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
158	0.00827	0.1845	stm1712	acnA	-14.47	0.143385	236 -- 294	48 -- 104	aconitate hydratase 1	_____________235_________________295\n_____________\|___________________\|\n5'-AUC...CAACC_______G_AU________CGCAA...GCG-3'\n______________CUGUGGA_A__CAGGGUAA\n______________\|\|:\|\|\|\|_\|__\|\|\|\|\|\|\|\|\n______________GAUACCU_U__GUCCCAUU\n3'-UUU...UUAGU_______G_CU________UACAU...UCA-5'\n_____________\|___________________\|\n_____________105_________________47\n	167 -- 173	149 -- 155	-24.0869 kcal/mol	10.3759 kcal/mol	4.11594 kcal/mol	235 295@LB@ \| \|@LB@5'-AUC...CAACC G AU CGCAA...GCG-3'@LB@ CUGUGGA A CAGGGUAA@LB@ \|\|:\|\|\|\| \| \|\|\|\|\|\|\|\|@LB@ GAUACCU U GUCCCAUU@LB@3'-UUU...UUAGU G CU UACAU...UCA-5'@LB@ \| \|@LB@ 105 47@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -24.0869 kcal/mol@LB@Unfolding Energy - mRNA 10.3759 kcal/mol@LB@Unfolding Energy - sRNA 4.11594 kcal/mol@LB@@LB@Position - mRNA 236 -- 294@LB@Position - sRNA 48 -- 104@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 149 -- 155@LB@
129	0.006472	0.1774	stm0158	acnB	-11.80	0.356459	140 -- 172	33 -- 60	bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase	_____________139________________173\n_____________\|__________________\|\n5'-AUU...CUUUU_________G_U______UUAAA...UGC-3'\n______________UUGUAAACA_A_UAACAC\n______________\|\|\|:\|\|\|\|\|_\|_:\|\|\|\|\|\n______________AACGUUUGU_U_GUUGUG\n3'-UUU...UGGUU_________G_U______UUGUA...UCA-5'\n_____________\|__________________\|\n_____________61_________________32\n	48 -- 54	84 -- 90	-17.8051 kcal/mol	3.41045 kcal/mol	3.73018 kcal/mol	139 173@LB@ \| \|@LB@5'-AUU...CUUUU G U UUAAA...UGC-3'@LB@ UUGUAAACA A UAACAC@LB@ \|\|\|:\|\|\|\|\| \| :\|\|\|\|\|@LB@ AACGUUUGU U GUUGUG@LB@3'-UUU...UGGUU G U UUGUA...UCA-5'@LB@ \| \|@LB@ 61 32@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -17.8051 kcal/mol@LB@Unfolding Energy - mRNA 3.41045 kcal/mol@LB@Unfolding Energy - sRNA 3.73018 kcal/mol@LB@@LB@Position - mRNA 140 -- 172@LB@Position - sRNA 33 -- 60@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 84 -- 90@LB@
137	0.006825	0.1774	stm1196	acpP	-14.14	0.161333	197 -- 223	36 -- 60	acyl carrier protein	_____________196___________________________________________224\n_____________\|_____________________________________________\|\n5'-ACU...AGAAC_______GAAA_____C____A____CU__GCGUUAA________AAGUA...UGG-3'\n______________GCGUUAA____AUUAU_GGCG_ACAG__GG_______GCAGGAAG\n______________:\|:\|\|\|\|____\|:\|\|\|_\|:\|:_\|\|\|\|__\|\|_______:\|\|\|\|\|\|\|\n______________UGUAAUU____UGAUA_CUGU_UGUC__CC_______UGUCCUUC\n3'-UUU...CACGA_______AG_______C____C________AUUUACA________ACUUU...UCA-5'\n_____________\|_____________________________________________\|\n_____________61____________________________________________35\n	258 -- 264	137 -- 143	-28.6095 kcal/mol	10.3633 kcal/mol	7.13805 kcal/mol	196 224@LB@ \| \|@LB@5'-ACU...AGAAC GAAA C A CU GCGUUAA AAGUA...UGG-3'@LB@ GCGUUAA AUUAU GGCG ACAG GG GCAGGAAG@LB@ :\|:\|\|\|\| \|:\|\|\| \|:\|: \|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ UGUAAUU UGAUA CUGU UGUC CC UGUCCUUC@LB@3'-UUU...CACGA AG C C AUUUACA ACUUU...UCA-5'@LB@ \| \|@LB@ 61 35@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -28.6095 kcal/mol@LB@Unfolding Energy - mRNA 10.3633 kcal/mol@LB@Unfolding Energy - sRNA 7.13805 kcal/mol@LB@@LB@Position - mRNA 197 -- 223@LB@Position - sRNA 36 -- 60@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 137 -- 143@LB@
19	0.0004167	0.0781	stm0475	acrB	-19.12	0.024591	69 -- 114	139 -- 185	aminoglycoside/multidrug transporter permease	_____________68_______________________115\n_____________\|________________________\|\n5'-AAG...GUCCU____C_____U_____________AAUUA...CGC-3'\n______________GGCG_ACAGG_UAAA_GUACAGGA\n______________\|:\|:_\|\|\|\|\|_\|\|\|\|_\|\|\|\|\|\|\|\|\n______________CUGU_UGUCC_AUUU_CAUGUCCU\n3'-UUU...GAUAC____C_____C____A________UCACU...UCA-5'\n_____________\|________________________\|\n_____________186______________________138\n	108 -- 114	139 -- 145	-25.274 kcal/mol	6.90525 kcal/mol	3.69132 kcal/mol	68 115@LB@ \| \|@LB@5'-AAG...GUCCU C U AAUUA...CGC-3'@LB@ GGCG ACAGG UAAA GUACAGGA@LB@ \|:\|: \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUGU UGUCC AUUU CAUGUCCU@LB@3'-UUU...GAUAC C C A UCACU...UCA-5'@LB@ \| \|@LB@ 186 138@LB@@LB@@LB@Energy -19.12 kcal/mol@LB@Hybridization Energy -25.274 kcal/mol@LB@Unfolding Energy - mRNA 6.90525 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 69 -- 114@LB@Position - sRNA 139 -- 185@LB@Position Seed - mRNA 108 -- 114@LB@Position Seed - sRNA 139 -- 145@LB@
170	0.009347	0.1945	stm0477	acrR	-17.70	0.042454	229 -- 246	74 -- 91	DNA-binding transcriptional repressor AcrR	_____________228________________247\n_____________\|__________________\|\n5'-AAG...AGCGC__G_______________UCCUG...CGC-3'\n______________UG_AGACACGACAACACA\n______________\|\|_\|:\|\|\|\|:\|\|\|\|\|\|\|\|\n______________AC_UUUGUGUUGUUGUGU\n3'-UUU...GGUUA__G_______________UGUAG...UCA-5'\n_____________\|__________________\|\n_____________92_________________73\n	240 -- 246	74 -- 80	-24.9092 kcal/mol	3.16809 kcal/mol	3.73631 kcal/mol	228 247@LB@ \| \|@LB@5'-AAG...AGCGC G UCCUG...CGC-3'@LB@ UG AGACACGACAACACA@LB@ \|\| \|:\|\|\|\|:\|\|\|\|\|\|\|\|@LB@ AC UUUGUGUUGUUGUGU@LB@3'-UUU...GGUUA G UGUAG...UCA-5'@LB@ \| \|@LB@ 92 73@LB@@LB@@LB@Energy -17.70 kcal/mol@LB@Hybridization Energy -24.9092 kcal/mol@LB@Unfolding Energy - mRNA 3.16809 kcal/mol@LB@Unfolding Energy - sRNA 3.73631 kcal/mol@LB@@LB@Position - mRNA 229 -- 246@LB@Position - sRNA 74 -- 91@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 74 -- 80@LB@
13	0.0002148	0.05681	stm4275	acs	-17.09	0.053801	176 -- 229	31 -- 87	acetate--CoA ligase	_____________175___________________230\n_____________\|_____________________\|\n5'-UUA...UGAGC________UA______C____CCCGC...ACG-3'\n______________CAAACACA__AACACG_CAUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:_\|\|\|:\n______________GUUUGUGU__UUGUGU_GUAG\n3'-UUU...UUAAC________UG______U____UGUUG...UCA-5'\n_____________\|_____________________\|\n_____________88____________________30\n	208 -- 214	82 -- 88	-19.539 kcal/mol	0.409404 kcal/mol	4.32311 kcal/mol	175 230@LB@ \| \|@LB@5'-UUA...UGAGC UA C CCCGC...ACG-3'@LB@ CAAACACA AACACG CAUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|:@LB@ GUUUGUGU UUGUGU GUAG@LB@3'-UUU...UUAAC UG U UGUUG...UCA-5'@LB@ \| \|@LB@ 88 30@LB@@LB@@LB@Energy -17.09 kcal/mol@LB@Hybridization Energy -19.539 kcal/mol@LB@Unfolding Energy - mRNA 0.409404 kcal/mol@LB@Unfolding Energy - sRNA 4.32311 kcal/mol@LB@@LB@Position - mRNA 176 -- 229@LB@Position - sRNA 31 -- 87@LB@Position Seed - mRNA 208 -- 214@LB@Position Seed - sRNA 82 -- 88@LB@
131	0.006551	0.1774	stm3217	aer	-17.88	0.039631	254 -- 298	36 -- 77	senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506	_____________253____________________________________________________________________________________299\n_____________\|______________________________________________________________________________________\|\n5'-UUU...AAGGC______UGA_____________________ACAAA____AA__AUU____________________UC__G______UUUA_____UAAAG...CCA-3'\n______________GCAGGA___GGUGAAAA_________UCGU_____UAUU__GG____AAUCGCA____AAUUGCGA__CA_AGCAAU____ACAAC\n______________:\|\|\|\|\|___:\|\|\|\|\|\|\|_________\|\|\|:_____\|\|::__\|\|____\|\|\|\|\|\|\|____\|\|\|\|\|\|:\|__\|\|_\|:\|\|\|:____\|\|\|\|\|\n______________UGUCCU___UCACUUUU_________AGCG_____AUGG__CC____UUAGCGU____UUAACGUU__GU_UUGUUG____UGUUG\n3'-UUU...UUACA_________________UCCCAUCAG_____________CA__AGAC_______CUGG________U___G_______________UAGUG...UCA-5'\n_____________\|______________________________________________________________________________________\|\n_____________78_____________________________________________________________________________________35\n	89 -- 95	99 -- 105	-43.6348 kcal/mol	13.4466 kcal/mol	20.9633 kcal/mol	253 299@LB@ \| \|@LB@5'-UUU...AAGGC UGA ACAAA AA AUU UC G UUUA UAAAG...CCA-3'@LB@ GCAGGA GGUGAAAA UCGU UAUU GG AAUCGCA AAUUGCGA CA AGCAAU ACAAC@LB@ :\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|: \|\|:: \|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\| \|\| \|:\|\|\|: \|\|\|\|\|@LB@ UGUCCU UCACUUUU AGCG AUGG CC UUAGCGU UUAACGUU GU UUGUUG UGUUG@LB@3'-UUU...UUACA UCCCAUCAG CA AGAC CUGG U G UAGUG...UCA-5'@LB@ \| \|@LB@ 78 35@LB@@LB@@LB@Energy -17.88 kcal/mol@LB@Hybridization Energy -43.6348 kcal/mol@LB@Unfolding Energy - mRNA 13.4466 kcal/mol@LB@Unfolding Energy - sRNA 20.9633 kcal/mol@LB@@LB@Position - mRNA 254 -- 298@LB@Position - sRNA 36 -- 77@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 99 -- 105@LB@
126	0.006333	0.1774	stm1584	ansP	-14.21	0.157463	122 -- 184	36 -- 93	amino acid permease	_____________121_________________185\n_____________\|___________________\|\n5'-AUA...UGUCA________UAUAACA____ACGUA...GUC-3'\n______________GGACAGGC_______GGUA\n______________\|\|\|\|\|\|:\|_______\|\|\|\|\n______________CCUGUCUG_______CCAU\n3'-UUU...UGAUA________UC_________UUACA...UCA-5'\n_____________\|___________________\|\n_____________94__________________35\n	178 -- 184	156 -- 162	-15.5225 kcal/mol	4.18435 kcal/mol	3.12041 kcal/mol	121 185@LB@ \| \|@LB@5'-AUA...UGUCA UAUAACA ACGUA...GUC-3'@LB@ GGACAGGC GGUA@LB@ \|\|\|\|\|\|:\| \|\|\|\|@LB@ CCUGUCUG CCAU@LB@3'-UUU...UGAUA UC UUACA...UCA-5'@LB@ \| \|@LB@ 94 35@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -15.5225 kcal/mol@LB@Unfolding Energy - mRNA 4.18435 kcal/mol@LB@Unfolding Energy - sRNA 3.12041 kcal/mol@LB@@LB@Position - mRNA 122 -- 184@LB@Position - sRNA 36 -- 93@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 156 -- 162@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@
2	2.663e-05	0.04123	stm2355	argT	-17.69	0.042680	144 -- 202	34 -- 91	histidine ABC transporter substrate-binding protein HisJ	_____________143____________________203\n_____________\|______________________\|\n5'-UUA...AAGUC_________________C____AAAAC...AUA-3'\n______________UGCAAACAC_ACAACGC_ACGU\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|\|:\|_\|\|:\|\n______________ACGUUUGUG_UGUUGUG_UGUA\n3'-UUU...GGUUA_________U_______U____GUGUU...UCA-5'\n_____________\|______________________\|\n_____________92_____________________33\n	153 -- 159	75 -- 81	-25.653 kcal/mol	2.98604 kcal/mol	4.21448 kcal/mol	143 203@LB@ \| \|@LB@5'-UUA...AAGUC C AAAAC...AUA-3'@LB@ UGCAAACAC ACAACGC ACGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|:\| \|\|:\|@LB@ ACGUUUGUG UGUUGUG UGUA@LB@3'-UUU...GGUUA U U GUGUU...UCA-5'@LB@ \| \|@LB@ 92 33@LB@@LB@@LB@Energy -17.69 kcal/mol@LB@Hybridization Energy -25.653 kcal/mol@LB@Unfolding Energy - mRNA 2.98604 kcal/mol@LB@Unfolding Energy - sRNA 4.21448 kcal/mol@LB@@LB@Position - mRNA 144 -- 202@LB@Position - sRNA 34 -- 91@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 75 -- 81@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

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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

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