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
164	0.006623	0.1421	b2278	nuoL	-8.77	0.099276	203 -- 221	5 -- 24	NADH:ubiquinone oxidoreductase membrane subunit L	_____________202___________________222\n_____________\|_____________________\|\n5'-GGU...CGGAU______G________A_____AUUAU...UCG-3'\n______________GAACAU_CUUGCCUU___ACC\n______________\|\|\|\|\|\|_\|\|\|:\|\|\|:___\|\|\|\n______________CUUGUA_GAAUGGAG___UGG\n3'-AUU...UCUAU_______________ACA___GAUG-5'\n_____________\|_____________________\|\n_____________25____________________4\n	211 -- 217	11 -- 17	-20.7037 kcal/mol	3.94864 kcal/mol	8.01095 kcal/mol	202 222@LB@ \| \|@LB@5'-GGU...CGGAU G A AUUAU...UCG-3'@LB@ GAACAU CUUGCCUU ACC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|: \|\|\|@LB@ CUUGUA GAAUGGAG UGG@LB@3'-AUU...UCUAU ACA GAUG-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -20.7037 kcal/mol@LB@Unfolding Energy - mRNA 3.94864 kcal/mol@LB@Unfolding Energy - sRNA 8.01095 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase	_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@LB@
4	8.02e-06	0.007054	b0425	panE	-14.83	0.000836	22 -- 49	1 -- 32	2-dehydropantoate reductase NADPH-specific	_____________21________________________________50\n_____________\|_________________________________\|\n5'-AUC...AUAUC_________________UU____________U_AUUUU...CGC-3'\n______________GAAAGAUGG__CAUCUU__CCUCU___CCCU_C\n______________\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|__\|\|\|\|\|___\|\|\|\|_\|\n______________CUUUCUAUC__GUAGAA__GGAGA___GGGA_G\n3'-AUU...CCAGA_________UU______U______CAU____U_-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	24 -- 30	24 -- 30	-28.6113 kcal/mol	4.98037 kcal/mol	8.82471 kcal/mol	21 50@LB@ \| \|@LB@5'-AUC...AUAUC UU U AUUUU...CGC-3'@LB@ GAAAGAUGG CAUCUU CCUCU CCCU C@LB@ \|\|\|\|\|\|\|:\| \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|@LB@ CUUUCUAUC GUAGAA GGAGA GGGA G@LB@3'-AUU...CCAGA UU U CAU U -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -28.6113 kcal/mol@LB@Unfolding Energy - mRNA 4.98037 kcal/mol@LB@Unfolding Energy - sRNA 8.82471 kcal/mol@LB@@LB@Position - mRNA 22 -- 49@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 24 -- 30@LB@
153	0.006198	0.1406	b3459	panM	-8.50	0.116540	144 -- 151	50 -- 57	PanD autocleavage accelerator panothenate synthesis	_____________143______152\n_____________\|________\|\n5'-AAA...AAGCC________AAUUA...UUG-3'\n______________UCCGAUUA\n______________\|\|\|\|\|\|\|\|\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	145 -- 151	50 -- 56	-10.246 kcal/mol	1.44461 kcal/mol	0.317388 kcal/mol	143 152@LB@ \| \|@LB@5'-AAA...AAGCC AAUUA...UUG-3'@LB@ UCCGAUUA@LB@ \|\|\|\|\|\|\|\|@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -10.246 kcal/mol@LB@Unfolding Energy - mRNA 1.44461 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 144 -- 151@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@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@
46	0.0005017	0.03778	b1713	pheT	-7.80	0.173677	95 -- 107	17 -- 29	phenylalanine tRNA synthetase beta subunit	_____________94____________108\n_____________\|_____________\|\n5'-CUG...GAUGG_____________GACUA...ACG-3'\n______________GGAUGGAGCGUCU\n______________:\|\|\|:\|\|:\|:\|\|\|\n______________UCUAUCUUGUAGA\n3'-AUU...GACUU_____________AUGGA...AUG-5'\n_____________\|_____________\|\n_____________30____________16\n	100 -- 106	18 -- 24	-17.5948 kcal/mol	5.55471 kcal/mol	4.26164 kcal/mol	94 108@LB@ \| \|@LB@5'-CUG...GAUGG GACUA...ACG-3'@LB@ GGAUGGAGCGUCU@LB@ :\|\|\|:\|\|:\|:\|\|\|@LB@ UCUAUCUUGUAGA@LB@3'-AUU...GACUU AUGGA...AUG-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.5948 kcal/mol@LB@Unfolding Energy - mRNA 5.55471 kcal/mol@LB@Unfolding Energy - sRNA 4.26164 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 18 -- 24@LB@
35	0.0003501	0.03519	b2700	pncC	-8.73	0.102058	11 -- 28	20 -- 37	nicotinamide-nucleotide amidohydrolase; NMN amidohydrolase	_____________10_________________29\n_____________\|__________________\|\n5'-ACG...AUGGC_______C__U_______AGCCG...GUU-3'\n______________GGUCUGG_AG_UAGGACA\n______________\|\|\|\|\|\|:_\|\|_\|\|\|:\|\|\|\n______________CCAGACU_UC_AUCUUGU\n3'-AUU...AUUUU_______U__U_______AGAAU...AUG-5'\n_____________\|__________________\|\n_____________38_________________19\n	22 -- 28	20 -- 26	-19.0339 kcal/mol	5.51285 kcal/mol	4.72108 kcal/mol	10 29@LB@ \| \|@LB@5'-ACG...AUGGC C U AGCCG...GUU-3'@LB@ GGUCUGG AG UAGGACA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ CCAGACU UC AUCUUGU@LB@3'-AUU...AUUUU U U AGAAU...AUG-5'@LB@ \| \|@LB@ 38 19@LB@@LB@@LB@Energy -8.73 kcal/mol@LB@Hybridization Energy -19.0339 kcal/mol@LB@Unfolding Energy - mRNA 5.51285 kcal/mol@LB@Unfolding Energy - sRNA 4.72108 kcal/mol@LB@@LB@Position - mRNA 11 -- 28@LB@Position - sRNA 20 -- 37@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 20 -- 26@LB@
6	1.448e-05	0.00754	b3863	polA	-11.40	0.016745	236 -- 262	1 -- 29	5' to 3' DNA polymerase and 3' to 5'/5' to 3' exonuclease	_____________235___________________________263\n_____________\|_____________________________\|\n5'-AGA...CUUGU______UU_________________GC__AUAUC...GCG-3'\n______________AGAUGG__CAUCUUAUCUU__UAUC__GC\n______________\|\|\|\|:\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|__:\|\n______________UCUAUC__GUAGAAUGGAG__AUGG__UG\n3'-AUU...GACUU______UU___________AC____GA__-5'\n_____________\|____________________________\|\n_____________30___________________________1\n	244 -- 250	15 -- 21	-25.0693 kcal/mol	5.64295 kcal/mol	8.05079 kcal/mol	235 263@LB@ \| \|@LB@5'-AGA...CUUGU UU GC AUAUC...GCG-3'@LB@ AGAUGG CAUCUUAUCUU UAUC GC@LB@ \|\|\|\|:\| \|\|\|\|\|\|\|:\|\|: \|\|:\| :\|@LB@ UCUAUC GUAGAAUGGAG AUGG UG@LB@3'-AUU...GACUU UU AC GA -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -11.40 kcal/mol@LB@Hybridization Energy -25.0693 kcal/mol@LB@Unfolding Energy - mRNA 5.64295 kcal/mol@LB@Unfolding Energy - sRNA 8.05079 kcal/mol@LB@@LB@Position - mRNA 236 -- 262@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 15 -- 21@LB@
73	0.001217	0.05856	b1702	ppsA	-8.47	0.118779	124 -- 132	50 -- 58	phosphoenolpyruvate synthase	_____________123_______133\n_____________\|_________\|\n5'-UAU...UUUUC_________AAUAU...AAA-3'\n______________AUCCGGUUA\n______________\|\|\|\|\|:\|\|\|\n______________UAGGCUAAU\n3'-AUU...CGGUU_________GCACU...AUG-5'\n_____________\|_________\|\n_____________59________49\n	126 -- 132	50 -- 56	-10.3571 kcal/mol	1.58803 kcal/mol	0.317553 kcal/mol	123 133@LB@ \| \|@LB@5'-UAU...UUUUC AAUAU...AAA-3'@LB@ AUCCGGUUA@LB@ \|\|\|\|\|:\|\|\|@LB@ UAGGCUAAU@LB@3'-AUU...CGGUU GCACU...AUG-5'@LB@ \| \|@LB@ 59 49@LB@@LB@@LB@Energy -8.47 kcal/mol@LB@Hybridization Energy -10.3571 kcal/mol@LB@Unfolding Energy - mRNA 1.58803 kcal/mol@LB@Unfolding Energy - sRNA 0.317553 kcal/mol@LB@@LB@Position - mRNA 124 -- 132@LB@Position - sRNA 50 -- 58@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 50 -- 56@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)	_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@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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