Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
194	0.008663	0.1558	b0213	yafS	-5.39	0.521143	17 -- 34	51 -- 73	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________16______________________35\n_____________\|_______________________\|\n5'-UGG...GGUGA_______________________GCCAG...UCA-3'\n______________GAAAUAU__GGCC___UCCGGUU\n______________:\|\|\|\|\|\|__:\|\|\|___\|\|\|\|:\|\|\n______________UUUUAUA__UCGG___AGGCUAA\n3'-AUU...GCCGA_______AG____UUU_______UGCAC...AUG-5'\n_____________\|_______________________\|\n_____________74______________________50\n	28 -- 34	51 -- 57	-15.2768 kcal/mol	3.69768 kcal/mol	6.213 kcal/mol	16 35@LB@ \| \|@LB@5'-UGG...GGUGA GCCAG...UCA-3'@LB@ GAAAUAU GGCC UCCGGUU@LB@ :\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|\|@LB@ UUUUAUA UCGG AGGCUAA@LB@3'-AUU...GCCGA AG UUU UGCAC...AUG-5'@LB@ \| \|@LB@ 74 50@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.2768 kcal/mol@LB@Unfolding Energy - mRNA 3.69768 kcal/mol@LB@Unfolding Energy - sRNA 6.213 kcal/mol@LB@@LB@Position - mRNA 17 -- 34@LB@Position - sRNA 51 -- 73@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
3	0	0	b2564	pdxJ	-5.03	0.588876	273 -- 283	52 -- 62	pyridoxine 5'-phosphate synthase	_____________272_________284\n_____________\|___________\|\n5'-AAA...CUUAC___________GCAGG...UUG-3'\n______________CCGGAUCCGGU\n______________\|\|::\|\|\|\|\|:\|\n______________GGUUUAGGCUA\n3'-AUU...AAGUC___________AUGCA...AUG-5'\n_____________\|___________\|\n_____________63__________51\n	277 -- 283	52 -- 58	-14.6263 kcal/mol	4.30712 kcal/mol	5.31395 kcal/mol	272 284@LB@ \| \|@LB@5'-AAA...CUUAC GCAGG...UUG-3'@LB@ CCGGAUCCGGU@LB@ \|\|::\|\|\|\|\|:\|@LB@ GGUUUAGGCUA@LB@3'-AUU...AAGUC AUGCA...AUG-5'@LB@ \| \|@LB@ 63 51@LB@@LB@@LB@Energy -5.03 kcal/mol@LB@Hybridization Energy -14.6263 kcal/mol@LB@Unfolding Energy - mRNA 4.30712 kcal/mol@LB@Unfolding Energy - sRNA 5.31395 kcal/mol@LB@@LB@Position - mRNA 273 -- 283@LB@Position - sRNA 52 -- 62@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 52 -- 58@LB@
18	6.719e-05	0.01313	b2935	tktA	-10.85	0.025018	263 -- 275	52 -- 64	transketolase 1 thiamine triphosphate-binding	_____________262___________276\n_____________\|_____________\|\n5'-AAG...CAGAA_____________CACCC...UGG-3'\n______________AGCCAAAUCCGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|\n______________UCGGUUUAGGCUA\n3'-AUU...AUAAG_____________AUGCA...AUG-5'\n_____________\|_____________\|\n_____________65____________51\n	269 -- 275	52 -- 58	-21.1603 kcal/mol	4.16811 kcal/mol	6.16128 kcal/mol	262 276@LB@ \| \|@LB@5'-AAG...CAGAA CACCC...UGG-3'@LB@ AGCCAAAUCCGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|@LB@ UCGGUUUAGGCUA@LB@3'-AUU...AUAAG AUGCA...AUG-5'@LB@ \| \|@LB@ 65 51@LB@@LB@@LB@Energy -10.85 kcal/mol@LB@Hybridization Energy -21.1603 kcal/mol@LB@Unfolding Energy - mRNA 4.16811 kcal/mol@LB@Unfolding Energy - sRNA 6.16128 kcal/mol@LB@@LB@Position - mRNA 263 -- 275@LB@Position - sRNA 52 -- 64@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 52 -- 58@LB@
57	0.0008523	0.0526	b3281	aroE	-7.63	0.189523	225 -- 232	52 -- 59	dehydroshikimate reductase NAD(P)-binding	_____________224______233\n_____________\|________\|\n5'-UUU...UUGGU________AGCCC...AUG-3'\n______________AAUCCGAU\n______________\|\|\|\|\|\|\|\|\n______________UUAGGCUA\n3'-AUU...UCGGU________AUGCA...AUG-5'\n_____________\|________\|\n_____________60_______51\n	226 -- 232	52 -- 58	-9.52512 kcal/mol	1.61129 kcal/mol	0.296943 kcal/mol	224 233@LB@ \| \|@LB@5'-UUU...UUGGU AGCCC...AUG-3'@LB@ AAUCCGAU@LB@ \|\|\|\|\|\|\|\|@LB@ UUAGGCUA@LB@3'-AUU...UCGGU AUGCA...AUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -9.52512 kcal/mol@LB@Unfolding Energy - mRNA 1.61129 kcal/mol@LB@Unfolding Energy - sRNA 0.296943 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 52 -- 58@LB@
127	0.004255	0.1179	b2838	lysA	-9.87	0.049362	214 -- 233	52 -- 69	diaminopimelate decarboxylase PLP-binding	_____________213__________________234\n_____________\|____________________\|\n5'-GGU...UUCAC________A_C___A_____CUCAC...CGC-3'\n______________UGUUCAGC_C_GAU_CCGAU\n______________\|:\|\|\|\|\|\|_\|_:\|\|_\|\|\|\|\|\n______________AUAAGUCG_G_UUA_GGCUA\n3'-AUU...AUUUU__________U_________AUGCA...AUG-5'\n_____________\|____________________\|\n_____________70___________________51\n	215 -- 221	62 -- 68	-18.1264 kcal/mol	2.0842 kcal/mol	6.19243 kcal/mol	213 234@LB@ \| \|@LB@5'-GGU...UUCAC A C A CUCAC...CGC-3'@LB@ UGUUCAGC C GAU CCGAU@LB@ \|:\|\|\|\|\|\| \| :\|\| \|\|\|\|\|@LB@ AUAAGUCG G UUA GGCUA@LB@3'-AUU...AUUUU U AUGCA...AUG-5'@LB@ \| \|@LB@ 70 51@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -18.1264 kcal/mol@LB@Unfolding Energy - mRNA 2.0842 kcal/mol@LB@Unfolding Energy - sRNA 6.19243 kcal/mol@LB@@LB@Position - mRNA 214 -- 233@LB@Position - sRNA 52 -- 69@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 62 -- 68@LB@
130	0.004431	0.1199	b3355	prkB	-7.29	0.227256	214 -- 220	52 -- 58	putative phosphoribulokinase	_____________213_____221\n_____________\|_______\|\n5'-GGC...CAAAC_______CAUUG...AUC-3'\n______________AUCCGGU\n______________\|\|\|\|\|:\|\n______________UAGGCUA\n3'-AUU...CGGUU_______AUGCA...AUG-5'\n_____________\|_______\|\n_____________59______51\n	214 -- 220	52 -- 58	-8.26146 kcal/mol	0.695321 kcal/mol	0.296688 kcal/mol	213 221@LB@ \| \|@LB@5'-GGC...CAAAC CAUUG...AUC-3'@LB@ AUCCGGU@LB@ \|\|\|\|\|:\|@LB@ UAGGCUA@LB@3'-AUU...CGGUU AUGCA...AUG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -8.26146 kcal/mol@LB@Unfolding Energy - mRNA 0.695321 kcal/mol@LB@Unfolding Energy - sRNA 0.296688 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 52 -- 58@LB@
142	0.005204	0.1284	b3931	hslU	-6.88	0.277791	3 -- 17	52 -- 65	molecular chaperone and ATPase component of HslUV protease	_____________2_______________18\n_____________\|_______________\|\n_________5'-UG________AAA____CUUAU...ACC-3'\n______________CAGCCAGA___CGAU\n______________\|\|\|\|\|\|:\|___\|\|\|\|\n______________GUCGGUUU___GCUA\n3'-AUU...UAUAA________AG_____AUGCA...AUG-5'\n_____________\|_______________\|\n_____________66______________51\n	4 -- 10	58 -- 64	-14.8174 kcal/mol	1.78514 kcal/mol	6.17277 kcal/mol	2 18@LB@ \| \|@LB@ 5'-UG AAA CUUAU...ACC-3'@LB@ CAGCCAGA CGAU@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ GUCGGUUU GCUA@LB@3'-AUU...UAUAA AG AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -6.88 kcal/mol@LB@Hybridization Energy -14.8174 kcal/mol@LB@Unfolding Energy - mRNA 1.78514 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 3 -- 17@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 58 -- 64@LB@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent	______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
188	0.008316	0.1556	b3406	greB	-8.11	0.146040	42 -- 55	52 -- 65	transcript cleavage factor	_____________41_____________56\n_____________\|______________\|\n5'-AUU...GUCAC______________AUGAA...UGA-3'\n______________CAGCUAAAUCUGGU\n______________\|\|\|\|:\|\|\|\|\|:\|:\|\n______________GUCGGUUUAGGCUA\n3'-AUU...UAUAA______________AUGCA...AUG-5'\n_____________\|______________\|\n_____________66_____________51\n	49 -- 55	52 -- 58	-18.5321 kcal/mol	4.27254 kcal/mol	6.17277 kcal/mol	41 56@LB@ \| \|@LB@5'-AUU...GUCAC AUGAA...UGA-3'@LB@ CAGCUAAAUCUGGU@LB@ \|\|\|\|:\|\|\|\|\|:\|:\|@LB@ GUCGGUUUAGGCUA@LB@3'-AUU...UAUAA AUGCA...AUG-5'@LB@ \| \|@LB@ 66 51@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -18.5321 kcal/mol@LB@Unfolding Energy - mRNA 4.27254 kcal/mol@LB@Unfolding Energy - sRNA 6.17277 kcal/mol@LB@@LB@Position - mRNA 42 -- 55@LB@Position - sRNA 52 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 52 -- 58@LB@
197	0.00873	0.1558	b2324	mnmC	-9.11	0.080832	111 -- 120	52 -- 61	fused 5-methylaminomethyl-2-thiouridine-forming enzyme methyltransferase and FAD-dependent demodification enzyme	_____________110________121\n_____________\|__________\|\n5'-GCU...CCGAA__________CAGCC...ACG-3'\n______________CAAGUCCGAU\n______________\|\|\|:\|\|\|\|\|\|\n______________GUUUAGGCUA\n3'-AUU...AGUCG__________AUGCA...AUG-5'\n_____________\|__________\|\n_____________62_________51\n	114 -- 120	52 -- 58	-12.6788 kcal/mol	1.38997 kcal/mol	2.20422 kcal/mol	110 121@LB@ \| \|@LB@5'-GCU...CCGAA CAGCC...ACG-3'@LB@ CAAGUCCGAU@LB@ \|\|\|:\|\|\|\|\|\|@LB@ GUUUAGGCUA@LB@3'-AUU...AGUCG AUGCA...AUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -12.6788 kcal/mol@LB@Unfolding Energy - mRNA 1.38997 kcal/mol@LB@Unfolding Energy - sRNA 2.20422 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 52 -- 58@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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