Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
173	0.009278	0.1803	b3495	uspA	-10.68	0.124344	253 -- 279	16 -- 40	universal stress global response regulator		_____________252_________________________280\n_____________\|___________________________\|\n5'-GUC...CAAAG________G__AA____GUCUC_____CUCGC...AAG-3'\n______________UUCUGGUA_AG__AGCA_____UAUGG\n______________\|:\|\|\|\|\|\|_\|\|__\|\|\|\|_____\|\|\|\|\|\n______________AGGACCAU_UC__UCGU_____AUACC\n3'-UUU...CACCA________G__GA____AAA_______CAAUA...UCG-5'\n_____________\|___________________________\|\n_____________41__________________________15\n	254 -- 260	33 -- 39	-24.2729 kcal/mol	9.02768 kcal/mol	4.56874 kcal/mol	252 280@LB@ \| \|@LB@5'-GUC...CAAAG G AA GUCUC CUCGC...AAG-3'@LB@ UUCUGGUA AG AGCA UAUGG@LB@ \|:\|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|@LB@ AGGACCAU UC UCGU AUACC@LB@3'-UUU...CACCA G GA AAA CAAUA...UCG-5'@LB@ \| \|@LB@ 41 15@LB@@LB@@LB@Energy -10.68 kcal/mol@LB@Hybridization Energy -24.2729 kcal/mol@LB@Unfolding Energy - mRNA 9.02768 kcal/mol@LB@Unfolding Energy - sRNA 4.56874 kcal/mol@LB@@LB@Position - mRNA 253 -- 279@LB@Position - sRNA 16 -- 40@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 33 -- 39@LB@
149	0.00724	0.1633	b3494	uspB	-9.24	0.227320	190 -- 228	15 -- 51	universal stress (ethanol tolerance) protein B		_____________189_____________________________________229\n_____________\|_______________________________________\|\n5'-AAU...UCGCC_______A___AUGAUAA___C_GUC_____AUUU____CUUUA...UGC-3'\n______________GGGGAGG_GGU_______GCA_C___GCAUU____UGGG\n______________::\|\|\|\|\|_\|\|\|_______:\|\|_\|___\|\|\|\|\|____\|\|\|\|\n______________UUCCUCC_CCA_______UGU_G___CGUAA____ACCC\n3'-UUU...UCCGA_______A___AGGACCA___C_AU______AAU_____AAUAC...UCG-5'\n_____________\|_______________________________________\|\n_____________52______________________________________14\n	190 -- 196	45 -- 51	-24.8188 kcal/mol	10.9257 kcal/mol	4.65724 kcal/mol	189 229@LB@ \| \|@LB@5'-AAU...UCGCC A AUGAUAA C GUC AUUU CUUUA...UGC-3'@LB@ GGGGAGG GGU GCA C GCAUU UGGG@LB@ ::\|\|\|\|\| \|\|\| :\|\| \| \|\|\|\|\| \|\|\|\|@LB@ UUCCUCC CCA UGU G CGUAA ACCC@LB@3'-UUU...UCCGA A AGGACCA C AU AAU AAUAC...UCG-5'@LB@ \| \|@LB@ 52 14@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -24.8188 kcal/mol@LB@Unfolding Energy - mRNA 10.9257 kcal/mol@LB@Unfolding Energy - sRNA 4.65724 kcal/mol@LB@@LB@Position - mRNA 190 -- 228@LB@Position - sRNA 15 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 45 -- 51@LB@
20	0.0001678	0.0282	b2056	wcaD	-17.66	0.001373	77 -- 104	24 -- 48	putative colanic acid polymerase		_____________76___________________________105\n_____________\|____________________________\|\n5'-GCC...AAGAA______CUGCAA____________A___AACCG...UCA-3'\n______________GAGGUG______CUGGUGCAGUUA_GCA\n______________\|\|\|\|\|\|______\|\|\|\|\|:\|\|\|:\|\|_\|\|\|\n______________CUCCAC______GACCAUGUCGAU_CGU\n3'-UUU...GAUUC______CAAG__________________AAAAU...UCG-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	94 -- 100	27 -- 33	-32.1729 kcal/mol	9.95006 kcal/mol	4.55899 kcal/mol	76 105@LB@ \| \|@LB@5'-GCC...AAGAA CUGCAA A AACCG...UCA-3'@LB@ GAGGUG CUGGUGCAGUUA GCA@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\|\|:\|\| \|\|\|@LB@ CUCCAC GACCAUGUCGAU CGU@LB@3'-UUU...GAUUC CAAG AAAAU...UCG-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -17.66 kcal/mol@LB@Hybridization Energy -32.1729 kcal/mol@LB@Unfolding Energy - mRNA 9.95006 kcal/mol@LB@Unfolding Energy - sRNA 4.55899 kcal/mol@LB@@LB@Position - mRNA 77 -- 104@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 27 -- 33@LB@
71	0.001933	0.09081	b2044	wcaL	-10.40	0.140507	12 -- 21	24 -- 33	putative glycosyl transferase		_____________11_________22\n_____________\|__________\|\n5'-GGG...AUGCA________G_CUACC...AGA-3'\n______________GCAGCUGG_A\n______________:\|\|\|\|\|:\|_\|\n______________UGUCGAUC_U\n3'-UUU...GACCA________G_AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	13 -- 19	26 -- 32	-13.1871 kcal/mol	1.35791 kcal/mol	1.42716 kcal/mol	11 22@LB@ \| \|@LB@5'-GGG...AUGCA G CUACC...AGA-3'@LB@ GCAGCUGG A@LB@ :\|\|\|\|\|:\| \|@LB@ UGUCGAUC U@LB@3'-UUU...GACCA G AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.40 kcal/mol@LB@Hybridization Energy -13.1871 kcal/mol@LB@Unfolding Energy - mRNA 1.35791 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 12 -- 21@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 26 -- 32@LB@
134	0.005847	0.146	b0065	yabI	-9.48	0.206647	266 -- 290	24 -- 46	DedA family inner membrane protein		_____________265_______________________291\n_____________\|_________________________\|\n5'-UGA...GUGUU_____CC_______AGUC_______CUGGU...GUU-3'\n______________GGUGG__UUUCUGG____GCUGGCG\n______________\|\|\|\|\|__\|\|:\|\|\|\|____\|\|\|:\|\|:\n______________CCACC__AAGGACC____CGAUCGU\n3'-UUU...UUCCU______________AUGU_______AAAAU...UCG-5'\n_____________\|_________________________\|\n_____________47________________________23\n	284 -- 290	24 -- 30	-26.6068 kcal/mol	12.5692 kcal/mol	4.55813 kcal/mol	265 291@LB@ \| \|@LB@5'-UGA...GUGUU CC AGUC CUGGU...GUU-3'@LB@ GGUGG UUUCUGG GCUGGCG@LB@ \|\|\|\|\| \|\|:\|\|\|\| \|\|\|:\|\|:@LB@ CCACC AAGGACC CGAUCGU@LB@3'-UUU...UUCCU AUGU AAAAU...UCG-5'@LB@ \| \|@LB@ 47 23@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -26.6068 kcal/mol@LB@Unfolding Energy - mRNA 12.5692 kcal/mol@LB@Unfolding Energy - sRNA 4.55813 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 24 -- 46@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
112	0.004445	0.1334	b0132	yadD	-7.85	0.370183	131 -- 161	16 -- 48	transposase_31 family protein	b3411 b2244 b2305	_____________130________________________________162\n_____________\|__________________________________\|\n5'-CCC...AUAAA_____________ACG_____GC__C__GAC___AUACU...UGG-3'\n______________GAGGUGG___CUG___AUAGC__GC_UU___UGG\n______________\|\|\|\|\|\|\|___\|\|\|___\|:\|\|\|__\|\|_\|\|___\|\|\|\n______________CUCCACC___GAC___UGUCG__CG_AA___ACC\n3'-UUU...GAUUC_______AAG___CA______AU__U__AAU___CAAUA...UCG-5'\n_____________\|__________________________________\|\n_____________49_________________________________15\n	131 -- 137	42 -- 48	-24.9925 kcal/mol	12.5665 kcal/mol	4.57255 kcal/mol	130 162@LB@ \| \|@LB@5'-CCC...AUAAA ACG GC C GAC AUACU...UGG-3'@LB@ GAGGUGG CUG AUAGC GC UU UGG@LB@ \|\|\|\|\|\|\| \|\|\| \|:\|\|\| \|\| \|\| \|\|\|@LB@ CUCCACC GAC UGUCG CG AA ACC@LB@3'-UUU...GAUUC AAG CA AU U AAU CAAUA...UCG-5'@LB@ \| \|@LB@ 49 15@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -24.9925 kcal/mol@LB@Unfolding Energy - mRNA 12.5665 kcal/mol@LB@Unfolding Energy - sRNA 4.57255 kcal/mol@LB@@LB@Position - mRNA 131 -- 161@LB@Position - sRNA 16 -- 48@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 42 -- 48@LB@
47	0.001093	0.07744	b0128	yadH	-6.67	0.521304	272 -- 286	25 -- 36	putative ABC transporter permease		_____________271_____________287\n_____________\|_______________\|\n5'-UUA...AUCUG_______ACG_____GCCGC...UCA-3'\n______________GGUGCAG___CUGGU\n______________\|\|\|:\|\|\|___\|\|:\|:\n______________CCAUGUC___GAUCG\n3'-UUU...AAGGA_______________UAAAA...UCG-5'\n_____________\|_______________\|\n_____________37______________24\n	272 -- 278	30 -- 36	-13.5693 kcal/mol	5.47586 kcal/mol	1.42738 kcal/mol	271 287@LB@ \| \|@LB@5'-UUA...AUCUG ACG GCCGC...UCA-3'@LB@ GGUGCAG CUGGU@LB@ \|\|\|:\|\|\| \|\|:\|:@LB@ CCAUGUC GAUCG@LB@3'-UUU...AAGGA UAAAA...UCG-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -6.67 kcal/mol@LB@Hybridization Energy -13.5693 kcal/mol@LB@Unfolding Energy - mRNA 5.47586 kcal/mol@LB@Unfolding Energy - sRNA 1.42738 kcal/mol@LB@@LB@Position - mRNA 272 -- 286@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 30 -- 36@LB@
111	0.004429	0.1334	b0141	yadN	-9.15	0.234499	216 -- 249	16 -- 43	putative fimbrial-like adhesin protein		_____________215____________________________________250\n_____________\|______________________________________\|\n5'-UUA...AAUUA_____UGCCCUGU_____CUUAU_______________UUGCA...GUG-3'\n______________GGUUU________CUGGU_____GCUGGCG____AUGG\n______________\|\|\|\|:________\|\|\|\|\|_____\|\|\|:\|\|:____\|\|\|\|\n______________CCAAG________GACCA_____CGAUCGU____UACC\n3'-UUU...CUCCA__________________UGU_________AAAA____CAAUA...UCG-5'\n_____________\|______________________________________\|\n_____________44_____________________________________15\n	239 -- 245	24 -- 30	-21.9877 kcal/mol	8.2619 kcal/mol	4.57091 kcal/mol	215 250@LB@ \| \|@LB@5'-UUA...AAUUA UGCCCUGU CUUAU UUGCA...GUG-3'@LB@ GGUUU CUGGU GCUGGCG AUGG@LB@ \|\|\|\|: \|\|\|\|\| \|\|\|:\|\|: \|\|\|\|@LB@ CCAAG GACCA CGAUCGU UACC@LB@3'-UUU...CUCCA UGU AAAA CAAUA...UCG-5'@LB@ \| \|@LB@ 44 15@LB@@LB@@LB@Energy -9.15 kcal/mol@LB@Hybridization Energy -21.9877 kcal/mol@LB@Unfolding Energy - mRNA 8.2619 kcal/mol@LB@Unfolding Energy - sRNA 4.57091 kcal/mol@LB@@LB@Position - mRNA 216 -- 249@LB@Position - sRNA 16 -- 43@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 24 -- 30@LB@
56	0.001349	0.08097	b0287	yagU	-10.29	0.147287	182 -- 196	14 -- 37	DUF1440 family inner membrane acid resistance protein		_____________181______________________197\n_____________\|________________________\|\n5'-AAC...CAUAA________________________AGAUA...GGG-3'\n______________UGGUACA___AGCA______GGGU\n______________\|\|\|\|\|\|\|___\|\|\|\|______\|\|\|\|\n______________ACCAUGU___UCGU______CCCA\n3'-UUU...CAAGG_______CGA____AAAAUA____AUACA...UCG-5'\n_____________\|________________________\|\n_____________38_______________________13\n	182 -- 188	31 -- 37	-16.1787 kcal/mol	3.22484 kcal/mol	2.65978 kcal/mol	181 197@LB@ \| \|@LB@5'-AAC...CAUAA AGAUA...GGG-3'@LB@ UGGUACA AGCA GGGU@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ ACCAUGU UCGU CCCA@LB@3'-UUU...CAAGG CGA AAAAUA AUACA...UCG-5'@LB@ \| \|@LB@ 38 13@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -16.1787 kcal/mol@LB@Unfolding Energy - mRNA 3.22484 kcal/mol@LB@Unfolding Energy - sRNA 2.65978 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 14 -- 37@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
148	0.00721	0.1633	b0643	ybeL	-14.84	0.012433	12 -- 39	23 -- 48	DUF1451 family protein		_____________11___________________________40\n_____________\|____________________________\|\n5'-AAU...GCGUU____________CAGAU_C__A______AGCCC...CGC-3'\n______________GAGGUGGUUUUU_____C_GC_UAGCAU\n______________\|\|\|\|\|\|\|\|\|::\|_____\|_\|\|_\|\|\|\|\|\|\n______________CUCCACCAAGGA_____G_CG_AUCGUA\n3'-UUU...GAUUC____________CCAU__U_________AAAUA...UCG-5'\n_____________\|____________________________\|\n_____________49___________________________22\n	17 -- 23	37 -- 43	-25.8201 kcal/mol	6.42089 kcal/mol	4.55935 kcal/mol	11 40@LB@ \| \|@LB@5'-AAU...GCGUU CAGAU C A AGCCC...CGC-3'@LB@ GAGGUGGUUUUU C GC UAGCAU@LB@ \|\|\|\|\|\|\|\|\|::\| \| \|\| \|\|\|\|\|\|@LB@ CUCCACCAAGGA G CG AUCGUA@LB@3'-UUU...GAUUC CCAU U AAAUA...UCG-5'@LB@ \| \|@LB@ 49 22@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -25.8201 kcal/mol@LB@Unfolding Energy - mRNA 6.42089 kcal/mol@LB@Unfolding Energy - sRNA 4.55935 kcal/mol@LB@@LB@Position - mRNA 12 -- 39@LB@Position - sRNA 23 -- 48@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 37 -- 43@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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