Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
122	0.004081	0.1177	b3940	metL	-10.48	0.032541	261 -- 280	41 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________260__________________281\n_____________\|____________________\|\n5'-ACG...GCAGU_______CUG__________UUAUU...GCA-3'\n______________AGUCUGG___AUGUGAAGUG\n______________\|:\|\|:\|:___\|:\|\|\|\|\|\|\|:\n______________UUAGGCU___UGCACUUCAU\n3'-AUU...UCGGU_______AA___________UUUCC...AUG-5'\n_____________\|____________________\|\n_____________60___________________40\n	274 -- 280	41 -- 47	-17.3741 kcal/mol	3.59224 kcal/mol	3.31634 kcal/mol	260 281@LB@ \| \|@LB@5'-ACG...GCAGU CUG UUAUU...GCA-3'@LB@ AGUCUGG AUGUGAAGUG@LB@ \|:\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ UUAGGCU UGCACUUCAU@LB@3'-AUU...UCGGU AA UUUCC...AUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.3741 kcal/mol@LB@Unfolding Energy - mRNA 3.59224 kcal/mol@LB@Unfolding Energy - sRNA 3.31634 kcal/mol@LB@@LB@Position - mRNA 261 -- 280@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
19	8.831e-05	0.01635	b3389	aroB	-10.54	0.031183	4 -- 17	42 -- 56	3-dehydroquinate synthase	_____________3_______________18\n_____________\|_______________\|\n________5'-ACA___CC__________UCUGG...CGG-3'\n______________CCG___GCGUGAAGU\n______________\|\|\|___:\|\|\|\|\|\|\|\|\n______________GGC___UGCACUUCA\n3'-AUU...GUUUA___UAA_________UUUUC...AUG-5'\n_____________\|_______________\|\n_____________57______________41\n	11 -- 17	42 -- 48	-15.9415 kcal/mol	2.13198 kcal/mol	3.27911 kcal/mol	3 18@LB@ \| \|@LB@ 5'-ACA CC UCUGG...CGG-3'@LB@ CCG GCGUGAAGU@LB@ \|\|\| :\|\|\|\|\|\|\|\|@LB@ GGC UGCACUUCA@LB@3'-AUU...GUUUA UAA UUUUC...AUG-5'@LB@ \| \|@LB@ 57 41@LB@@LB@@LB@Energy -10.54 kcal/mol@LB@Hybridization Energy -15.9415 kcal/mol@LB@Unfolding Energy - mRNA 2.13198 kcal/mol@LB@Unfolding Energy - sRNA 3.27911 kcal/mol@LB@@LB@Position - mRNA 4 -- 17@LB@Position - sRNA 42 -- 56@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 42 -- 48@LB@
25	0.0002052	0.02687	b0885	aat	-14.70	0.000956	173 -- 191	42 -- 59	leucyl/phenylalanyl-tRNA-protein transferase	_____________172_________________192\n_____________\|___________________\|\n5'-CGU...UGAAC_______C___________UUUGC...UUA-3'\n______________GAUCCGA_UUGCGUGGAGU\n______________:\|\|\|\|\|\|_\|\|:\|\|\|\|:\|\|\|\n______________UUAGGCU_AAUGCACUUCA\n3'-AUU...UCGGU___________________UUUUC...AUG-5'\n_____________\|___________________\|\n_____________60__________________41\n	185 -- 191	42 -- 48	-23.9715 kcal/mol	6.00825 kcal/mol	3.27976 kcal/mol	172 192@LB@ \| \|@LB@5'-CGU...UGAAC C UUUGC...UUA-3'@LB@ GAUCCGA UUGCGUGGAGU@LB@ :\|\|\|\|\|\| \|\|:\|\|\|\|:\|\|\|@LB@ UUAGGCU AAUGCACUUCA@LB@3'-AUU...UCGGU UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -14.70 kcal/mol@LB@Hybridization Energy -23.9715 kcal/mol@LB@Unfolding Energy - mRNA 6.00825 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 173 -- 191@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 42 -- 48@LB@
28	0.0002139	0.02687	b4174	hflK	-10.82	0.025576	125 -- 140	42 -- 58	modulator for HflB protease specific for phage lambda cII repressor	_____________124_______________141\n_____________\|_________________\|\n5'-AGA...GUAGC______A__________CAUAU...GUC-3'\n______________GUCUGA__GCGUGGAGU\n______________:\|\|:\|\|__:\|\|\|\|:\|\|\|\n______________UAGGCU__UGCACUUCA\n3'-AUU...CGGUU______AA_________UUUUC...AUG-5'\n_____________\|_________________\|\n_____________59________________41\n	134 -- 140	42 -- 48	-18.0833 kcal/mol	3.99428 kcal/mol	3.27972 kcal/mol	124 141@LB@ \| \|@LB@5'-AGA...GUAGC A CAUAU...GUC-3'@LB@ GUCUGA GCGUGGAGU@LB@ :\|\|:\|\| :\|\|\|\|:\|\|\|@LB@ UAGGCU UGCACUUCA@LB@3'-AUU...CGGUU AA UUUUC...AUG-5'@LB@ \| \|@LB@ 59 41@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -18.0833 kcal/mol@LB@Unfolding Energy - mRNA 3.99428 kcal/mol@LB@Unfolding Energy - sRNA 3.27972 kcal/mol@LB@@LB@Position - mRNA 125 -- 140@LB@Position - sRNA 42 -- 58@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 42 -- 48@LB@
59	0.0008996	0.0531	b1310	ycjN	-10.87	0.024752	113 -- 129	42 -- 59	putative ABC sugar transporter periplasmic binding protein	_____________112________________130\n_____________\|__________________\|\n5'-UUC...GUCGG__________________UGAUA...UUA-3'\n______________GAUCUGAUUA_GUGAAGU\n______________:\|\|\|:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAGGCUAAU_CACUUCA\n3'-AUU...UCGGU__________G_______UUUUC...AUG-5'\n_____________\|__________________\|\n_____________60_________________41\n	123 -- 129	42 -- 48	-20.0101 kcal/mol	5.87569 kcal/mol	3.27976 kcal/mol	112 130@LB@ \| \|@LB@5'-UUC...GUCGG UGAUA...UUA-3'@LB@ GAUCUGAUUA GUGAAGU@LB@ :\|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUAGGCUAAU CACUUCA@LB@3'-AUU...UCGGU G UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -20.0101 kcal/mol@LB@Unfolding Energy - mRNA 5.87569 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 113 -- 129@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 42 -- 48@LB@
156	0.006236	0.1406	b2922	yggE	-5.46	0.507768	199 -- 207	42 -- 50	oxidative stress defense protein	_____________198_______208\n_____________\|_________\|\n5'-GCA...GACUA_________UCAAA...CCG-3'\n______________ACGUGAAGU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCACUUCA\n3'-AUU...GCUAA_________UUUUC...AUG-5'\n_____________\|_________\|\n_____________51________41\n	201 -- 207	42 -- 48	-12.7727 kcal/mol	4.07491 kcal/mol	3.2504 kcal/mol	198 208@LB@ \| \|@LB@5'-GCA...GACUA UCAAA...CCG-3'@LB@ ACGUGAAGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCACUUCA@LB@3'-AUU...GCUAA UUUUC...AUG-5'@LB@ \| \|@LB@ 51 41@LB@@LB@@LB@Energy -5.46 kcal/mol@LB@Hybridization Energy -12.7727 kcal/mol@LB@Unfolding Energy - mRNA 4.07491 kcal/mol@LB@Unfolding Energy - sRNA 3.2504 kcal/mol@LB@@LB@Position - mRNA 199 -- 207@LB@Position - sRNA 42 -- 50@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 42 -- 48@LB@
186	0.008252	0.1556	b2026	hisI	-8.65	0.106637	17 -- 26	42 -- 51	phosphoribosyl-AMP cyclohydrolase and phosphoribosyl-ATP pyrophosphatase	_____________16_________27\n_____________\|__________\|\n5'-GAA...AAAAG__________UUGCC...UGC-3'\n______________UGCGUGAAGU\n______________\|:\|\|\|\|\|\|\|\|\n______________AUGCACUUCA\n3'-AUU...GGCUA__________UUUUC...AUG-5'\n_____________\|__________\|\n_____________52_________41\n	20 -- 26	42 -- 48	-13.8545 kcal/mol	1.95631 kcal/mol	3.26026 kcal/mol	16 27@LB@ \| \|@LB@5'-GAA...AAAAG UUGCC...UGC-3'@LB@ UGCGUGAAGU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ AUGCACUUCA@LB@3'-AUU...GGCUA UUUUC...AUG-5'@LB@ \| \|@LB@ 52 41@LB@@LB@@LB@Energy -8.65 kcal/mol@LB@Hybridization Energy -13.8545 kcal/mol@LB@Unfolding Energy - mRNA 1.95631 kcal/mol@LB@Unfolding Energy - sRNA 3.26026 kcal/mol@LB@@LB@Position - mRNA 17 -- 26@LB@Position - sRNA 42 -- 51@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 42 -- 48@LB@
12	3.867e-05	0.01134	b0728	sucC	-9.87	0.049323	145 -- 186	43 -- 73	succinyl-CoA synthetase beta subunit	_____________144_________________________________________187\n_____________\|___________________________________________\|\n5'-CGC...GAUAC_____________UACGGUUUAAA____AA_____________GAUGG...AAG-3'\n______________GAAAUAUUCGGUC___________AGAU__CGAUUAC_UGAAG\n______________:\|\|\|\|\|\|\|\|:\|:\|___________\|:\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUUAUAAGUCGG___________UUUA__GCUAAUG_ACUUC\n3'-AUU...GCCGA____________________________G________C_____AUUUU...AUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________42\n	175 -- 181	49 -- 55	-26.5157 kcal/mol	7.48621 kcal/mol	9.17828 kcal/mol	144 187@LB@ \| \|@LB@5'-CGC...GAUAC UACGGUUUAAA AA GAUGG...AAG-3'@LB@ GAAAUAUUCGGUC AGAU CGAUUAC UGAAG@LB@ :\|\|\|\|\|\|\|\|:\|:\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUUAUAAGUCGG UUUA GCUAAUG ACUUC@LB@3'-AUU...GCCGA G C AUUUU...AUG-5'@LB@ \| \|@LB@ 74 42@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -26.5157 kcal/mol@LB@Unfolding Energy - mRNA 7.48621 kcal/mol@LB@Unfolding Energy - sRNA 9.17828 kcal/mol@LB@@LB@Position - mRNA 145 -- 186@LB@Position - sRNA 43 -- 73@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@LB@
37	0.0003769	0.03584	b1212	prmC	-14.52	0.001141	215 -- 228	43 -- 56	RF-1 and RF-2 N5-glutamine methyltransferase	_____________214____________229\n_____________\|______________\|\n5'-CGU...CAACA______________CAAUA...GCA-3'\n______________CUGGUUACGUGAAG\n______________\|:\|:\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACUUC\n3'-AUU...GUUUA______________AUUUU...AUG-5'\n_____________\|______________\|\n_____________57_____________42\n	222 -- 228	43 -- 49	-20.863 kcal/mol	3.08488 kcal/mol	3.27327 kcal/mol	214 229@LB@ \| \|@LB@5'-CGU...CAACA CAAUA...GCA-3'@LB@ CUGGUUACGUGAAG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACUUC@LB@3'-AUU...GUUUA AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -14.52 kcal/mol@LB@Hybridization Energy -20.863 kcal/mol@LB@Unfolding Energy - mRNA 3.08488 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 43 -- 49@LB@
52	0.0006736	0.04557	b3964	yijD	-9.23	0.074829	177 -- 192	43 -- 57	DUF1422 family inner membrane protein	_____________176______________193\n_____________\|________________\|\n5'-ACU...AUUAU_____GAA________GACGA...UGC-3'\n______________UCCGG___AUGUGAAG\n______________\|\|\|\|:___\|:\|\|\|\|\|\|\n______________AGGCU___UGCACUUC\n3'-AUU...GGUUU_____AA_________AUUUU...AUG-5'\n_____________\|________________\|\n_____________58_______________42\n	186 -- 192	43 -- 49	-16.7307 kcal/mol	4.24116 kcal/mol	3.27382 kcal/mol	176 193@LB@ \| \|@LB@5'-ACU...AUUAU GAA GACGA...UGC-3'@LB@ UCCGG AUGUGAAG@LB@ \|\|\|\|: \|:\|\|\|\|\|\|@LB@ AGGCU UGCACUUC@LB@3'-AUU...GGUUU AA AUUUU...AUG-5'@LB@ \| \|@LB@ 58 42@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -16.7307 kcal/mol@LB@Unfolding Energy - mRNA 4.24116 kcal/mol@LB@Unfolding Energy - sRNA 3.27382 kcal/mol@LB@@LB@Position - mRNA 177 -- 192@LB@Position - sRNA 43 -- 57@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 43 -- 49@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