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
54	0.003913	0.237	b0387	yaiI	-8.67	0.221647	168 -- 177	9 -- 18	UPF0178 family protein	_____________167________178\n_____________\|__________\|\n5'-CAC...GCGAC__________AUUAC...CAA-3'\n______________ACAAUAGAGG\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUUAUUUCC\n3'-UUU...GACAC__________GUAUAUUG-5'\n_____________\|__________\|\n_____________19_________8\n	171 -- 177	9 -- 15	-10.6786 kcal/mol	1.38452 kcal/mol	0.627418 kcal/mol	167 178@LB@ \| \|@LB@5'-CAC...GCGAC AUUAC...CAA-3'@LB@ ACAAUAGAGG@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUUAUUUCC@LB@3'-UUU...GACAC GUAUAUUG-5'@LB@ \| \|@LB@ 19 8@LB@@LB@@LB@Energy -8.67 kcal/mol@LB@Hybridization Energy -10.6786 kcal/mol@LB@Unfolding Energy - mRNA 1.38452 kcal/mol@LB@Unfolding Energy - sRNA 0.627418 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 9 -- 18@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 9 -- 15@LB@
62	0.004714	0.2539	b0973	hyaB	-9.08	0.185506	169 -- 187	48 -- 64	hydrogenase 1 large subunit	_____________168_________________188\n_____________\|___________________\|\n5'-GGU...AAACC___C_____CCA_______AGGAU...GCG-3'\n______________GAA_AUCAG___GGCAAUG\n______________\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|\n______________CUU_UAGUC___CCGUUAC\n3'-UUU...ACAAC___U_____A_________GUUAC...UUG-5'\n_____________\|___________________\|\n_____________65__________________47\n	181 -- 187	48 -- 54	-17.0784 kcal/mol	4.02672 kcal/mol	3.97302 kcal/mol	168 188@LB@ \| \|@LB@5'-GGU...AAACC C CCA AGGAU...GCG-3'@LB@ GAA AUCAG GGCAAUG@LB@ \|\|\| \|\|\|\|\| \|\|\|\|\|\|\|@LB@ CUU UAGUC CCGUUAC@LB@3'-UUU...ACAAC U A GUUAC...UUG-5'@LB@ \| \|@LB@ 65 47@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -17.0784 kcal/mol@LB@Unfolding Energy - mRNA 4.02672 kcal/mol@LB@Unfolding Energy - sRNA 3.97302 kcal/mol@LB@@LB@Position - mRNA 169 -- 187@LB@Position - sRNA 48 -- 64@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 48 -- 54@LB@
150	0.01784	0.3828	b2412	zipA	-13.80	0.016156	169 -- 198	28 -- 57	FtsZ stabilizer	_____________168____________________________199\n_____________\|______________________________\|\n5'-CAG...GCCGU________G___UUA_AA____________UAAUG...CUU-3'\n______________GGUGGCAA_GUG___G__CAACAGAGAAUA\n______________:\|\|\|\|\|\|\|_\|::___\|__\|\|\|\|\|\|\|:\|\|\|\|\n______________UCACCGUU_CGU___C__GUUGUCUUUUAU\n3'-UUU...UUUAG________A___UAC_GG____________UUUAG...UUG-5'\n_____________\|______________________________\|\n_____________58_____________________________27\n	189 -- 195	31 -- 37	-29.7049 kcal/mol	6.01867 kcal/mol	9.88595 kcal/mol	168 199@LB@ \| \|@LB@5'-CAG...GCCGU G UUA AA UAAUG...CUU-3'@LB@ GGUGGCAA GUG G CAACAGAGAAUA@LB@ :\|\|\|\|\|\|\| \|:: \| \|\|\|\|\|\|\|:\|\|\|\|@LB@ UCACCGUU CGU C GUUGUCUUUUAU@LB@3'-UUU...UUUAG A UAC GG UUUAG...UUG-5'@LB@ \| \|@LB@ 58 27@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -29.7049 kcal/mol@LB@Unfolding Energy - mRNA 6.01867 kcal/mol@LB@Unfolding Energy - sRNA 9.88595 kcal/mol@LB@@LB@Position - mRNA 169 -- 198@LB@Position - sRNA 28 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@LB@
184	0.02285	0.4143	b4312	fimB	-10.59	0.091292	169 -- 221	1 -- 58	tyrosine recombinase/inversion of on/off regulator of fimA	_____________168________________________________________________________________222\n_____________\|__________________________________________________________________\|\n5'-AUG...ACAGC_____C___UC______UA_____G________________________AGAAUA____UG_____AAAAA...GUA-3'\n______________UAGUG_GCG__UGUAAU____UAA_GGAAAA___________ACGAUGA______AGGC__AUAAC\n______________:\|\|\|\|_\|\|:__\|\|:\|\|\|____:\|\|_:\|\|\|\|\|___________\|\|:\|\|:\|______\|\|\|\|__\|\|\|\|\|\n______________GUCAC_CGU__ACGUUA____GUU_UCUUUU___________UGUUAUU______UCCG__UAUUG\n3'-UUU...UUUUA_________U_______CCGG___G______AUUUUAGACAC_________________UA_____-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	198 -- 204	12 -- 18	-31.4649 kcal/mol	8.72248 kcal/mol	12.1476 kcal/mol	168 222@LB@ \| \|@LB@5'-AUG...ACAGC C UC UA G AGAAUA UG AAAAA...GUA-3'@LB@ UAGUG GCG UGUAAU UAA GGAAAA ACGAUGA AGGC AUAAC@LB@ :\|\|\|\| \|\|: \|\|:\|\|\| :\|\| :\|\|\|\|\| \|\|:\|\|:\| \|\|\|\| \|\|\|\|\|@LB@ GUCAC CGU ACGUUA GUU UCUUUU UGUUAUU UCCG UAUUG@LB@3'-UUU...UUUUA U CCGG G AUUUUAGACAC UA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -31.4649 kcal/mol@LB@Unfolding Energy - mRNA 8.72248 kcal/mol@LB@Unfolding Energy - sRNA 12.1476 kcal/mol@LB@@LB@Position - mRNA 169 -- 221@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@LB@
65	0.005052	0.2614	b0451	amtB	-9.90	0.127883	170 -- 220	11 -- 61	ammonium transporter	_____________169____________________________________________________221\n_____________\|______________________________________________________\|\n5'-CCA...GCUGU____UC_____CACA____CA__AA_______________AUA_C_________AACUG...CGU-3'\n______________AAUC__UGGCA____GCAA__GG__CGA___AAAAUGAAG___G_GACGAUAAA\n______________\|\|\|\|__\|\|\|\|\|____\|\|\|\|__\|\|__\|:\|___\|\|\|\|\|:\|\|:___\|_\|\|\|:\|\|\|\|\|\n______________UUAG__ACCGU____CGUU__CC__GUU___UUUUAUUUU___C_CUGUUAUUU\n3'-UUU...ACCUU____UC_____UA______A___GG___GUC_________AGA_A_________CCGUA...UUG-5'\n_____________\|______________________________________________________\|\n_____________62_____________________________________________________10\n	214 -- 220	11 -- 17	-30.4323 kcal/mol	9.41224 kcal/mol	11.1248 kcal/mol	169 221@LB@ \| \|@LB@5'-CCA...GCUGU UC CACA CA AA AUA C AACUG...CGU-3'@LB@ AAUC UGGCA GCAA GG CGA AAAAUGAAG G GACGAUAAA@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\| \|\| \|:\| \|\|\|\|\|:\|\|: \| \|\|\|:\|\|\|\|\|@LB@ UUAG ACCGU CGUU CC GUU UUUUAUUUU C CUGUUAUUU@LB@3'-UUU...ACCUU UC UA A GG GUC AGA A CCGUA...UUG-5'@LB@ \| \|@LB@ 62 10@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -30.4323 kcal/mol@LB@Unfolding Energy - mRNA 9.41224 kcal/mol@LB@Unfolding Energy - sRNA 11.1248 kcal/mol@LB@@LB@Position - mRNA 170 -- 220@LB@Position - sRNA 11 -- 61@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 11 -- 17@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@
10	0.0004066	0.1262	b3429	glgA	-9.74	0.137242	173 -- 185	51 -- 64	glycogen synthase	_____________172____________186\n_____________\|______________\|\n5'-GUA...GCUAC______________UAAAC...ACG-3'\n______________GGAAGUUAG_GGCA\n______________\|:\|\|:\|:\|\|_\|\|\|\|\n______________CUUUUAGUC_CCGU\n3'-UUU...ACAAC_________A____UACGU...UUG-5'\n_____________\|______________\|\n_____________65_____________50\n	175 -- 181	56 -- 62	-15.3924 kcal/mol	2.76007 kcal/mol	2.8882 kcal/mol	172 186@LB@ \| \|@LB@5'-GUA...GCUAC UAAAC...ACG-3'@LB@ GGAAGUUAG GGCA@LB@ \|:\|\|:\|:\|\| \|\|\|\|@LB@ CUUUUAGUC CCGU@LB@3'-UUU...ACAAC A UACGU...UUG-5'@LB@ \| \|@LB@ 65 50@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -15.3924 kcal/mol@LB@Unfolding Energy - mRNA 2.76007 kcal/mol@LB@Unfolding Energy - sRNA 2.8882 kcal/mol@LB@@LB@Position - mRNA 173 -- 185@LB@Position - sRNA 51 -- 64@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 56 -- 62@LB@
167	0.01994	0.3993	b1982	amn	-7.06	0.411594	174 -- 215	8 -- 54	AMP nucleosidase	_____________173______________________________________________216\n_____________\|________________________________________________\|\n5'-UUU...UGUGC_____U____________________CACACA___A____________UCCGG...GCA-3'\n______________GGUAA_UGU_AUGG___AACAGGAGA_______UG__AUAAUAAGGGC\n______________\|\|:\|\|_\|\|:_\|\|\|\|___\|\|\|\|\|:\|:\|_______\|\|__\|:\|\|\|\|\|:\|\|\|\n______________CCGUU_ACG_UACC___UUGUCUUUU_______AC__UGUUAUUUCCG\n3'-UUU...AGUCA_________U____GGG_________AUUUUAG__AC___________UAUAUUG-5'\n_____________\|________________________________________________\|\n_____________55_______________________________________________7\n	209 -- 215	8 -- 14	-29.9928 kcal/mol	10.9089 kcal/mol	12.019 kcal/mol	173 216@LB@ \| \|@LB@5'-UUU...UGUGC U CACACA A UCCGG...GCA-3'@LB@ GGUAA UGU AUGG AACAGGAGA UG AUAAUAAGGGC@LB@ \|\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|:\|:\| \|\| \|:\|\|\|\|\|:\|\|\|@LB@ CCGUU ACG UACC UUGUCUUUU AC UGUUAUUUCCG@LB@3'-UUU...AGUCA U GGG AUUUUAG AC UAUAUUG-5'@LB@ \| \|@LB@ 55 7@LB@@LB@@LB@Energy -7.06 kcal/mol@LB@Hybridization Energy -29.9928 kcal/mol@LB@Unfolding Energy - mRNA 10.9089 kcal/mol@LB@Unfolding Energy - sRNA 12.019 kcal/mol@LB@@LB@Position - mRNA 174 -- 215@LB@Position - sRNA 8 -- 54@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 8 -- 14@LB@
76	0.006626	0.2822	b1658	purR	-10.59	0.091499	175 -- 205	41 -- 63	transcriptional repressor hypoxanthine-binding	_____________174______________________________206\n_____________\|________________________________\|\n5'-UUU...GAGCU____________CUGGAGUGA____G______AACAA...GCA-3'\n______________GAAGUUAG_GGU_________AAUG_AAUGGC\n______________:\|\|:\|:\|\|_\|\|:_________\|\|\|\|_\|\|\|\|\|\|\n______________UUUUAGUC_CCG_________UUAC_UUACCG\n3'-UUU...CAACC________A________________G______GGUUG...UUG-5'\n_____________\|________________________________\|\n_____________64_______________________________40\n	176 -- 182	56 -- 62	-19.9152 kcal/mol	5.04846 kcal/mol	4.27657 kcal/mol	174 206@LB@ \| \|@LB@5'-UUU...GAGCU CUGGAGUGA G AACAA...GCA-3'@LB@ GAAGUUAG GGU AAUG AAUGGC@LB@ :\|\|:\|:\|\| \|\|: \|\|\|\| \|\|\|\|\|\|@LB@ UUUUAGUC CCG UUAC UUACCG@LB@3'-UUU...CAACC A G GGUUG...UUG-5'@LB@ \| \|@LB@ 64 40@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -19.9152 kcal/mol@LB@Unfolding Energy - mRNA 5.04846 kcal/mol@LB@Unfolding Energy - sRNA 4.27657 kcal/mol@LB@@LB@Position - mRNA 175 -- 205@LB@Position - sRNA 41 -- 63@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 56 -- 62@LB@
59	0.004284	0.2442	b0094	ftsA	-10.23	0.109208	176 -- 218	1 -- 63	ATP-binding cell division FtsK recruitment protein	_____________175________________________________________________________________219\n_____________\|__________________________________________________________________\|\n5'-AAU...GCAAC__________________CA___AG___________________________UCA_____ACG___AGAAA...UCA-3'\n______________AAAAUCAG_______GCA__GGC__AACA________________ACAAUGA___AGGCG___GAC\n______________\|\|\|\|\|\|\|\|_______\|\|\|__\|\|\|__\|\|\|\|________________\|\|\|\|\|:\|___\|\|\|\|:___:\|\|\n______________UUUUAGUC_______CGU__CCG__UUGU________________UGUUAUU___UCCGU___UUG\n3'-UUU...CAACC________ACCGUUA___UA___GG____CUUUUAUUUUAGACAC_______________AUA___-5'\n_____________\|_________________________________________________________________\|\n_____________64________________________________________________________________1\n	198 -- 204	12 -- 18	-27.1283 kcal/mol	4.74085 kcal/mol	12.1605 kcal/mol	175 219@LB@ \| \|@LB@5'-AAU...GCAAC CA AG UCA ACG AGAAA...UCA-3'@LB@ AAAAUCAG GCA GGC AACA ACAAUGA AGGCG GAC@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:\| \|\|\|\|: :\|\|@LB@ UUUUAGUC CGU CCG UUGU UGUUAUU UCCGU UUG@LB@3'-UUU...CAACC ACCGUUA UA GG CUUUUAUUUUAGACAC AUA -5'@LB@ \| \|@LB@ 64 1@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -27.1283 kcal/mol@LB@Unfolding Energy - mRNA 4.74085 kcal/mol@LB@Unfolding Energy - sRNA 12.1605 kcal/mol@LB@@LB@Position - mRNA 176 -- 218@LB@Position - sRNA 1 -- 63@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 12 -- 18@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