Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
159	0.01815	0.3828	b2418	pdxK	-7.58	0.341503	51 -- 77	38 -- 65	pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase	_____________50___________________________78\n_____________\|____________________________\|\n5'-CAU...AACGG____U____UUA___________A____GACAA...GCA-3'\n______________GGAG_GUCA___GUAGUGUAAUG__CCA\n______________\|\|\|:_:\|\|\|___\|:\|:\|\|:\|\|\|\|__\|\|\|\n______________CCUU_UAGU___CGUUACGUUAC__GGU\n3'-UUU...UACAA____U____CAC___________CG___UGUCU...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________37\n	67 -- 73	43 -- 49	-23.6415 kcal/mol	9.38399 kcal/mol	6.67322 kcal/mol	50 78@LB@ \| \|@LB@5'-CAU...AACGG U UUA A GACAA...GCA-3'@LB@ GGAG GUCA GUAGUGUAAUG CCA@LB@ \|\|\|: :\|\|\| \|:\|:\|\|:\|\|\|\| \|\|\|@LB@ CCUU UAGU CGUUACGUUAC GGU@LB@3'-UUU...UACAA U CAC CG UGUCU...UUG-5'@LB@ \| \|@LB@ 66 37@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -23.6415 kcal/mol@LB@Unfolding Energy - mRNA 9.38399 kcal/mol@LB@Unfolding Energy - sRNA 6.67322 kcal/mol@LB@@LB@Position - mRNA 51 -- 77@LB@Position - sRNA 38 -- 65@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 43 -- 49@LB@
186	0.02292	0.4143	b2717	hycI	-8.63	0.225035	220 -- 254	38 -- 70	protease involved in processing C-terminal end of HycE	_____________219___________________________________255\n_____________\|_____________________________________\|\n5'-AGC...ACUCU_______C__UAG__UGAUG______________G__GGUCC...ACU-3'\n______________GUGUUGG_AA___CA_____GGCGAUG__AUGGC_CA\n______________:\|\|\|\|\|\|_\|\|___\|\|_____\|\|\|:\|\|\|__\|\|\|\|\|_\|\|\n______________UACAACC_UU___GU_____CCGUUAC__UACCG_GU\n3'-UUU...AAAUA__________UUA__CA__________GU_____G__UGUCU...UUG-5'\n_____________\|_____________________________________\|\n_____________71____________________________________37\n	240 -- 246	48 -- 54	-27.127 kcal/mol	11.1995 kcal/mol	7.29667 kcal/mol	219 255@LB@ \| \|@LB@5'-AGC...ACUCU C UAG UGAUG G GGUCC...ACU-3'@LB@ GUGUUGG AA CA GGCGAUG AUGGC CA@LB@ :\|\|\|\|\|\| \|\| \|\| \|\|\|:\|\|\| \|\|\|\|\| \|\|@LB@ UACAACC UU GU CCGUUAC UACCG GU@LB@3'-UUU...AAAUA UUA CA GU G UGUCU...UUG-5'@LB@ \| \|@LB@ 71 37@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -27.127 kcal/mol@LB@Unfolding Energy - mRNA 11.1995 kcal/mol@LB@Unfolding Energy - sRNA 7.29667 kcal/mol@LB@@LB@Position - mRNA 220 -- 254@LB@Position - sRNA 38 -- 70@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 48 -- 54@LB@
13	0.0005138	0.1268	b0055	djlA	-16.40	0.003186	213 -- 240	39 -- 65	membrane-anchored DnaK co-chaperone DNA-binding protein	_____________212__________________________241\n_____________\|____________________________\|\n5'-GAC...AUUGG__A_______U_____UG__C_______UACUG...UUG-3'\n______________GG_AAAAUCA_UGGCG__GC_GUGGCCU\n______________\|\|_\|\|\|\|\|\|\|_\|\|\|\|:__\|\|_:\|\|\|\|\|:\n______________CC_UUUUAGU_ACCGU__CG_UACCGGG\n3'-UUU...UACAA__________C_____UA__U_______UUGUC...UUG-5'\n_____________\|____________________________\|\n_____________66___________________________38\n	234 -- 240	39 -- 45	-30.8595 kcal/mol	7.7929 kcal/mol	6.66922 kcal/mol	212 241@LB@ \| \|@LB@5'-GAC...AUUGG A U UG C UACUG...UUG-3'@LB@ GG AAAAUCA UGGCG GC GUGGCCU@LB@ \|\| \|\|\|\|\|\|\| \|\|\|\|: \|\| :\|\|\|\|\|:@LB@ CC UUUUAGU ACCGU CG UACCGGG@LB@3'-UUU...UACAA C UA U UUGUC...UUG-5'@LB@ \| \|@LB@ 66 38@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -30.8595 kcal/mol@LB@Unfolding Energy - mRNA 7.7929 kcal/mol@LB@Unfolding Energy - sRNA 6.66922 kcal/mol@LB@@LB@Position - mRNA 213 -- 240@LB@Position - sRNA 39 -- 65@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 39 -- 45@LB@
51	0.003814	0.237	b3888	yiiD	-11.06	0.072417	149 -- 179	39 -- 72	GNAT family putative N-acetyltransferase	_____________148_________________________________180\n_____________\|___________________________________\|\n5'-UUU...UGCGG_____CA__U______C___U______________CGUGA...AUC-3'\n______________AUAUG__GG___AUCG_UGG_CAAUG__AUGGCCC\n______________\|\|\|\|\|__\|\|___\|\|\|:_\|\|\|_\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UAUAC__CC___UAGU_ACC_GUUAC__UACCGGG\n3'-UUU...AAAAA_____AA__UUU____C_________GU_______UUGUC...UUG-5'\n_____________\|___________________________________\|\n_____________73__________________________________38\n	173 -- 179	39 -- 45	-28.8621 kcal/mol	10.5098 kcal/mol	7.29447 kcal/mol	148 180@LB@ \| \|@LB@5'-UUU...UGCGG CA U C U CGUGA...AUC-3'@LB@ AUAUG GG AUCG UGG CAAUG AUGGCCC@LB@ \|\|\|\|\| \|\| \|\|\|: \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ UAUAC CC UAGU ACC GUUAC UACCGGG@LB@3'-UUU...AAAAA AA UUU C GU UUGUC...UUG-5'@LB@ \| \|@LB@ 73 38@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -28.8621 kcal/mol@LB@Unfolding Energy - mRNA 10.5098 kcal/mol@LB@Unfolding Energy - sRNA 7.29447 kcal/mol@LB@@LB@Position - mRNA 149 -- 179@LB@Position - sRNA 39 -- 72@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 39 -- 45@LB@
56	0.003989	0.237	b0453	ybaY	-12.27	0.038324	59 -- 73	39 -- 55	outer membrane lipoprotein	_____________58________________74\n_____________\|_________________\|\n5'-AAG...UCCGA_________________GAAUU...CAA-3'\n______________UGG__GUGCAAUGGUCU\n______________\|\|\|__:\|\|\|\|\|\|\|\|:\|:\n______________ACC__UACGUUACCGGG\n3'-UUU...UAGUC___GU____________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	67 -- 73	39 -- 45	-20.8095 kcal/mol	3.77686 kcal/mol	4.76312 kcal/mol	58 74@LB@ \| \|@LB@5'-AAG...UCCGA GAAUU...CAA-3'@LB@ UGG GUGCAAUGGUCU@LB@ \|\|\| :\|\|\|\|\|\|\|\|:\|:@LB@ ACC UACGUUACCGGG@LB@3'-UUU...UAGUC GU UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -12.27 kcal/mol@LB@Hybridization Energy -20.8095 kcal/mol@LB@Unfolding Energy - mRNA 3.77686 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 59 -- 73@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 67 -- 73@LB@Position Seed - sRNA 39 -- 45@LB@
60	0.004583	0.2539	b0674	asnB	-9.07	0.186262	281 -- 298	39 -- 51	asparagine synthetase B	_____________280________________299\n_____________\|__________________\|\n5'-ACA...CGCCU______UCAUC_______GG-3'\n______________GAUGCG_____GUGGCCC\n______________:\|\|\|\|:_____:\|\|\|\|\|\|\n______________UUACGU_____UACCGGG\n3'-UUU...CACCG__________________UUGUC...UUG-5'\n_____________\|__________________\|\n_____________52_________________38\n	292 -- 298	39 -- 45	-18.7239 kcal/mol	4.90882 kcal/mol	4.74571 kcal/mol	280 299@LB@ \| \|@LB@5'-ACA...CGCCU UCAUC GG-3'@LB@ GAUGCG GUGGCCC@LB@ :\|\|\|\|: :\|\|\|\|\|\|@LB@ UUACGU UACCGGG@LB@3'-UUU...CACCG UUGUC...UUG-5'@LB@ \| \|@LB@ 52 38@LB@@LB@@LB@Energy -9.07 kcal/mol@LB@Hybridization Energy -18.7239 kcal/mol@LB@Unfolding Energy - mRNA 4.90882 kcal/mol@LB@Unfolding Energy - sRNA 4.74571 kcal/mol@LB@@LB@Position - mRNA 281 -- 298@LB@Position - sRNA 39 -- 51@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 39 -- 45@LB@
74	0.006275	0.2822	b3298	rpsM	-14.03	0.014091	187 -- 207	39 -- 57	30S ribosomal subunit protein S13	_____________186___________________208\n_____________\|_____________________\|\n5'-GUC...UAAAU___A_G______UA_______GUAUA...UCC-3'\n______________AGU_G_AGUGCA__GUGGCCC\n______________\|\|\|_\|_\|:\|\|\|\|__:\|\|\|\|\|\|\n______________UCA_C_UUACGU__UACCGGG\n3'-UUU...UUUAG___C_G_______________UUGUC...UUG-5'\n_____________\|_____________________\|\n_____________58____________________38\n	201 -- 207	39 -- 45	-23.7565 kcal/mol	4.54468 kcal/mol	5.17956 kcal/mol	186 208@LB@ \| \|@LB@5'-GUC...UAAAU A G UA GUAUA...UCC-3'@LB@ AGU G AGUGCA GUGGCCC@LB@ \|\|\| \| \|:\|\|\|\| :\|\|\|\|\|\|@LB@ UCA C UUACGU UACCGGG@LB@3'-UUU...UUUAG C G UUGUC...UUG-5'@LB@ \| \|@LB@ 58 38@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -23.7565 kcal/mol@LB@Unfolding Energy - mRNA 4.54468 kcal/mol@LB@Unfolding Energy - sRNA 5.17956 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 39 -- 57@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 39 -- 45@LB@
79	0.006804	0.2822	b2947	gshB	-11.48	0.058268	213 -- 229	39 -- 54	glutathione synthetase	_____________212_______________230\n_____________\|_________________\|\n5'-UGC...AGCUC____UC_______A___CAUCG...ACG-3'\n______________GGCA__GUGAUGG_CCC\n______________\|\|\|\|__\|::\|\|\|\|_\|\|\|\n______________CCGU__CGUUACC_GGG\n3'-UUU...AGUCA____UA___________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________55________________38\n	219 -- 225	42 -- 48	-21.2333 kcal/mol	4.99211 kcal/mol	4.76022 kcal/mol	212 230@LB@ \| \|@LB@5'-UGC...AGCUC UC A CAUCG...ACG-3'@LB@ GGCA GUGAUGG CCC@LB@ \|\|\|\| \|::\|\|\|\| \|\|\|@LB@ CCGU CGUUACC GGG@LB@3'-UUU...AGUCA UA UUGUC...UUG-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -21.2333 kcal/mol@LB@Unfolding Energy - mRNA 4.99211 kcal/mol@LB@Unfolding Energy - sRNA 4.76022 kcal/mol@LB@@LB@Position - mRNA 213 -- 229@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 42 -- 48@LB@
84	0.00705	0.2822	b2341	fadJ	-9.52	0.152421	171 -- 187	39 -- 55	enoyl-CoA hydratase/epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase	_____________170_______________188\n_____________\|_________________\|\n5'-CAU...GGGCU_____CG__________UGGAG...CGG-3'\n______________UGGCG__GCAAUGGUUC\n______________\|\|\|\|:__\|\|\|\|\|\|\|::\|\n______________ACCGU__CGUUACCGGG\n3'-UUU...UAGUC_____UA__________UUGUC...UUG-5'\n_____________\|_________________\|\n_____________56________________38\n	181 -- 187	39 -- 45	-22.4983 kcal/mol	8.21876 kcal/mol	4.76312 kcal/mol	170 188@LB@ \| \|@LB@5'-CAU...GGGCU CG UGGAG...CGG-3'@LB@ UGGCG GCAAUGGUUC@LB@ \|\|\|\|: \|\|\|\|\|\|\|::\|@LB@ ACCGU CGUUACCGGG@LB@3'-UUU...UAGUC UA UUGUC...UUG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -22.4983 kcal/mol@LB@Unfolding Energy - mRNA 8.21876 kcal/mol@LB@Unfolding Energy - sRNA 4.76312 kcal/mol@LB@@LB@Position - mRNA 171 -- 187@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 39 -- 45@LB@
93	0.008233	0.2977	b2669	stpA	-8.51	0.236304	244 -- 255	39 -- 50	DNA binding protein nucleoid-associated	_____________243__________256\n_____________\|____________\|\n5'-UUC...CCUCC____________GCGAA...UCA-3'\n______________GUGCGAUGGCUC\n______________:\|\|\|:\|\|\|\|\|:\|\n______________UACGUUACCGGG\n3'-UUU...ACCGU____________UUGUC...UUG-5'\n_____________\|____________\|\n_____________51___________38\n	249 -- 255	39 -- 45	-19.1222 kcal/mol	5.86982 kcal/mol	4.73799 kcal/mol	243 256@LB@ \| \|@LB@5'-UUC...CCUCC GCGAA...UCA-3'@LB@ GUGCGAUGGCUC@LB@ :\|\|\|:\|\|\|\|\|:\|@LB@ UACGUUACCGGG@LB@3'-UUU...ACCGU UUGUC...UUG-5'@LB@ \| \|@LB@ 51 38@LB@@LB@@LB@Energy -8.51 kcal/mol@LB@Hybridization Energy -19.1222 kcal/mol@LB@Unfolding Energy - mRNA 5.86982 kcal/mol@LB@Unfolding Energy - sRNA 4.73799 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 39 -- 50@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 39 -- 45@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