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
67	0.004159	0.2071	bsu31830	yueE	-13.48	0.058566	169 -- 197	28 -- 51	phosphohydrolase YueE	_____________168___________________________198\n_____________\|_____________________________\|\n5'-UAG...UGUUA___U___AAAAAU____AAA_________UCCAU...AUG-3'\n______________GGA_UCU______AUCU___GGAGGGGUU\n______________\|\|\|_\|\|\|______\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CCU_AGA______UAGA___UCUCCCCAA\n3'-UUU...AAAAG_______AC________CUA_________CCCCU...AUA-5'\n_____________\|_____________________________\|\n_____________52____________________________27\n	191 -- 197	28 -- 34	-19.6632 kcal/mol	5.21125 kcal/mol	0.974859 kcal/mol	168 198@LB@ \| \|@LB@5'-UAG...UGUUA U AAAAAU AAA UCCAU...AUG-3'@LB@ GGA UCU AUCU GGAGGGGUU@LB@ \|\|\| \|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CCU AGA UAGA UCUCCCCAA@LB@3'-UUU...AAAAG AC CUA CCCCU...AUA-5'@LB@ \| \|@LB@ 52 27@LB@@LB@@LB@Energy -13.48 kcal/mol@LB@Hybridization Energy -19.6632 kcal/mol@LB@Unfolding Energy - mRNA 5.21125 kcal/mol@LB@Unfolding Energy - sRNA 0.974859 kcal/mol@LB@@LB@Position - mRNA 169 -- 197@LB@Position - sRNA 28 -- 51@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
57	0.003091	0.1809	bsu19720	yodR	-13.42	0.059995	155 -- 217	11 -- 51	coenzyme A transferase subunit beta	_____________154_________________________________________________________________218\n_____________\|___________________________________________________________________\|\n5'-GCU...ACCGG_______UG________________UACGAAGCGA____GUGAAGUGGAAAUGG__UU_________AGAAA...CCU-3'\n______________GGGUUUU___UUGA___GGGGGUUG__________GGGA_______________GC__GGGAGUAGC\n______________\|\|:\|:\|\|___:\|\|\|___:\|\|\|\|\|\|\|__________\|\|\|\|_______________:\|__\|:\|\|\|\|\|\|\|\n______________CCUAGAA___GACU___UCCCCAAC__________CCCU_______________UG__CUCUCAUCG\n3'-UUU...AAAAG_______CUA____AUC_______________________________________U__________AAGAG...AUA-5'\n_____________\|___________________________________________________________________\|\n_____________52__________________________________________________________________10\n	211 -- 217	11 -- 17	-37.5623 kcal/mol	14.1868 kcal/mol	9.95641 kcal/mol	154 218@LB@ \| \|@LB@5'-GCU...ACCGG UG UACGAAGCGA GUGAAGUGGAAAUGG UU AGAAA...CCU-3'@LB@ GGGUUUU UUGA GGGGGUUG GGGA GC GGGAGUAGC@LB@ \|\|:\|:\|\| :\|\|\| :\|\|\|\|\|\|\| \|\|\|\| :\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA GACU UCCCCAAC CCCU UG CUCUCAUCG@LB@3'-UUU...AAAAG CUA AUC U AAGAG...AUA-5'@LB@ \| \|@LB@ 52 10@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -37.5623 kcal/mol@LB@Unfolding Energy - mRNA 14.1868 kcal/mol@LB@Unfolding Energy - sRNA 9.95641 kcal/mol@LB@@LB@Position - mRNA 155 -- 217@LB@Position - sRNA 11 -- 51@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 11 -- 17@LB@
184	0.01795	0.3254	bsu30470	ytzC	-13.40	0.060457	189 -- 197	28 -- 36	Evidence 4: Homologs of previously reported genes of unknown function	_____________188_______198\n_____________\|_________\|\n5'-UUC...CAAGA_________ACUGU...AUU-3'\n______________GGAGGGGUU\n______________:\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-16.1349 kcal/mol	2.59994 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UUC...CAAGA ACUGU...AUU-3'@LB@ GGAGGGGUU@LB@ :\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -13.40 kcal/mol@LB@Hybridization Energy -16.1349 kcal/mol@LB@Unfolding Energy - mRNA 2.59994 kcal/mol@LB@Unfolding Energy - sRNA 0.134381 kcal/mol@LB@@LB@Position - mRNA 189 -- 197@LB@Position - sRNA 28 -- 36@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 28 -- 34@LB@
183	0.01776	0.3237	bsu08550	sspK	-13.38	0.060997	172 -- 193	31 -- 48	small acid-soluble spore protein K	_____________171____________________194\n_____________\|______________________\|\n5'-UUU...CAACU_________C__ACC_______AUAUG...ACG-3'\n______________UUUUGAUCU_GA___UAGGGGG\n______________\|:\|\|\|\|\|\|\|_\|\|___\|\|\|:\|\|\|\n______________AGAACUAGA_CU___AUCUCCC\n3'-UUU...AGCCU______________________CAACC...AUA-5'\n_____________\|______________________\|\n_____________49_____________________30\n	187 -- 193	31 -- 37	-20.1262 kcal/mol	5.7766 kcal/mol	0.970395 kcal/mol	171 194@LB@ \| \|@LB@5'-UUU...CAACU C ACC AUAUG...ACG-3'@LB@ UUUUGAUCU GA UAGGGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ AGAACUAGA CU AUCUCCC@LB@3'-UUU...AGCCU CAACC...AUA-5'@LB@ \| \|@LB@ 49 30@LB@@LB@@LB@Energy -13.38 kcal/mol@LB@Hybridization Energy -20.1262 kcal/mol@LB@Unfolding Energy - mRNA 5.7766 kcal/mol@LB@Unfolding Energy - sRNA 0.970395 kcal/mol@LB@@LB@Position - mRNA 172 -- 193@LB@Position - sRNA 31 -- 48@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
111	0.009313	0.2778	bsu16780	rnjB	-13.26	0.064171	155 -- 177	29 -- 51	ribonuclease J 2	_____________154_____________________178\n_____________\|_______________________\|\n5'-GCA...UAAUA___ACAAGUGA_______C____AUGAG...UAU-3'\n______________GGA________UGAUGGA_GGGU\n______________\|\|\|________\|\|\|\|:\|\|_\|\|\|\|\n______________CCU________ACUAUCU_CCCA\n3'-UUU...AAAAG___AGAACUAG_______C____ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	166 -- 172	34 -- 40	-18.6769 kcal/mol	4.44629 kcal/mol	0.974539 kcal/mol	154 178@LB@ \| \|@LB@5'-GCA...UAAUA ACAAGUGA C AUGAG...UAU-3'@LB@ GGA UGAUGGA GGGU@LB@ \|\|\| \|\|\|\|:\|\| \|\|\|\|@LB@ CCU ACUAUCU CCCA@LB@3'-UUU...AAAAG AGAACUAG C ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -18.6769 kcal/mol@LB@Unfolding Energy - mRNA 4.44629 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 155 -- 177@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 34 -- 40@LB@
27	0.0005687	0.07027	bsu32550	yurJ	-13.20	0.065709	183 -- 191	31 -- 39	ABC transporter ATP-binding protein	_____________182_______192\n_____________\|_________\|\n5'-AAC...CAAAA_________ACUUU...UGC-3'\n______________GAUAGGGGG\n______________\|\|\|\|\|:\|\|\|\n______________CUAUCUCCC\n3'-UUU...CUAGA_________CAACC...AUA-5'\n_____________\|_________\|\n_____________40________30\n	185 -- 191	31 -- 37	-15.8488 kcal/mol	1.87568 kcal/mol	0.774822 kcal/mol	182 192@LB@ \| \|@LB@5'-AAC...CAAAA ACUUU...UGC-3'@LB@ GAUAGGGGG@LB@ \|\|\|\|\|:\|\|\|@LB@ CUAUCUCCC@LB@3'-UUU...CUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 40 30@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -15.8488 kcal/mol@LB@Unfolding Energy - mRNA 1.87568 kcal/mol@LB@Unfolding Energy - sRNA 0.774822 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 31 -- 39@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 31 -- 37@LB@
173	0.01667	0.3152	bsu28970	ytxB	-13.17	0.066474	182 -- 201	13 -- 34	tvp38/tmem64 family membrane protein YtxB	_____________181____________________202\n_____________\|______________________\|\n5'-UGC...UUCAA_____AA_______U_______UGAAA...AAA-3'\n______________AGGGG____GGAAC_GAGGGUA\n______________\|\|\|\|\|____\|\|\|\|\|_\|\|\|:\|\|\|\n______________UCCCC____CCUUG_CUCUCAU\n3'-UUU...CUAUC_____AACC_____U_______CGAAG...AUA-5'\n_____________\|______________________\|\n_____________35_____________________12\n	195 -- 201	13 -- 19	-25.067 kcal/mol	2.85387 kcal/mol	9.04315 kcal/mol	181 202@LB@ \| \|@LB@5'-UGC...UUCAA AA U UGAAA...AAA-3'@LB@ AGGGG GGAAC GAGGGUA@LB@ \|\|\|\|\| \|\|\|\|\| \|\|\|:\|\|\|@LB@ UCCCC CCUUG CUCUCAU@LB@3'-UUU...CUAUC AACC U CGAAG...AUA-5'@LB@ \| \|@LB@ 35 12@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -25.067 kcal/mol@LB@Unfolding Energy - mRNA 2.85387 kcal/mol@LB@Unfolding Energy - sRNA 9.04315 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 13 -- 34@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@LB@
53	0.002724	0.1697	bsu06970	yesO	-13.13	0.067695	188 -- 199	26 -- 36	ABC transporter substrate-binding protein	_____________187__________200\n_____________\|____________\|\n5'-CGA...AUUAA_______A____UUUGA...UUA-3'\n______________AGGGGGG_UUGG\n______________\|\|:\|\|\|\|_\|\|\|\|\n______________UCUCCCC_AACC\n3'-UUU...GACUA____________CCUUG...AUA-5'\n_____________\|____________\|\n_____________37___________25\n	188 -- 194	30 -- 36	-17.5942 kcal/mol	4.33325 kcal/mol	0.135623 kcal/mol	187 200@LB@ \| \|@LB@5'-CGA...AUUAA A UUUGA...UUA-3'@LB@ AGGGGGG UUGG@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UCUCCCC AACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -17.5942 kcal/mol@LB@Unfolding Energy - mRNA 4.33325 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
174	0.01668	0.3152	bsu22210	yprB	-13.05	0.069799	168 -- 191	31 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'	_____________167______________________192\n_____________\|________________________\|\n5'-AUU...AGCUG_______AAAU___GUAA______AGGCC...AUG-3'\n______________UUGGAUC____GUC____GGAGGG\n______________\|:\|\|\|\|\|____:\|\|____:\|\|\|\|\|\n______________AGCCUAG____UAG____UCUCCC\n3'-UUU...AAAAA_______AAC____ACUA______CAACC...AUA-5'\n_____________\|________________________\|\n_____________54_______________________30\n	168 -- 174	47 -- 53	-20.3327 kcal/mol	6.30079 kcal/mol	0.981784 kcal/mol	167 192@LB@ \| \|@LB@5'-AUU...AGCUG AAAU GUAA AGGCC...AUG-3'@LB@ UUGGAUC GUC GGAGGG@LB@ \|:\|\|\|\|\| :\|\| :\|\|\|\|\|@LB@ AGCCUAG UAG UCUCCC@LB@3'-UUU...AAAAA AAC ACUA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.05 kcal/mol@LB@Hybridization Energy -20.3327 kcal/mol@LB@Unfolding Energy - mRNA 6.30079 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 168 -- 191@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 47 -- 53@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@

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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