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	Additional homologs
116	0.003844	0.1165	b1004	wrbA	-12.42	0.007537	123 -- 145	10 -- 35	NAD(P)H:quinone oxidoreductase		_____________122________________________146\n_____________\|__________________________\|\n5'-UUA...UGCAC__________________________AAAUA...AAG-3'\n______________UCUGAAA___AGGACGUCUUAUCUUU\n______________\|\|\|\|\|\|\|___\|\|:\|\|:\|\|\|\|\|:\|\|:\|\n______________AGACUUU___UCUUGUAGAAUGGAGA\n3'-AUU...UUUCC_______CUA________________CAUGG...AUG-5'\n_____________\|__________________________\|\n_____________36_________________________9\n	133 -- 139	16 -- 22	-25.4666 kcal/mol	4.32254 kcal/mol	8.70229 kcal/mol	122 146@LB@ \| \|@LB@5'-UUA...UGCAC AAAUA...AAG-3'@LB@ UCUGAAA AGGACGUCUUAUCUUU@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\|\|:\|\|:\|@LB@ AGACUUU UCUUGUAGAAUGGAGA@LB@3'-AUU...UUUCC CUA CAUGG...AUG-5'@LB@ \| \|@LB@ 36 9@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -25.4666 kcal/mol@LB@Unfolding Energy - mRNA 4.32254 kcal/mol@LB@Unfolding Energy - sRNA 8.70229 kcal/mol@LB@@LB@Position - mRNA 123 -- 145@LB@Position - sRNA 10 -- 35@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 16 -- 22@LB@
46	0.0005017	0.03778	b1713	pheT	-7.80	0.173677	95 -- 107	17 -- 29	phenylalanine tRNA synthetase beta subunit		_____________94____________108\n_____________\|_____________\|\n5'-CUG...GAUGG_____________GACUA...ACG-3'\n______________GGAUGGAGCGUCU\n______________:\|\|\|:\|\|:\|:\|\|\|\n______________UCUAUCUUGUAGA\n3'-AUU...GACUU_____________AUGGA...AUG-5'\n_____________\|_____________\|\n_____________30____________16\n	100 -- 106	18 -- 24	-17.5948 kcal/mol	5.55471 kcal/mol	4.26164 kcal/mol	94 108@LB@ \| \|@LB@5'-CUG...GAUGG GACUA...ACG-3'@LB@ GGAUGGAGCGUCU@LB@ :\|\|\|:\|\|:\|:\|\|\|@LB@ UCUAUCUUGUAGA@LB@3'-AUU...GACUU AUGGA...AUG-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.5948 kcal/mol@LB@Unfolding Energy - mRNA 5.55471 kcal/mol@LB@Unfolding Energy - sRNA 4.26164 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 18 -- 24@LB@
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent		_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
128	0.004347	0.1195	b3690	cbrA	-9.56	0.060736	197 -- 211	17 -- 31	colicin M resistance protein; FAD-binding protein putative oxidoreductase		_____________196_____________212\n_____________\|_______________\|\n5'-CAG...AGUGA_______________CGACG...AAA-3'\n______________AAAGAUGGAACAUUU\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\n______________UUUCUAUCUUGUAGA\n3'-AUU...CAGAC_______________AUGGA...AUG-5'\n_____________\|_______________\|\n_____________32______________16\n	204 -- 210	18 -- 24	-17.0326 kcal/mol	3.22818 kcal/mol	4.26586 kcal/mol	196 212@LB@ \| \|@LB@5'-CAG...AGUGA CGACG...AAA-3'@LB@ AAAGAUGGAACAUUU@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|@LB@ UUUCUAUCUUGUAGA@LB@3'-AUU...CAGAC AUGGA...AUG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -17.0326 kcal/mol@LB@Unfolding Energy - mRNA 3.22818 kcal/mol@LB@Unfolding Energy - sRNA 4.26586 kcal/mol@LB@@LB@Position - mRNA 197 -- 211@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
13	4.485e-05	0.01183	b0511	ybbW	-13.60	0.002717	173 -- 210	18 -- 58	putative allantoin transporter		_____________172________________________________________211\n_____________\|__________________________________________\|\n5'-UGG...ACGUU_______________AU____________UUU__________AGAGA...UUA-3'\n______________AUUCGA_UACGUGAA__UAAGAGG___GA___AUGGAACAUC\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|\|__\|\|\|:\|\|\|___\|\|___\|\|:\|\|\|\|\|\|\|\n______________UAGGCU_AUGCACUU__AUUUUCC___CU___UAUCUUGUAG\n3'-AUU...CGGUU______A________C________AGA__UUC__________AAUGG...AUG-5'\n_____________\|__________________________________________\|\n_____________59_________________________________________17\n	204 -- 210	18 -- 24	-34.0515 kcal/mol	8.25655 kcal/mol	12.1809 kcal/mol	172 211@LB@ \| \|@LB@5'-UGG...ACGUU AU UUU AGAGA...UUA-3'@LB@ AUUCGA UACGUGAA UAAGAGG GA AUGGAACAUC@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|:\|\|\| \|\| \|\|:\|\|\|\|\|\|\|@LB@ UAGGCU AUGCACUU AUUUUCC CU UAUCUUGUAG@LB@3'-AUU...CGGUU A C AGA UUC AAUGG...AUG-5'@LB@ \| \|@LB@ 59 17@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -34.0515 kcal/mol@LB@Unfolding Energy - mRNA 8.25655 kcal/mol@LB@Unfolding Energy - sRNA 12.1809 kcal/mol@LB@@LB@Position - mRNA 173 -- 210@LB@Position - sRNA 18 -- 58@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
67	0.001147	0.05856	b2319	usg	-10.96	0.023185	203 -- 221	18 -- 36	putative semialdehyde dehydrogenase		_____________202_________________222\n_____________\|___________________\|\n5'-GAG...ACCAU_________C_________GCCGU...AAA-3'\n______________GUCUGAAGG_UGGAACAUU\n______________\|\|\|\|\|\|\|:\|_\|:\|\|\|\|\|\|:\n______________CAGACUUUC_AUCUUGUAG\n3'-AUU...UUUUC_________U_________AAUGG...AUG-5'\n_____________\|___________________\|\n_____________37__________________17\n	215 -- 221	18 -- 24	-22.956 kcal/mol	5.32254 kcal/mol	6.60045 kcal/mol	202 222@LB@ \| \|@LB@5'-GAG...ACCAU C GCCGU...AAA-3'@LB@ GUCUGAAGG UGGAACAUU@LB@ \|\|\|\|\|\|\|:\| \|:\|\|\|\|\|\|:@LB@ CAGACUUUC AUCUUGUAG@LB@3'-AUU...UUUUC U AAUGG...AUG-5'@LB@ \| \|@LB@ 37 17@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -22.956 kcal/mol@LB@Unfolding Energy - mRNA 5.32254 kcal/mol@LB@Unfolding Energy - sRNA 6.60045 kcal/mol@LB@@LB@Position - mRNA 203 -- 221@LB@Position - sRNA 18 -- 36@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 18 -- 24@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@
53	0.0007581	0.04961	b1302	puuE	-16.93	0.000076	166 -- 207	20 -- 57	4-aminobutyrate aminotransferase PLP-dependent	b2662	_____________165_________________________________________208\n_____________\|___________________________________________\|\n5'-AGC...UAAUU________AC_______AGUC_______G_____C________ACAAU...CGC-3'\n______________UCCGAUUA__CGUGAAG____AAAAGGU_UGAAA_AU_GAGCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|____\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|_\|\|:\|\|\n______________AGGCUAAU__GCACUUC____UUUUCCA_ACUUU_UA_CUUGU\n3'-AUU...GGUUU_________________A__________G_____C__U_____AGAAU...AUG-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________19\n	176 -- 182	43 -- 49	-36.956 kcal/mol	7.85943 kcal/mol	12.1551 kcal/mol	165 208@LB@ \| \|@LB@5'-AGC...UAAUU AC AGUC G C ACAAU...CGC-3'@LB@ UCCGAUUA CGUGAAG AAAAGGU UGAAA AU GAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|:\|\|@LB@ AGGCUAAU GCACUUC UUUUCCA ACUUU UA CUUGU@LB@3'-AUU...GGUUU A G C U AGAAU...AUG-5'@LB@ \| \|@LB@ 58 19@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -36.956 kcal/mol@LB@Unfolding Energy - mRNA 7.85943 kcal/mol@LB@Unfolding Energy - sRNA 12.1551 kcal/mol@LB@@LB@Position - mRNA 166 -- 207@LB@Position - sRNA 20 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 43 -- 49@LB@
110	0.003442	0.1101	b0528	ybcJ	-8.36	0.126664	258 -- 272	21 -- 34	ribosome-associated protein; putative RNA-binding protein		_____________257_____________273\n_____________\|_______________\|\n5'-AGG...UGAAA________C______GAAAG...CGA-3'\n______________CUGGAAGG_UGGAGC\n______________\|\|\|:\|\|\|:_\|:\|\|:\|\n______________GACUUUCU_AUCUUG\n3'-AUU...UUCCA_______________UAGAA...AUG-5'\n_____________\|_______________\|\n_____________35______________20\n	259 -- 265	27 -- 33	-15.4755 kcal/mol	3.05057 kcal/mol	4.02417 kcal/mol	257 273@LB@ \| \|@LB@5'-AGG...UGAAA C GAAAG...CGA-3'@LB@ CUGGAAGG UGGAGC@LB@ \|\|\|:\|\|\|: \|:\|\|:\|@LB@ GACUUUCU AUCUUG@LB@3'-AUU...UUCCA UAGAA...AUG-5'@LB@ \| \|@LB@ 35 20@LB@@LB@@LB@Energy -8.36 kcal/mol@LB@Hybridization Energy -15.4755 kcal/mol@LB@Unfolding Energy - mRNA 3.05057 kcal/mol@LB@Unfolding Energy - sRNA 4.02417 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 21 -- 34@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 27 -- 33@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase		_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@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