Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
41	0.008018	0.6129	b1740	nadE	-11.27	0.022577	258 -- 272	38 -- 52	NAD synthetase NH3/glutamine-dependent	_____________257_____________273\n_____________\|_______________\|\n5'-UUC...AUGCU_________A_____CGUAG...ACC-3'\n______________GAAGAGGAA_UUCGU\n______________:\|\|\|\|\|\|\|\|_\|\|\|:\|\n______________UUUCUCCUU_AAGUA\n3'-UUU...GGCAG_________A_____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	260 -- 266	44 -- 50	-15.8385 kcal/mol	3.49717 kcal/mol	1.0693 kcal/mol	257 273@LB@ \| \|@LB@5'-UUC...AUGCU A CGUAG...ACC-3'@LB@ GAAGAGGAA UUCGU@LB@ :\|\|\|\|\|\|\|\| \|\|\|:\|@LB@ UUUCUCCUU AAGUA@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -15.8385 kcal/mol@LB@Unfolding Energy - mRNA 3.49717 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 260 -- 266@LB@Position Seed - sRNA 44 -- 50@LB@
25	0.004737	0.5992	b1093	fabG	-11.25	0.022809	188 -- 202	38 -- 52	3-oxoacyl-[acyl-carrier-protein] reductase	_____________187_____________203\n_____________\|_______________\|\n5'-UAC...CUUUA_________AA____GAAUU...UUG-3'\n______________AAAGAGGAA__UCAU\n______________\|\|\|\|\|\|\|\|\|__\|\|\|\|\n______________UUUCUCCUU__AGUA\n3'-UUU...GGCAG_________AA____AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	190 -- 196	44 -- 50	-14.2885 kcal/mol	1.96871 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-UAC...CUUUA AA GAAUU...UUG-3'@LB@ AAAGAGGAA UCAU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUUCUCCUU AGUA@LB@3'-UUU...GGCAG AA AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -14.2885 kcal/mol@LB@Unfolding Energy - mRNA 1.96871 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 44 -- 50@LB@
18	0.003456	0.593	b0867	amiD	-11.23	0.023022	276 -- 289	39 -- 52	1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein	_____________275____________290\n_____________\|______________\|\n5'-GAU...UCGAG__________A___GCUUG...CCC-3'\n______________AAAGAGGGAU_UCA\n______________\|\|\|\|\|\|\|:\|\|_\|\|\|\n______________UUUCUCCUUA_AGU\n3'-UUU...GGCAG__________A___AAAAA...ACA-5'\n_____________\|______________\|\n_____________53_____________38\n	279 -- 285	43 -- 49	-14.4178 kcal/mol	2.13665 kcal/mol	1.05043 kcal/mol	275 290@LB@ \| \|@LB@5'-GAU...UCGAG A GCUUG...CCC-3'@LB@ AAAGAGGGAU UCA@LB@ \|\|\|\|\|\|\|:\|\| \|\|\|@LB@ UUUCUCCUUA AGU@LB@3'-UUU...GGCAG A AAAAA...ACA-5'@LB@ \| \|@LB@ 53 38@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -14.4178 kcal/mol@LB@Unfolding Energy - mRNA 2.13665 kcal/mol@LB@Unfolding Energy - sRNA 1.05043 kcal/mol@LB@@LB@Position - mRNA 276 -- 289@LB@Position - sRNA 39 -- 52@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 43 -- 49@LB@
39	0.007917	0.6129	b3657	yicJ	-11.19	0.023423	220 -- 230	47 -- 57	putative transporter	_____________219_________231\n_____________\|___________\|\n5'-CAG...GUUGU___________AAAAU...UGU-3'\n______________CCGUUAAAGAG\n______________\|\|\|\|:\|\|\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	224 -- 230	47 -- 53	-15.9196 kcal/mol	1.98973 kcal/mol	2.73556 kcal/mol	219 231@LB@ \| \|@LB@5'-CAG...GUUGU AAAAU...UGU-3'@LB@ CCGUUAAAGAG@LB@ \|\|\|\|:\|\|\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -15.9196 kcal/mol@LB@Unfolding Energy - mRNA 1.98973 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 220 -- 230@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 47 -- 53@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
4	0.0002658	0.2138	b1040	csgD	-11.06	0.024985	185 -- 199	38 -- 52	csgBAC operon transcriptional regulator	_____________184_____________200\n_____________\|_______________\|\n5'-UUA...UAAAA____C__________CAUGU...CGC-3'\n______________AAAG_GGGGUUUCAU\n______________\|\|\|\|_\|\|::\|\|\|\|\|\|\n______________UUUC_CCUUAAAGUA\n3'-UUU...GGCAG____U__________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	193 -- 199	38 -- 44	-14.3947 kcal/mol	2.26766 kcal/mol	1.0693 kcal/mol	184 200@LB@ \| \|@LB@5'-UUA...UAAAA C CAUGU...CGC-3'@LB@ AAAG GGGGUUUCAU@LB@ \|\|\|\| \|\|::\|\|\|\|\|\|@LB@ UUUC CCUUAAAGUA@LB@3'-UUU...GGCAG U AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -14.3947 kcal/mol@LB@Unfolding Energy - mRNA 2.26766 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 185 -- 199@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 38 -- 44@LB@
28	0.005242	0.6024	b0785	moaE	-11.01	0.025514	211 -- 232	52 -- 74	molybdopterin synthase large subunit	_____________210_____________________233\n_____________\|_______________________\|\n5'-AGA...AGAAA____A__________________GCCGU...CCU-3'\n______________CCAA_AUUGUUGUUGGUCCG_CA\n______________\|\|\|\|_\|\|:\|:\|:\|\|\|\|:\|\|\|_\|\|\n______________GGUU_UAGCGAUAACCGGGC_GU\n3'-UUU...UUACC____A_______________A__UUCUC...ACA-5'\n_____________\|_______________________\|\n_____________75______________________51\n	216 -- 222	63 -- 69	-28.4518 kcal/mol	6.10798 kcal/mol	11.3304 kcal/mol	210 233@LB@ \| \|@LB@5'-AGA...AGAAA A GCCGU...CCU-3'@LB@ CCAA AUUGUUGUUGGUCCG CA@LB@ \|\|\|\| \|\|:\|:\|:\|\|\|\|:\|\|\| \|\|@LB@ GGUU UAGCGAUAACCGGGC GU@LB@3'-UUU...UUACC A A UUCUC...ACA-5'@LB@ \| \|@LB@ 75 51@LB@@LB@@LB@Energy -11.01 kcal/mol@LB@Hybridization Energy -28.4518 kcal/mol@LB@Unfolding Energy - mRNA 6.10798 kcal/mol@LB@Unfolding Energy - sRNA 11.3304 kcal/mol@LB@@LB@Position - mRNA 211 -- 232@LB@Position - sRNA 52 -- 74@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 63 -- 69@LB@
182	0.03771	0.6177	b0397	sbcC	-11.00	0.025718	84 -- 100	39 -- 56	exonuclease dsDNA ATP-dependent	_____________83_________________101\n_____________\|__________________\|\n5'-GAA...CUCAG___________UG_____AUCGC...UUG-3'\n______________CGUCGAAGAGG___UUCA\n______________\|\|\|\|:\|\|\|\|\|\|___\|\|\|\|\n______________GCAGUUUCUCC___AAGU\n3'-UUU...ACCGG___________UUA____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	88 -- 94	46 -- 52	-19.0672 kcal/mol	6.9127 kcal/mol	1.15786 kcal/mol	83 101@LB@ \| \|@LB@5'-GAA...CUCAG UG AUCGC...UUG-3'@LB@ CGUCGAAGAGG UUCA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ GCAGUUUCUCC AAGU@LB@3'-UUU...ACCGG UUA AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0672 kcal/mol@LB@Unfolding Energy - mRNA 6.9127 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 84 -- 100@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 46 -- 52@LB@
87	0.01794	0.6177	b3499	rlmJ	-10.99	0.025859	12 -- 21	46 -- 55	23S rRNA m(6)A2030 methyltransferase SAM-dependent	_____________11_________22\n_____________\|__________\|\n5'-GCG...UCCUG__________UUAAG...AUA-3'\n______________GUUAAAGAGG\n______________\|\|:\|\|\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	15 -- 21	46 -- 52	-14.3615 kcal/mol	2.45195 kcal/mol	0.924411 kcal/mol	11 22@LB@ \| \|@LB@5'-GCG...UCCUG UUAAG...AUA-3'@LB@ GUUAAAGAGG@LB@ \|\|:\|\|\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -14.3615 kcal/mol@LB@Unfolding Energy - mRNA 2.45195 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 46 -- 52@LB@
14	0.003078	0.593	b0886	cydC	-10.90	0.026971	183 -- 199	39 -- 56	glutathione/cysteine ABC transporter export permease/ATPase	_____________182________________200\n_____________\|__________________\|\n5'-GCG...CCCAU_____________A____AAUGC...UCG-3'\n______________CGUC_AGGAGGAG_UUUA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|:\|\n______________GCAG_UUCUCCUU_AAGU\n3'-UUU...ACCGG____U________A____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	188 -- 194	44 -- 50	-16.2318 kcal/mol	4.17801 kcal/mol	1.15786 kcal/mol	182 200@LB@ \| \|@LB@5'-GCG...CCCAU A AAUGC...UCG-3'@LB@ CGUC AGGAGGAG UUUA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|:\|@LB@ GCAG UUCUCCUU AAGU@LB@3'-UUU...ACCGG U A AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -10.90 kcal/mol@LB@Hybridization Energy -16.2318 kcal/mol@LB@Unfolding Energy - mRNA 4.17801 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 183 -- 199@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@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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