Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
45	0.002879	0.2151	b3319	rplD	-8.41	0.246804	191 -- 204	42 -- 54	50S ribosomal subunit protein L4	_____________190____________205\n_____________\|______________\|\n5'-UCA...CGUAA__A___A_______AAUUA...UUG-3'\n______________GG_GAU_GCAAUGG\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CC_UUA_CGUUACC\n3'-UUU...AGUCA__G___________GGGUU...UUG-5'\n_____________\|______________\|\n_____________55_____________41\n	198 -- 204	42 -- 48	-13.9027 kcal/mol	1.99374 kcal/mol	3.49932 kcal/mol	190 205@LB@ \| \|@LB@5'-UCA...CGUAA A A AAUUA...UUG-3'@LB@ GG GAU GCAAUGG@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CC UUA CGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -13.9027 kcal/mol@LB@Unfolding Energy - mRNA 1.99374 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 191 -- 204@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
49	0.003464	0.237	b4260	pepA	-9.32	0.166975	186 -- 204	42 -- 59	multifunctional aminopeptidase A: a cyteinylglycinase transcription regulator and site-specific recombination factor	_____________185__________________205\n_____________\|____________________\|\n5'-UUA...AAGAU____GA_C____________AGUUU...AAC-3'\n______________UCAG__G_GUAGUGCA_UGG\n______________\|\|\|\|__\|_\|:\|:\|\|\|\|_\|\|\|\n______________AGUC__C_CGUUACGU_ACC\n3'-UUU...CUUUU____A___________U___GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	195 -- 201	46 -- 52	-17.4947 kcal/mol	4.48384 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-UUA...AAGAU GA C AGUUU...AAC-3'@LB@ UCAG G GUAGUGCA UGG@LB@ \|\|\|\| \| \|:\|:\|\|\|\| \|\|\|@LB@ AGUC C CGUUACGU ACC@LB@3'-UUU...CUUUU A U GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -17.4947 kcal/mol@LB@Unfolding Energy - mRNA 4.48384 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 46 -- 52@LB@
57	0.004077	0.237	b4198	ulaF	-9.90	0.127727	21 -- 37	42 -- 55	L-ribulose 5-phosphate 4-epimerase	_____________20________________38\n_____________\|_________________\|\n5'-GUC...CCGUU_____AAG_________AUUUC...GCG-3'\n______________UGGCG___GUGUAGUGG\n______________\|\|\|\|:___:\|\|:\|:\|\|\|\n______________ACCGU___UACGUUACC\n3'-UUU...UAGUC_________________GGGUU...UUG-5'\n_____________\|_________________\|\n_____________56________________41\n	31 -- 37	42 -- 48	-17.0201 kcal/mol	3.6214 kcal/mol	3.50097 kcal/mol	20 38@LB@ \| \|@LB@5'-GUC...CCGUU AAG AUUUC...GCG-3'@LB@ UGGCG GUGUAGUGG@LB@ \|\|\|\|: :\|\|:\|:\|\|\|@LB@ ACCGU UACGUUACC@LB@3'-UUU...UAGUC GGGUU...UUG-5'@LB@ \| \|@LB@ 56 41@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -17.0201 kcal/mol@LB@Unfolding Energy - mRNA 3.6214 kcal/mol@LB@Unfolding Energy - sRNA 3.50097 kcal/mol@LB@@LB@Position - mRNA 21 -- 37@LB@Position - sRNA 42 -- 55@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 42 -- 48@LB@
71	0.005918	0.2791	b4348	hsdS	-11.53	0.056880	66 -- 85	42 -- 60	specificity determinant for hsdM and hsdR	_____________65___________________86\n_____________\|____________________\|\n5'-CUG...GAUGU_____C_____AA_______GCGAA...UAA-3'\n______________AUUAG_GGCAG__GCGAUGG\n______________\|\|:\|\|_\|\|\|\|:__\|\|:\|\|\|\|\n______________UAGUC_CCGUU__CGUUACC\n3'-UUU...CCUUU_____A_____A________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________61___________________41\n	79 -- 85	42 -- 48	-21.0522 kcal/mol	5.82821 kcal/mol	3.69672 kcal/mol	65 86@LB@ \| \|@LB@5'-CUG...GAUGU C AA GCGAA...UAA-3'@LB@ AUUAG GGCAG GCGAUGG@LB@ \|\|:\|\| \|\|\|\|: \|\|:\|\|\|\|@LB@ UAGUC CCGUU CGUUACC@LB@3'-UUU...CCUUU A A GGGUU...UUG-5'@LB@ \| \|@LB@ 61 41@LB@@LB@@LB@Energy -11.53 kcal/mol@LB@Hybridization Energy -21.0522 kcal/mol@LB@Unfolding Energy - mRNA 5.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.69672 kcal/mol@LB@@LB@Position - mRNA 66 -- 85@LB@Position - sRNA 42 -- 60@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 42 -- 48@LB@
96	0.009004	0.3118	b3981	secE	-8.82	0.207803	253 -- 270	42 -- 57	preprotein translocase membrane subunit	_____________252________________271\n_____________\|__________________\|\n5'-UAA...GAUGA_____GUCGU________CAUUG...ACU-3'\n______________AGUGG_____UGUGGUGG\n______________\|\|\|\|\|_____\|\|:::\|\|\|\n______________UCACC_____ACGUUACC\n3'-UUU...UUUAG_____GUU__________GGGUU...UUG-5'\n_____________\|__________________\|\n_____________58_________________41\n	264 -- 270	42 -- 48	-15.0916 kcal/mol	2.64473 kcal/mol	3.62906 kcal/mol	252 271@LB@ \| \|@LB@5'-UAA...GAUGA GUCGU CAUUG...ACU-3'@LB@ AGUGG UGUGGUGG@LB@ \|\|\|\|\| \|\|:::\|\|\|@LB@ UCACC ACGUUACC@LB@3'-UUU...UUUAG GUU GGGUU...UUG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -8.82 kcal/mol@LB@Hybridization Energy -15.0916 kcal/mol@LB@Unfolding Energy - mRNA 2.64473 kcal/mol@LB@Unfolding Energy - sRNA 3.62906 kcal/mol@LB@@LB@Position - mRNA 253 -- 270@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 42 -- 48@LB@
117	0.01164	0.3326	b1119	nagK	-13.64	0.017780	246 -- 275	42 -- 70	N-acetyl-D-glucosamine kinase	_____________245_____________________________276\n_____________\|_______________________________\|\n5'-UCA...UUGGC_____U__UAG_____C_____U________GAAAA...GUG-3'\n______________GUGUU_GA____CGGU_GGCAG_UGCAGUGG\n______________:\|\|\|\|_\|\|____\|:\|\|_\|\|\|\|:_\|\|\|\|:\|\|\|\n______________UACAA_CU____GUCA_CCGUU_ACGUUACC\n3'-UUU...AAAUA_____C__UUUA___________________GGGUU...UUG-5'\n_____________\|_______________________________\|\n_____________71______________________________41\n	269 -- 275	42 -- 48	-28.344 kcal/mol	8.3584 kcal/mol	6.34928 kcal/mol	245 276@LB@ \| \|@LB@5'-UCA...UUGGC U UAG C U GAAAA...GUG-3'@LB@ GUGUU GA CGGU GGCAG UGCAGUGG@LB@ :\|\|\|\| \|\| \|:\|\| \|\|\|\|: \|\|\|\|:\|\|\|@LB@ UACAA CU GUCA CCGUU ACGUUACC@LB@3'-UUU...AAAUA C UUUA GGGUU...UUG-5'@LB@ \| \|@LB@ 71 41@LB@@LB@@LB@Energy -13.64 kcal/mol@LB@Hybridization Energy -28.344 kcal/mol@LB@Unfolding Energy - mRNA 8.3584 kcal/mol@LB@Unfolding Energy - sRNA 6.34928 kcal/mol@LB@@LB@Position - mRNA 246 -- 275@LB@Position - sRNA 42 -- 70@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 42 -- 48@LB@
131	0.01428	0.3654	b2099	yegU	-10.27	0.106798	246 -- 258	42 -- 54	ADP-ribosylglycohydrolase family protein	_____________245___________259\n_____________\|_____________\|\n5'-GUG...CGUUA__G__________GGAUG...CAC-3'\n______________GG_GAUGCGAUGG\n______________\|\|_:\|\|\|\|:\|\|\|\|\n______________CC_UUACGUUACC\n3'-UUU...AGUCA__G__________GGGUU...UUG-5'\n_____________\|_____________\|\n_____________55____________41\n	252 -- 258	42 -- 48	-19.8763 kcal/mol	6.10373 kcal/mol	3.49932 kcal/mol	245 259@LB@ \| \|@LB@5'-GUG...CGUUA G GGAUG...CAC-3'@LB@ GG GAUGCGAUGG@LB@ \|\| :\|\|\|\|:\|\|\|\|@LB@ CC UUACGUUACC@LB@3'-UUU...AGUCA G GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -10.27 kcal/mol@LB@Hybridization Energy -19.8763 kcal/mol@LB@Unfolding Energy - mRNA 6.10373 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 258@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 42 -- 48@LB@
134	0.01498	0.3759	b3388	damX	-9.22	0.174550	186 -- 204	42 -- 59	cell division protein that binds to the septal ring	_____________185__________________205\n_____________\|____________________\|\n5'-GGG...ACCUU_____________UA_____AUGAA...AAC-3'\n______________UUAGUGG_GGUGU__AAUGG\n______________\|:\|\|\|\|\|_::\|\|:__\|\|\|\|\|\n______________AGUCACC_UUACG__UUACC\n3'-UUU...CUUUU_______G____________GGGUU...UUG-5'\n_____________\|____________________\|\n_____________60___________________41\n	186 -- 192	53 -- 59	-16.4488 kcal/mol	3.53707 kcal/mol	3.69565 kcal/mol	185 205@LB@ \| \|@LB@5'-GGG...ACCUU UA AUGAA...AAC-3'@LB@ UUAGUGG GGUGU AAUGG@LB@ \|:\|\|\|\|\| ::\|\|: \|\|\|\|\|@LB@ AGUCACC UUACG UUACC@LB@3'-UUU...CUUUU G GGGUU...UUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -9.22 kcal/mol@LB@Hybridization Energy -16.4488 kcal/mol@LB@Unfolding Energy - mRNA 3.53707 kcal/mol@LB@Unfolding Energy - sRNA 3.69565 kcal/mol@LB@@LB@Position - mRNA 186 -- 204@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 53 -- 59@LB@
160	0.01821	0.3828	b0106	hofC	-9.30	0.168390	246 -- 262	42 -- 54	assembly protein in type IV pilin biogenesis transmembrane protein	_____________245_______________263\n_____________\|_________________\|\n5'-UUA...GCGAC________GCAA_____GAUGC...UGG-3'\n______________GGCAAUGC____GAUGG\n______________\|\|\|\|\|\|\|\|____:\|\|\|\|\n______________CCGUUACG____UUACC\n3'-UUU...AGUCA_________________GGGUU...UUG-5'\n_____________\|_________________\|\n_____________55________________41\n	247 -- 253	47 -- 53	-17.2549 kcal/mol	4.45921 kcal/mol	3.49932 kcal/mol	245 263@LB@ \| \|@LB@5'-UUA...GCGAC GCAA GAUGC...UGG-3'@LB@ GGCAAUGC GAUGG@LB@ \|\|\|\|\|\|\|\| :\|\|\|\|@LB@ CCGUUACG UUACC@LB@3'-UUU...AGUCA GGGUU...UUG-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -9.30 kcal/mol@LB@Hybridization Energy -17.2549 kcal/mol@LB@Unfolding Energy - mRNA 4.45921 kcal/mol@LB@Unfolding Energy - sRNA 3.49932 kcal/mol@LB@@LB@Position - mRNA 246 -- 262@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 247 -- 253@LB@Position Seed - sRNA 47 -- 53@LB@
163	0.01899	0.3918	b0037	caiC	-9.20	0.176089	195 -- 204	42 -- 51	putative crotonobetaine/carnitine-CoA ligase	_____________194________205\n_____________\|__________\|\n5'-CGG...AUAGA__________AUAUC...GAG-3'\n______________GGUGCAAUGG\n______________::\|\|\|\|\|\|\|\|\n______________UUACGUUACC\n3'-UUU...CACCG__________GGGUU...UUG-5'\n_____________\|__________\|\n_____________52_________41\n	198 -- 204	42 -- 48	-13.9036 kcal/mol	2.50026 kcal/mol	2.20704 kcal/mol	194 205@LB@ \| \|@LB@5'-CGG...AUAGA AUAUC...GAG-3'@LB@ GGUGCAAUGG@LB@ ::\|\|\|\|\|\|\|\|@LB@ UUACGUUACC@LB@3'-UUU...CACCG GGGUU...UUG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -13.9036 kcal/mol@LB@Unfolding Energy - mRNA 2.50026 kcal/mol@LB@Unfolding Energy - sRNA 2.20704 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@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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