Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
15	0.003313	0.593	b3133	agaV	-12.53	0.012445	185 -- 194	44 -- 53	N-acetylgalactosamine-specific enzyme IIB component of PTS	_____________184________195\n_____________\|__________\|\n5'-UCA...CAAAA__________CACGC...UAG-3'\n______________CAAAGAGGAA\n______________\|\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-14.1596 kcal/mol	0.702602 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UCA...CAAAA CACGC...UAG-3'@LB@ CAAAGAGGAA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -14.1596 kcal/mol@LB@Unfolding Energy - mRNA 0.702602 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
37	0.007616	0.6129	b4141	yjeH	-11.12	0.024259	30 -- 40	44 -- 54	putative transporter	_____________29__________41\n_____________\|___________\|\n5'-CAG...CCCCU___________AAAGA...CUG-3'\n______________UCAAGGGGGAA\n______________\|\|\|\|:\|:\|\|\|\|\n______________AGUUUCUCCUU\n3'-UUU...CGGGC___________AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	34 -- 40	44 -- 50	-14.4219 kcal/mol	2.36204 kcal/mol	0.939671 kcal/mol	29 41@LB@ \| \|@LB@5'-CAG...CCCCU AAAGA...CUG-3'@LB@ UCAAGGGGGAA@LB@ \|\|\|\|:\|:\|\|\|\|@LB@ AGUUUCUCCUU@LB@3'-UUU...CGGGC AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.4219 kcal/mol@LB@Unfolding Energy - mRNA 2.36204 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 30 -- 40@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 34 -- 40@LB@Position Seed - sRNA 44 -- 50@LB@
42	0.008125	0.6129	b2431	yfeX	-9.88	0.043594	266 -- 278	44 -- 56	porphyrinogen oxidase cytoplasmic	_____________265___________279\n_____________\|_____________\|\n5'-AUU...GCCAA___G_________GUUGA...CCA-3'\n______________CGU_AAAGGGGAA\n______________\|\|\|_\|\|\|\|:\|\|\|\|\n______________GCA_UUUCUCCUU\n3'-UUU...ACCGG___G_________AAAGU...ACA-5'\n_____________\|_____________\|\n_____________57____________43\n	272 -- 278	44 -- 50	-15.4775 kcal/mol	4.65199 kcal/mol	0.948902 kcal/mol	265 279@LB@ \| \|@LB@5'-AUU...GCCAA G GUUGA...CCA-3'@LB@ CGU AAAGGGGAA@LB@ \|\|\| \|\|\|\|:\|\|\|\|@LB@ GCA UUUCUCCUU@LB@3'-UUU...ACCGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 57 43@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.4775 kcal/mol@LB@Unfolding Energy - mRNA 4.65199 kcal/mol@LB@Unfolding Energy - sRNA 0.948902 kcal/mol@LB@@LB@Position - mRNA 266 -- 278@LB@Position - sRNA 44 -- 56@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 44 -- 50@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase	_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB	_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@LB@
51	0.009714	0.6129	b1736	chbA	-9.09	0.063099	186 -- 194	44 -- 52	N N'-diacetylchitobiose-specific enzyme IIA component of PTS	_____________185_______195\n_____________\|_________\|\n5'-GGU...AGAAA_________CGAUG...GCC-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	188 -- 194	44 -- 50	-11.469 kcal/mol	1.52278 kcal/mol	0.860683 kcal/mol	185 195@LB@ \| \|@LB@5'-GGU...AGAAA CGAUG...GCC-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -11.469 kcal/mol@LB@Unfolding Energy - mRNA 1.52278 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 186 -- 194@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
53	0.01077	0.6177	b3429	glgA	-6.74	0.182373	105 -- 111	44 -- 50	glycogen synthase	_____________104_____112\n_____________\|_______\|\n5'-GUA...AACGC_______GAUGC...ACG-3'\n______________AGAGGAA\n______________\|\|\|\|\|\|\|\n______________UCUCCUU\n3'-UUU...CAGUU_______AAAGU...ACA-5'\n_____________\|_______\|\n_____________51______43\n	105 -- 111	44 -- 50	-9.00959 kcal/mol	1.43957 kcal/mol	0.825028 kcal/mol	104 112@LB@ \| \|@LB@5'-GUA...AACGC GAUGC...ACG-3'@LB@ AGAGGAA@LB@ \|\|\|\|\|\|\|@LB@ UCUCCUU@LB@3'-UUU...CAGUU AAAGU...ACA-5'@LB@ \| \|@LB@ 51 43@LB@@LB@@LB@Energy -6.74 kcal/mol@LB@Hybridization Energy -9.00959 kcal/mol@LB@Unfolding Energy - mRNA 1.43957 kcal/mol@LB@Unfolding Energy - sRNA 0.825028 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 44 -- 50@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 44 -- 50@LB@
66	0.01414	0.6177	b0440	hupB	-10.30	0.035643	184 -- 193	44 -- 53	HU DNA-binding transcriptional regulator beta subunit	_____________183________194\n_____________\|__________\|\n5'-CGC...AAUUA__________GAGAA...CUG-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	187 -- 193	44 -- 50	-11.552 kcal/mol	0.319105 kcal/mol	0.927997 kcal/mol	183 194@LB@ \| \|@LB@5'-CGC...AAUUA GAGAA...CUG-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -11.552 kcal/mol@LB@Unfolding Energy - mRNA 0.319105 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 44 -- 50@LB@
70	0.01448	0.6177	b4012	yjaB	-8.12	0.098308	234 -- 242	44 -- 52	GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein	_____________233_______243\n_____________\|_________\|\n5'-AAG...AUGAG_________GAACU...CAG-3'\n______________GAAGGGGAG\n______________:\|\|\|:\|\|\|:\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	236 -- 242	44 -- 50	-9.78668 kcal/mol	0.80114 kcal/mol	0.860683 kcal/mol	233 243@LB@ \| \|@LB@5'-AAG...AUGAG GAACU...CAG-3'@LB@ GAAGGGGAG@LB@ :\|\|\|:\|\|\|:@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -9.78668 kcal/mol@LB@Unfolding Energy - mRNA 0.80114 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 234 -- 242@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 44 -- 50@LB@
71	0.01472	0.6177	b0846	rcdA	-10.28	0.035999	187 -- 195	44 -- 52	transcriptional regulator of csgD and ybiJI; autoregulator	_____________186_______196\n_____________\|_________\|\n5'-GCG...UGCAG_________AUGAC...AAA-3'\n______________AGAGAGGAA\n______________\|:\|\|\|\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	189 -- 195	44 -- 50	-11.6116 kcal/mol	0.46711 kcal/mol	0.860683 kcal/mol	186 196@LB@ \| \|@LB@5'-GCG...UGCAG AUGAC...AAA-3'@LB@ AGAGAGGAA@LB@ \|:\|\|\|\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -10.28 kcal/mol@LB@Hybridization Energy -11.6116 kcal/mol@LB@Unfolding Energy - mRNA 0.46711 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 187 -- 195@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@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