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
57	0.001403	0.08147	b0948	rlmL	-12.46	0.051711	286 -- 300	33 -- 47	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent	_____________285____________300\n_____________\|______________\|\n5'-GAC...AUGCC_________AG____-3'\n______________AGGUGGUUC__GGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________UCCACCAAG__CCAU\n3'-UUU...AUUCC_________GA____GUCGA...UCG-5'\n_____________\|_______________\|\n_____________48______________32\n	288 -- 294	39 -- 45	-21.3846 kcal/mol	5.67574 kcal/mol	3.25146 kcal/mol	285 300@LB@ \| \|@LB@5'-GAC...AUGCC AG -3'@LB@ AGGUGGUUC GGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:@LB@ UCCACCAAG CCAU@LB@3'-UUU...AUUCC GA GUCGA...UCG-5'@LB@ \| \|@LB@ 48 32@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.3846 kcal/mol@LB@Unfolding Energy - mRNA 5.67574 kcal/mol@LB@Unfolding Energy - sRNA 3.25146 kcal/mol@LB@@LB@Position - mRNA 286 -- 300@LB@Position - sRNA 33 -- 47@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 39 -- 45@LB@
11	3.883e-05	0.01168	b4074	nrfE	-17.71	0.001322	131 -- 144	35 -- 48	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE	_____________130____________145\n_____________\|______________\|\n5'-ACC...GAAAA______________ACGUA...UGC-3'\n______________GAGGUGGUUUCUGG\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\|\n______________CUCCACCAAGGACC\n3'-UUU...GAUUC______________AUGUC...UCG-5'\n_____________\|______________\|\n_____________49_____________34\n	138 -- 144	35 -- 41	-26.5218 kcal/mol	5.67902 kcal/mol	3.13693 kcal/mol	130 145@LB@ \| \|@LB@5'-ACC...GAAAA ACGUA...UGC-3'@LB@ GAGGUGGUUUCUGG@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|\|@LB@ CUCCACCAAGGACC@LB@3'-UUU...GAUUC AUGUC...UCG-5'@LB@ \| \|@LB@ 49 34@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -26.5218 kcal/mol@LB@Unfolding Energy - mRNA 5.67902 kcal/mol@LB@Unfolding Energy - sRNA 3.13693 kcal/mol@LB@@LB@Position - mRNA 131 -- 144@LB@Position - sRNA 35 -- 48@LB@Position Seed - mRNA 138 -- 144@LB@Position Seed - sRNA 35 -- 41@LB@
64	0.001739	0.09016	b4463	ygcU	-11.99	0.066010	140 -- 150	36 -- 46	putative FAD-linked oxidoreductase	_____________139_________151\n_____________\|___________\|\n5'-AUC...AUAAC___________UUUUC...UUG-3'\n______________GGUGGUUUCUG\n______________\|\|\|\|\|\|\|:\|\|\|\n______________CCACCAAGGAC\n3'-UUU...UUCCU___________CAUGU...UCG-5'\n_____________\|___________\|\n_____________47__________35\n	144 -- 150	36 -- 42	-19.2157 kcal/mol	4.08908 kcal/mol	3.13564 kcal/mol	139 151@LB@ \| \|@LB@5'-AUC...AUAAC UUUUC...UUG-3'@LB@ GGUGGUUUCUG@LB@ \|\|\|\|\|\|\|:\|\|\|@LB@ CCACCAAGGAC@LB@3'-UUU...UUCCU CAUGU...UCG-5'@LB@ \| \|@LB@ 47 35@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -19.2157 kcal/mol@LB@Unfolding Energy - mRNA 4.08908 kcal/mol@LB@Unfolding Energy - sRNA 3.13564 kcal/mol@LB@@LB@Position - mRNA 140 -- 150@LB@Position - sRNA 36 -- 46@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 36 -- 42@LB@
84	0.00278	0.1082	b1418	cybB	-11.15	0.099871	281 -- 297	37 -- 49	cytochrome b561	_____________280_______________298\n_____________\|_________________\|\n5'-AAC...GCAAU____UUUC_________UCC-3'\n______________GGAG____GUGGUUUCU\n______________\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CCUC____CACCAAGGA\n3'-UUU...CGAUU_________________CCAUG...UCG-5'\n_____________\|_________________\|\n_____________50________________36\n	291 -- 297	37 -- 43	-16.7846 kcal/mol	2.49998 kcal/mol	3.13428 kcal/mol	280 298@LB@ \| \|@LB@5'-AAC...GCAAU UUUC UCC-3'@LB@ GGAG GUGGUUUCU@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CCUC CACCAAGGA@LB@3'-UUU...CGAUU CCAUG...UCG-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -16.7846 kcal/mol@LB@Unfolding Energy - mRNA 2.49998 kcal/mol@LB@Unfolding Energy - sRNA 3.13428 kcal/mol@LB@@LB@Position - mRNA 281 -- 297@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 37 -- 43@LB@
90	0.002979	0.1113	b3328	gspG	-12.13	0.061461	284 -- 293	37 -- 46	pseudopilin cryptic general secretion pathway	_____________283________294\n_____________\|__________\|\n5'-AAA...AGCCU__________AACCUAA-3'\n______________GGUGGUUCCU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCACCAAGGA\n3'-UUU...UUCCU__________CCAUG...UCG-5'\n_____________\|__________\|\n_____________47_________36\n	287 -- 293	37 -- 43	-18.4741 kcal/mol	3.21142 kcal/mol	3.13317 kcal/mol	283 294@LB@ \| \|@LB@5'-AAA...AGCCU AACCUAA-3'@LB@ GGUGGUUCCU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCACCAAGGA@LB@3'-UUU...UUCCU CCAUG...UCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.4741 kcal/mol@LB@Unfolding Energy - mRNA 3.21142 kcal/mol@LB@Unfolding Energy - sRNA 3.13317 kcal/mol@LB@@LB@Position - mRNA 284 -- 293@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
33	0.0006117	0.0623	b1795	yeaQ	-12.41	0.053010	276 -- 283	42 -- 49	UPF0410 family protein	_____________275______284\n_____________\|________\|\n5'-AUA...AAGAU________AUUCU...UCC-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	277 -- 283	42 -- 48	-16.41 kcal/mol	1.22894 kcal/mol	2.77009 kcal/mol	275 284@LB@ \| \|@LB@5'-AUA...AAGAU AUUCU...UCC-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -12.41 kcal/mol@LB@Hybridization Energy -16.41 kcal/mol@LB@Unfolding Energy - mRNA 1.22894 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 276 -- 283@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 277 -- 283@LB@Position Seed - sRNA 42 -- 48@LB@
91	0.003099	0.1126	b2343	yfcZ	-10.72	0.122030	27 -- 34	42 -- 49	UPF0381 family protein	_____________26_______35\n_____________\|________\|\n5'-GAA...AAUUU________CGCAC...UGU-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	28 -- 34	42 -- 48	-16.5707 kcal/mol	3.08276 kcal/mol	2.77009 kcal/mol	26 35@LB@ \| \|@LB@5'-GAA...AAUUU CGCAC...UGU-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -16.5707 kcal/mol@LB@Unfolding Energy - mRNA 3.08276 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 27 -- 34@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 42 -- 48@LB@
94	0.003268	0.1162	b2687	luxS	-10.18	0.155002	189 -- 196	42 -- 49	S-ribosylhomocysteine lyase	_____________188______197\n_____________\|________\|\n5'-GAA...UUACC________CUAAA...UCA-3'\n______________GGAGGUGG\n______________\|\|\|\|\|\|\|\|\n______________CCUCCACC\n3'-UUU...CGAUU________AAGGA...UCG-5'\n_____________\|________\|\n_____________50_______41\n	190 -- 196	42 -- 48	-16.7111 kcal/mol	3.76521 kcal/mol	2.77009 kcal/mol	188 197@LB@ \| \|@LB@5'-GAA...UUACC CUAAA...UCA-3'@LB@ GGAGGUGG@LB@ \|\|\|\|\|\|\|\|@LB@ CCUCCACC@LB@3'-UUU...CGAUU AAGGA...UCG-5'@LB@ \| \|@LB@ 50 41@LB@@LB@@LB@Energy -10.18 kcal/mol@LB@Hybridization Energy -16.7111 kcal/mol@LB@Unfolding Energy - mRNA 3.76521 kcal/mol@LB@Unfolding Energy - sRNA 2.77009 kcal/mol@LB@@LB@Position - mRNA 189 -- 196@LB@Position - sRNA 42 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 42 -- 48@LB@
165	0.008583	0.1748	b4075	nrfF	-7.99	0.354712	71 -- 77	63 -- 69	heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfF	_____________70______78\n_____________\|_______\|\n5'-AGC...UCAUG_______AAACU...AAC-3'\n______________GGGGAGA\n______________:\|\|\|\|\|\|\n______________UCCCUCU\n3'-UUU...CACAU_______AAUGU...UCG-5'\n_____________\|_______\|\n_____________70______62\n	71 -- 77	63 -- 69	-11.2965 kcal/mol	2.37125 kcal/mol	0.939295 kcal/mol	70 78@LB@ \| \|@LB@5'-AGC...UCAUG AAACU...AAC-3'@LB@ GGGGAGA@LB@ :\|\|\|\|\|\|@LB@ UCCCUCU@LB@3'-UUU...CACAU AAUGU...UCG-5'@LB@ \| \|@LB@ 70 62@LB@@LB@@LB@Energy -7.99 kcal/mol@LB@Hybridization Energy -11.2965 kcal/mol@LB@Unfolding Energy - mRNA 2.37125 kcal/mol@LB@Unfolding Energy - sRNA 0.939295 kcal/mol@LB@@LB@Position - mRNA 71 -- 77@LB@Position - sRNA 63 -- 69@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 63 -- 69@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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching