Input and runtime details for job 5774122 (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 5774122 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:30:38 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:16:08 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 23:32:42 CET 2018
	Post-Processing Finished		@ Fri Feb 16 23:32:50 CET 2018
	Job Completed		@ Fri Feb 16 23:33:10 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5774122&toolName=CopraRNA ( 30 days expiry )

Description of the job

FsrA

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_000964 Bacillus subtilis subsp. subtilis str. 168

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
108	0.009234	0.2778	bsu12360	exuT	-9.24	0.271038	118 -- 128	32 -- 43	hexuronate transporter	_____________117__________129\n_____________\|____________\|\n5'-AAA...UUCCU____________AUUUA...UUA-3'\n______________GUC_GAUGGAGG\n______________:\|\|_\|\|\|:\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	122 -- 128	32 -- 38	-13.9988 kcal/mol	3.80022 kcal/mol	0.959872 kcal/mol	117 129@LB@ \| \|@LB@5'-AAA...UUCCU AUUUA...UUA-3'@LB@ GUC GAUGGAGG@LB@ :\|\| \|\|\|:\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -13.9988 kcal/mol@LB@Unfolding Energy - mRNA 3.80022 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 118 -- 128@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
185	0.01858	0.3269	bsu27560	hisS	-8.40	0.345340	122 -- 132	25 -- 38	histidine--tRNA ligase	_____________121____________133\n_____________\|______________\|\n5'-GCG...GUAUA_______C______AGUUU...CUU-3'\n______________GUAGGGG____GGG\n______________:\|\|\|:\|\|____\|\|\|\n______________UAUCUCC____CCC\n3'-UUU...UAGAC_______CCAA___CUUGU...AUA-5'\n_____________\|______________\|\n_____________39_____________24\n	122 -- 128	32 -- 38	-11.8618 kcal/mol	2.79445 kcal/mol	0.662893 kcal/mol	121 133@LB@ \| \|@LB@5'-GCG...GUAUA C AGUUU...CUU-3'@LB@ GUAGGGG GGG@LB@ :\|\|\|:\|\| \|\|\|@LB@ UAUCUCC CCC@LB@3'-UUU...UAGAC CCAA CUUGU...AUA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -11.8618 kcal/mol@LB@Unfolding Energy - mRNA 2.79445 kcal/mol@LB@Unfolding Energy - sRNA 0.662893 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 32 -- 38@LB@
110	0.009311	0.2778	bsu18230	yngG	-6.09	0.597733	269 -- 285	32 -- 53	hydroxymethylglutaryl-CoA lyase YngG	_____________268____________________286\n_____________\|______________________\|\n5'-AAA...CCCGU_______GCAAC__________AUAAA...GGA-3'\n______________UUGGAUC__________AGAGG\n______________\|:\|\|\|\|\|__________\|\|\|\|\|\n______________AGCCUAG__________UCUCC\n3'-UUU...AAAAA_______AACUAGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	269 -- 275	47 -- 53	-12.5955 kcal/mol	5.52332 kcal/mol	0.981755 kcal/mol	268 286@LB@ \| \|@LB@5'-AAA...CCCGU GCAAC AUAAA...GGA-3'@LB@ UUGGAUC AGAGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGCCUAG UCUCC@LB@3'-UUU...AAAAA AACUAGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -12.5955 kcal/mol@LB@Unfolding Energy - mRNA 5.52332 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 47 -- 53@LB@
133	0.01175	0.2883	bsu11610	ppnK	-12.45	0.088788	273 -- 294	32 -- 53	inorganic polyphosphate/ATP-NAD kinase 1	_____________272____________________295\n_____________\|______________________\|\n5'-CCA...AUUUA____________A___AACU__AUGAAA-3'\n______________UUGGAUUUUGAU_UGG____GG\n______________\|:\|\|\|\|:\|\|\|\|\|_\|\|:____\|\|\n______________AGCCUAGAACUA_ACU____CC\n3'-UUU...AAAAA____________G___AUCU__CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	278 -- 284	42 -- 48	-17.5759 kcal/mol	4.14878 kcal/mol	0.981755 kcal/mol	272 295@LB@ \| \|@LB@5'-CCA...AUUUA A AACU AUGAAA-3'@LB@ UUGGAUUUUGAU UGG GG@LB@ \|:\|\|\|\|:\|\|\|\|\| \|\|: \|\|@LB@ AGCCUAGAACUA ACU CC@LB@3'-UUU...AAAAA G AUCU CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -17.5759 kcal/mol@LB@Unfolding Energy - mRNA 4.14878 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 273 -- 294@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 42 -- 48@LB@
164	0.01535	0.3122	bsu39720	iolE	-13.03	0.070250	182 -- 189	30 -- 37	inosose dehydratase	_____________181______190\n_____________\|________\|\n5'-GUU...AGUAU________AGGCA...UAA-3'\n______________UAGAGGGG\n______________\|\|\|\|\|\|\|\|\n______________AUCUCCCC\n3'-UUU...AGACU________AACCC...AUA-5'\n_____________\|________\|\n_____________38_______29\n	183 -- 189	30 -- 36	-14.5397 kcal/mol	1.33978 kcal/mol	0.165704 kcal/mol	181 190@LB@ \| \|@LB@5'-GUU...AGUAU AGGCA...UAA-3'@LB@ UAGAGGGG@LB@ \|\|\|\|\|\|\|\|@LB@ AUCUCCCC@LB@3'-UUU...AGACU AACCC...AUA-5'@LB@ \| \|@LB@ 38 29@LB@@LB@@LB@Energy -13.03 kcal/mol@LB@Hybridization Energy -14.5397 kcal/mol@LB@Unfolding Energy - mRNA 1.33978 kcal/mol@LB@Unfolding Energy - sRNA 0.165704 kcal/mol@LB@@LB@Position - mRNA 182 -- 189@LB@Position - sRNA 30 -- 37@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
59	0.003314	0.1874	bsu01560	kbaA	-8.60	0.327174	11 -- 30	33 -- 52	kinB-signaling pathway activation protein	_____________10___________________31\n_____________\|____________________\|\n5'-AGU...AUAUC__CUG________UU_____CGCAA...AUA-3'\n______________CG___CUUGGUCU__UGGAG\n______________\|\|___\|\|\|\|:\|\|\|__\|:\|\|\|\n______________GC___GAACUAGA__AUCUC\n3'-UUU...AAAAA__CUA________CU_____CCCAA...AUA-5'\n_____________\|____________________\|\n_____________53___________________32\n	17 -- 23	40 -- 46	-17.5678 kcal/mol	7.9942 kcal/mol	0.976367 kcal/mol	10 31@LB@ \| \|@LB@5'-AGU...AUAUC CUG UU CGCAA...AUA-3'@LB@ CG CUUGGUCU UGGAG@LB@ \|\| \|\|\|\|:\|\|\| \|:\|\|\|@LB@ GC GAACUAGA AUCUC@LB@3'-UUU...AAAAA CUA CU CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -17.5678 kcal/mol@LB@Unfolding Energy - mRNA 7.9942 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 11 -- 30@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 17 -- 23@LB@Position Seed - sRNA 40 -- 46@LB@
10	0.0001049	0.035	bsu34190	yvfH	-16.62	0.013859	188 -- 201	23 -- 36	L-lactate permease	_____________187____________202\n_____________\|______________\|\n5'-UGG...UUCAA_________U____UGCAA...CGA-3'\n______________GGAGGGGUU_GGGA\n______________:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UCUCCCCAA_CCCU\n3'-UUU...GACUA_________C____UGUCU...AUA-5'\n_____________\|______________\|\n_____________37_____________22\n	190 -- 196	28 -- 34	-23.4111 kcal/mol	6.64684 kcal/mol	0.139628 kcal/mol	187 202@LB@ \| \|@LB@5'-UGG...UUCAA U UGCAA...CGA-3'@LB@ GGAGGGGUU GGGA@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UCUCCCCAA CCCU@LB@3'-UUU...GACUA C UGUCU...AUA-5'@LB@ \| \|@LB@ 37 22@LB@@LB@@LB@Energy -16.62 kcal/mol@LB@Hybridization Energy -23.4111 kcal/mol@LB@Unfolding Energy - mRNA 6.64684 kcal/mol@LB@Unfolding Energy - sRNA 0.139628 kcal/mol@LB@@LB@Position - mRNA 188 -- 201@LB@Position - sRNA 23 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@LB@
48	0.002156	0.1498	bsu34050	yvfV	-12.63	0.082536	177 -- 196	28 -- 46	lactate utilization protein A	_____________176__________________197\n_____________\|____________________\|\n5'-UCG...AUAUA____GGA___G_________CAUCA...UUG-3'\n______________UUGG___UGA_AGAGGGGUU\n______________\|\|\|:___\|\|\|_\|\|\|\|\|\|\|\|\|\n______________AACU___ACU_UCUCCCCAA\n3'-UUU...CCUAG____AG____A_________CCCCU...AUA-5'\n_____________\|____________________\|\n_____________47___________________27\n	190 -- 196	28 -- 34	-21.1804 kcal/mol	7.57881 kcal/mol	0.97023 kcal/mol	176 197@LB@ \| \|@LB@5'-UCG...AUAUA GGA G CAUCA...UUG-3'@LB@ UUGG UGA AGAGGGGUU@LB@ \|\|\|: \|\|\| \|\|\|\|\|\|\|\|\|@LB@ AACU ACU UCUCCCCAA@LB@3'-UUU...CCUAG AG A CCCCU...AUA-5'@LB@ \| \|@LB@ 47 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -21.1804 kcal/mol@LB@Unfolding Energy - mRNA 7.57881 kcal/mol@LB@Unfolding Energy - sRNA 0.97023 kcal/mol@LB@@LB@Position - mRNA 177 -- 196@LB@Position - sRNA 28 -- 46@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 28 -- 34@LB@
45	0.002015	0.1494	bsu34040	yvfW	-14.27	0.041807	34 -- 68	10 -- 49	lactate utilization protein B	_____________33_______________________________________69\n_____________\|________________________________________\|\n5'-GCG...AAAAA___GA___G_________AAAC__________________GAUCG...GUC-3'\n______________GUC___AU_UG_UGGAGG_____GGGAGCAGAG_GU_GCU\n______________:\|\|___\|\|_\|\|_\|:\|\|\|\|_____\|\|\|\|:\|\|\|\|\|_\|\|_\|\|\|\n______________UAG___UA_AC_AUCUCC_____CCCUUGUCUC_CA_CGA\n3'-UUU...AAGCC___AAC__G__U______CCAAC__________U__U___AGAGA...AUA-5'\n_____________\|________________________________________\|\n_____________50_______________________________________9\n	55 -- 61	19 -- 25	-34.7578 kcal/mol	10.5343 kcal/mol	9.9558 kcal/mol	33 69@LB@ \| \|@LB@5'-GCG...AAAAA GA G AAAC GAUCG...GUC-3'@LB@ GUC AU UG UGGAGG GGGAGCAGAG GU GCU@LB@ :\|\| \|\| \|\| \|:\|\|\|\| \|\|\|\|:\|\|\|\|\| \|\| \|\|\|@LB@ UAG UA AC AUCUCC CCCUUGUCUC CA CGA@LB@3'-UUU...AAGCC AAC G U CCAAC U U AGAGA...AUA-5'@LB@ \| \|@LB@ 50 9@LB@@LB@@LB@Energy -14.27 kcal/mol@LB@Hybridization Energy -34.7578 kcal/mol@LB@Unfolding Energy - mRNA 10.5343 kcal/mol@LB@Unfolding Energy - sRNA 9.9558 kcal/mol@LB@@LB@Position - mRNA 34 -- 68@LB@Position - sRNA 10 -- 49@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 19 -- 25@LB@
109	0.009307	0.2778	bsu07880	yfkJ	-15.70	0.021808	288 -- 299	30 -- 51	low molecular weight protein-tyrosine-phosphatase YfkJ	_____________287____________________300\n_____________\|______________________\|\n5'-GGU...AAAAA______________________A-3'\n______________GGAU__________UAGAGGGG\n______________\|\|\|\|__________\|\|\|\|\|\|\|\|\n______________CCUA__________AUCUCCCC\n3'-UUU...AAAAG____GAACUAGACU________AACCC...AUA-5'\n_____________\|______________________\|\n_____________52_____________________29\n	293 -- 299	30 -- 36	-17.0834 kcal/mol	0.412933 kcal/mol	0.974282 kcal/mol	287 300@LB@ \| \|@LB@5'-GGU...AAAAA A-3'@LB@ GGAU UAGAGGGG@LB@ \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCUA AUCUCCCC@LB@3'-UUU...AAAAG GAACUAGACU AACCC...AUA-5'@LB@ \| \|@LB@ 52 29@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -17.0834 kcal/mol@LB@Unfolding Energy - mRNA 0.412933 kcal/mol@LB@Unfolding Energy - sRNA 0.974282 kcal/mol@LB@@LB@Position - mRNA 288 -- 299@LB@Position - sRNA 30 -- 51@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 30 -- 36@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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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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