Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
108	0.01118	0.3104	b2565	recO	-9.71	0.135448	294 -- 300	5 -- 11	gap repair protein	_____________293____300\n_____________\|______\|\n5'-GAA...GGCGC_______-3'\n______________GUGCGUC\n______________\|:\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	294 -- 300	5 -- 11	-11.8762 kcal/mol	1.05403 kcal/mol	1.11145 kcal/mol	293 300@LB@ \| \|@LB@5'-GAA...GGCGC -3'@LB@ GUGCGUC@LB@ \|:\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -11.8762 kcal/mol@LB@Unfolding Energy - mRNA 1.05403 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 5 -- 11@LB@
192	0.01895	0.3104	b3333	gspL	-4.89	0.645256	110 -- 132	1 -- 21	general secretory pathway component cryptic	_____________109______________________133\n_____________\|________________________\|\n5'-GAU...CCAGG____________CAUAUU______AACCG...CGC-3'\n______________GAUGGCAAA_GC______UUUUUC\n______________\|\|\|::\|\|\|\|_\|\|______\|:\|\|\|\|\n______________CUAUUGUUU_CG______AGAAAG\n3'-UUU...UACUA_________A__CGC_________-5'\n_____________\|_______________________\|\n_____________22______________________1\n	110 -- 116	15 -- 21	-12.6455 kcal/mol	6.50221 kcal/mol	1.25763 kcal/mol	109 133@LB@ \| \|@LB@5'-GAU...CCAGG CAUAUU AACCG...CGC-3'@LB@ GAUGGCAAA GC UUUUUC@LB@ \|\|\|::\|\|\|\| \|\| \|:\|\|\|\|@LB@ CUAUUGUUU CG AGAAAG@LB@3'-UUU...UACUA A CGC -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -4.89 kcal/mol@LB@Hybridization Energy -12.6455 kcal/mol@LB@Unfolding Energy - mRNA 6.50221 kcal/mol@LB@Unfolding Energy - sRNA 1.25763 kcal/mol@LB@@LB@Position - mRNA 110 -- 132@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 15 -- 21@LB@
140	0.01344	0.3104	b2388	glk	-4.25	0.738023	201 -- 214	10 -- 20	glucokinase	_____________200____________215\n_____________\|______________\|\n5'-CUA...GAAGA_______AGU____AUUAG...AUU-3'\n______________AUGACAA___AUGC\n______________\|\|:\|\|\|\|___\|\|\|\|\n______________UAUUGUU___UACG\n3'-UUU...ACUAC______________CGCAG...AAG-5'\n_____________\|______________\|\n_____________21_____________9\n	201 -- 207	14 -- 20	-8.41213 kcal/mol	2.93934 kcal/mol	1.22774 kcal/mol	200 215@LB@ \| \|@LB@5'-CUA...GAAGA AGU AUUAG...AUU-3'@LB@ AUGACAA AUGC@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UAUUGUU UACG@LB@3'-UUU...ACUAC CGCAG...AAG-5'@LB@ \| \|@LB@ 21 9@LB@@LB@@LB@Energy -4.25 kcal/mol@LB@Hybridization Energy -8.41213 kcal/mol@LB@Unfolding Energy - mRNA 2.93934 kcal/mol@LB@Unfolding Energy - sRNA 1.22774 kcal/mol@LB@@LB@Position - mRNA 201 -- 214@LB@Position - sRNA 10 -- 20@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 14 -- 20@LB@
181	0.01793	0.3104	b1594	mlc	-11.10	0.078496	11 -- 37	1 -- 18	glucosamine anaerobic growth regulon transcriptional repressor; autorepressor	_____________10__________________________38\n_____________\|___________________________\|\n5'-AAA...UCAUG______GUCCGGC_______AA_____GUAUU...GUA-3'\n______________AACAAA_______UGCGCGU__CUUUC\n______________\|\|\|\|\|\|_______\|\|\|\|\|\|\|__\|\|\|\|\|\n______________UUGUUU_______ACGCGCA__GAAAG\n3'-UUU...UACUA___________________________-5'\n_____________\|__________________________\|\n_____________19_________________________1\n	24 -- 30	6 -- 12	-16.8416 kcal/mol	4.49753 kcal/mol	1.24077 kcal/mol	10 38@LB@ \| \|@LB@5'-AAA...UCAUG GUCCGGC AA GUAUU...GUA-3'@LB@ AACAAA UGCGCGU CUUUC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUU ACGCGCA GAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -16.8416 kcal/mol@LB@Unfolding Energy - mRNA 4.49753 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 11 -- 37@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 6 -- 12@LB@
172	0.01719	0.3104	b0678	nagB	-13.42	0.030481	5 -- 26	1 -- 17	glucosamine-6-phosphate deaminase	_____________4______________________27\n_____________\|______________________\|\n_______5'-UAUC______UAAAC___________GUGAG...GUC-3'\n______________GCAAAU_____GCGUGUCUUUU\n______________:\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|:\n______________UGUUUA_____CGCGCAGAAAG\n3'-UUU...ACUAU______________________-5'\n_____________\|_____________________\|\n_____________18____________________1\n	20 -- 26	1 -- 7	-18.2092 kcal/mol	3.54695 kcal/mol	1.23994 kcal/mol	4 27@LB@ \| \|@LB@ 5'-UAUC UAAAC GUGAG...GUC-3'@LB@ GCAAAU GCGUGUCUUUU@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:@LB@ UGUUUA CGCGCAGAAAG@LB@3'-UUU...ACUAU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -18.2092 kcal/mol@LB@Unfolding Energy - mRNA 3.54695 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 5 -- 26@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
148	0.01421	0.3104	b2379	alaC	-8.54	0.209762	290 -- 297	5 -- 12	glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase	_____________289______298\n_____________\|________\|\n5'-UGU...AUGGC________GGC-3'\n______________UGCGCGUC\n______________\|\|\|\|\|\|\|\|\n______________ACGCGCAG\n3'-UUU...UGUUU________AAAG-5'\n_____________\|________\|\n_____________13_______4\n	291 -- 297	5 -- 11	-14.909 kcal/mol	5.25295 kcal/mol	1.11508 kcal/mol	289 298@LB@ \| \|@LB@5'-UGU...AUGGC GGC-3'@LB@ UGCGCGUC@LB@ \|\|\|\|\|\|\|\|@LB@ ACGCGCAG@LB@3'-UUU...UGUUU AAAG-5'@LB@ \| \|@LB@ 13 4@LB@@LB@@LB@Energy -8.54 kcal/mol@LB@Hybridization Energy -14.909 kcal/mol@LB@Unfolding Energy - mRNA 5.25295 kcal/mol@LB@Unfolding Energy - sRNA 1.11508 kcal/mol@LB@@LB@Position - mRNA 290 -- 297@LB@Position - sRNA 5 -- 12@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 5 -- 11@LB@
77	0.007102	0.3087	b0832	gsiD	-8.78	0.192254	77 -- 85	7 -- 15	glutathione ABC transporter permease	_____________76________86\n_____________\|_________\|\n5'-UUG...CGUAG_________AUUAC...GAU-3'\n______________AAAUGCGUG\n______________\|\|\|\|\|\|\|:\|\n______________UUUACGCGC\n3'-UUU...UAUUG_________AGAAAG-5'\n_____________\|_________\|\n_____________16________6\n	79 -- 85	7 -- 13	-12.0627 kcal/mol	2.10506 kcal/mol	1.17837 kcal/mol	76 86@LB@ \| \|@LB@5'-UUG...CGUAG AUUAC...GAU-3'@LB@ AAAUGCGUG@LB@ \|\|\|\|\|\|\|:\|@LB@ UUUACGCGC@LB@3'-UUU...UAUUG AGAAAG-5'@LB@ \| \|@LB@ 16 6@LB@@LB@@LB@Energy -8.78 kcal/mol@LB@Hybridization Energy -12.0627 kcal/mol@LB@Unfolding Energy - mRNA 2.10506 kcal/mol@LB@Unfolding Energy - sRNA 1.17837 kcal/mol@LB@@LB@Position - mRNA 77 -- 85@LB@Position - sRNA 7 -- 15@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 7 -- 13@LB@
102	0.01008	0.3104	b3500	gor	-8.16	0.240292	285 -- 295	4 -- 15	glutathione oxidoreductase	_____________284__________296\n_____________\|____________\|\n5'-GGC...GCCAG____________GAUUG-3'\n______________AAAUGUGCG_CU\n______________\|\|\|\|\|:\|\|\|_\|\|\n______________UUUACGCGC_GA\n3'-UUU...UAUUG_________A__AAG-5'\n_____________\|____________\|\n_____________16___________3\n	287 -- 293	7 -- 13	-12.6909 kcal/mol	3.32128 kcal/mol	1.20666 kcal/mol	284 296@LB@ \| \|@LB@5'-GGC...GCCAG GAUUG-3'@LB@ AAAUGUGCG CU@LB@ \|\|\|\|\|:\|\|\| \|\|@LB@ UUUACGCGC GA@LB@3'-UUU...UAUUG A AAG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -12.6909 kcal/mol@LB@Unfolding Energy - mRNA 3.32128 kcal/mol@LB@Unfolding Energy - sRNA 1.20666 kcal/mol@LB@@LB@Position - mRNA 285 -- 295@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 7 -- 13@LB@
14	0.0004057	0.09812	b0886	cydC	-15.95	0.010534	194 -- 211	2 -- 21	glutathione/cysteine ABC transporter export permease/ATPase	_____________193__________________212\n_____________\|____________________\|\n5'-GCG...GAGGA___U________________GCUAC...UCG-3'\n______________GAU__UAAAUGCGCG_CUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUA__GUUUACGCGC_GAAA\n3'-UUU...UACUA___UU__________A____G-5'\n_____________\|____________________\|\n_____________22___________________1\n	201 -- 207	7 -- 13	-19.6155 kcal/mol	2.41081 kcal/mol	1.25756 kcal/mol	193 212@LB@ \| \|@LB@5'-GCG...GAGGA U GCUAC...UCG-3'@LB@ GAU UAAAUGCGCG CUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUA GUUUACGCGC GAAA@LB@3'-UUU...UACUA UU A G-5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -19.6155 kcal/mol@LB@Unfolding Energy - mRNA 2.41081 kcal/mol@LB@Unfolding Energy - sRNA 1.25756 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 2 -- 21@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
166	0.01595	0.3104	b3560	glyQ	-10.24	0.110293	22 -- 29	7 -- 14	glycine tRNA synthetase alpha subunit	_____________21_______30\n_____________\|________\|\n5'-ACA...UAUGA________GUUAU...UGG-3'\n______________AAUGCGCG\n______________\|\|\|\|\|\|\|\|\n______________UUACGCGC\n3'-UUU...AUUGU________AGAAAG-5'\n_____________\|________\|\n_____________15_______6\n	23 -- 29	7 -- 13	-12.7168 kcal/mol	1.35517 kcal/mol	1.11978 kcal/mol	21 30@LB@ \| \|@LB@5'-ACA...UAUGA GUUAU...UGG-3'@LB@ AAUGCGCG@LB@ \|\|\|\|\|\|\|\|@LB@ UUACGCGC@LB@3'-UUU...AUUGU AGAAAG-5'@LB@ \| \|@LB@ 15 6@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -12.7168 kcal/mol@LB@Unfolding Energy - mRNA 1.35517 kcal/mol@LB@Unfolding Energy - sRNA 1.11978 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 7 -- 14@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 7 -- 13@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