Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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	Additional homologs
51	0.005002	0.3217	b0115	aceF	-12.52	0.087110	146 -- 171	149 -- 173	pyruvate dehydrogenase dihydrolipoyltransacetylase component E2		_____________145______________________________________172\n_____________\|________________________________________\|\n5'-GAU...GCAAU_____________________C_______AUA________CCGCG...CGC-3'\n______________CGCCAA_AUUCA_____ACAU_GAUGCAG___AAGUUAAC\n______________\|:\|\|\|\|_\|:\|\|\|_____\|\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|:\|\|\|\n______________GUGGUU_UGAGU_____UGUA_CUACGUC___UUCAGUUG\n3'-UUU...AAAAU______A_____CAGUG____________CG_________AAAGU...UAG-5'\n_____________\|________________________________________\|\n_____________174______________________________________148\n	165 -- 171	149 -- 155	-31.6788 kcal/mol	5.24034 kcal/mol	12.6269 kcal/mol	145 172@LB@ \| \|@LB@5'-GAU...GCAAU C AUA CCGCG...CGC-3'@LB@ CGCCAA AUUCA ACAU GAUGCAG AAGUUAAC@LB@ \|:\|\|\|\| \|:\|\|\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|\|:\|\|\|@LB@ GUGGUU UGAGU UGUA CUACGUC UUCAGUUG@LB@3'-UUU...AAAAU A CAGUG CG AAAGU...UAG-5'@LB@ \| \|@LB@ 174 148@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -31.6788 kcal/mol@LB@Unfolding Energy - mRNA 5.24034 kcal/mol@LB@Unfolding Energy - sRNA 12.6269 kcal/mol@LB@@LB@Position - mRNA 146 -- 171@LB@Position - sRNA 149 -- 173@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 149 -- 155@LB@
27	0.002233	0.2633	b3525	yhjH	-10.03	0.271118	185 -- 216	151 -- 171	cyclic-di-GMP phosphodiesterase FlhDC-regulated		_____________184_______________________________217\n_____________\|_________________________________\|\n5'-UUA...UUUAA__A___G_____CUU_____AUA__________UCCAG...CCU-3'\n______________AC_CAG__ACAU___UGAUG___AGGCAGGUUA\n______________\|\|_\|\|\|__\|\|\|:___\|\|\|\|\|___\|\|\|\|\|:\|\|:\|\n______________UG_GUC__UGUG___ACUAC___UCCGUUCAGU\n3'-UUU...GGUUA__A___AG____U_______G____________UGAAA...UAG-5'\n_____________\|_________________________________\|\n_____________172_______________________________150\n	209 -- 215	152 -- 158	-24.6278 kcal/mol	4.97701 kcal/mol	8.14531 kcal/mol	184 217@LB@ \| \|@LB@5'-UUA...UUUAA A G CUU AUA UCCAG...CCU-3'@LB@ AC CAG ACAU UGAUG AGGCAGGUUA@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\| \|\|\|\|\|:\|\|:\|@LB@ UG GUC UGUG ACUAC UCCGUUCAGU@LB@3'-UUU...GGUUA A AG U G UGAAA...UAG-5'@LB@ \| \|@LB@ 172 150@LB@@LB@@LB@Energy -10.03 kcal/mol@LB@Hybridization Energy -24.6278 kcal/mol@LB@Unfolding Energy - mRNA 4.97701 kcal/mol@LB@Unfolding Energy - sRNA 8.14531 kcal/mol@LB@@LB@Position - mRNA 185 -- 216@LB@Position - sRNA 151 -- 171@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 152 -- 158@LB@
158	0.01775	0.3749	b1187	fadR	-13.89	0.045798	42 -- 66	152 -- 176	fatty acid metabolism regulon transcriptional regulator		_____________41________________________67\n_____________\|_________________________\|\n5'-AAA...CUUAA______G___G__GUG_________UUGAU...CAG-3'\n______________CGGUCA_GCA_GA___AGGCAAGUC\n______________\|:\|\|\|\|_:\|\|_\|\|___\|\|\|\|\|\|\|\|\|\n______________GUCAGU_UGU_CU___UCCGUUCAG\n3'-UUU...UAUGA______G___A__ACG_________UUGAA...UAG-5'\n_____________\|_________________________\|\n_____________177_______________________151\n	60 -- 66	152 -- 158	-31.5031 kcal/mol	7.04431 kcal/mol	8.02398 kcal/mol	41 67@LB@ \| \|@LB@5'-AAA...CUUAA G G GUG UUGAU...CAG-3'@LB@ CGGUCA GCA GA AGGCAAGUC@LB@ \|:\|\|\|\| :\|\| \|\| \|\|\|\|\|\|\|\|\|@LB@ GUCAGU UGU CU UCCGUUCAG@LB@3'-UUU...UAUGA G A ACG UUGAA...UAG-5'@LB@ \| \|@LB@ 177 151@LB@@LB@@LB@Energy -13.89 kcal/mol@LB@Hybridization Energy -31.5031 kcal/mol@LB@Unfolding Energy - mRNA 7.04431 kcal/mol@LB@Unfolding Energy - sRNA 8.02398 kcal/mol@LB@@LB@Position - mRNA 42 -- 66@LB@Position - sRNA 152 -- 176@LB@Position Seed - mRNA 60 -- 66@LB@Position Seed - sRNA 152 -- 158@LB@
52	0.005023	0.3217	b0403	malZ	-9.64	0.320537	253 -- 286	155 -- 185	maltodextrin glucosidase		_____________252___________________________287\n_____________\|_____________________________\|\n5'-UUU...UCAAC_____________U____C__A_______AGACC...AGC-3'\n______________UGCUCA_UUACAC_GUGG_UG_CGGGCGA\n______________\|:\|\|\|\|_\|:\|\|\|\|_:\|\|:_\|\|_\|:\|\|\|:\|\n______________AUGAGU_AGUGUG_UACU_AC_GUCCGUU\n3'-UUU...UGGUU______C______________________CAGUU...UAG-5'\n_____________\|_____________________________\|\n_____________186___________________________154\n	280 -- 286	155 -- 161	-27.4446 kcal/mol	6.9929 kcal/mol	7.82707 kcal/mol	252 287@LB@ \| \|@LB@5'-UUU...UCAAC U C A AGACC...AGC-3'@LB@ UGCUCA UUACAC GUGG UG CGGGCGA@LB@ \|:\|\|\|\| \|:\|\|\|\| :\|\|: \|\| \|:\|\|\|:\|@LB@ AUGAGU AGUGUG UACU AC GUCCGUU@LB@3'-UUU...UGGUU C CAGUU...UAG-5'@LB@ \| \|@LB@ 186 154@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -27.4446 kcal/mol@LB@Unfolding Energy - mRNA 6.9929 kcal/mol@LB@Unfolding Energy - sRNA 7.82707 kcal/mol@LB@@LB@Position - mRNA 253 -- 286@LB@Position - sRNA 155 -- 185@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 155 -- 161@LB@
98	0.01073	0.3575	b0424	yajL	-11.45	0.143367	14 -- 29	155 -- 170	oxidative-stress-resistance chaperone		_____________13_______________30\n_____________\|________________\|\n5'-AGA...GUGAU________________UUGAU...CCA-3'\n______________UACGUGAUGCAGGUGA\n______________:\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GUGUACUACGUCCGUU\n3'-UUU...UCAGU________________CAGUU...UAG-5'\n_____________\|________________\|\n_____________171______________154\n	22 -- 28	156 -- 162	-24.1359 kcal/mol	6.48358 kcal/mol	7.06607 kcal/mol	13 30@LB@ \| \|@LB@5'-AGA...GUGAU UUGAU...CCA-3'@LB@ UACGUGAUGCAGGUGA@LB@ :\|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GUGUACUACGUCCGUU@LB@3'-UUU...UCAGU CAGUU...UAG-5'@LB@ \| \|@LB@ 171 154@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -24.1359 kcal/mol@LB@Unfolding Energy - mRNA 6.48358 kcal/mol@LB@Unfolding Energy - sRNA 7.06607 kcal/mol@LB@@LB@Position - mRNA 14 -- 29@LB@Position - sRNA 155 -- 170@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 156 -- 162@LB@
191	0.02237	0.3833	b1658	purR	-11.05	0.172432	254 -- 265	163 -- 174	transcriptional repressor hypoxanthine-binding		_____________253_______________266\n_____________\|_________________\|\n5'-UUU...CUACA___GU____________CAACA...GCA-3'\n______________ACU__GUCACACGUGAU\n______________\|\|\|__\|\|\|\|\|\|\|:\|\|\|\|\n______________UGA__CAGUGUGUACUA\n3'-UUU...GGUUA___GU____________CGUCC...UAG-5'\n_____________\|_________________\|\n_____________175_______________162\n	259 -- 265	163 -- 169	-20.3148 kcal/mol	3.57431 kcal/mol	4.30742 kcal/mol	253 266@LB@ \| \|@LB@5'-UUU...CUACA GU CAACA...GCA-3'@LB@ ACU GUCACACGUGAU@LB@ \|\|\| \|\|\|\|\|\|\|:\|\|\|\|@LB@ UGA CAGUGUGUACUA@LB@3'-UUU...GGUUA GU CGUCC...UAG-5'@LB@ \| \|@LB@ 175 162@LB@@LB@@LB@Energy -11.05 kcal/mol@LB@Hybridization Energy -20.3148 kcal/mol@LB@Unfolding Energy - mRNA 3.57431 kcal/mol@LB@Unfolding Energy - sRNA 4.30742 kcal/mol@LB@@LB@Position - mRNA 254 -- 265@LB@Position - sRNA 163 -- 174@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 163 -- 169@LB@
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter		_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@LB@
15	0.0008498	0.1886	b4254	argI	-15.11	0.025648	62 -- 84	167 -- 185	ornithine carbamoyltransferase 1	b0273	_____________61______________________85\n_____________\|_______________________\|\n5'-UUC...GUCCU__________UUAUU________CCACU...AUA-3'\n______________GCCGAUACUC_____GUCACACA\n______________:\|\|:\|\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UGGUUAUGAG_____CAGUGUGU\n3'-UUU...AAAUG__________U____________ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________186_____________________166\n	78 -- 84	167 -- 173	-24.735 kcal/mol	3.62809 kcal/mol	5.02083 kcal/mol	61 85@LB@ \| \|@LB@5'-UUC...GUCCU UUAUU CCACU...AUA-3'@LB@ GCCGAUACUC GUCACACA@LB@ :\|\|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGGUUAUGAG CAGUGUGU@LB@3'-UUU...AAAUG U ACUAC...UAG-5'@LB@ \| \|@LB@ 186 166@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -24.735 kcal/mol@LB@Unfolding Energy - mRNA 3.62809 kcal/mol@LB@Unfolding Energy - sRNA 5.02083 kcal/mol@LB@@LB@Position - mRNA 62 -- 84@LB@Position - sRNA 167 -- 185@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 167 -- 173@LB@
53	0.005067	0.3217	b3666	uhpT	-10.07	0.266829	134 -- 177	167 -- 215	hexose phosphate transporter		_____________133_______________________________________________________178\n_____________\|_________________________________________________________\|\n5'-GCC...UGGAC____UCU____CC______________________UA________AUGCC_______GGUAU...UGG-3'\n______________GCUA___CAGG__UGAUUUGCU_GC___UGAUUUU____CAAUGC_____UCACGCA\n______________:\|:\|___\|\|\|\|__\|:\|\|:\|\|\|\|_\|\|___\|\|\|\|\|\|\|____\|\|\|\|:\|_____\|\|\|\|:\|\|\n______________UGGU___GUCC__AUUAGACGA_CG___ACUAAAA____GUUAUG_____AGUGUGU\n____3'-UUUUUUU____C______AU_________C__CCC_______UGUG______AGUC________ACUAC...UAG-5'\n_____________\|_________________________________________________________\|\n_____________216_______________________________________________________166\n	171 -- 177	167 -- 173	-37.7334 kcal/mol	11.6521 kcal/mol	18.4949 kcal/mol	133 178@LB@ \| \|@LB@5'-GCC...UGGAC UCU CC UA AUGCC GGUAU...UGG-3'@LB@ GCUA CAGG UGAUUUGCU GC UGAUUUU CAAUGC UCACGCA@LB@ :\|:\| \|\|\|\| \|:\|\|:\|\|\|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\| \|\|\|\|:\|\|@LB@ UGGU GUCC AUUAGACGA CG ACUAAAA GUUAUG AGUGUGU@LB@ 3'-UUUUUUU C AU C CCC UGUG AGUC ACUAC...UAG-5'@LB@ \| \|@LB@ 216 166@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -37.7334 kcal/mol@LB@Unfolding Energy - mRNA 11.6521 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 134 -- 177@LB@Position - sRNA 167 -- 215@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 167 -- 173@LB@
97	0.01056	0.3575	b2372	yfdV	-22.84	0.000764	17 -- 36	167 -- 186	putative transporter		_____________16___________________37\n_____________\|____________________\|\n5'-UUC...UUAAC____________________AACCG...CUC-3'\n______________CACCGGUAUUCAGUCGCGCA\n______________\|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|\n______________GUGGUUAUGAGUCAGUGUGU\n3'-UUU...AAAAU____________________ACUAC...UAG-5'\n_____________\|____________________\|\n_____________187__________________166\n	30 -- 36	167 -- 173	-32.2779 kcal/mol	2.6891 kcal/mol	5.05466 kcal/mol	16 37@LB@ \| \|@LB@5'-UUC...UUAAC AACCG...CUC-3'@LB@ CACCGGUAUUCAGUCGCGCA@LB@ \|\|\|\|::\|\|:\|\|\|\|\|\|:\|:\|\|@LB@ GUGGUUAUGAGUCAGUGUGU@LB@3'-UUU...AAAAU ACUAC...UAG-5'@LB@ \| \|@LB@ 187 166@LB@@LB@@LB@Energy -22.84 kcal/mol@LB@Hybridization Energy -32.2779 kcal/mol@LB@Unfolding Energy - mRNA 2.6891 kcal/mol@LB@Unfolding Energy - sRNA 5.05466 kcal/mol@LB@@LB@Position - mRNA 17 -- 36@LB@Position - sRNA 167 -- 186@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 167 -- 173@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)

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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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