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
130	0.004431	0.1199	b3355	prkB	-7.29	0.227256	214 -- 220	52 -- 58	putative phosphoribulokinase		_____________213_____221\n_____________\|_______\|\n5'-GGC...CAAAC_______CAUUG...AUC-3'\n______________AUCCGGU\n______________\|\|\|\|\|:\|\n______________UAGGCUA\n3'-AUU...CGGUU_______AUGCA...AUG-5'\n_____________\|_______\|\n_____________59______51\n	214 -- 220	52 -- 58	-8.26146 kcal/mol	0.695321 kcal/mol	0.296688 kcal/mol	213 221@LB@ \| \|@LB@5'-GGC...CAAAC CAUUG...AUC-3'@LB@ AUCCGGU@LB@ \|\|\|\|\|:\|@LB@ UAGGCUA@LB@3'-AUU...CGGUU AUGCA...AUG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -8.26146 kcal/mol@LB@Unfolding Energy - mRNA 0.695321 kcal/mol@LB@Unfolding Energy - sRNA 0.296688 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 52 -- 58@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@
179	0.007709	0.1511	b4111	proP	-8.76	0.100034	225 -- 232	49 -- 56	proline/glycine betaine transporter		_____________224______233\n_____________\|________\|\n5'-CAC...UAAAA________CCUUC...GUA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	226 -- 232	49 -- 55	-10.6643 kcal/mol	1.60159 kcal/mol	0.317884 kcal/mol	224 233@LB@ \| \|@LB@5'-CAC...UAAAA CCUUC...GUA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -10.6643 kcal/mol@LB@Unfolding Energy - mRNA 1.60159 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 49 -- 55@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@
169	0.006985	0.1454	b0384	psiF	-5.27	0.543574	221 -- 228	1 -- 8	PsiF family protein		_____________220______229\n_____________\|________\|\n5'-CCC...CUGGU________UUUUC...UGA-3'\n______________UACCUUGC\n______________\|\|\|\|:\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	222 -- 228	1 -- 7	-9.62499 kcal/mol	2.26355 kcal/mol	2.11603 kcal/mol	220 229@LB@ \| \|@LB@5'-CCC...CUGGU UUUUC...UGA-3'@LB@ UACCUUGC@LB@ \|\|\|\|:\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -5.27 kcal/mol@LB@Hybridization Energy -9.62499 kcal/mol@LB@Unfolding Energy - mRNA 2.26355 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 222 -- 228@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@
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@
119	0.003968	0.1172	b2765	queD	-8.07	0.149030	164 -- 172	1 -- 9	6-pyruvoyl tetrahydrobiopterin synthase (PTPS)		_____________163_______173\n_____________\|_________\|\n5'-AAC...UUCCG_________GGCGG...AUU-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	166 -- 172	1 -- 7	-12.1088 kcal/mol	1.92954 kcal/mol	2.12872 kcal/mol	163 173@LB@ \| \|@LB@5'-AAC...UUCCG GGCGG...AUU-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.07 kcal/mol@LB@Hybridization Energy -12.1088 kcal/mol@LB@Unfolding Energy - mRNA 1.92954 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 164 -- 172@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 1 -- 7@LB@
90	0.002406	0.09404	b0551	quuD	-13.47	0.003063	177 -- 196	40 -- 58	DLP12 prophage; putative antitermination protein		_____________176__________________197\n_____________\|____________________\|\n5'-ACU...UUCUG________UU__________GUUGA...GAU-3'\n______________GUCUGAUU__UGUGGAGUAA\n______________:\|\|:\|\|\|\|__:\|\|\|:\|\|\|\|\|\n______________UAGGCUAA__GCACUUCAUU\n3'-AUU...CGGUU________U___________UUCCA...AUG-5'\n_____________\|____________________\|\n_____________59___________________39\n	190 -- 196	40 -- 46	-19.625 kcal/mol	2.82746 kcal/mol	3.34877 kcal/mol	176 197@LB@ \| \|@LB@5'-ACU...UUCUG UU GUUGA...GAU-3'@LB@ GUCUGAUU UGUGGAGUAA@LB@ :\|\|:\|\|\|\| :\|\|\|:\|\|\|\|\|@LB@ UAGGCUAA GCACUUCAUU@LB@3'-AUU...CGGUU U UUCCA...AUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -19.625 kcal/mol@LB@Unfolding Energy - mRNA 2.82746 kcal/mol@LB@Unfolding Energy - sRNA 3.34877 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@LB@
189	0.008373	0.1558	b1559	quuQ	-11.90	0.011421	197 -- 219	1 -- 24	Qin prophage; putative antitermination protein Q		_____________196______________________220\n_____________\|________________________\|\n5'-UCU...AGAAC______GA______GAA_______CAAAA...AUG-3'\n______________GAGCAU___ACCUU___GCCUUAC\n______________\|\|:\|\|\|___\|\|\|\|:___:\|\|:\|\|\|\n______________CUUGUA___UGGAG___UGGGAUG\n3'-AUU...UCUAU______GAA_____ACA_______-5'\n_____________\|_______________________\|\n_____________25______________________1\n	213 -- 219	1 -- 7	-21.9861 kcal/mol	2.0909 kcal/mol	8.02158 kcal/mol	196 220@LB@ \| \|@LB@5'-UCU...AGAAC GA GAA CAAAA...AUG-3'@LB@ GAGCAU ACCUU GCCUUAC@LB@ \|\|:\|\|\| \|\|\|\|: :\|\|:\|\|\|@LB@ CUUGUA UGGAG UGGGAUG@LB@3'-AUU...UCUAU GAA ACA -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -21.9861 kcal/mol@LB@Unfolding Energy - mRNA 2.0909 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 197 -- 219@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@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