Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
61	0.0009386	0.05413	b0574	cusB	-12.39	0.007718	27 -- 84	1 -- 59	copper/silver efflux system membrane fusion protein	_____________26_____________________________________________________________85\n_____________\|______________________________________________________________\|\n5'-AAA...AUCAC______________CC_____CU__C_G____U__CCAU___C______A_________C__AGACG...AAA-3'\n______________GAUCCGAUUGC_UG__GUGAA__GG_C_GAGA_GA____GCG_UUUACC_UC___ACCC_GC\n______________:\|\|\|\|\|\|\|\|:\|_\|\|__\|\|:\|\|__\|\|_\|_\|\|:\|_\|\|____:\|:_:\|\|\|\|\|_\|\|___\|\|\|\|_:\|\n______________UUAGGCUAAUG_AC__CAUUU__CC_G_CUUU_CU____UGU_GAAUGG_AG___UGGG_UG\n3'-AUU...UCGGU___________C__UU_____U___A_A_______AUCU___A_________ACA____A__-5'\n_____________\|_____________________________________________________________\|\n_____________60____________________________________________________________1\n	31 -- 37	49 -- 55	-39.7476 kcal/mol	14.6812 kcal/mol	12.7027 kcal/mol	26 85@LB@ \| \|@LB@5'-AAA...AUCAC CC CU C G U CCAU C A C AGACG...AAA-3'@LB@ GAUCCGAUUGC UG GUGAA GG C GAGA GA GCG UUUACC UC ACCC GC@LB@ :\|\|\|\|\|\|\|\|:\| \|\| \|\|:\|\| \|\| \| \|\|:\| \|\| :\|: :\|\|\|\|\| \|\| \|\|\|\| :\|@LB@ UUAGGCUAAUG AC CAUUU CC G CUUU CU UGU GAAUGG AG UGGG UG@LB@3'-AUU...UCGGU C UU U A A AUCU A ACA A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -39.7476 kcal/mol@LB@Unfolding Energy - mRNA 14.6812 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 27 -- 84@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 49 -- 55@LB@
65	0.001093	0.05856	b1519	tam	-11.83	0.011992	187 -- 231	1 -- 50	trans-aconitate methyltransferase	_____________186____________________________________________________232\n_____________\|______________________________________________________\|\n5'-UUU...CGCUG_____________AAAU______C_________C__________U___A_____ACUUU...AAU-3'\n______________ACG_GGAGUAAAA____GUCUGA____UGGAAC______CCUCU_UAU_UCUAC\n______________\|\|\|_\|:\|\|\|\|\|\|\|____\|\|\|\|\|\|____\|:\|\|\|\|______\|\|\|\|\|_\|\|:_:\|\|\|\|\n______________UGC_CUUCAUUUU____CAGACU____AUCUUG______GGAGA_AUG_GGAUG\n3'-AUU...GCUAA___A_________C_________UUCU______UAGAAU_____C_________-5'\n_____________\|_____________________________________________________\|\n_____________51____________________________________________________1\n	191 -- 197	39 -- 45	-32.7669 kcal/mol	8.27841 kcal/mol	12.6772 kcal/mol	186 232@LB@ \| \|@LB@5'-UUU...CGCUG AAAU C C U A ACUUU...AAU-3'@LB@ ACG GGAGUAAAA GUCUGA UGGAAC CCUCU UAU UCUAC@LB@ \|\|\| \|:\|\|\|\|\|\|\| \|\|\|\|\|\| \|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|@LB@ UGC CUUCAUUUU CAGACU AUCUUG GGAGA AUG GGAUG@LB@3'-AUU...GCUAA A C UUCU UAGAAU C -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.83 kcal/mol@LB@Hybridization Energy -32.7669 kcal/mol@LB@Unfolding Energy - mRNA 8.27841 kcal/mol@LB@Unfolding Energy - sRNA 12.6772 kcal/mol@LB@@LB@Position - mRNA 187 -- 231@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 39 -- 45@LB@
69	0.001182	0.05856	b2962	yggX	-12.92	0.004967	226 -- 272	1 -- 57	oxidative damage protective factor for iron-sulfur proteins	_____________225________________________________________________________273\n_____________\|__________________________________________________________\|\n5'-UCA...UACUU___UGCA________C____________________G_______AG________CG__GAGCU...AGA-3'\n______________UCC____ACGUGAAG_AGAAGGUC__________AG_AUUUU_C__CUGUACCC__GC\n______________\|\|\|____\|\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|__________\|:_\|\|:\|\|_\|__\|\|\|\|\|\|\|\|__:\|\n______________AGG____UGCACUUC_UUUUCCAG__________UU_UAGAA_G__GACAUGGG__UG\n3'-AUU...GGUUU___CUAA________A________ACUUUCUAUC__G_____U_GA________A___-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	262 -- 268	4 -- 10	-42.3698 kcal/mol	16.7751 kcal/mol	12.7026 kcal/mol	225 273@LB@ \| \|@LB@5'-UCA...UACUU UGCA C G AG CG GAGCU...AGA-3'@LB@ UCC ACGUGAAG AGAAGGUC AG AUUUU C CUGUACCC GC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\| \|: \|\|:\|\| \| \|\|\|\|\|\|\|\| :\|@LB@ AGG UGCACUUC UUUUCCAG UU UAGAA G GACAUGGG UG@LB@3'-AUU...GGUUU CUAA A ACUUUCUAUC G U GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -42.3698 kcal/mol@LB@Unfolding Energy - mRNA 16.7751 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 226 -- 272@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 4 -- 10@LB@
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
75	0.001328	0.06227	b1748	astC	-8.39	0.124654	121 -- 127	1 -- 7	succinylornithine transaminase PLP-dependent	_____________120_____128\n_____________\|_______\|\n5'-UCA...CACGA_______AAUCU...UGU-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	121 -- 127	1 -- 7	-11.9071 kcal/mol	1.50434 kcal/mol	2.03949 kcal/mol	120 128@LB@ \| \|@LB@5'-UCA...CACGA AAUCU...UGU-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.39 kcal/mol@LB@Hybridization Energy -11.9071 kcal/mol@LB@Unfolding Energy - mRNA 1.50434 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 121 -- 127@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 121 -- 127@LB@Position Seed - sRNA 1 -- 7@LB@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA	_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@LB@
81	0.001761	0.07647	b3311	rpsQ	-9.62	0.058411	217 -- 225	1 -- 9	30S ribosomal subunit protein S17	_____________216_______226\n_____________\|_________\|\n5'-GGU...AAUCC_________AAGGU...UCU-3'\n______________GUACUCUGC\n______________\|\|\|\|:\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	219 -- 225	1 -- 7	-13.7932 kcal/mol	2.07071 kcal/mol	2.12872 kcal/mol	216 226@LB@ \| \|@LB@5'-GGU...AAUCC AAGGU...UCU-3'@LB@ GUACUCUGC@LB@ \|\|\|\|:\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -13.7932 kcal/mol@LB@Unfolding Energy - mRNA 2.07071 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 217 -- 225@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 1 -- 7@LB@
83	0.001985	0.08414	b1901	araF	-10.36	0.035498	164 -- 171	1 -- 8	L-arabinose ABC transporter periplasmic binding protein	_____________163______172\n_____________\|________\|\n5'-UCC...GUUUU________ACAAA...AGC-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	165 -- 171	1 -- 7	-13.292 kcal/mol	0.840759 kcal/mol	2.11603 kcal/mol	163 172@LB@ \| \|@LB@5'-UCC...GUUUU ACAAA...AGC-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -13.292 kcal/mol@LB@Unfolding Energy - mRNA 0.840759 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 164 -- 171@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 1 -- 7@LB@
84	0.002084	0.08729	b2067	yegE	-5.99	0.414041	137 -- 150	1 -- 15	putative diguanylate cyclase	_____________136_____________151\n_____________\|_______________\|\n5'-AGU...GUAAA___________A___AUAAA...CGC-3'\n______________ACUUUUGUACU__GC\n______________\|\|:\|:\|\|\|\|\|:__:\|\n______________UGGAGACAUGG__UG\n3'-AUU...UAGAA___________GA__-5'\n_____________\|______________\|\n_____________16_____________1\n	141 -- 147	5 -- 11	-13.6769 kcal/mol	1.88278 kcal/mol	5.82808 kcal/mol	136 151@LB@ \| \|@LB@5'-AGU...GUAAA A AUAAA...CGC-3'@LB@ ACUUUUGUACU GC@LB@ \|\|:\|:\|\|\|\|\|: :\|@LB@ UGGAGACAUGG UG@LB@3'-AUU...UAGAA GA -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -5.99 kcal/mol@LB@Hybridization Energy -13.6769 kcal/mol@LB@Unfolding Energy - mRNA 1.88278 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 137 -- 150@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 5 -- 11@LB@
85	0.002234	0.09158	b0118	acnB	-9.43	0.065848	121 -- 128	1 -- 8	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________120______129\n_____________\|________\|\n5'-GAG...GCAUU________AAACU...UGC-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	122 -- 128	1 -- 7	-13.4001 kcal/mol	1.87598 kcal/mol	2.11603 kcal/mol	120 129@LB@ \| \|@LB@5'-GAG...GCAUU AAACU...UGC-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.4001 kcal/mol@LB@Unfolding Energy - mRNA 1.87598 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 121 -- 128@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 1 -- 7@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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