Input and runtime details for job 3202356 (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 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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	Additional homologs
87	0.004009	0.1596	stm2067	sbcB	-11.70	0.367652	220 -- 292	35 -- 90	exodeoxyribonuclease I		_____________219_____________________293\n_____________\|_______________________\|\n5'-AUU...AUGUA______U________________AUUGG...CCG-3'\n______________CGAACA_UAGCA__ACAAUAUCA\n______________\|:\|\|\|\|_:\|:\|\|__\|\|\|\|:\|\|\|\|\n______________GUUUGU_GUUGU__UGUUGUAGU\n3'-UUU...UUAAC____________UG_________GUUGG...UCA-5'\n_____________\|_______________________\|\n_____________91______________________34\n	110 -- 116	68 -- 74	-17.8808 kcal/mol	2.08887 kcal/mol	5.27986 kcal/mol	219 293@LB@ \| \|@LB@5'-AUU...AUGUA U AUUGG...CCG-3'@LB@ CGAACA UAGCA ACAAUAUCA@LB@ \|:\|\|\|\| :\|:\|\| \|\|\|\|:\|\|\|\|@LB@ GUUUGU GUUGU UGUUGUAGU@LB@3'-UUU...UUAAC UG GUUGG...UCA-5'@LB@ \| \|@LB@ 91 34@LB@@LB@@LB@Energy -11.70 kcal/mol@LB@Hybridization Energy -17.8808 kcal/mol@LB@Unfolding Energy - mRNA 2.08887 kcal/mol@LB@Unfolding Energy - sRNA 5.27986 kcal/mol@LB@@LB@Position - mRNA 220 -- 292@LB@Position - sRNA 35 -- 90@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 68 -- 74@LB@
149	0.007892	0.1845	stm2071	hisG	-15.61	0.094042	166 -- 245	36 -- 100	ATP phosphoribosyltransferase		_____________165________________________246\n_____________\|__________________________\|\n5'-UUU...AGACC__UU________A________G____ACGCA...AUU-3'\n______________GG__CAGACAGG_UAA____A_AGGA\n______________\|\|__\|\|\|\|\|\|\|\|_\|\|\|____\|_\|\|\|\|\n______________CC__GUCUGUCC_AUU____U_UCCU\n3'-UUU...UGAUA__U_________C___UACA_G____UCACU...UCA-5'\n_____________\|__________________________\|\n_____________101________________________35\n	177 -- 183	153 -- 159	-19.7047 kcal/mol	3.01127 kcal/mol	3.70983 kcal/mol	165 246@LB@ \| \|@LB@5'-UUU...AGACC UU A G ACGCA...AUU-3'@LB@ GG CAGACAGG UAA A AGGA@LB@ \|\| \|\|\|\|\|\|\|\| \|\|\| \| \|\|\|\|@LB@ CC GUCUGUCC AUU U UCCU@LB@3'-UUU...UGAUA U C UACA G UCACU...UCA-5'@LB@ \| \|@LB@ 101 35@LB@@LB@@LB@Energy -15.61 kcal/mol@LB@Hybridization Energy -19.7047 kcal/mol@LB@Unfolding Energy - mRNA 3.01127 kcal/mol@LB@Unfolding Energy - sRNA 3.70983 kcal/mol@LB@@LB@Position - mRNA 166 -- 245@LB@Position - sRNA 36 -- 100@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 153 -- 159@LB@
108	0.005311	0.1728	stm2183	cdd	-16.35	0.071230	31 -- 68	151 -- 187	cytidine deaminase		_____________30_________________69\n_____________\|__________________\|\n5'-UGG...AGAUC_____UUAA_________GGCCC...UGA-3'\n______________ACAUA____GACAUAGCA\n______________\|\|\|:\|____:\|\|\|:\|:\|\|\n______________UGUGU____UUGUGUUGU\n3'-UUU...ACGUU_____UG___________AGUGU...UCA-5'\n_____________\|__________________\|\n_____________188________________150\n	150 -- 156	71 -- 77	-12.389 kcal/mol	1.12571 kcal/mol	3.50787 kcal/mol	30 69@LB@ \| \|@LB@5'-UGG...AGAUC UUAA GGCCC...UGA-3'@LB@ ACAUA GACAUAGCA@LB@ \|\|\|:\| :\|\|\|:\|:\|\|@LB@ UGUGU UUGUGUUGU@LB@3'-UUU...ACGUU UG AGUGU...UCA-5'@LB@ \| \|@LB@ 188 150@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -12.389 kcal/mol@LB@Unfolding Energy - mRNA 1.12571 kcal/mol@LB@Unfolding Energy - sRNA 3.50787 kcal/mol@LB@@LB@Position - mRNA 31 -- 68@LB@Position - sRNA 151 -- 187@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 71 -- 77@LB@
58	0.002307	0.14	stm2234	N/A	-13.92	0.174542	131 -- 196	38 -- 89	phage tail protein	stm2705 stm2233	_____________130______197\n_____________\|________\|\n5'-CUG...UACAC________AUCCA...CAG-3'\n______________CAGACAGG\n______________\|\|\|\|\|\|\|\|\n______________GUCUGUCC\n3'-UUU...UACCU________CAUUU...UCA-5'\n_____________\|________\|\n_____________90_______37\n	132 -- 138	153 -- 159	-13.9425 kcal/mol	2.61206 kcal/mol	2.72972 kcal/mol	130 197@LB@ \| \|@LB@5'-CUG...UACAC AUCCA...CAG-3'@LB@ CAGACAGG@LB@ \|\|\|\|\|\|\|\|@LB@ GUCUGUCC@LB@3'-UUU...UACCU CAUUU...UCA-5'@LB@ \| \|@LB@ 90 37@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -13.9425 kcal/mol@LB@Unfolding Energy - mRNA 2.61206 kcal/mol@LB@Unfolding Energy - sRNA 2.72972 kcal/mol@LB@@LB@Position - mRNA 131 -- 196@LB@Position - sRNA 38 -- 89@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 153 -- 159@LB@
181	0.01001	0.1966	stm2266	apbE	-12.19	0.314808	267 -- 297	62 -- 90	FAD:protein FMN transferase ApbE		_____________266_____________________________298\n_____________\|_______________________________\|\n5'-ACC...AUGAG__UCCCGA______A__________CU____CUC-3'\n______________GC______AACGAC_ACAGCGUCAC__GCCG\n______________\|\|______\|\|\|:\|\|_\|\|\|:\|:\|\|\|\|__:\|\|\|\n______________CG______UUGUUG_UGUUGUAGUG__UGGC\n3'-UUU...GUUAA__UUUGUG_________________U_____AUUCG...UCA-5'\n_____________\|_______________________________\|\n_____________91______________________________61\n	285 -- 291	67 -- 73	-27.9543 kcal/mol	7.52451 kcal/mol	8.62576 kcal/mol	266 298@LB@ \| \|@LB@5'-ACC...AUGAG UCCCGA A CU CUC-3'@LB@ GC AACGAC ACAGCGUCAC GCCG@LB@ \|\| \|\|\|:\|\| \|\|\|:\|:\|\|\|\| :\|\|\|@LB@ CG UUGUUG UGUUGUAGUG UGGC@LB@3'-UUU...GUUAA UUUGUG U AUUCG...UCA-5'@LB@ \| \|@LB@ 91 61@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -27.9543 kcal/mol@LB@Unfolding Energy - mRNA 7.52451 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 267 -- 297@LB@Position - sRNA 62 -- 90@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 67 -- 73@LB@
143	0.007336	0.182	stm2276	ubiG	-14.65	0.134291	225 -- 278	36 -- 81	2-octaprenyl-6-hydroxy phenol methylase		_____________224_________________279\n_____________\|___________________\|\n5'-CAC...CGGCA____________CA_____UUUGC...AAU-3'\n______________GUAGAUAUAACG__GCGAC\n______________\|:\|:\|:\|:\|\|\|:__:\|:\|\|\n______________CGUUUGUGUUGU__UGUUG\n3'-UUU...GUUAA____________UG_____UAGUG...UCA-5'\n_____________\|___________________\|\n_____________82__________________35\n	134 -- 140	80 -- 86	-18.0681 kcal/mol	5.41873 kcal/mol	3.80362 kcal/mol	224 279@LB@ \| \|@LB@5'-CAC...CGGCA CA UUUGC...AAU-3'@LB@ GUAGAUAUAACG GCGAC@LB@ \|:\|:\|:\|:\|\|\|: :\|:\|\|@LB@ CGUUUGUGUUGU UGUUG@LB@3'-UUU...GUUAA UG UAGUG...UCA-5'@LB@ \| \|@LB@ 82 35@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -18.0681 kcal/mol@LB@Unfolding Energy - mRNA 5.41873 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 225 -- 278@LB@Position - sRNA 36 -- 81@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 80 -- 86@LB@
46	0.001637	0.1267	stm2313	elaC	-17.21	0.051329	250 -- 300	51 -- 90	ribonuclease Z	stm1109	_____________249_____________________________________________301\n_____________\|_______________________________________________\|\n5'-UCG...CUCAC____UGUA________UUUAUUACAUCU________CAAC_______GGAG-3'\n______________GCAA____ACGGCAAU____________GCAACAUC____GCAGCCG\n______________\|\|\|\|____\|\|::\|\|\|:____________:\|\|\|\|\|\|\|____:\|\|:\|\|\|\n______________CGUU____UGUUGUUG____________UGUUGUAG____UGUUGGC\n3'-UUU...GUUAA____UG_________________________________________AUUCG...UCA-5'\n_____________\|_______________________________________________\|\n_____________91______________________________________________50\n	290 -- 296	62 -- 68	-28.5454 kcal/mol	7.10881 kcal/mol	8.62576 kcal/mol	249 301@LB@ \| \|@LB@5'-UCG...CUCAC UGUA UUUAUUACAUCU CAAC GGAG-3'@LB@ GCAA ACGGCAAU GCAACAUC GCAGCCG@LB@ \|\|\|\| \|\|::\|\|\|: :\|\|\|\|\|\|\| :\|\|:\|\|\|@LB@ CGUU UGUUGUUG UGUUGUAG UGUUGGC@LB@3'-UUU...GUUAA UG AUUCG...UCA-5'@LB@ \| \|@LB@ 91 50@LB@@LB@@LB@Energy -17.21 kcal/mol@LB@Hybridization Energy -28.5454 kcal/mol@LB@Unfolding Energy - mRNA 7.10881 kcal/mol@LB@Unfolding Energy - sRNA 8.62576 kcal/mol@LB@@LB@Position - mRNA 250 -- 300@LB@Position - sRNA 51 -- 90@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 62 -- 68@LB@
148	0.007836	0.1845	stm2318	nuoL	-12.84	0.254324	144 -- 178	37 -- 76	NADH-quinone oxidoreductase subunit L		_____________143___________________179\n_____________\|_____________________\|\n5'-GGG...AGACC_____U____U__________UUCUC...UUG-3'\n______________GAUGG_CAGG___GAUGUACA\n______________\|\|::\|_\|\|\|\|___:\|\|\|\|\|\|\|\n______________CUGUC_GUCC___UUACAUGU\n3'-UUU...GAUAC_____U____CAU________CCUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________36\n	82 -- 88	142 -- 148	-19.9967 kcal/mol	7.20144 kcal/mol	3.50251 kcal/mol	143 179@LB@ \| \|@LB@5'-GGG...AGACC U U UUCUC...UUG-3'@LB@ GAUGG CAGG GAUGUACA@LB@ \|\|::\| \|\|\|\| :\|\|\|\|\|\|\|@LB@ CUGUC GUCC UUACAUGU@LB@3'-UUU...GAUAC U CAU CCUUC...UCA-5'@LB@ \| \|@LB@ 77 36@LB@@LB@@LB@Energy -12.84 kcal/mol@LB@Hybridization Energy -19.9967 kcal/mol@LB@Unfolding Energy - mRNA 7.20144 kcal/mol@LB@Unfolding Energy - sRNA 3.50251 kcal/mol@LB@@LB@Position - mRNA 144 -- 178@LB@Position - sRNA 37 -- 76@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 142 -- 148@LB@
141	0.007251	0.182	stm2325	nuoE	-19.46	0.021521	159 -- 233	56 -- 129	NADH-quinone oxidoreductase subunit E		_____________158_____________________________________________________________________________234\n_____________\|_______________________________________________________________________________\|\n5'-AUG...UAUCU_______A___AUU____UAU___A_____________CUAAUUAU______G_________AC___A___________UUUGA...GUG-3'\n______________GGGUAGU_UCG___UUGU___GUC_GA__UGUGGACCG________GCACGA_AAU_CAACA__CAC_AACCG_AGGCU\n______________\|\|\|\|\|\|\|_\|\|\|___::\|\|___\|\|\|_\|\|__:\|::\|\|\|\|:________:\|\|\|:\|_\|\|:_\|\|\|\|\|__\|\|\|_\|\|\|\|\|_\|:\|\|:\n______________CCCAUCA_AGC___GGCA___CAG_CU__GCGUCUGGU________UGUGUU_UUG_GUUGU__GUG_UUGGC_UUCGG\n3'-UUU...UUUUU_______G___GAU____C_____A__UA_________UAACGUU_______G___U_____A__________A_____UUUUC...UCA-5'\n_____________\|_______________________________________________________________________________\|\n_____________130_____________________________________________________________________________55\n	159 -- 165	123 -- 129	-58.9967 kcal/mol	15.8863 kcal/mol	27.1281 kcal/mol	158 234@LB@ \| \|@LB@5'-AUG...UAUCU A AUU UAU A CUAAUUAU G AC A UUUGA...GUG-3'@LB@ GGGUAGU UCG UUGU GUC GA UGUGGACCG GCACGA AAU CAACA CAC AACCG AGGCU@LB@ \|\|\|\|\|\|\| \|\|\| ::\|\| \|\|\| \|\| :\|::\|\|\|\|: :\|\|\|:\| \|\|: \|\|\|\|\| \|\|\| \|\|\|\|\| \|:\|\|:@LB@ CCCAUCA AGC GGCA CAG CU GCGUCUGGU UGUGUU UUG GUUGU GUG UUGGC UUCGG@LB@3'-UUU...UUUUU G GAU C A UA UAACGUU G U A A UUUUC...UCA-5'@LB@ \| \|@LB@ 130 55@LB@@LB@@LB@Energy -19.46 kcal/mol@LB@Hybridization Energy -58.9967 kcal/mol@LB@Unfolding Energy - mRNA 15.8863 kcal/mol@LB@Unfolding Energy - sRNA 27.1281 kcal/mol@LB@@LB@Position - mRNA 159 -- 233@LB@Position - sRNA 56 -- 129@LB@Position Seed - mRNA 159 -- 165@LB@Position Seed - sRNA 123 -- 129@LB@
45	0.001635	0.1267	stm2351	hisP	-13.82	0.180688	258 -- 282	115 -- 140	histidine and lysine/arginine/ornithine transport protein		_____________257__________________________283\n_____________\|____________________________\|\n5'-UAC...GUCAU______CU____________________AGGCC...AUG-3'\n______________GAAGUG__GAAAGGGGUA___UCGCUGC\n______________\|\|\|\|\|\|__:\|\|\|:\|\|\|\|\|___\|\|\|\|\|:\|\n______________CUUCAC__UUUUUCCCAU___AGCGAUG\n3'-UUU...AUGUC__________________CAG_______GCACC...UCA-5'\n_____________\|____________________________\|\n_____________141__________________________114\n	276 -- 282	115 -- 121	-29.6028 kcal/mol	6.54228 kcal/mol	8.52785 kcal/mol	257 283@LB@ \| \|@LB@5'-UAC...GUCAU CU AGGCC...AUG-3'@LB@ GAAGUG GAAAGGGGUA UCGCUGC@LB@ \|\|\|\|\|\| :\|\|\|:\|\|\|\|\| \|\|\|\|\|:\|@LB@ CUUCAC UUUUUCCCAU AGCGAUG@LB@3'-UUU...AUGUC CAG GCACC...UCA-5'@LB@ \| \|@LB@ 141 114@LB@@LB@@LB@Energy -13.82 kcal/mol@LB@Hybridization Energy -29.6028 kcal/mol@LB@Unfolding Energy - mRNA 6.54228 kcal/mol@LB@Unfolding Energy - sRNA 8.52785 kcal/mol@LB@@LB@Position - mRNA 258 -- 282@LB@Position - sRNA 115 -- 140@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 115 -- 121@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