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
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@
78	0.002256	0.09621	b0509	glxR	-14.00	0.021344	191 -- 236	14 -- 48	tartronate semialdehyde reductase NADH-dependent	b3882 b3125	_____________190______________________________________________237\n_____________\|________________________________________________\|\n5'-AGG...UAAAA_____UAAUUAUGAAA____GAUUUAU_____UA______________ACACC...CGG-3'\n______________GAGGU___________CUGG_______UGGCU__GGCAU__UAUGGGU\n______________\|\|\|\|\|___________\|\|\|\|_______::\|\|\|__:\|\|\|\|__\|\|\|\|\|\|\|\n______________CUCCA___________GACC_______GUCGA__UCGUA__AUACCCA\n3'-UUU...GAUUC_____CCAAG__________AU_________________AA_______AUACA...UCG-5'\n_____________\|________________________________________________\|\n_____________49_______________________________________________13\n	230 -- 236	14 -- 20	-26.1649 kcal/mol	7.59311 kcal/mol	4.57384 kcal/mol	190 237@LB@ \| \|@LB@5'-AGG...UAAAA UAAUUAUGAAA GAUUUAU UA ACACC...CGG-3'@LB@ GAGGU CUGG UGGCU GGCAU UAUGGGU@LB@ \|\|\|\|\| \|\|\|\| ::\|\|\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUCCA GACC GUCGA UCGUA AUACCCA@LB@3'-UUU...GAUUC CCAAG AU AA AUACA...UCG-5'@LB@ \| \|@LB@ 49 13@LB@@LB@@LB@Energy -14.00 kcal/mol@LB@Hybridization Energy -26.1649 kcal/mol@LB@Unfolding Energy - mRNA 7.59311 kcal/mol@LB@Unfolding Energy - sRNA 4.57384 kcal/mol@LB@@LB@Position - mRNA 191 -- 236@LB@Position - sRNA 14 -- 48@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 14 -- 20@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB		_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
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@
53	0.001234	0.07744	b0884	infA	-13.12	0.035785	57 -- 86	2 -- 40	translation initiation factor IF-1		_____________56_______________________________________87\n_____________\|________________________________________\|\n5'-UUU...UGCGC____________U____CG_____________________AGUAA...CUG-3'\n______________UUUUGGUGCGGC_UAGC___________UGUG_UUUUCGG\n______________\|::\|\|\|\|:\|:\|\|_\|\|\|\|___________\|:\|\|_\|\|\|\|\|:\|\n______________AGGACCAUGUCG_AUCG___________AUAC_AAAAGUC\n3'-UUU...CACCA_________________UAAAAUACCCA____A_______G-5'\n_____________\|________________________________________\|\n_____________41_______________________________________1\n	80 -- 86	2 -- 8	-28.8253 kcal/mol	11.0921 kcal/mol	4.60818 kcal/mol	56 87@LB@ \| \|@LB@5'-UUU...UGCGC U CG AGUAA...CUG-3'@LB@ UUUUGGUGCGGC UAGC UGUG UUUUCGG@LB@ \|::\|\|\|\|:\|:\|\| \|\|\|\| \|:\|\| \|\|\|\|\|:\|@LB@ AGGACCAUGUCG AUCG AUAC AAAAGUC@LB@3'-UUU...CACCA UAAAAUACCCA A G-5'@LB@ \| \|@LB@ 41 1@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -28.8253 kcal/mol@LB@Unfolding Energy - mRNA 11.0921 kcal/mol@LB@Unfolding Energy - sRNA 4.60818 kcal/mol@LB@@LB@Position - mRNA 57 -- 86@LB@Position - sRNA 2 -- 40@LB@Position Seed - mRNA 80 -- 86@LB@Position Seed - sRNA 2 -- 8@LB@
142	0.006672	0.1579	b3168	infB	-12.04	0.064271	249 -- 267	29 -- 45	translation initiation factor IF-2		_____________248_________________268\n_____________\|___________________\|\n5'-AAG...CCUCC____AACG___________AAUUU...CUG-3'\n______________GUGG____CCUGGUACAGC\n______________\|\|\|\|____\|\|\|\|\|\|\|\|\|\|\|\n______________CACC____GGACCAUGUCG\n3'-UUU...UCCUC____AA_____________AUCGU...UCG-5'\n_____________\|___________________\|\n_____________46__________________28\n	261 -- 267	29 -- 35	-27.2517 kcal/mol	10.9083 kcal/mol	4.30037 kcal/mol	248 268@LB@ \| \|@LB@5'-AAG...CCUCC AACG AAUUU...CUG-3'@LB@ GUGG CCUGGUACAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CACC GGACCAUGUCG@LB@3'-UUU...UCCUC AA AUCGU...UCG-5'@LB@ \| \|@LB@ 46 28@LB@@LB@@LB@Energy -12.04 kcal/mol@LB@Hybridization Energy -27.2517 kcal/mol@LB@Unfolding Energy - mRNA 10.9083 kcal/mol@LB@Unfolding Energy - sRNA 4.30037 kcal/mol@LB@@LB@Position - mRNA 249 -- 267@LB@Position - sRNA 29 -- 45@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 29 -- 35@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@
110	0.004262	0.1302	b1871	cmoB	-11.44	0.086999	165 -- 182	22 -- 44	tRNA (cmo5U34)-carboxymethyltransferase carboxy-SAM-dependent		_____________164______________________183\n_____________\|________________________\|\n5'-CAC...AACUU______A_________________AAAAG...AGC-3'\n______________UGGUUC_CUGG______UGGCAUU\n______________\|\|\|\|\|\|_\|\|\|\|______\|:\|\|\|\|\|\n______________ACCAAG_GACC______AUCGUAA\n3'-UUU...CCUCC___________AUGUCG_______AAUAC...UCG-5'\n_____________\|________________________\|\n_____________45_______________________21\n	176 -- 182	22 -- 28	-20.1895 kcal/mol	4.19283 kcal/mol	4.55859 kcal/mol	164 183@LB@ \| \|@LB@5'-CAC...AACUU A AAAAG...AGC-3'@LB@ UGGUUC CUGG UGGCAUU@LB@ \|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ ACCAAG GACC AUCGUAA@LB@3'-UUU...CCUCC AUGUCG AAUAC...UCG-5'@LB@ \| \|@LB@ 45 21@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.1895 kcal/mol@LB@Unfolding Energy - mRNA 4.19283 kcal/mol@LB@Unfolding Energy - sRNA 4.55859 kcal/mol@LB@@LB@Position - mRNA 165 -- 182@LB@Position - sRNA 22 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 22 -- 28@LB@
189	0.01085	0.1919	b3606	trmL	-8.64	0.283903	120 -- 126	63 -- 69	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent		_____________119_____127\n_____________\|_______\|\n5'-UAG...CCUCC_______GGGCC...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	120 -- 126	63 -- 69	-10.8913 kcal/mol	1.31422 kcal/mol	0.939295 kcal/mol	119 127@LB@ \| \|@LB@5'-UAG...CCUCC GGGCC...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -10.8913 kcal/mol@LB@Unfolding Energy - mRNA 1.31422 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 120 -- 126@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 63 -- 69@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase		_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 27 -- 33@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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