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: https://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
39	0.001399	0.1215	stm4007	glnA	-20.44	0.014679	143 -- 217	36 -- 106	type I glutamate--ammonia ligase		_____________142_____________________________________________________________________________218\n_____________\|_______________________________________________________________________________\|\n5'-CAC...CAGCA______A_____UC____UAC_____________C___G_C___U___GGA____A____UAU_______U________UUUGA...CGA-3'\n______________GAAUUG_AGAUC____GU___CACGACGAC_CGA_CAU_A_CAA_CCG___GAGU_CAAG___GUCCG_C_GAACACGU\n______________\|\|\|\|:\|_\|\|\|:\|____\|:___\|\|\|:\|\|:\|\|_\|:\|_\|\|\|_\|_\|\|\|_\|\|\|___:\|\|:_\|\|\|:___\|:\|\|:_\|_\|\|\|\|\|\|\|:\n______________CUUAGC_UCUGG____CG___GUGUUGUUG_GUU_GUA_U_GUU_GGC___UUCG_GUUU___CGGGU_G_CUUGUGCG\n3'-UUU...CCAGA______G_____UUAA__UUU_________U_______G_________A___________U_______A_U________UAAGG...UCA-5'\n_____________\|_______________________________________________________________________________\|\n_____________107_____________________________________________________________________________35\n	211 -- 217	36 -- 42	-55.3576 kcal/mol	10.964 kcal/mol	31.8708 kcal/mol	142 218@LB@ \| \|@LB@5'-CAC...CAGCA A UC UAC C G C U GGA A UAU U UUUGA...CGA-3'@LB@ GAAUUG AGAUC GU CACGACGAC CGA CAU A CAA CCG GAGU CAAG GUCCG C GAACACGU@LB@ \|\|\|\|:\| \|\|\|:\| \|: \|\|\|:\|\|:\|\| \|:\| \|\|\| \| \|\|\| \|\|\| :\|\|: \|\|\|: \|:\|\|: \| \|\|\|\|\|\|\|:@LB@ CUUAGC UCUGG CG GUGUUGUUG GUU GUA U GUU GGC UUCG GUUU CGGGU G CUUGUGCG@LB@3'-UUU...CCAGA G UUAA UUU U G A U A U UAAGG...UCA-5'@LB@ \| \|@LB@ 107 35@LB@@LB@@LB@Energy -20.44 kcal/mol@LB@Hybridization Energy -55.3576 kcal/mol@LB@Unfolding Energy - mRNA 10.964 kcal/mol@LB@Unfolding Energy - sRNA 31.8708 kcal/mol@LB@@LB@Position - mRNA 143 -- 217@LB@Position - sRNA 36 -- 106@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 36 -- 42@LB@
190	0.01053	0.1967	stm4032	N/A	-12.98	0.242168	37 -- 92	31 -- 85	lipase	stm0490	_____________36__________________93\n_____________\|___________________\|\n5'-CUU...UCGCG____G______G_______GAGGG...GCU-3'\n______________AACA_AAUAUU_AUGACCG\n______________\|\|\|\|_\|\|:\|\|:_\|::\|\|\|\|\n______________UUGU_UUGUAG_UGUUGGC\n3'-UUU...UGUUG____G______________AUUCG...UCA-5'\n_____________\|___________________\|\n_____________86__________________30\n	283 -- 289	62 -- 68	-14.8704 kcal/mol	1.51414 kcal/mol	6.51321 kcal/mol	36 93@LB@ \| \|@LB@5'-CUU...UCGCG G G GAGGG...GCU-3'@LB@ AACA AAUAUU AUGACCG@LB@ \|\|\|\| \|\|:\|\|: \|::\|\|\|\|@LB@ UUGU UUGUAG UGUUGGC@LB@3'-UUU...UGUUG G AUUCG...UCA-5'@LB@ \| \|@LB@ 86 30@LB@@LB@@LB@Energy -12.98 kcal/mol@LB@Hybridization Energy -14.8704 kcal/mol@LB@Unfolding Energy - mRNA 1.51414 kcal/mol@LB@Unfolding Energy - sRNA 6.51321 kcal/mol@LB@@LB@Position - mRNA 37 -- 92@LB@Position - sRNA 31 -- 85@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 62 -- 68@LB@
59	0.00232	0.14	stm4105	metF	-16.51	0.066936	223 -- 245	40 -- 59	methylenetetrahydrofolate reductase [NAD(P)H]		_____________222__________________246\n_____________\|____________________\|\n5'-AAG...UUUAC__________AUA_______GCGAU...GCA-3'\n______________AACACAACAA___AUAACAU\n______________\|\|\|\|\|\|\|\|\|\|___\|:\|\|\|\|\|\n______________UUGUGUUGUU___UGUUGUA\n3'-UUU...AACGU__________G_________GUGUU...UCA-5'\n_____________\|____________________\|\n_____________60___________________39\n	175 -- 181	70 -- 76	-16.6304 kcal/mol	0.675865 kcal/mol	3.87174 kcal/mol	222 246@LB@ \| \|@LB@5'-AAG...UUUAC AUA GCGAU...GCA-3'@LB@ AACACAACAA AUAACAU@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|@LB@ UUGUGUUGUU UGUUGUA@LB@3'-UUU...AACGU G GUGUU...UCA-5'@LB@ \| \|@LB@ 60 39@LB@@LB@@LB@Energy -16.51 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 0.675865 kcal/mol@LB@Unfolding Energy - sRNA 3.87174 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 40 -- 59@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 70 -- 76@LB@
95	0.004301	0.1596	stm4114	pflD	-11.77	0.360092	46 -- 100	34 -- 88	formate C-acetyltransferase	stm0843	_____________45_____________________101\n_____________\|______________________\|\n5'-UUU...CGGUA_______C______________GAACA...AGA-3'\n______________AAACGCG_CGACGC__CAUUAU\n______________\|\|\|\|:\|:_\|:\|\|:\|__\|\|\|:\|:\n______________UUUGUGU_GUUGUG__GUAGUG\n3'-UUU...UAACG_______U______UU______UUGGC...UCA-5'\n_____________\|______________________\|\n_____________89_____________________33\n	46 -- 52	82 -- 88	-16.7675 kcal/mol	5.49067 kcal/mol	5.48747 kcal/mol	45 101@LB@ \| \|@LB@5'-UUU...CGGUA C GAACA...AGA-3'@LB@ AAACGCG CGACGC CAUUAU@LB@ \|\|\|\|:\|: \|:\|\|:\| \|\|\|:\|:@LB@ UUUGUGU GUUGUG GUAGUG@LB@3'-UUU...UAACG U UU UUGGC...UCA-5'@LB@ \| \|@LB@ 89 33@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -16.7675 kcal/mol@LB@Unfolding Energy - mRNA 5.49067 kcal/mol@LB@Unfolding Energy - sRNA 5.48747 kcal/mol@LB@@LB@Position - mRNA 46 -- 100@LB@Position - sRNA 34 -- 88@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 82 -- 88@LB@
64	0.003108	0.1596	stm4162	thiF	-13.53	0.200092	247 -- 294	34 -- 76	molybdopterin/thiamine biosynthesis adenylyltransferase		_____________246___________________295\n_____________\|_____________________\|\n5'-GCA...GCUCG_______________A_____AGCAA...UUG-3'\n______________GCGAUAUCGCGAUUG_AGGCC\n______________:\|:\|:\|\|\|:\|:\|::\|_\|:\|\|\|\n______________UGUUGUAGUGUUGGC_UUCGG\n3'-UUU...UGUUG_______________A_____UUUUC...UCA-5'\n_____________\|_____________________\|\n_____________77____________________33\n	248 -- 254	69 -- 75	-25.2172 kcal/mol	7.66984 kcal/mol	8.92374 kcal/mol	246 295@LB@ \| \|@LB@5'-GCA...GCUCG A AGCAA...UUG-3'@LB@ GCGAUAUCGCGAUUG AGGCC@LB@ :\|:\|:\|\|\|:\|:\|::\| \|:\|\|\|@LB@ UGUUGUAGUGUUGGC UUCGG@LB@3'-UUU...UGUUG A UUUUC...UCA-5'@LB@ \| \|@LB@ 77 33@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -25.2172 kcal/mol@LB@Unfolding Energy - mRNA 7.66984 kcal/mol@LB@Unfolding Energy - sRNA 8.92374 kcal/mol@LB@@LB@Position - mRNA 247 -- 294@LB@Position - sRNA 34 -- 76@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 69 -- 75@LB@
162	0.00849	0.1864	stm4221	pgi	-15.16	0.111294	249 -- 289	56 -- 88	glucose-6-phosphate isomerase		_____________248_______________________________________290\n_____________\|_________________________________________\|\n5'-GCU...UCCAG______U_____GAAAUGAAA_____________C______UUUCG...ACG-3'\n______________AAACAC_ACGAU_________GACGUUACGAUCG_UGAGCU\n______________\|\|\|\|\|\|_\|\|:\|:_________:\|\|:\|:\|\|:\|:\|\|_\|:\|\|\|:\n______________UUUGUG_UGUUG_________UUGUAGUGUUGGC_AUUCGG\n3'-UUU...UAACG______U_____UG___________________________UUUUC...UCA-5'\n_____________\|_________________________________________\|\n_____________89________________________________________55\n	272 -- 278	66 -- 72	-30.3131 kcal/mol	6.22888 kcal/mol	11.698 kcal/mol	248 290@LB@ \| \|@LB@5'-GCU...UCCAG U GAAAUGAAA C UUUCG...ACG-3'@LB@ AAACAC ACGAU GACGUUACGAUCG UGAGCU@LB@ \|\|\|\|\|\| \|\|:\|: :\|\|:\|:\|\|:\|:\|\| \|:\|\|\|:@LB@ UUUGUG UGUUG UUGUAGUGUUGGC AUUCGG@LB@3'-UUU...UAACG U UG UUUUC...UCA-5'@LB@ \| \|@LB@ 89 55@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -30.3131 kcal/mol@LB@Unfolding Energy - mRNA 6.22888 kcal/mol@LB@Unfolding Energy - sRNA 11.698 kcal/mol@LB@@LB@Position - mRNA 249 -- 289@LB@Position - sRNA 56 -- 88@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 66 -- 72@LB@
130	0.00652	0.1774	stm4228	malF	-14.47	0.143021	162 -- 175	1 -- 15	maltose ABC transporter permease MalF		_____________161_____________176\n_____________\|_______________\|\n5'-AAC...ACAUC_______________UUCAA...UAA-3'\n______________UCCGGC_CAGGAAGU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|\n______________AGGCCG_GUCCUUCA\n3'-UUU...AAGCA______A________-5'\n_____________\|______________\|\n_____________16_____________1\n	169 -- 175	1 -- 7	-25.2779 kcal/mol	6.67863 kcal/mol	4.81264 kcal/mol	161 176@LB@ \| \|@LB@5'-AAC...ACAUC UUCAA...UAA-3'@LB@ UCCGGC CAGGAAGU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ AGGCCG GUCCUUCA@LB@3'-UUU...AAGCA A -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -25.2779 kcal/mol@LB@Unfolding Energy - mRNA 6.67863 kcal/mol@LB@Unfolding Energy - sRNA 4.81264 kcal/mol@LB@@LB@Position - mRNA 162 -- 175@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@LB@
96	0.004303	0.1596	stm4243	yjbN	-11.74	0.363864	272 -- 280	155 -- 163	tRNA dihydrouridine(20/20a) synthase DusA		_____________271______________________________281\n_____________\|________________________________\|\n5'-UUA...UUAAU___AC_________C____A_____CCU____GGCAG...GUU-3'\n______________GGG____UGUACGG_GAAG_UGAAA___GGGG\n______________\|\|\|____\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\|___:\|\|\|\n______________CCC____ACAUGUC_CUUC_ACUUU___UCCC\n3'-UUU...UCUGU___AUUU__________________U______AUCAG...UCA-5'\n_____________\|________________________________\|\n_____________164______________________________154\n	58 -- 64	141 -- 147	-26.0653 kcal/mol	8.12251 kcal/mol	7.07058 kcal/mol	271 281@LB@ \| \|@LB@5'-UUA...UUAAU AC C A CCU GGCAG...GUU-3'@LB@ GGG UGUACGG GAAG UGAAA GGGG@LB@ \|\|\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|\| :\|\|\|@LB@ CCC ACAUGUC CUUC ACUUU UCCC@LB@3'-UUU...UCUGU AUUU U AUCAG...UCA-5'@LB@ \| \|@LB@ 164 154@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -26.0653 kcal/mol@LB@Unfolding Energy - mRNA 8.12251 kcal/mol@LB@Unfolding Energy - sRNA 7.07058 kcal/mol@LB@@LB@Position - mRNA 272 -- 280@LB@Position - sRNA 155 -- 163@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 141 -- 147@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@
142	0.007269	0.182	stm4341	frdC	-12.15	0.319206	131 -- 234	54 -- 160	fumarate reductase subunit C		_____________130__________________235\n_____________\|____________________\|\n5'-AGA...AGGAG_______________UA___GCAAA...CGG-3'\n______________UGC_AACAUGACGAC__AAC\n______________\|\|\|_\|\|\|\|::\|\|:\|\|__\|\|\|\n______________ACG_UUGUGUUGUUG__UUG\n3'-UUU...GGUUA___U___________UG___UAGUG...UCA-5'\n_____________\|____________________\|\n_____________161__________________53\n	202 -- 208	77 -- 83	-18.8897 kcal/mol	4.02107 kcal/mol	3.80548 kcal/mol	130 235@LB@ \| \|@LB@5'-AGA...AGGAG UA GCAAA...CGG-3'@LB@ UGC AACAUGACGAC AAC@LB@ \|\|\| \|\|\|\|::\|\|:\|\| \|\|\|@LB@ ACG UUGUGUUGUUG UUG@LB@3'-UUU...GGUUA U UG UAGUG...UCA-5'@LB@ \| \|@LB@ 161 53@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.8897 kcal/mol@LB@Unfolding Energy - mRNA 4.02107 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 131 -- 234@LB@Position - sRNA 54 -- 160@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 77 -- 83@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

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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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