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
76	0.002251	0.09621	b0020	nhaR	-13.73	0.025158	90 -- 112	25 -- 46	transcriptional activator of nhaA		_____________89______________________113\n_____________\|_______________________\|\n5'-AUC...UCUUC__C___AA____A__________UACGC...CUC-3'\n______________GG_GGU__UUGG_UACAGCUGGU\n______________\|\|_\|\|\|__:\|\|\|_\|\|\|\|\|\|\|:\|:\n______________CC_CCA__GACC_AUGUCGAUCG\n3'-UUU...UUCCU__A___AG_______________UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________47______________________24\n	106 -- 112	25 -- 31	-27.2836 kcal/mol	8.99906 kcal/mol	4.55673 kcal/mol	89 113@LB@ \| \|@LB@5'-AUC...UCUUC C AA A UACGC...CUC-3'@LB@ GG GGU UUGG UACAGCUGGU@LB@ \|\| \|\|\| :\|\|\| \|\|\|\|\|\|\|:\|:@LB@ CC CCA GACC AUGUCGAUCG@LB@3'-UUU...UUCCU A AG UAAAA...UCG-5'@LB@ \| \|@LB@ 47 24@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -27.2836 kcal/mol@LB@Unfolding Energy - mRNA 8.99906 kcal/mol@LB@Unfolding Energy - sRNA 4.55673 kcal/mol@LB@@LB@Position - mRNA 90 -- 112@LB@Position - sRNA 25 -- 46@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 25 -- 31@LB@
200	0.01185	0.1975	b0025	ribF	-6.09	0.598433	35 -- 41	28 -- 34	bifunctional riboflavin kinase/FAD synthetase		_____________34______42\n_____________\|_______\|\n5'-UGG...GUGAA_______UUUCC...GCG-3'\n______________UACAGCU\n______________\|\|\|\|\|\|\|\n______________AUGUCGA\n3'-UUU...GGACC_______UCGUA...UCG-5'\n_____________\|_______\|\n_____________35______27\n	35 -- 41	28 -- 34	-8.9914 kcal/mol	1.72675 kcal/mol	1.17027 kcal/mol	34 42@LB@ \| \|@LB@5'-UGG...GUGAA UUUCC...GCG-3'@LB@ UACAGCU@LB@ \|\|\|\|\|\|\|@LB@ AUGUCGA@LB@3'-UUU...GGACC UCGUA...UCG-5'@LB@ \| \|@LB@ 35 27@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.9914 kcal/mol@LB@Unfolding Energy - mRNA 1.72675 kcal/mol@LB@Unfolding Energy - sRNA 1.17027 kcal/mol@LB@@LB@Position - mRNA 35 -- 41@LB@Position - sRNA 28 -- 34@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 28 -- 34@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@
199	0.0118	0.1975	b0077	ilvI	-11.98	0.066447	6 -- 27	1 -- 30	acetolactate synthase 3 large subunit		_____________5______________________________28\n_____________\|______________________________\|\n______5'-AAAUU_______AG_______A_____________CGAUU...UUU-3'\n______________GCU_GUA__UUGUGGG________UUCAGC\n______________\|\|\|_\|:\|__\|\|:\|\|\|\|________\|\|\|\|\|\|\n______________CGA_CGU__AAUACCC________AAGUCG\n3'-UUU...CAUGU___U___AA_______AAUACAAA______-5'\n_____________\|_____________________________\|\n_____________31____________________________1\n	14 -- 20	15 -- 21	-19.3299 kcal/mol	5.86615 kcal/mol	1.48556 kcal/mol	5 28@LB@ \| \|@LB@ 5'-AAAUU AG A CGAUU...UUU-3'@LB@ GCU GUA UUGUGGG UUCAGC@LB@ \|\|\| \|:\| \|\|:\|\|\|\| \|\|\|\|\|\|@LB@ CGA CGU AAUACCC AAGUCG@LB@3'-UUU...CAUGU U AA AAUACAAA -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.86615 kcal/mol@LB@Unfolding Energy - sRNA 1.48556 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 15 -- 21@LB@
104	0.003825	0.1236	b0081	mraZ	-12.90	0.040525	169 -- 210	15 -- 49	RsmH methytransferase inhibitor		_____________168________________________________________211\n_____________\|__________________________________________\|\n5'-GAU...AUUGU____CAAA____GAAUAAGG____A_________GUUCC___GAGCA...AAA-3'\n______________GGGG____GUGG________GGUG_GGCUGGCAU_____GGG\n______________\|\|:\|____\|\|\|\|________\|\|\|:_:\|\|\|:\|\|\|\|_____\|\|\|\n______________CCUC____CACC________CCAU_UCGAUCGUA_____CCC\n3'-UUU...CGAUU____________AAGGA_______G_________AAAUA___AAUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________50_________________________________________14\n	196 -- 202	23 -- 29	-32.8076 kcal/mol	15.3299 kcal/mol	4.57366 kcal/mol	168 211@LB@ \| \|@LB@5'-GAU...AUUGU CAAA GAAUAAGG A GUUCC GAGCA...AAA-3'@LB@ GGGG GUGG GGUG GGCUGGCAU GGG@LB@ \|\|:\| \|\|\|\| \|\|\|: :\|\|\|:\|\|\|\| \|\|\|@LB@ CCUC CACC CCAU UCGAUCGUA CCC@LB@3'-UUU...CGAUU AAGGA G AAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 50 14@LB@@LB@@LB@Energy -12.90 kcal/mol@LB@Hybridization Energy -32.8076 kcal/mol@LB@Unfolding Energy - mRNA 15.3299 kcal/mol@LB@Unfolding Energy - sRNA 4.57366 kcal/mol@LB@@LB@Position - mRNA 169 -- 210@LB@Position - sRNA 15 -- 49@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 23 -- 29@LB@
21	0.0001799	0.02879	b0107	hofB	-20.93	0.000028	267 -- 289	25 -- 48	T2SE secretion family protein; P-loop ATPase superfamily protein		_____________266______________________290\n_____________\|________________________\|\n5'-CCA...GCGAA__________A__U__________CGAUG...CUU-3'\n______________GAGGUGGUUC_UG_UGCGG_UAGU\n______________\|\|\|\|\|\|\|\|\|\|_\|\|_\|:\|:\|_\|\|\|:\n______________CUCCACCAAG_AC_AUGUC_AUCG\n3'-UUU...GAUUC__________G__C_____G____UAAAA...UCG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	270 -- 276	39 -- 45	-28.7026 kcal/mol	3.21789 kcal/mol	4.55759 kcal/mol	266 290@LB@ \| \|@LB@5'-CCA...GCGAA A U CGAUG...CUU-3'@LB@ GAGGUGGUUC UG UGCGG UAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\| \|:\|:\| \|\|\|:@LB@ CUCCACCAAG AC AUGUC AUCG@LB@3'-UUU...GAUUC G C G UAAAA...UCG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -20.93 kcal/mol@LB@Hybridization Energy -28.7026 kcal/mol@LB@Unfolding Energy - mRNA 3.21789 kcal/mol@LB@Unfolding Energy - sRNA 4.55759 kcal/mol@LB@@LB@Position - mRNA 267 -- 289@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 270 -- 276@LB@Position Seed - sRNA 39 -- 45@LB@
144	0.006813	0.158	b0111	ampE	-6.38	0.559697	294 -- 300	1 -- 7	ampicillin resistance inner membrane protein; putative signaling protein in beta-lactamase regulation		_____________293____300\n_____________\|______\|\n5'-CUU...CGUUC_______-3'\n______________UUUCGGC\n______________\|\|\|\|:\|\|\n______________AAAGUCG\n3'-UUU...UACAA_______-5'\n_____________\|______\|\n_____________8______1\n	294 -- 300	1 -- 7	-7.27697 kcal/mol	0.0992979 kcal/mol	0.796773 kcal/mol	293 300@LB@ \| \|@LB@5'-CUU...CGUUC -3'@LB@ UUUCGGC@LB@ \|\|\|\|:\|\|@LB@ AAAGUCG@LB@3'-UUU...UACAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -7.27697 kcal/mol@LB@Unfolding Energy - mRNA 0.0992979 kcal/mol@LB@Unfolding Energy - sRNA 0.796773 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 1 -- 7@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@
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@
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@

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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