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
31	0.0003178	0.03519	b3588	aldB	-11.98	0.010708	83 -- 100	1 -- 16	aldehyde dehydrogenase B	_____________82_________________101\n_____________\|__________________\|\n5'-GAA...UCAAC__________A___U___CCGUA...GGG-3'\n______________UAUCUCUGUA_CCC_UGC\n______________\|\|:\|\|\|\|\|\|\|_\|\|\|_\|:\|\n______________AUGGAGACAU_GGG_AUG\n3'-AUU...GUAGA__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	86 -- 92	7 -- 13	-19.6311 kcal/mol	1.07825 kcal/mol	6.59719 kcal/mol	82 101@LB@ \| \|@LB@5'-GAA...UCAAC A U CCGUA...GGG-3'@LB@ UAUCUCUGUA CCC UGC@LB@ \|\|:\|\|\|\|\|\|\| \|\|\| \|:\|@LB@ AUGGAGACAU GGG AUG@LB@3'-AUU...GUAGA -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.6311 kcal/mol@LB@Unfolding Energy - mRNA 1.07825 kcal/mol@LB@Unfolding Energy - sRNA 6.59719 kcal/mol@LB@@LB@Position - mRNA 83 -- 100@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 7 -- 13@LB@
32	0.0003261	0.03519	b2789	gudP	-8.38	0.124980	121 -- 127	1 -- 7	putative D-glucarate transporter	_____________120_____128\n_____________\|_______\|\n5'-UGA...AAAAC_______GUCAC...ACG-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.2076 kcal/mol	0.809325 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UGA...AAAAC GUCAC...ACG-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.38 kcal/mol@LB@Hybridization Energy -11.2076 kcal/mol@LB@Unfolding Energy - mRNA 0.809325 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
33	0.0003369	0.03519	b0523	purE	-12.01	0.010423	150 -- 160	3 -- 13	N5-carboxyaminoimidazole ribonucleotide mutase	_____________149__________161\n_____________\|____________\|\n5'-UGG...GCUAU____________CUAAA...UGA-3'\n______________UCUCUGUGCCCU\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GGAGACAUGGGA\n3'-AUU...AGAAU____________UG-5'\n_____________\|____________\|\n_____________14___________2\n	154 -- 160	3 -- 9	-20.2448 kcal/mol	2.89849 kcal/mol	5.35591 kcal/mol	149 161@LB@ \| \|@LB@5'-UGG...GCUAU CUAAA...UGA-3'@LB@ UCUCUGUGCCCU@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GGAGACAUGGGA@LB@3'-AUU...AGAAU UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -20.2448 kcal/mol@LB@Unfolding Energy - mRNA 2.89849 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 150 -- 160@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
34	0.0003499	0.03519	b0333	prpC	-9.01	0.085770	169 -- 175	1 -- 7	2-methylcitrate synthase	_____________168_____176\n_____________\|_______\|\n5'-ACU...UCUCG_______AAAUG...GCA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	169 -- 175	1 -- 7	-11.7504 kcal/mol	0.722985 kcal/mol	2.03949 kcal/mol	168 176@LB@ \| \|@LB@5'-ACU...UCUCG AAAUG...GCA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -11.7504 kcal/mol@LB@Unfolding Energy - mRNA 0.722985 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 169 -- 175@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
35	0.0003501	0.03519	b2700	pncC	-8.73	0.102058	11 -- 28	20 -- 37	nicotinamide-nucleotide amidohydrolase; NMN amidohydrolase	_____________10_________________29\n_____________\|__________________\|\n5'-ACG...AUGGC_______C__U_______AGCCG...GUU-3'\n______________GGUCUGG_AG_UAGGACA\n______________\|\|\|\|\|\|:_\|\|_\|\|\|:\|\|\|\n______________CCAGACU_UC_AUCUUGU\n3'-AUU...AUUUU_______U__U_______AGAAU...AUG-5'\n_____________\|__________________\|\n_____________38_________________19\n	22 -- 28	20 -- 26	-19.0339 kcal/mol	5.51285 kcal/mol	4.72108 kcal/mol	10 29@LB@ \| \|@LB@5'-ACG...AUGGC C U AGCCG...GUU-3'@LB@ GGUCUGG AG UAGGACA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|\|@LB@ CCAGACU UC AUCUUGU@LB@3'-AUU...AUUUU U U AGAAU...AUG-5'@LB@ \| \|@LB@ 38 19@LB@@LB@@LB@Energy -8.73 kcal/mol@LB@Hybridization Energy -19.0339 kcal/mol@LB@Unfolding Energy - mRNA 5.51285 kcal/mol@LB@Unfolding Energy - sRNA 4.72108 kcal/mol@LB@@LB@Position - mRNA 11 -- 28@LB@Position - sRNA 20 -- 37@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 20 -- 26@LB@
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase	_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@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@
38	0.0004278	0.03766	b3092	uxaC	-12.53	0.006845	206 -- 269	1 -- 57	uronate isomerase	_____________205_________________________________________________________________270\n_____________\|___________________________________________________________________\|\n5'-UUG...AUGAC____U_____AC_____AUUUC______UU_____CC____UUGCCC___G________ACGA____GCAAA...AUU-3'\n______________UCCG_UUAUG__UGAAG________CUG__AGAUA__GAAU______GCC_UCUGUAUC____CUAC\n______________\|\|\|\|_\|\|\|:\|__\|\|\|\|\|________\|\|\|__\|\|\|\|\|__\|\|\|:______:\|\|_\|\|\|\|\|\|:\|____\|\|\|\|\n______________AGGC_AAUGC__ACUUC________GAC__UCUAU__CUUG______UGG_AGACAUGG____GAUG\n3'-AUU...GGUUU____U____________AUUUUCCA___UU___________UAGAA_____________________-5'\n_____________\|__________________________________________________________________\|\n_____________58_________________________________________________________________1\n	255 -- 261	5 -- 11	-36.5836 kcal/mol	11.3711 kcal/mol	12.7026 kcal/mol	205 270@LB@ \| \|@LB@5'-UUG...AUGAC U AC AUUUC UU CC UUGCCC G ACGA GCAAA...AUU-3'@LB@ UCCG UUAUG UGAAG CUG AGAUA GAAU GCC UCUGUAUC CUAC@LB@ \|\|\|\| \|\|\|:\| \|\|\|\|\| \|\|\| \|\|\|\|\| \|\|\|: :\|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ AGGC AAUGC ACUUC GAC UCUAU CUUG UGG AGACAUGG GAUG@LB@3'-AUU...GGUUU U AUUUUCCA UU UAGAA -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -36.5836 kcal/mol@LB@Unfolding Energy - mRNA 11.3711 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 206 -- 269@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 5 -- 11@LB@
39	0.0004396	0.03766	b3669	uhpA	-8.50	0.116685	77 -- 96	47 -- 66	response regulator in two-component regulatory system wtih UhpB	_____________76___________________97\n_____________\|____________________\|\n5'-UCA...CGUAA______C_______CG____UUAAC...UUG-3'\n______________UCAGUC_GAUCCGA__AUGU\n______________\|\|\|\|:\|_:\|\|\|\|\|\|__\|:\|\|\n______________AGUCGG_UUAGGCU__UGCA\n3'-AUU...UUAUA______U_______AA____CUUCA...AUG-5'\n_____________\|____________________\|\n_____________67___________________46\n	84 -- 90	53 -- 59	-21.6061 kcal/mol	5.63687 kcal/mol	7.4916 kcal/mol	76 97@LB@ \| \|@LB@5'-UCA...CGUAA C CG UUAAC...UUG-3'@LB@ UCAGUC GAUCCGA AUGU@LB@ \|\|\|\|:\| :\|\|\|\|\|\| \|:\|\|@LB@ AGUCGG UUAGGCU UGCA@LB@3'-AUU...UUAUA U AA CUUCA...AUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -21.6061 kcal/mol@LB@Unfolding Energy - mRNA 5.63687 kcal/mol@LB@Unfolding Energy - sRNA 7.4916 kcal/mol@LB@@LB@Position - mRNA 77 -- 96@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 53 -- 59@LB@
40	0.0004513	0.03766	b3291	mscL	-6.99	0.263134	48 -- 58	55 -- 65	mechanosensitive channel protein high conductance	_____________47__________59\n_____________\|___________\|\n5'-UGU...UCUUC________C__UUUCU...UCU-3'\n______________CAGCCAAG_CC\n______________\|\|\|\|\|\|\|:_\|\|\n______________GUCGGUUU_GG\n3'-AUU...UAUAA________A__CUAAU...AUG-5'\n_____________\|___________\|\n_____________66__________54\n	49 -- 55	58 -- 64	-14.9389 kcal/mol	1.90813 kcal/mol	6.05961 kcal/mol	47 59@LB@ \| \|@LB@5'-UGU...UCUUC C UUUCU...UCU-3'@LB@ CAGCCAAG CC@LB@ \|\|\|\|\|\|\|: \|\|@LB@ GUCGGUUU GG@LB@3'-AUU...UAUAA A CUAAU...AUG-5'@LB@ \| \|@LB@ 66 54@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -14.9389 kcal/mol@LB@Unfolding Energy - mRNA 1.90813 kcal/mol@LB@Unfolding Energy - sRNA 6.05961 kcal/mol@LB@@LB@Position - mRNA 48 -- 58@LB@Position - sRNA 55 -- 65@LB@Position Seed - mRNA 49 -- 55@LB@Position Seed - sRNA 58 -- 64@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