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
11	0.0001804	0.05681	stm0959	lrp	-12.80	0.257711	163 -- 181	139 -- 159	leucine-responsive transcriptional regulator	_____________162_______________________________________________182\n_____________\|_________________________________________________\|\n5'-UGA...AGAGU________A_____GA________UAC______ACAAUAAUAAU_____AUAGC...AGC-3'\n______________CAGGCAGG_GUAGG_____AGGAA___AGAGAG___________GGUAG\n______________\|\|\|:\|\|\|\|_\|\|\|::_____\|\|\|\|\|___\|:\|:\|\|___________\|\|\|\|\|\n______________GUCUGUCC_CAUUU_____UCCUU___UUUUUC___________CCAUC\n3'-UUU...UACCU______________ACAUG_____CAC______________________AGAGC...UCA-5'\n_____________\|_________________________________________________\|\n_____________160_______________________________________________138\n	163 -- 169	153 -- 159	-28.6161 kcal/mol	5.81197 kcal/mol	10.0349 kcal/mol	162 182@LB@ \| \|@LB@5'-UGA...AGAGU A GA UAC ACAAUAAUAAU AUAGC...AGC-3'@LB@ CAGGCAGG GUAGG AGGAA AGAGAG GGUAG@LB@ \|\|\|:\|\|\|\| \|\|\|:: \|\|\|\|\| \|:\|:\|\| \|\|\|\|\|@LB@ GUCUGUCC CAUUU UCCUU UUUUUC CCAUC@LB@3'-UUU...UACCU ACAUG CAC AGAGC...UCA-5'@LB@ \| \|@LB@ 160 138@LB@@LB@@LB@Energy -12.80 kcal/mol@LB@Hybridization Energy -28.6161 kcal/mol@LB@Unfolding Energy - mRNA 5.81197 kcal/mol@LB@Unfolding Energy - sRNA 10.0349 kcal/mol@LB@@LB@Position - mRNA 163 -- 181@LB@Position - sRNA 139 -- 159@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 153 -- 159@LB@
12	0.0002098	0.05681	stm3344	rpsI	-21.57	0.009451	131 -- 172	57 -- 102	30S ribosomal protein S9	_____________130__________________________173\n_____________\|____________________________\|\n5'-GUG...GGCAA__________C________CA_______CAAGU...GUU-3'\n______________CGAGCACAAC_ACGCGGCA__GCAACCG\n______________\|:\|:\|\|\|\|\|\|_\|\|:\|::\|\|__:\|\|\|\|\|\|\n______________GUUUGUGUUG_UGUGUUGU__UGUUGGC\n3'-UUU...UUAAC__________U________AG_______AUUCG...UCA-5'\n_____________\|____________________________\|\n_____________103__________________________56\n	161 -- 167	62 -- 68	-36.1701 kcal/mol	9.00411 kcal/mol	8.61223 kcal/mol	130 173@LB@ \| \|@LB@5'-GUG...GGCAA C CA CAAGU...GUU-3'@LB@ CGAGCACAAC ACGCGGCA GCAACCG@LB@ \|:\|:\|\|\|\|\|\| \|\|:\|::\|\| :\|\|\|\|\|\|@LB@ GUUUGUGUUG UGUGUUGU UGUUGGC@LB@3'-UUU...UUAAC U AG AUUCG...UCA-5'@LB@ \| \|@LB@ 103 56@LB@@LB@@LB@Energy -21.57 kcal/mol@LB@Hybridization Energy -36.1701 kcal/mol@LB@Unfolding Energy - mRNA 9.00411 kcal/mol@LB@Unfolding Energy - sRNA 8.61223 kcal/mol@LB@@LB@Position - mRNA 131 -- 172@LB@Position - sRNA 57 -- 102@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 62 -- 68@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@
14	0.0002233	0.05681	stm3843	trmE	-16.53	0.066478	207 -- 249	37 -- 85	tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE	_____________206______________250\n_____________\|________________\|\n5'-UGA...CAUGA________________UAUCG...CGC-3'\n______________GC___CAUAACGACAC\n______________\|\|___\|\|:\|\|\|:\|\|\|\|\n______________CG___GUGUUGUUGUG\n3'-UUU...GUUAA__UUU___________UUGUA...UCA-5'\n_____________\|________________\|\n_____________86_______________36\n	211 -- 217	75 -- 81	-15.3625 kcal/mol	2.22645 kcal/mol	3.72363 kcal/mol	206 250@LB@ \| \|@LB@5'-UGA...CAUGA UAUCG...CGC-3'@LB@ GC CAUAACGACAC@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ CG GUGUUGUUGUG@LB@3'-UUU...GUUAA UUU UUGUA...UCA-5'@LB@ \| \|@LB@ 86 36@LB@@LB@@LB@Energy -16.53 kcal/mol@LB@Hybridization Energy -15.3625 kcal/mol@LB@Unfolding Energy - mRNA 2.22645 kcal/mol@LB@Unfolding Energy - sRNA 3.72363 kcal/mol@LB@@LB@Position - mRNA 207 -- 249@LB@Position - sRNA 37 -- 85@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
15	0.000269	0.06194	stm3630	dppA	-21.81	0.008578	158 -- 199	51 -- 92	ABC transporter substrate-binding protein	_____________157_____________________________________200\n_____________\|_______________________________________\|\n5'-AUU...AGCCU______AGG___A__________________________AGAAG...AUU-3'\n______________UUGCAA___GCA_AACAACAU_ACAUCACAAUUG_GAGC\n______________\|\|\|\|\|\|___:\|\|_\|\|\|\|\|\|\|:_\|\|\|\|\|\|\|\|\|::\|_:\|\|\|\n______________AACGUU___UGU_UUGUUGUG_UGUAGUGUUGGC_UUCG\n3'-UUU...UGGUU____________G________U____________A____GUUUU...UCA-5'\n_____________\|_______________________________________\|\n_____________93______________________________________50\n	183 -- 189	63 -- 69	-36.2763 kcal/mol	6.81868 kcal/mol	11.5217 kcal/mol	157 200@LB@ \| \|@LB@5'-AUU...AGCCU AGG A AGAAG...AUU-3'@LB@ UUGCAA GCA AACAACAU ACAUCACAAUUG GAGC@LB@ \|\|\|\|\|\| :\|\| \|\|\|\|\|\|\|: \|\|\|\|\|\|\|\|\|::\| :\|\|\|@LB@ AACGUU UGU UUGUUGUG UGUAGUGUUGGC UUCG@LB@3'-UUU...UGGUU G U A GUUUU...UCA-5'@LB@ \| \|@LB@ 93 50@LB@@LB@@LB@Energy -21.81 kcal/mol@LB@Hybridization Energy -36.2763 kcal/mol@LB@Unfolding Energy - mRNA 6.81868 kcal/mol@LB@Unfolding Energy - sRNA 11.5217 kcal/mol@LB@@LB@Position - mRNA 158 -- 199@LB@Position - sRNA 51 -- 92@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 63 -- 69@LB@
16	0.0002876	0.06194	stm1378	pykF	-16.63	0.064116	5 -- 66	31 -- 91	pyruvate kinase	_____________4____________________________________________________________________67\n_____________\|____________________________________________________________________\|\n_______5'-GGAC___A____U_______UA__AU____CCCUUC___U__________C______________A______UCUGC...UGA-3'\n______________UGU_AAAC_CAACGAC__AA__UAUC______CCG_UGGGCUGAAA_GC______GAGCAC_CAUUCC\n______________\|\|:_\|\|\|\|_\|\|\|\|:\|\|__\|\|__:\|\|\|______\|\|\|_\|::\|\|::\|\|\|_\|\|______\|\|:\|\|\|_\|\|\|\|\|\|\n______________ACG_UUUG_GUUGUUG__UU__GUAG______GGC_AUUCGGUUUU_CG______CUUGUG_GUAAGG\n3'-UUU...GGUUA________U_______UG________UGUU___________________GGUAGU______C______CUAUU...UCA-5'\n_____________\|____________________________________________________________________\|\n_____________92___________________________________________________________________30\n	14 -- 20	77 -- 83	-44.7981 kcal/mol	9.74365 kcal/mol	24.1415 kcal/mol	4 67@LB@ \| \|@LB@ 5'-GGAC A U UA AU CCCUUC U C A UCUGC...UGA-3'@LB@ UGU AAAC CAACGAC AA UAUC CCG UGGGCUGAAA GC GAGCAC CAUUCC@LB@ \|\|: \|\|\|\| \|\|\|\|:\|\| \|\| :\|\|\| \|\|\| \|::\|\|::\|\|\| \|\| \|\|:\|\|\| \|\|\|\|\|\|@LB@ ACG UUUG GUUGUUG UU GUAG GGC AUUCGGUUUU CG CUUGUG GUAAGG@LB@3'-UUU...GGUUA U UG UGUU GGUAGU C CUAUU...UCA-5'@LB@ \| \|@LB@ 92 30@LB@@LB@@LB@Energy -16.63 kcal/mol@LB@Hybridization Energy -44.7981 kcal/mol@LB@Unfolding Energy - mRNA 9.74365 kcal/mol@LB@Unfolding Energy - sRNA 24.1415 kcal/mol@LB@@LB@Position - mRNA 5 -- 66@LB@Position - sRNA 31 -- 91@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 77 -- 83@LB@
17	0.0003055	0.06194	stm2694	N/A	-22.95	0.005498	261 -- 295	52 -- 90	Fels-2 prophage protein	_____________260_____________________________________296\n_____________\|_______________________________________\|\n5'-ACG...UAUCA_____________A_G____________AGU________UAUAA-3'\n______________GC___UACGACAA_A_AACGUUACAACC____GCCAAAA\n______________\|\|___:\|\|:\|\|\|\|_\|_\|\|\|:\|:\|\|\|\|\|\|____\|\|\|\|\|\|\|\n______________CG___GUGUUGUU_U_UUGUAGUGUUGG____CGGUUUU\n3'-UUU...GUUAA__UUU________G_G____________CAUU_______CGGGU...UCA-5'\n_____________\|_______________________________________\|\n_____________91______________________________________51\n	289 -- 295	52 -- 58	-35.4487 kcal/mol	2.51857 kcal/mol	14.0353 kcal/mol	260 296@LB@ \| \|@LB@5'-ACG...UAUCA A G AGU UAUAA-3'@LB@ GC UACGACAA A AACGUUACAACC GCCAAAA@LB@ \|\| :\|\|:\|\|\|\| \| \|\|\|:\|:\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ CG GUGUUGUU U UUGUAGUGUUGG CGGUUUU@LB@3'-UUU...GUUAA UUU G G CAUU CGGGU...UCA-5'@LB@ \| \|@LB@ 91 51@LB@@LB@@LB@Energy -22.95 kcal/mol@LB@Hybridization Energy -35.4487 kcal/mol@LB@Unfolding Energy - mRNA 2.51857 kcal/mol@LB@Unfolding Energy - sRNA 14.0353 kcal/mol@LB@@LB@Position - mRNA 261 -- 295@LB@Position - sRNA 52 -- 90@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 52 -- 58@LB@
18	0.0003131	0.06194	stm0112	leuB	-16.29	0.072835	153 -- 217	44 -- 93	3-isopropylmalate dehydrogenase	_____________152___________218\n_____________\|_____________\|\n5'-AAA...AAAGA_____________AGCUC...GUU-3'\n______________AUUGC_AACGCAA\n______________\|\|\|\|\|_\|\|\|:\|\|\|\n______________UAACG_UUGUGUU\n3'-UUU...CUGGU_____U_______GUUGU...UCA-5'\n_____________\|_____________\|\n_____________94____________43\n	158 -- 164	81 -- 87	-11.6192 kcal/mol	1.90811 kcal/mol	3.57619 kcal/mol	152 218@LB@ \| \|@LB@5'-AAA...AAAGA AGCUC...GUU-3'@LB@ AUUGC AACGCAA@LB@ \|\|\|\|\| \|\|\|:\|\|\|@LB@ UAACG UUGUGUU@LB@3'-UUU...CUGGU U GUUGU...UCA-5'@LB@ \| \|@LB@ 94 43@LB@@LB@@LB@Energy -16.29 kcal/mol@LB@Hybridization Energy -11.6192 kcal/mol@LB@Unfolding Energy - mRNA 1.90811 kcal/mol@LB@Unfolding Energy - sRNA 3.57619 kcal/mol@LB@@LB@Position - mRNA 153 -- 217@LB@Position - sRNA 44 -- 93@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@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@
20	0.0004512	0.08034	stm2384	aroC	-21.00	0.011794	171 -- 223	39 -- 90	chorismate synthase	_____________170___________________224\n_____________\|_____________________\|\n5'-GUU...AACAC______G________G_____GGAGC...GCA-3'\n______________GCAAAC_ACAACAAC_AUAAC\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|_\|:\|\|\|\n______________CGUUUG_UGUUGUUG_UGUUG\n3'-UUU...GUUAA_____________________UAGUG...UCA-5'\n_____________\|_____________________\|\n_____________91____________________38\n	179 -- 185	77 -- 83	-22.4295 kcal/mol	1.97696 kcal/mol	3.80362 kcal/mol	170 224@LB@ \| \|@LB@5'-GUU...AACAC G G GGAGC...GCA-3'@LB@ GCAAAC ACAACAAC AUAAC@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|@LB@ CGUUUG UGUUGUUG UGUUG@LB@3'-UUU...GUUAA UAGUG...UCA-5'@LB@ \| \|@LB@ 91 38@LB@@LB@@LB@Energy -21.00 kcal/mol@LB@Hybridization Energy -22.4295 kcal/mol@LB@Unfolding Energy - mRNA 1.97696 kcal/mol@LB@Unfolding Energy - sRNA 3.80362 kcal/mol@LB@@LB@Position - mRNA 171 -- 223@LB@Position - sRNA 39 -- 90@LB@Position Seed - mRNA 179 -- 185@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

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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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