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
111	0.01033	0.313	b1120	cobB	-14.51	0.010573	178 -- 236	7 -- 64	deacetylase of acs and cheY chemotaxis regulator	_____________177______________________________________________________________237\n_____________\|________________________________________________________________\|\n5'-CGC...UUUCA____UAA______GCCG__A_______AAA___CA______C____GUAC______________GGAAU...AUC-3'\n______________GAGA___AGUGGU____GA_GCAAUGG___AAC__AGAGUA___UC____UGACAG___GGGCA\n______________\|\|:\|___\|\|\|\|\|:____:\|_\|\|\|\|\|\|\|___\|\|\|__\|:\|:\|\|___\|\|____\|\|\|\|\|:___:\|\|\|\|\n______________CUUU___UCACCG____UU_CGUUACC___UUG__UUUUAU___AG____ACUGUU___UCCGU\n3'-UUU...ACAAC____UAG____________A_______GGG___UC______UUU__AC________AUU_____AUAUUG-5'\n_____________\|________________________________________________________________\|\n_____________65_______________________________________________________________6\n	198 -- 204	42 -- 48	-37.7371 kcal/mol	11.0723 kcal/mol	12.1536 kcal/mol	177 237@LB@ \| \|@LB@5'-CGC...UUUCA UAA GCCG A AAA CA C GUAC GGAAU...AUC-3'@LB@ GAGA AGUGGU GA GCAAUGG AAC AGAGUA UC UGACAG GGGCA@LB@ \|\|:\| \|\|\|\|\|: :\| \|\|\|\|\|\|\| \|\|\| \|:\|:\|\| \|\| \|\|\|\|\|: :\|\|\|\|@LB@ CUUU UCACCG UU CGUUACC UUG UUUUAU AG ACUGUU UCCGU@LB@3'-UUU...ACAAC UAG A GGG UC UUU AC AUU AUAUUG-5'@LB@ \| \|@LB@ 65 6@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -37.7371 kcal/mol@LB@Unfolding Energy - mRNA 11.0723 kcal/mol@LB@Unfolding Energy - sRNA 12.1536 kcal/mol@LB@@LB@Position - mRNA 178 -- 236@LB@Position - sRNA 7 -- 64@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 42 -- 48@LB@
112	0.0105	0.3154	b2136	yohD	-14.01	0.014269	227 -- 295	6 -- 72	DedA family inner membrane protein	_____________226_____________________________________________________________________296\n_____________\|_______________________________________________________________________\|\n5'-GAU...UCACA_____GUUAUGCCG__C____________A____________________C_____UUUGCUG________UGCGG-3'\n______________AUAUG_________CG_UGGUGAU_CGGU_GCCUGGCGGAAGGUGAAA_C_GUGAC_______GGAGGCGU\n______________\|\|\|\|\|_________\|:_\|\|\|::\|\|_\|::\|_\|\|\|:::\|:\|\|\|::\|:\|\|\|_\|_\|\|\|\|\|_______::\|\|\|\|:\|\n______________UAUAC_________GU_ACCGUUA_GUUA_CGGGUUGUCUUUUAUUUU_G_CACUG_______UUUCCGUA\n3'-UUU...AAAAA_____AACCUUUUA__C_______C____C__________________A_A_____UUA____________UAUUG-5'\n_____________\|_______________________________________________________________________\|\n_____________73______________________________________________________________________5\n	289 -- 295	6 -- 12	-51.7055 kcal/mol	25.533 kcal/mol	12.1614 kcal/mol	226 296@LB@ \| \|@LB@5'-GAU...UCACA GUUAUGCCG C A C UUUGCUG UGCGG-3'@LB@ AUAUG CG UGGUGAU CGGU GCCUGGCGGAAGGUGAAA C GUGAC GGAGGCGU@LB@ \|\|\|\|\| \|: \|\|\|::\|\| \|::\| \|\|\|:::\|:\|\|\|::\|:\|\|\| \| \|\|\|\|\| ::\|\|\|\|:\|@LB@ UAUAC GU ACCGUUA GUUA CGGGUUGUCUUUUAUUUU G CACUG UUUCCGUA@LB@3'-UUU...AAAAA AACCUUUUA C C C A A UUA UAUUG-5'@LB@ \| \|@LB@ 73 5@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -51.7055 kcal/mol@LB@Unfolding Energy - mRNA 25.533 kcal/mol@LB@Unfolding Energy - sRNA 12.1614 kcal/mol@LB@@LB@Position - mRNA 227 -- 295@LB@Position - sRNA 6 -- 72@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 6 -- 12@LB@
113	0.01136	0.3326	b3417	malP	-12.46	0.034450	250 -- 272	38 -- 60	maltodextrin phosphorylase	_____________249_____________________273\n_____________\|_______________________\|\n5'-ACA...UUCAC___________C__U________AAUUC...GCC-3'\n______________GUCAGUGGCAG_GU_AUGGCUUA\n______________:\|\|\|\|\|\|\|\|\|:_\|:_\|\|\|\|\|::\|\n______________UAGUCACCGUU_CG_UACCGGGU\n3'-UUU...CCUUU___________A__U________UGUCU...UUG-5'\n_____________\|_______________________\|\n_____________61______________________37\n	266 -- 272	38 -- 44	-30.8718 kcal/mol	11.793 kcal/mol	6.61394 kcal/mol	249 273@LB@ \| \|@LB@5'-ACA...UUCAC C U AAUUC...GCC-3'@LB@ GUCAGUGGCAG GU AUGGCUUA@LB@ :\|\|\|\|\|\|\|\|\|: \|: \|\|\|\|\|::\|@LB@ UAGUCACCGUU CG UACCGGGU@LB@3'-UUU...CCUUU A U UGUCU...UUG-5'@LB@ \| \|@LB@ 61 37@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -30.8718 kcal/mol@LB@Unfolding Energy - mRNA 11.793 kcal/mol@LB@Unfolding Energy - sRNA 6.61394 kcal/mol@LB@@LB@Position - mRNA 250 -- 272@LB@Position - sRNA 38 -- 60@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 38 -- 44@LB@
114	0.01136	0.3326	b2203	napB	-12.98	0.025868	242 -- 255	39 -- 54	nitrate reductase small cytochrome C550 subunit periplasmic	_____________241______________256\n_____________\|________________\|\n5'-ACC...UGGAC________________UGGUG...UUA-3'\n______________GGCGAUGC__UGGCCC\n______________\|\|\|:\|\|\|\|__\|\|\|\|\|\|\n______________CCGUUACG__ACCGGG\n3'-UUU...AGUCA________UU______UUGUC...UUG-5'\n_____________\|________________\|\n_____________55_______________38\n	243 -- 249	47 -- 53	-25.1467 kcal/mol	7.40583 kcal/mol	4.76022 kcal/mol	241 256@LB@ \| \|@LB@5'-ACC...UGGAC UGGUG...UUA-3'@LB@ GGCGAUGC UGGCCC@LB@ \|\|\|:\|\|\|\| \|\|\|\|\|\|@LB@ CCGUUACG ACCGGG@LB@3'-UUU...AGUCA UU UUGUC...UUG-5'@LB@ \| \|@LB@ 55 38@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -25.1467 kcal/mol@LB@Unfolding Energy - mRNA 7.40583 kcal/mol@LB@Unfolding Energy - sRNA 4.76022 kcal/mol@LB@@LB@Position - mRNA 242 -- 255@LB@Position - sRNA 39 -- 54@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 47 -- 53@LB@
115	0.0114	0.3326	b2531	iscR	-8.61	0.227442	42 -- 64	8 -- 31	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________41_______________________65\n_____________\|________________________\|\n5'-AUG...GCCAC_______AAA______C_______UAAAU...AAC-3'\n______________GAUAAAA____UGGCA_UGAAGGU\n______________:\|\|\|\|\|\|____\|\|:\|\|_\|:\|\|\|\|:\n______________UUAUUUU____ACUGU_AUUUCCG\n3'-UUU...GUCUU_______AGAC_____U_______UAUAUUG-5'\n_____________\|________________________\|\n_____________32_______________________7\n	58 -- 64	8 -- 14	-15.5579 kcal/mol	1.96266 kcal/mol	4.98963 kcal/mol	41 65@LB@ \| \|@LB@5'-AUG...GCCAC AAA C UAAAU...AAC-3'@LB@ GAUAAAA UGGCA UGAAGGU@LB@ :\|\|\|\|\|\| \|\|:\|\| \|:\|\|\|\|:@LB@ UUAUUUU ACUGU AUUUCCG@LB@3'-UUU...GUCUU AGAC U UAUAUUG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -8.61 kcal/mol@LB@Hybridization Energy -15.5579 kcal/mol@LB@Unfolding Energy - mRNA 1.96266 kcal/mol@LB@Unfolding Energy - sRNA 4.98963 kcal/mol@LB@@LB@Position - mRNA 42 -- 64@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 8 -- 14@LB@
116	0.0115	0.3326	b3770	ilvE	-6.73	0.460342	227 -- 277	1 -- 67	branched-chain amino acid aminotransferase	_____________226__________________________________________________________________278\n_____________\|____________________________________________________________________\|\n5'-UUU...UACAU____U______A___G______________C_____________________CG____U_________GUCGC...GCA-3'\n______________UUGG____UCA_UGG_GA___GAUGGUUCG_UGGGAA___________GACG__AAGG_GCAUGUGAU\n______________\|\|\|\|____\|\|\|_\|\|\|_:\|___:\|\|\|\|::\|:_::\|:\|\|___________\|\|\|:__\|\|:\|_\|\|\|\|:\|:\|:\n______________AACC____AGU_ACC_UU___UUACCGGGU_GUCUUU___________CUGU__UUUC_CGUAUAUUG\n3'-UUU...UAUAC____UUUU___C___G__ACG_________U______UAUUUUAGACA____UA______________-5'\n_____________\|___________________________________________________________________\|\n_____________68__________________________________________________________________1\n	269 -- 275	3 -- 9	-35.2937 kcal/mol	16.4013 kcal/mol	12.1612 kcal/mol	226 278@LB@ \| \|@LB@5'-UUU...UACAU U A G C CG U GUCGC...GCA-3'@LB@ UUGG UCA UGG GA GAUGGUUCG UGGGAA GACG AAGG GCAUGUGAU@LB@ \|\|\|\| \|\|\| \|\|\| :\| :\|\|\|\|::\|: ::\|:\|\| \|\|\|: \|\|:\| \|\|\|\|:\|:\|:@LB@ AACC AGU ACC UU UUACCGGGU GUCUUU CUGU UUUC CGUAUAUUG@LB@3'-UUU...UAUAC UUUU C G ACG U UAUUUUAGACA UA -5'@LB@ \| \|@LB@ 68 1@LB@@LB@@LB@Energy -6.73 kcal/mol@LB@Hybridization Energy -35.2937 kcal/mol@LB@Unfolding Energy - mRNA 16.4013 kcal/mol@LB@Unfolding Energy - sRNA 12.1612 kcal/mol@LB@@LB@Position - mRNA 227 -- 277@LB@Position - sRNA 1 -- 67@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 3 -- 9@LB@
117	0.01164	0.3326	b1119	nagK	-13.64	0.017780	246 -- 275	42 -- 70	N-acetyl-D-glucosamine kinase	_____________245_____________________________276\n_____________\|_______________________________\|\n5'-UCA...UUGGC_____U__UAG_____C_____U________GAAAA...GUG-3'\n______________GUGUU_GA____CGGU_GGCAG_UGCAGUGG\n______________:\|\|\|\|_\|\|____\|:\|\|_\|\|\|\|:_\|\|\|\|:\|\|\|\n______________UACAA_CU____GUCA_CCGUU_ACGUUACC\n3'-UUU...AAAUA_____C__UUUA___________________GGGUU...UUG-5'\n_____________\|_______________________________\|\n_____________71______________________________41\n	269 -- 275	42 -- 48	-28.344 kcal/mol	8.3584 kcal/mol	6.34928 kcal/mol	245 276@LB@ \| \|@LB@5'-UCA...UUGGC U UAG C U GAAAA...GUG-3'@LB@ GUGUU GA CGGU GGCAG UGCAGUGG@LB@ :\|\|\|\| \|\| \|:\|\| \|\|\|\|: \|\|\|\|:\|\|\|@LB@ UACAA CU GUCA CCGUU ACGUUACC@LB@3'-UUU...AAAUA C UUUA GGGUU...UUG-5'@LB@ \| \|@LB@ 71 41@LB@@LB@@LB@Energy -13.64 kcal/mol@LB@Hybridization Energy -28.344 kcal/mol@LB@Unfolding Energy - mRNA 8.3584 kcal/mol@LB@Unfolding Energy - sRNA 6.34928 kcal/mol@LB@@LB@Position - mRNA 246 -- 275@LB@Position - sRNA 42 -- 70@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 42 -- 48@LB@
118	0.01176	0.3326	b3601	mtlR	-9.20	0.175568	190 -- 199	44 -- 53	mannitol operon repressor	_____________189________200\n_____________\|__________\|\n5'-UAU...AUAAA__________AAUGG...UUG-3'\n______________GCAAUGCAAU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGUUACGUUA\n3'-UUU...GUCAC__________CCGGG...UUG-5'\n_____________\|__________\|\n_____________54_________43\n	193 -- 199	44 -- 50	-14.2394 kcal/mol	1.82821 kcal/mol	3.20822 kcal/mol	189 200@LB@ \| \|@LB@5'-UAU...AUAAA AAUGG...UUG-3'@LB@ GCAAUGCAAU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGUUACGUUA@LB@3'-UUU...GUCAC CCGGG...UUG-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -14.2394 kcal/mol@LB@Unfolding Energy - mRNA 1.82821 kcal/mol@LB@Unfolding Energy - sRNA 3.20822 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 44 -- 50@LB@
119	0.01177	0.3326	b4262	lptG	-9.06	0.186805	47 -- 70	7 -- 29	lipopolysaccharide export ABC permease	_____________46_______________________71\n_____________\|________________________\|\n5'-CCA...CUCCC_______GAAC_____________AGCUG...UCA-3'\n______________UGAAAUC____GGCGGUAAAGGUA\n______________\|:\|\|\|\|\|____\|:\|::\|\|\|\|\|\|:\|\n______________AUUUUAG____CUGUUAUUUCCGU\n3'-UUU...CUUUU_______ACA______________AUAUUG-5'\n_____________\|________________________\|\n_____________30_______________________6\n	64 -- 70	7 -- 13	-21.2282 kcal/mol	7.28231 kcal/mol	4.88318 kcal/mol	46 71@LB@ \| \|@LB@5'-CCA...CUCCC GAAC AGCUG...UCA-3'@LB@ UGAAAUC GGCGGUAAAGGUA@LB@ \|:\|\|\|\|\| \|:\|::\|\|\|\|\|\|:\|@LB@ AUUUUAG CUGUUAUUUCCGU@LB@3'-UUU...CUUUU ACA AUAUUG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -21.2282 kcal/mol@LB@Unfolding Energy - mRNA 7.28231 kcal/mol@LB@Unfolding Energy - sRNA 4.88318 kcal/mol@LB@@LB@Position - mRNA 47 -- 70@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 7 -- 13@LB@
120	0.01191	0.3337	b0354	yaiL	-10.86	0.080118	189 -- 207	50 -- 67	DUF2058 family protein	_____________188_________________208\n_____________\|___________________\|\n5'-GUA...CGGGU_______CAA__A______AACUU...UUC-3'\n______________UUGGAAA___AG_UGGCAA\n______________\|\|\|\|\|\|\|___\|\|_\|\|\|\|\|\|\n______________AACCUUU___UC_ACCGUU\n3'-UUU...UAUAC_______UAG_________ACGUU...UUG-5'\n_____________\|___________________\|\n_____________68__________________49\n	189 -- 195	61 -- 67	-16.0374 kcal/mol	2.05851 kcal/mol	3.12147 kcal/mol	188 208@LB@ \| \|@LB@5'-GUA...CGGGU CAA A AACUU...UUC-3'@LB@ UUGGAAA AG UGGCAA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|@LB@ AACCUUU UC ACCGUU@LB@3'-UUU...UAUAC UAG ACGUU...UUG-5'@LB@ \| \|@LB@ 68 49@LB@@LB@@LB@Energy -10.86 kcal/mol@LB@Hybridization Energy -16.0374 kcal/mol@LB@Unfolding Energy - mRNA 2.05851 kcal/mol@LB@Unfolding Energy - sRNA 3.12147 kcal/mol@LB@@LB@Position - mRNA 189 -- 207@LB@Position - sRNA 50 -- 67@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 61 -- 67@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