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	Additional homologs
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@
82	0.001877	0.08053	b3199	lptC	-13.73	0.002422	95 -- 106	45 -- 56	periplasmic membrane-anchored LPS-binding protein; LPS export protein		_____________94___________107\n_____________\|____________\|\n5'-UAU...GCGCG____________CGCGC...UGG-3'\n______________CCGAUUACGUGA\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACU\n3'-AUU...GUUUA____________UCAUU...AUG-5'\n_____________\|____________\|\n_____________57___________44\n	100 -- 106	45 -- 51	-18.6784 kcal/mol	2.68909 kcal/mol	2.27945 kcal/mol	94 107@LB@ \| \|@LB@5'-UAU...GCGCG CGCGC...UGG-3'@LB@ CCGAUUACGUGA@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACU@LB@3'-AUU...GUUUA UCAUU...AUG-5'@LB@ \| \|@LB@ 57 44@LB@@LB@@LB@Energy -13.73 kcal/mol@LB@Hybridization Energy -18.6784 kcal/mol@LB@Unfolding Energy - mRNA 2.68909 kcal/mol@LB@Unfolding Energy - sRNA 2.27945 kcal/mol@LB@@LB@Position - mRNA 95 -- 106@LB@Position - sRNA 45 -- 56@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 45 -- 51@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@
86	0.002239	0.09158	b0434	yajG	-10.16	0.040736	167 -- 223	4 -- 56	putative lipoprotein		_____________166____________________________________________________________224\n_____________\|______________________________________________________________\|\n5'-UGG...UUUUA__AAAC___CU_________UC________CCC______G__CAAAAAAAU_____U_____GUUAG...UGC-3'\n______________CC____ACG_____UAAGAG__UCUGAGAG___GAACAU_UU_________CCUCU___CCC\n______________\|\|____\|\|\|_____\|\|\|:\|\|__\|\|\|\|\|:\|\|___\|\|\|\|\|\|_\|\|_________\|\|\|\|\|___\|\|\|\n______________GG____UGC_____AUUUUC__AGACUUUC___CUUGUA_AA_________GGAGA___GGG\n3'-AUU...GUUUA__CUAA___ACUUC______C_________UAU______G__U_____________CAU___AUG-5'\n_____________\|______________________________________________________________\|\n_____________57_____________________________________________________________3\n	187 -- 193	28 -- 34	-29.9553 kcal/mol	7.1187 kcal/mol	12.7017 kcal/mol	166 224@LB@ \| \|@LB@5'-UGG...UUUUA AAAC CU UC CCC G CAAAAAAAU U GUUAG...UGC-3'@LB@ CC ACG UAAGAG UCUGAGAG GAACAU UU CCUCU CCC@LB@ \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|:\|\| \|\|\|\|\|\| \|\| \|\|\|\|\| \|\|\|@LB@ GG UGC AUUUUC AGACUUUC CUUGUA AA GGAGA GGG@LB@3'-AUU...GUUUA CUAA ACUUC C UAU G U CAU AUG-5'@LB@ \| \|@LB@ 57 3@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -29.9553 kcal/mol@LB@Unfolding Energy - mRNA 7.1187 kcal/mol@LB@Unfolding Energy - sRNA 12.7017 kcal/mol@LB@@LB@Position - mRNA 167 -- 223@LB@Position - sRNA 4 -- 56@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 28 -- 34@LB@
87	0.00233	0.09349	b2522	sseB	-8.85	0.094489	280 -- 288	1 -- 9	rhodanase-like enzyme sulfur transfer from thiosulfate		_____________279_______289\n_____________\|_________\|\n5'-GGU...UUUCC_________UGGAA...CCG-3'\n______________GUACUCUAC\n______________\|\|\|\|:\|\|\|\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	282 -- 288	1 -- 7	-12.3435 kcal/mol	1.38525 kcal/mol	2.12872 kcal/mol	279 289@LB@ \| \|@LB@5'-GGU...UUUCC UGGAA...CCG-3'@LB@ GUACUCUAC@LB@ \|\|\|\|:\|\|\|\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.3435 kcal/mol@LB@Unfolding Energy - mRNA 1.38525 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 280 -- 288@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 1 -- 7@LB@
88	0.002339	0.09349	b3878	yihQ	-11.00	0.022508	260 -- 267	1 -- 8	putative sulpholipid alpha-glucosidase; alpha-glucosyl fluoride glucosidase	b3656	_____________259______268\n_____________\|________\|\n5'-AAC...AGUUU________AUUUU...GCA-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	261 -- 267	1 -- 7	-13.427 kcal/mol	0.33456 kcal/mol	2.11603 kcal/mol	259 268@LB@ \| \|@LB@5'-AAC...AGUUU AUUUU...GCA-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -13.427 kcal/mol@LB@Unfolding Energy - mRNA 0.33456 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 260 -- 267@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 1 -- 7@LB@
89	0.002377	0.09395	b4136	dsbD	-10.47	0.032769	211 -- 231	1 -- 22	thiol:disulfide interchange protein and activator of DsbC		_____________210____________________232\n_____________\|______________________\|\n5'-UGC...UCAAC_______UA_G___________UACUU...CGG-3'\n______________GCAUCUU__C_CUG_AUCCUGC\n______________:\|\|\|\|\|\|__\|_\|\|\|_\|:\|\|\|:\|\n______________UGUAGAA__G_GAC_UGGGAUG\n3'-AUU...UAUCU_______UG_A___A_______-5'\n_____________\|_____________________\|\n_____________23____________________1\n	225 -- 231	1 -- 7	-23.5098 kcal/mol	5.0672 kcal/mol	7.99236 kcal/mol	210 232@LB@ \| \|@LB@5'-UGC...UCAAC UA G UACUU...CGG-3'@LB@ GCAUCUU C CUG AUCCUGC@LB@ :\|\|\|\|\|\| \| \|\|\| \|:\|\|\|:\|@LB@ UGUAGAA G GAC UGGGAUG@LB@3'-AUU...UAUCU UG A A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.47 kcal/mol@LB@Hybridization Energy -23.5098 kcal/mol@LB@Unfolding Energy - mRNA 5.0672 kcal/mol@LB@Unfolding Energy - sRNA 7.99236 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
90	0.002406	0.09404	b0551	quuD	-13.47	0.003063	177 -- 196	40 -- 58	DLP12 prophage; putative antitermination protein		_____________176__________________197\n_____________\|____________________\|\n5'-ACU...UUCUG________UU__________GUUGA...GAU-3'\n______________GUCUGAUU__UGUGGAGUAA\n______________:\|\|:\|\|\|\|__:\|\|\|:\|\|\|\|\|\n______________UAGGCUAA__GCACUUCAUU\n3'-AUU...CGGUU________U___________UUCCA...AUG-5'\n_____________\|____________________\|\n_____________59___________________39\n	190 -- 196	40 -- 46	-19.625 kcal/mol	2.82746 kcal/mol	3.34877 kcal/mol	176 197@LB@ \| \|@LB@5'-ACU...UUCUG UU GUUGA...GAU-3'@LB@ GUCUGAUU UGUGGAGUAA@LB@ :\|\|:\|\|\|\| :\|\|\|:\|\|\|\|\|@LB@ UAGGCUAA GCACUUCAUU@LB@3'-AUU...CGGUU U UUCCA...AUG-5'@LB@ \| \|@LB@ 59 39@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -19.625 kcal/mol@LB@Unfolding Energy - mRNA 2.82746 kcal/mol@LB@Unfolding Energy - sRNA 3.34877 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 40 -- 58@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 40 -- 46@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

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching