domain		_____________224______________241\n_____________\|________________\|\n5'-GCG...UUCUG__________G_____AUGAC...GUG-3'\n______________AGCGGAUGCG_CGUCU\n______________\|:\|::\|\|\|\|\|_\|\|\|\|\|\n______________UUGUUUACGC_GCAGA\n3'-UUU...UACUA________________AAG-5'\n_____________\|________________\|\n_____________19_______________3\n	228 -- 234	9 -- 15	-20.315 kcal/mol	6.5132 kcal/mol	1.22995 kcal/mol	224 241@LB@ \| \|@LB@5'-GCG...UUCUG G AUGAC...GUG-3'@LB@ AGCGGAUGCG CGUCU@LB@ \|:\|::\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUUACGC GCAGA@LB@3'-UUU...UACUA AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -20.315 kcal/mol@LB@Unfolding Energy - mRNA 6.5132 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 9 -- 15@LB@
96	0.009671	0.3104	b0941	elfG	-12.70	0.041082	222 -- 232	5 -- 15	putative fimbrial-like adhesin protein	b3145 b0533	_____________221_________233\n_____________\|___________\|\n5'-UUU...GAGAA___________AUUAC...GGC-3'\n______________AAAUGCGUGUC\n______________\|\|\|\|\|\|\|:\|\|\|\n______________UUUACGCGCAG\n3'-UUU...UAUUG___________AAAG-5'\n_____________\|___________\|\n_____________16__________4\n	226 -- 232	5 -- 11	-17.0283 kcal/mol	3.13128 kcal/mol	1.19708 kcal/mol	221 233@LB@ \| \|@LB@5'-UUU...GAGAA AUUAC...GGC-3'@LB@ AAAUGCGUGUC@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ UUUACGCGCAG@LB@3'-UUU...UAUUG AAAG-5'@LB@ \| \|@LB@ 16 4@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -17.0283 kcal/mol@LB@Unfolding Energy - mRNA 3.13128 kcal/mol@LB@Unfolding Energy - sRNA 1.19708 kcal/mol@LB@@LB@Position - mRNA 222 -- 232@LB@Position - sRNA 5 -- 15@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 5 -- 11@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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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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