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
131	0.004483	0.1204	b2069	yegD	-6.32	0.360285	213 -- 222	48 -- 57	Hsp70 chaperone family protein	_____________212________223\n_____________\|__________\|\n5'-CAC...UUGGU__________GUACA...UGC-3'\n______________UUUGAUUACG\n______________\|::\|\|\|\|\|\|\|\n______________AGGCUAAUGC\n3'-AUU...GGUUU__________ACUUC...AUG-5'\n_____________\|__________\|\n_____________58_________47\n	216 -- 222	48 -- 54	-10.2333 kcal/mol	2.33693 kcal/mol	1.55976 kcal/mol	212 223@LB@ \| \|@LB@5'-CAC...UUGGU GUACA...UGC-3'@LB@ UUUGAUUACG@LB@ \|::\|\|\|\|\|\|\|@LB@ AGGCUAAUGC@LB@3'-AUU...GGUUU ACUUC...AUG-5'@LB@ \| \|@LB@ 58 47@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -10.2333 kcal/mol@LB@Unfolding Energy - mRNA 2.33693 kcal/mol@LB@Unfolding Energy - sRNA 1.55976 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 48 -- 57@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 48 -- 54@LB@
132	0.004657	0.1239	b1200	dhaK	-7.52	0.201505	172 -- 179	1 -- 8	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit	_____________171______180\n_____________\|________\|\n5'-UUC...AUCCA________CGUAA...UGU-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	173 -- 179	1 -- 7	-12.1513 kcal/mol	2.5392 kcal/mol	2.11603 kcal/mol	171 180@LB@ \| \|@LB@5'-UUC...AUCCA CGUAA...UGU-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -12.1513 kcal/mol@LB@Unfolding Energy - mRNA 2.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 172 -- 179@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.004686	0.1239	b3081	fadH	-11.00	0.022420	2 -- 21	1 -- 24	2 4-dienoyl-CoA reductase NADH and FMN-linked	_____________1________________________22\n_____________\|________________________\|\n__________5'-U_____C__________________AUGUG...ACC-3'\n______________GGACG_CUUAUC_C___GCCCUAC\n______________\|:\|\|:_\|\|\|\|:\|_\|___:\|\|\|\|\|\|\n______________CUUGU_GAAUGG_G___UGGGAUG\n3'-AUU...UCUAU_____A______A_ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	15 -- 21	1 -- 7	-21.5738 kcal/mol	2.57038 kcal/mol	8.02158 kcal/mol	1 22@LB@ \| \|@LB@ 5'-U C AUGUG...ACC-3'@LB@ GGACG CUUAUC C GCCCUAC@LB@ \|:\|\|: \|\|\|\|:\| \| :\|\|\|\|\|\|@LB@ CUUGU GAAUGG G UGGGAUG@LB@3'-AUU...UCUAU A A ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -21.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.57038 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 2 -- 21@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 1 -- 7@LB@
134	0.004727	0.1241	b1655	mepH	-9.70	0.055155	231 -- 243	1 -- 13	murein DD-endopeptidase space-maker hydrolase	_____________230___________244\n_____________\|_____________\|\n5'-CGU...UCACG_____________UUUUU...AGA-3'\n______________CUCUGUGCUUUAC\n______________\|\|\|\|\|\|:\|::\|\|\|\n______________GAGACAUGGGAUG\n3'-AUU...GAAUG_____________-5'\n_____________\|____________\|\n_____________14___________1\n	237 -- 243	1 -- 7	-18.9465 kcal/mol	4.13106 kcal/mol	5.13393 kcal/mol	230 244@LB@ \| \|@LB@5'-CGU...UCACG UUUUU...AGA-3'@LB@ CUCUGUGCUUUAC@LB@ \|\|\|\|\|\|:\|::\|\|\|@LB@ GAGACAUGGGAUG@LB@3'-AUU...GAAUG -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -18.9465 kcal/mol@LB@Unfolding Energy - mRNA 4.13106 kcal/mol@LB@Unfolding Energy - sRNA 5.13393 kcal/mol@LB@@LB@Position - mRNA 231 -- 243@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
135	0.004796	0.125	b3634	coaD	-9.06	0.083023	69 -- 85	49 -- 66	pantetheine-phosphate adenylyltransferase	_____________68_________________86\n_____________\|__________________\|\n5'-GGA...UUUAC________CG________CGUAG...UUC-3'\n______________UCA_CCGA__CCGAUUAC\n______________\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|\n______________AGU_GGUU__GGCUAAUG\n3'-AUU...UUAUA___C____UA________CACUU...AUG-5'\n_____________\|__________________\|\n_____________67_________________48\n	79 -- 85	49 -- 55	-17.7938 kcal/mol	2.54845 kcal/mol	6.20469 kcal/mol	68 86@LB@ \| \|@LB@5'-GGA...UUUAC CG CGUAG...UUC-3'@LB@ UCA CCGA CCGAUUAC@LB@ \|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AGU GGUU GGCUAAUG@LB@3'-AUU...UUAUA C UA CACUU...AUG-5'@LB@ \| \|@LB@ 67 48@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -17.7938 kcal/mol@LB@Unfolding Energy - mRNA 2.54845 kcal/mol@LB@Unfolding Energy - sRNA 6.20469 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 49 -- 66@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 49 -- 55@LB@
136	0.004892	0.1265	b2349	intS	-8.19	0.139381	273 -- 281	3 -- 11	CPS-53 (KpLE1) prophage; putative prophage CPS-53 integrase	_____________272_______282\n_____________\|_________\|\n5'-AAG...AUGGC_________UAUGU...GGA-3'\n______________CUGUACCUU\n______________\|\|\|\|\|\|\|:\|\n______________GACAUGGGA\n3'-AUU...AUGGA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	275 -- 281	3 -- 9	-13.0022 kcal/mol	1.37836 kcal/mol	3.45478 kcal/mol	272 282@LB@ \| \|@LB@5'-AAG...AUGGC UAUGU...GGA-3'@LB@ CUGUACCUU@LB@ \|\|\|\|\|\|\|:\|@LB@ GACAUGGGA@LB@3'-AUU...AUGGA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -13.0022 kcal/mol@LB@Unfolding Energy - mRNA 1.37836 kcal/mol@LB@Unfolding Energy - sRNA 3.45478 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
137	0.004974	0.127	b0092	ddlB	-6.99	0.263821	283 -- 297	43 -- 56	D-alanine:D-alanine ligase	_____________282_____________298\n_____________\|_______________\|\n5'-UUC...GUUAG____AC_________GCG-3'\n______________CCGG__UGCGUGAAG\n______________\|\|\|:__\|:\|\|\|\|\|\|\|\n______________GGCU__AUGCACUUC\n3'-AUU...GUUUA____A__________AUUUU...AUG-5'\n_____________\|_______________\|\n_____________57______________42\n	291 -- 297	43 -- 49	-17.3937 kcal/mol	7.14584 kcal/mol	3.27327 kcal/mol	282 298@LB@ \| \|@LB@5'-UUC...GUUAG AC GCG-3'@LB@ CCGG UGCGUGAAG@LB@ \|\|\|: \|:\|\|\|\|\|\|\|@LB@ GGCU AUGCACUUC@LB@3'-AUU...GUUUA A AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -17.3937 kcal/mol@LB@Unfolding Energy - mRNA 7.14584 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
138	0.004994	0.127	b3633	waaA	-9.37	0.068643	230 -- 259	48 -- 75	3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)	_____________229____________________________260\n_____________\|______________________________\|\n5'-UCG...CUUCU___CCU__________CU_______A____GCUCU...AAC-3'\n______________CUA___UAUUCAGCCG__GAUCUGG_UACG\n______________\|\|\|___\|\|\|\|\|\|\|\|\|:__:\|\|\|:\|:_\|\|\|\|\n______________GAU___AUAAGUCGGU__UUAGGCU_AUGC\n3'-AUU...CCGCC___UUU___________________A____ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________76_____________________________47\n	248 -- 254	53 -- 59	-25.3567 kcal/mol	8.33931 kcal/mol	7.67232 kcal/mol	229 260@LB@ \| \|@LB@5'-UCG...CUUCU CCU CU A GCUCU...AAC-3'@LB@ CUA UAUUCAGCCG GAUCUGG UACG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|: :\|\|\|:\|: \|\|\|\|@LB@ GAU AUAAGUCGGU UUAGGCU AUGC@LB@3'-AUU...CCGCC UUU A ACUUC...AUG-5'@LB@ \| \|@LB@ 76 47@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -25.3567 kcal/mol@LB@Unfolding Energy - mRNA 8.33931 kcal/mol@LB@Unfolding Energy - sRNA 7.67232 kcal/mol@LB@@LB@Position - mRNA 230 -- 259@LB@Position - sRNA 48 -- 75@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 53 -- 59@LB@
139	0.005017	0.127	b2603	yfiR	-11.92	0.011246	223 -- 243	1 -- 19	putative periplasmic inhibitor of YfiN activity	_____________222___________________244\n_____________\|_____________________\|\n5'-GUA...ACUGU___________AUUC______UGACG...GUA-3'\n______________UCUUACUUCUG____UCCUGC\n______________\|\|\|\|\|\|:\|\|\|\|____:\|\|\|:\|\n______________AGAAUGGAGAC____GGGAUG\n3'-AUU...CUUGU___________AU________-5'\n_____________\|____________________\|\n_____________20___________________1\n	227 -- 233	9 -- 15	-21.8705 kcal/mol	2.00959 kcal/mol	7.96751 kcal/mol	222 244@LB@ \| \|@LB@5'-GUA...ACUGU AUUC UGACG...GUA-3'@LB@ UCUUACUUCUG UCCUGC@LB@ \|\|\|\|\|\|:\|\|\|\| :\|\|\|:\|@LB@ AGAAUGGAGAC GGGAUG@LB@3'-AUU...CUUGU AU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -21.8705 kcal/mol@LB@Unfolding Energy - mRNA 2.00959 kcal/mol@LB@Unfolding Energy - sRNA 7.96751 kcal/mol@LB@@LB@Position - mRNA 223 -- 243@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 9 -- 15@LB@
140	0.005114	0.1284	b3993	thiE	-7.64	0.188958	243 -- 250	4 -- 11	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)	_____________242______251\n_____________\|________\|\n5'-CAC...CAGGA________GGUGG...UAC-3'\n______________CUGUACCC\n______________\|\|\|\|\|\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	244 -- 250	4 -- 10	-13.9053 kcal/mol	2.83489 kcal/mol	3.45361 kcal/mol	242 251@LB@ \| \|@LB@5'-CAC...CAGGA GGUGG...UAC-3'@LB@ CUGUACCC@LB@ \|\|\|\|\|\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -13.9053 kcal/mol@LB@Unfolding Energy - mRNA 2.83489 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 243 -- 250@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 4 -- 10@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