Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
191	0.009733	0.1776	b0190	yaeQ	-9.83	0.261410	113 -- 128	45 -- 75	PDDEXK superfamily protein	_____________112_____________________________129\n_____________\|_______________________________\|\n5'-UAC...AAGGU_______________________________UUUCU...CUU-3'\n______________GACUAUAC_CA______________CACUCA\n______________\|\|\|\|\|:\|\|_\|\|______________\|\|\|\|\|\|\n______________CUGAUGUG_GU______________GUGAGU\n3'-UUU...CGUUU________U__CGUUAAGCAACAAA______CCCCU...GCA-5'\n_____________\|_______________________________\|\n_____________76______________________________44\n	114 -- 120	68 -- 74	-15.3898 kcal/mol	1.82074 kcal/mol	3.74078 kcal/mol	112 129@LB@ \| \|@LB@5'-UAC...AAGGU UUUCU...CUU-3'@LB@ GACUAUAC CA CACUCA@LB@ \|\|\|\|\|:\|\| \|\| \|\|\|\|\|\|@LB@ CUGAUGUG GU GUGAGU@LB@3'-UUU...CGUUU U CGUUAAGCAACAAA CCCCU...GCA-5'@LB@ \| \|@LB@ 76 44@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -15.3898 kcal/mol@LB@Unfolding Energy - mRNA 1.82074 kcal/mol@LB@Unfolding Energy - sRNA 3.74078 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 45 -- 75@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 68 -- 74@LB@
136	0.006258	0.1605	b0219	yafV	-11.82	0.112632	212 -- 233	61 -- 78	putative NAD(P)-binding C-N hydrolase family amidase	_____________211____________________234\n_____________\|______________________\|\n5'-GUC...GGUUU___________UUUU_______CCACU...CCG-3'\n______________GAAGAUUACGC____GCAGCAA\n______________:\|\|\|\|:\|\|\|:\|____:\|\|\|\|\|\|\n______________UUUCUGAUGUG____UGUCGUU\n3'-UUU...ACCCG______________________AAGCA...GCA-5'\n_____________\|______________________\|\n_____________79_____________________60\n	227 -- 233	61 -- 67	-20.0989 kcal/mol	5.01896 kcal/mol	3.25783 kcal/mol	211 234@LB@ \| \|@LB@5'-GUC...GGUUU UUUU CCACU...CCG-3'@LB@ GAAGAUUACGC GCAGCAA@LB@ :\|\|\|\|:\|\|\|:\| :\|\|\|\|\|\|@LB@ UUUCUGAUGUG UGUCGUU@LB@3'-UUU...ACCCG AAGCA...GCA-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -20.0989 kcal/mol@LB@Unfolding Energy - mRNA 5.01896 kcal/mol@LB@Unfolding Energy - sRNA 3.25783 kcal/mol@LB@@LB@Position - mRNA 212 -- 233@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 61 -- 67@LB@
140	0.006445	0.1605	b0325	yahK	-13.93	0.038719	67 -- 79	43 -- 55	broad specificity NADPH-dependent aldehyde reductase Zn-containing	_____________66____________80\n_____________\|_____________\|\n5'-UUA...UGCUC_____________CUCGC...AAA-3'\n______________UGUUUCAUUCAGG\n______________\|\|\|\|\|\|\|:\|\|\|\|\|\n______________ACAAAGUGAGUCC\n3'-UUU...AAGCA_____________CCUAA...GCA-5'\n_____________\|_____________\|\n_____________56____________42\n	73 -- 79	43 -- 49	-18.9036 kcal/mol	3.47822 kcal/mol	1.49792 kcal/mol	66 80@LB@ \| \|@LB@5'-UUA...UGCUC CUCGC...AAA-3'@LB@ UGUUUCAUUCAGG@LB@ \|\|\|\|\|\|\|:\|\|\|\|\|@LB@ ACAAAGUGAGUCC@LB@3'-UUU...AAGCA CCUAA...GCA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -13.93 kcal/mol@LB@Hybridization Energy -18.9036 kcal/mol@LB@Unfolding Energy - mRNA 3.47822 kcal/mol@LB@Unfolding Energy - sRNA 1.49792 kcal/mol@LB@@LB@Position - mRNA 67 -- 79@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 43 -- 49@LB@
102	0.004593	0.1538	b0343	lacY	-16.22	0.009713	12 -- 55	39 -- 78	lactose permease	_____________11___________________________________________56\n_____________\|____________________________________________\|\n5'-UGC...ACGCG_____AG_________UG___A___ACG_____CA_AU______UGGUG...GGC-3'\n______________GAAGA__GCACAUGGC__AAU_UCG___GUUUC__U__GGGGAU\n______________:\|\|\|\|__:\|\|\|\|::\|\|__\|\|\|_\|\|\|___\|\|\|\|\|__\|__\|\|\|\|\|\|\n______________UUUCU__UGUGUGUCG__UUA_AGC___CAAAG__A__CCCCUA\n3'-UUU...ACCCG_____GA__________________AA______UG_GU______AAGGU...GCA-5'\n_____________\|____________________________________________\|\n_____________79___________________________________________38\n	21 -- 27	63 -- 69	-31.4377 kcal/mol	10.4352 kcal/mol	4.77966 kcal/mol	11 56@LB@ \| \|@LB@5'-UGC...ACGCG AG UG A ACG CA AU UGGUG...GGC-3'@LB@ GAAGA GCACAUGGC AAU UCG GUUUC U GGGGAU@LB@ :\|\|\|\| :\|\|\|\|::\|\| \|\|\| \|\|\| \|\|\|\|\| \| \|\|\|\|\|\|@LB@ UUUCU UGUGUGUCG UUA AGC CAAAG A CCCCUA@LB@3'-UUU...ACCCG GA AA UG GU AAGGU...GCA-5'@LB@ \| \|@LB@ 79 38@LB@@LB@@LB@Energy -16.22 kcal/mol@LB@Hybridization Energy -31.4377 kcal/mol@LB@Unfolding Energy - mRNA 10.4352 kcal/mol@LB@Unfolding Energy - sRNA 4.77966 kcal/mol@LB@@LB@Position - mRNA 12 -- 55@LB@Position - sRNA 39 -- 78@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 63 -- 69@LB@
196	0.01003	0.1776	b0344	lacZ	-8.86	0.369200	215 -- 237	48 -- 76	beta-D-galactosidase	_____________214___________________________238\n_____________\|_____________________________\|\n5'-ACC...AUUAC_____________________C_______AACGU...CUU-3'\n______________GGAUU_CAC_UGGC____CGU_GUUUUAC\n______________:\|\|:\|_\|\|\|_::\|\|____\|\|\|_\|\|\|\|:\|\|\n______________UCUGA_GUG_GUCG____GCA_CAAAGUG\n3'-UUU...CCGUU_____U___U____UUAA___A_______AGUCC...GCA-5'\n_____________\|_____________________________\|\n_____________77____________________________47\n	231 -- 237	48 -- 54	-17.9156 kcal/mol	5.37156 kcal/mol	3.68714 kcal/mol	214 238@LB@ \| \|@LB@5'-ACC...AUUAC C AACGU...CUU-3'@LB@ GGAUU CAC UGGC CGU GUUUUAC@LB@ :\|\|:\| \|\|\| ::\|\| \|\|\| \|\|\|\|:\|\|@LB@ UCUGA GUG GUCG GCA CAAAGUG@LB@3'-UUU...CCGUU U U UUAA A AGUCC...GCA-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -8.86 kcal/mol@LB@Hybridization Energy -17.9156 kcal/mol@LB@Unfolding Energy - mRNA 5.37156 kcal/mol@LB@Unfolding Energy - sRNA 3.68714 kcal/mol@LB@@LB@Position - mRNA 215 -- 237@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 48 -- 54@LB@
138	0.006392	0.1605	b0345	lacI	-7.62	0.533808	7 -- 17	61 -- 71	lactose-inducible lac operon transcriptional repressor	_____________6___________18\n_____________\|___________\|\n_____5'-CAUUGA___G_______AAAAG...AAA-3'\n______________ACA_GCAGCGG\n______________\|\|\|_:\|\|\|\|::\n______________UGU_UGUCGUU\n3'-UUU...UCUGA___G_______AAGCA...GCA-5'\n_____________\|___________\|\n_____________72__________60\n	11 -- 17	61 -- 67	-13.1569 kcal/mol	2.35774 kcal/mol	3.17655 kcal/mol	6 18@LB@ \| \|@LB@ 5'-CAUUGA G AAAAG...AAA-3'@LB@ ACA GCAGCGG@LB@ \|\|\| :\|\|\|\|::@LB@ UGU UGUCGUU@LB@3'-UUU...UCUGA G AAGCA...GCA-5'@LB@ \| \|@LB@ 72 60@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -13.1569 kcal/mol@LB@Unfolding Energy - mRNA 2.35774 kcal/mol@LB@Unfolding Energy - sRNA 3.17655 kcal/mol@LB@@LB@Position - mRNA 7 -- 17@LB@Position - sRNA 61 -- 71@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 61 -- 67@LB@
133	0.006126	0.1605	b0387	yaiI	-9.01	0.350598	46 -- 81	33 -- 74	UPF0178 family protein	_____________45_________________________________________82\n_____________\|__________________________________________\|\n5'-CAC...CCCAU____________CAAUAAAACCG______UCU__________UGCCU...CAA-3'\n______________AUUGC_CGCAGC_____________AUUU______UUUCCAU\n______________\|:\|:\|_\|:\|\|\|\|_____________\|:\|:______\|\|\|\|\|\|\|\n______________UGAUG_GUGUCG_____________UGAG______AAAGGUA\n3'-UUU...GUUUC_____U______UUAAGCAACAAAG____UCCCCU_______CGAAU...GCA-5'\n_____________\|__________________________________________\|\n_____________75_________________________________________32\n	75 -- 81	33 -- 39	-16.9561 kcal/mol	3.12923 kcal/mol	4.81602 kcal/mol	45 82@LB@ \| \|@LB@5'-CAC...CCCAU CAAUAAAACCG UCU UGCCU...CAA-3'@LB@ AUUGC CGCAGC AUUU UUUCCAU@LB@ \|:\|:\| \|:\|\|\|\| \|:\|: \|\|\|\|\|\|\|@LB@ UGAUG GUGUCG UGAG AAAGGUA@LB@3'-UUU...GUUUC U UUAAGCAACAAAG UCCCCU CGAAU...GCA-5'@LB@ \| \|@LB@ 75 32@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -16.9561 kcal/mol@LB@Unfolding Energy - mRNA 3.12923 kcal/mol@LB@Unfolding Energy - sRNA 4.81602 kcal/mol@LB@@LB@Position - mRNA 46 -- 81@LB@Position - sRNA 33 -- 74@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 33 -- 39@LB@
163	0.007762	0.1668	b0394	mak	-14.23	0.032787	242 -- 265	40 -- 75	manno(fructo)kinase	_____________241__________________________________266\n_____________\|____________________________________\|\n5'-GUU...GAAGU________UG______G___________________GCAGU...GUG-3'\n______________GAUUGCAC__GGCGAU_____________CAGGGGA\n______________\|\|:\|:\|\|\|__:\|\|:\|\|_____________\|\|\|\|\|\|\|\n______________CUGAUGUG__UCGUUA_____________GUCCCCU\n3'-UUU...CGUUU________UG______AGCAACAAAGUGA_______AAAGG...GCA-5'\n_____________\|____________________________________\|\n_____________76___________________________________39\n	259 -- 265	40 -- 46	-27.5886 kcal/mol	8.58508 kcal/mol	4.77786 kcal/mol	241 266@LB@ \| \|@LB@5'-GUU...GAAGU UG G GCAGU...GUG-3'@LB@ GAUUGCAC GGCGAU CAGGGGA@LB@ \|\|:\|:\|\|\| :\|\|:\|\| \|\|\|\|\|\|\|@LB@ CUGAUGUG UCGUUA GUCCCCU@LB@3'-UUU...CGUUU UG AGCAACAAAGUGA AAAGG...GCA-5'@LB@ \| \|@LB@ 76 39@LB@@LB@@LB@Energy -14.23 kcal/mol@LB@Hybridization Energy -27.5886 kcal/mol@LB@Unfolding Energy - mRNA 8.58508 kcal/mol@LB@Unfolding Energy - sRNA 4.77786 kcal/mol@LB@@LB@Position - mRNA 242 -- 265@LB@Position - sRNA 40 -- 75@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 40 -- 46@LB@
81	0.003429	0.1462	b0413	nrdR	-16.32	0.009130	136 -- 177	33 -- 64	Nrd regulon repressor	_____________135_________________________________________178\n_____________\|___________________________________________\|\n5'-AGG...GUUGC__C_________A___UCAG_______UAAAAUA_________UAACC...UGU-3'\n______________GC__UUUGUUGU_UCG____UUCAGGG_______GAUUUCCGU\n______________\|\|__\|\|:\|\|\|\|\|_\|\|:____:\|\|\|\|\|\|_______\|\|\|\|\|\|\|:\|\n______________CG__AAGCAACA_AGU____GAGUCCC_______CUAAAGGUA\n3'-UUU...UGUGU__UU________A______________________________CGAAU...GCA-5'\n_____________\|___________________________________________\|\n_____________65__________________________________________32\n	171 -- 177	33 -- 39	-28.4719 kcal/mol	7.3911 kcal/mol	4.76435 kcal/mol	135 178@LB@ \| \|@LB@5'-AGG...GUUGC C A UCAG UAAAAUA UAACC...UGU-3'@LB@ GC UUUGUUGU UCG UUCAGGG GAUUUCCGU@LB@ \|\| \|\|:\|\|\|\|\| \|\|: :\|\|\|\|\|\| \|\|\|\|\|\|\|:\|@LB@ CG AAGCAACA AGU GAGUCCC CUAAAGGUA@LB@3'-UUU...UGUGU UU A CGAAU...GCA-5'@LB@ \| \|@LB@ 65 32@LB@@LB@@LB@Energy -16.32 kcal/mol@LB@Hybridization Energy -28.4719 kcal/mol@LB@Unfolding Energy - mRNA 7.3911 kcal/mol@LB@Unfolding Energy - sRNA 4.76435 kcal/mol@LB@@LB@Position - mRNA 136 -- 177@LB@Position - sRNA 33 -- 64@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 33 -- 39@LB@
159	0.007688	0.1668	b0454	ybaZ	-17.74	0.003345	226 -- 245	34 -- 52	excision repair protein alkyltransferase-like protein ATL	_____________225__________________246\n_____________\|____________________\|\n5'-AGG...GCGAC__________C_UU______GAUUA...UUC-3'\n______________UUCACUCGGG_G__UUUCCA\n______________\|\|\|\|\|\|\|:\|\|_\|__\|\|\|\|\|\|\n______________AAGUGAGUCC_C__AAAGGU\n3'-UUU...CAACA____________CU______ACGAA...GCA-5'\n_____________\|____________________\|\n_____________53___________________33\n	229 -- 235	43 -- 49	-23.7092 kcal/mol	4.0826 kcal/mol	1.88482 kcal/mol	225 246@LB@ \| \|@LB@5'-AGG...GCGAC C UU GAUUA...UUC-3'@LB@ UUCACUCGGG G UUUCCA@LB@ \|\|\|\|\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ AAGUGAGUCC C AAAGGU@LB@3'-UUU...CAACA CU ACGAA...GCA-5'@LB@ \| \|@LB@ 53 33@LB@@LB@@LB@Energy -17.74 kcal/mol@LB@Hybridization Energy -23.7092 kcal/mol@LB@Unfolding Energy - mRNA 4.0826 kcal/mol@LB@Unfolding Energy - sRNA 1.88482 kcal/mol@LB@@LB@Position - mRNA 226 -- 245@LB@Position - sRNA 34 -- 52@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 43 -- 49@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