Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
120	0.01317	0.3575	b1158	pinE	-11.56	0.136715	30 -- 59	115 -- 145	e14 prophage; site-specific DNA recombinase	_____________29_____________________60\n_____________\|______________________\|\n5'-AGC...CCGGG______________GUA_____GAGCC...ACA-3'\n______________ACACCAA____CAG___AUGCA\n______________\|\|\|\|\|\|\|____\|\|\|___\|::\|\|\n______________UGUGGUU____GUC___UGUGU\n3'-UUU...UAAAA_______AUGA___AG______ACUAC...UAG-5'\n_____________\|______________________\|\n_____________146____________________114\n	98 -- 104	181 -- 187	-13.8739 kcal/mol	4.34554 kcal/mol	5.05492 kcal/mol	29 60@LB@ \| \|@LB@5'-AGC...CCGGG GUA GAGCC...ACA-3'@LB@ ACACCAA CAG AUGCA@LB@ \|\|\|\|\|\|\| \|\|\| \|::\|\|@LB@ UGUGGUU GUC UGUGU@LB@3'-UUU...UAAAA AUGA AG ACUAC...UAG-5'@LB@ \| \|@LB@ 146 114@LB@@LB@@LB@Energy -11.56 kcal/mol@LB@Hybridization Energy -13.8739 kcal/mol@LB@Unfolding Energy - mRNA 4.34554 kcal/mol@LB@Unfolding Energy - sRNA 5.05492 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 115 -- 145@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 181 -- 187@LB@
138	0.01487	0.3575	b3771	ilvD	-15.83	0.018324	35 -- 66	67 -- 98	dihydroxyacid dehydratase	_____________34______67\n_____________\|_______\|\n5'-GCG...AAAAA_______GCACG...GUA-3'\n______________UGGGACG\n______________\|\|\|\|\|\|\|\n______________ACCCUGC\n3'-UUU...GCAAC_______GAAUU...UAG-5'\n_____________\|_______\|\n_____________99______66\n	147 -- 153	87 -- 93	-12.7493 kcal/mol	2.26202 kcal/mol	4.21173 kcal/mol	34 67@LB@ \| \|@LB@5'-GCG...AAAAA GCACG...GUA-3'@LB@ UGGGACG@LB@ \|\|\|\|\|\|\|@LB@ ACCCUGC@LB@3'-UUU...GCAAC GAAUU...UAG-5'@LB@ \| \|@LB@ 99 66@LB@@LB@@LB@Energy -15.83 kcal/mol@LB@Hybridization Energy -12.7493 kcal/mol@LB@Unfolding Energy - mRNA 2.26202 kcal/mol@LB@Unfolding Energy - sRNA 4.21173 kcal/mol@LB@@LB@Position - mRNA 35 -- 66@LB@Position - sRNA 67 -- 98@LB@Position Seed - mRNA 147 -- 153@LB@Position Seed - sRNA 87 -- 93@LB@
74	0.007724	0.3458	b1261	trpB	-16.40	0.014006	36 -- 47	195 -- 206	tryptophan synthase beta subunit	_____________35___________48\n_____________\|____________\|\n5'-UGG...AACGU____________GGGCU...UCA-3'\n______________UCUGCUGGCGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACGACCGCCC\n3'-UUU...AUAUU____________ACUAA...UAG-5'\n_____________\|____________\|\n_____________207__________194\n	41 -- 47	195 -- 201	-26.9412 kcal/mol	6.0368 kcal/mol	9.05854 kcal/mol	35 48@LB@ \| \|@LB@5'-UGG...AACGU GGGCU...UCA-3'@LB@ UCUGCUGGCGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACGACCGCCC@LB@3'-UUU...AUAUU ACUAA...UAG-5'@LB@ \| \|@LB@ 207 194@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -26.9412 kcal/mol@LB@Unfolding Energy - mRNA 6.0368 kcal/mol@LB@Unfolding Energy - sRNA 9.05854 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 195 -- 206@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 195 -- 201@LB@
192	0.02246	0.3833	b4340	yjiR	-11.68	0.128907	36 -- 62	126 -- 153	putative DNA-binding transcriptional regulator/putative aminotransferase	_____________35_______63\n_____________\|________\|\n5'-AGC...CAGAG________AUCCA...GUC-3'\n______________GCUUCAUC\n______________\|\|\|\|\|\|\|\|\n______________CGAAGUAG\n3'-UUU...GGGAA________-5'\n_____________\|_______\|\n_____________154_____126\n	50 -- 56	1 -- 7	-12.7164 kcal/mol	1.73081 kcal/mol	0.703102 kcal/mol	35 63@LB@ \| \|@LB@5'-AGC...CAGAG AUCCA...GUC-3'@LB@ GCUUCAUC@LB@ \|\|\|\|\|\|\|\|@LB@ CGAAGUAG@LB@3'-UUU...GGGAA -5'@LB@ \| \|@LB@ 154 126@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -12.7164 kcal/mol@LB@Unfolding Energy - mRNA 1.73081 kcal/mol@LB@Unfolding Energy - sRNA 0.703102 kcal/mol@LB@@LB@Position - mRNA 36 -- 62@LB@Position - sRNA 126 -- 153@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 1 -- 7@LB@
193	0.0225	0.3833	b3751	rbsB	-14.76	0.030308	38 -- 56	74 -- 93	D-ribose ABC transporter periplasmic binding protein; ribose chemotaxis receptor	_____________37________________________________________________57\n_____________\|_________________________________________________\|\n___5'-GCGGUACG_____GG______GAAAA_____CA___U____________________UUAAU...UCU-3'\n______________AGUCU__CGGGCG_____GGUCG__UUG_UGGGACGUU_GAUCGGCGCA\n______________\|\|\|\|:__\|::\|\|:_____::\|\|\|__\|\|\|_\|\|\|\|\|\|\|:\|_:\|:\|::\|\|\|\|\n______________UCAGG__GUUCGU_____UUAGC__AAC_ACCCUGCGA_UUGGUUGCGU\n3'-UUU...CGUAG_____AA______ACCAA____________________A__________UGGUC...UAG-5'\n_____________\|_________________________________________________\|\n_____________94________________________________________________73\n	40 -- 46	85 -- 91	-47.7546 kcal/mol	17.619 kcal/mol	19.1533 kcal/mol	37 57@LB@ \| \|@LB@ 5'-GCGGUACG GG GAAAA CA U UUAAU...UCU-3'@LB@ AGUCU CGGGCG GGUCG UUG UGGGACGUU GAUCGGCGCA@LB@ \|\|\|\|: \|::\|\|: ::\|\|\| \|\|\| \|\|\|\|\|\|\|:\| :\|:\|::\|\|\|\|@LB@ UCAGG GUUCGU UUAGC AAC ACCCUGCGA UUGGUUGCGU@LB@3'-UUU...CGUAG AA ACCAA A UGGUC...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.76 kcal/mol@LB@Hybridization Energy -47.7546 kcal/mol@LB@Unfolding Energy - mRNA 17.619 kcal/mol@LB@Unfolding Energy - sRNA 19.1533 kcal/mol@LB@@LB@Position - mRNA 38 -- 56@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 85 -- 91@LB@
155	0.01733	0.3749	b3542	dppC	-14.36	0.036537	40 -- 62	74 -- 93	dipeptide/heme ABC transporter permease	_____________39_______________________________________________________63\n_____________\|________________________________________________________\|\n5'-GGG...UCGUC____U__U___C__________UA___C_____GA_______C_____________AGAAG...UCG-3'\n______________AACU_GC_GGU__GAUCUGCUG__CGG_GUGGU___AC_CCG_GUAUUC_GUCAUA\n______________\|\|\|:_\|\|_\|\|\|__:\|\|\|\|\|\|\|\|__\|\|\|_\|\|\|:\|___\|\|_\|\|:_:\|\|:\|\|_\|\|\|\|:\|\n______________UUGG_CG_CCA__UUAGACGAC__GCC_CACUA___UG_GGU_UAUGAG_CAGUGU\n_____3'-UUUUUU____U__U___UA_________C__________AAA__U__________U______GUACU...UAG-5'\n_____________\|________________________________________________________\|\n_____________94_______________________________________________________73\n	146 -- 152	200 -- 206	-46.3163 kcal/mol	15.5571 kcal/mol	18.3074 kcal/mol	39 63@LB@ \| \|@LB@5'-GGG...UCGUC U U C UA C GA C AGAAG...UCG-3'@LB@ AACU GC GGU GAUCUGCUG CGG GUGGU AC CCG GUAUUC GUCAUA@LB@ \|\|\|: \|\| \|\|\| :\|\|\|\|\|\|\|\| \|\|\| \|\|\|:\| \|\| \|\|: :\|\|:\|\| \|\|\|\|:\|@LB@ UUGG CG CCA UUAGACGAC GCC CACUA UG GGU UAUGAG CAGUGU@LB@ 3'-UUUUUU U U UA C AAA U U GUACU...UAG-5'@LB@ \| \|@LB@ 94 73@LB@@LB@@LB@Energy -14.36 kcal/mol@LB@Hybridization Energy -46.3163 kcal/mol@LB@Unfolding Energy - mRNA 15.5571 kcal/mol@LB@Unfolding Energy - sRNA 18.3074 kcal/mol@LB@@LB@Position - mRNA 40 -- 62@LB@Position - sRNA 74 -- 93@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 200 -- 206@LB@
158	0.01775	0.3749	b1187	fadR	-13.89	0.045798	42 -- 66	152 -- 176	fatty acid metabolism regulon transcriptional regulator	_____________41________________________67\n_____________\|_________________________\|\n5'-AAA...CUUAA______G___G__GUG_________UUGAU...CAG-3'\n______________CGGUCA_GCA_GA___AGGCAAGUC\n______________\|:\|\|\|\|_:\|\|_\|\|___\|\|\|\|\|\|\|\|\|\n______________GUCAGU_UGU_CU___UCCGUUCAG\n3'-UUU...UAUGA______G___A__ACG_________UUGAA...UAG-5'\n_____________\|_________________________\|\n_____________177_______________________151\n	60 -- 66	152 -- 158	-31.5031 kcal/mol	7.04431 kcal/mol	8.02398 kcal/mol	41 67@LB@ \| \|@LB@5'-AAA...CUUAA G G GUG UUGAU...CAG-3'@LB@ CGGUCA GCA GA AGGCAAGUC@LB@ \|:\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ GUCAGU UGU CU UCCGUUCAG@LB@3'-UUU...UAUGA G A ACG UUGAA...UAG-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -13.89 kcal/mol@LB@Hybridization Energy -31.5031 kcal/mol@LB@Unfolding Energy - mRNA 7.04431 kcal/mol@LB@Unfolding Energy - sRNA 8.02398 kcal/mol@LB@@LB@Position - mRNA 42 -- 66@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 152 -- 158@LB@
153	0.01719	0.3749	b2997	hybO	-10.59	0.212773	44 -- 57	176 -- 189	hydrogenase 2 small subunit	_____________43_________________58\n_____________\|__________________\|\n5'-CUC...AUUAA______________CU__CCUUC...GCA-3'\n______________UUACACUAAUGCUU__UC\n______________\|\|\|\|\|\|:\|\|\|:\|\|:__\|\|\n______________AAUGUGGUUAUGAG__AG\n3'-UUU...ACUAA______________UC__UGUGU...UAG-5'\n_____________\|__________________\|\n_____________190________________175\n	51 -- 57	176 -- 182	-17.3647 kcal/mol	0.828093 kcal/mol	4.66778 kcal/mol	43 58@LB@ \| \|@LB@5'-CUC...AUUAA CU CCUUC...GCA-3'@LB@ UUACACUAAUGCUU UC@LB@ \|\|\|\|\|\|:\|\|\|:\|\|: \|\|@LB@ AAUGUGGUUAUGAG AG@LB@3'-UUU...ACUAA UC UGUGU...UAG-5'@LB@ \| \|@LB@ 190 175@LB@@LB@@LB@Energy -10.59 kcal/mol@LB@Hybridization Energy -17.3647 kcal/mol@LB@Unfolding Energy - mRNA 0.828093 kcal/mol@LB@Unfolding Energy - sRNA 4.66778 kcal/mol@LB@@LB@Position - mRNA 44 -- 57@LB@Position - sRNA 176 -- 189@LB@Position Seed - mRNA 51 -- 57@LB@Position Seed - sRNA 176 -- 182@LB@
64	0.006252	0.3261	b3195	mlaF	-10.58	0.212925	52 -- 62	81 -- 91	ABC transporter maintaining OM lipid asymmetry ATP-binding protein	_____________51____________________________________63\n_____________\|_____________________________________\|\n5'-UUU...UUCAA___UAA___GA______________AAAA__A_____AGACG...GAG-3'\n______________GGU___AUU__GCGCC_AUGCUUAG____UC_ACGCA\n______________\|\|\|___\|\|\|__:\|:\|\|_\|\|:\|\|:\|\|____\|\|_\|\|:\|\|\n______________CCA___UAA__UGUGG_UAUGAGUC____AG_UGUGU\n3'-UUU...ACCGC___C_____AA_____U____________________ACUAC...UAG-5'\n_____________\|_____________________________________\|\n_____________92____________________________________80\n	166 -- 172	174 -- 180	-23.2269 kcal/mol	9.4943 kcal/mol	5.22711 kcal/mol	51 63@LB@ \| \|@LB@5'-UUU...UUCAA UAA GA AAAA A AGACG...GAG-3'@LB@ GGU AUU GCGCC AUGCUUAG UC ACGCA@LB@ \|\|\| \|\|\| :\|:\|\| \|\|:\|\|:\|\| \|\| \|\|:\|\|@LB@ CCA UAA UGUGG UAUGAGUC AG UGUGU@LB@3'-UUU...ACCGC C AA U ACUAC...UAG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -10.58 kcal/mol@LB@Hybridization Energy -23.2269 kcal/mol@LB@Unfolding Energy - mRNA 9.4943 kcal/mol@LB@Unfolding Energy - sRNA 5.22711 kcal/mol@LB@@LB@Position - mRNA 52 -- 62@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 174 -- 180@LB@
118	0.01293	0.3575	b1598	ydgD	-17.08	0.010207	53 -- 140	115 -- 186	putative peptidase	_____________52______________________________________________________________________141\n_____________\|_______________________________________________________________________\|\n5'-CUU...AUCCU_____UAUG__________UACC__CC___UUUAU_____CU______A____UCUGAUUUUAC_______UUCAU...AGG-3'\n______________UAUUU____CGCAC_UGAU____GC__GUU_____CUUUC__GAUUGU_GUUA___________UCCCACU\n______________\|\|:\|:____\|:\|\|\|_\|\|\|\|____\|\|__\|\|:_____\|\|\|\|\|__:\|\|\|\|:_\|\|:\|___________\|\|\|\|\|\|\|\n______________AUGAG____GUGUG_ACUA____CG__CAG_____GAAAG__UUAACG_CAGU___________AGGGUGA\n3'-UUU...UGGUU_____UCA______U____CGUC__UU___UU________UC______C______________________CGUAG...UAG-5'\n_____________\|_______________________________________________________________________\|\n_____________187_____________________________________________________________________114\n	122 -- 128	125 -- 131	-34.2678 kcal/mol	6.55961 kcal/mol	16.6417 kcal/mol	52 141@LB@ \| \|@LB@5'-CUU...AUCCU UAUG UACC CC UUUAU CU A UCUGAUUUUAC UUCAU...AGG-3'@LB@ UAUUU CGCAC UGAU GC GUU CUUUC GAUUGU GUUA UCCCACU@LB@ \|\|:\|: \|:\|\|\| \|\|\|\| \|\| \|\|: \|\|\|\|\| :\|\|\|\|: \|\|:\| \|\|\|\|\|\|\|@LB@ AUGAG GUGUG ACUA CG CAG GAAAG UUAACG CAGU AGGGUGA@LB@3'-UUU...UGGUU UCA U CGUC UU UU UC C CGUAG...UAG-5'@LB@ \| \|@LB@ 187 114@LB@@LB@@LB@Energy -17.08 kcal/mol@LB@Hybridization Energy -34.2678 kcal/mol@LB@Unfolding Energy - mRNA 6.55961 kcal/mol@LB@Unfolding Energy - sRNA 16.6417 kcal/mol@LB@@LB@Position - mRNA 53 -- 140@LB@Position - sRNA 115 -- 186@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 125 -- 131@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