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
175	0.01672	0.3152	bsu04630	ydcC	-11.64	0.120416	196 -- 203	27 -- 34	sporulation protein YdcC	_____________195______204\n_____________\|________\|\n5'-CCG...GAAAA________AAAAA...UGG-3'\n______________AGGGGUUG\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAAC\n3'-UUU...CUAUC________CCCUU...AUA-5'\n_____________\|________\|\n_____________35_______26\n	197 -- 203	27 -- 33	-14.5305 kcal/mol	2.76844 kcal/mol	0.118612 kcal/mol	195 204@LB@ \| \|@LB@5'-CCG...GAAAA AAAAA...UGG-3'@LB@ AGGGGUUG@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAAC@LB@3'-UUU...CUAUC CCCUU...AUA-5'@LB@ \| \|@LB@ 35 26@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -14.5305 kcal/mol@LB@Unfolding Energy - mRNA 2.76844 kcal/mol@LB@Unfolding Energy - sRNA 0.118612 kcal/mol@LB@@LB@Position - mRNA 196 -- 203@LB@Position - sRNA 27 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 27 -- 33@LB@
15	0.0002364	0.05257	bsu19290	yozO	-13.57	0.056229	184 -- 195	28 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183__________196\n_____________\|____________\|\n5'-AAA...AUGCA__A_________CUUCA...UGG-3'\n______________GA_AGAGGGGUU\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CU_UCUCCCCAA\n3'-UUU...CUAGA__A_________CCCCU...AUA-5'\n_____________\|____________\|\n_____________40___________27\n	189 -- 195	28 -- 34	-16.9963 kcal/mol	2.64187 kcal/mol	0.77983 kcal/mol	183 196@LB@ \| \|@LB@5'-AAA...AUGCA A CUUCA...UGG-3'@LB@ GA AGAGGGGUU@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CU UCUCCCCAA@LB@3'-UUU...CUAGA A CCCCU...AUA-5'@LB@ \| \|@LB@ 40 27@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -16.9963 kcal/mol@LB@Unfolding Energy - mRNA 2.64187 kcal/mol@LB@Unfolding Energy - sRNA 0.77983 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 28 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
25	0.0005172	0.06638	bsu30210	bioD	-10.94	0.155183	179 -- 210	28 -- 53	ATP-dependent dethiobiotin synthetase BioD	_____________178_______________________________211\n_____________\|_________________________________\|\n5'-GUC...UUCAA_____AAG___G___CACAUCAUUU________UUUUU...UCG-3'\n______________UCGGA____GA_CUG__________GAGGGGUU\n______________\|\|\|\|\|____\|\|_\|\|\|__________\|\|\|\|\|\|\|\|\n______________AGCCU____CU_GAC__________CUCCCCAA\n3'-UUU...AAAAA_____AGAA__A___UAU_______________CCCCU...AUA-5'\n_____________\|_________________________________\|\n_____________54________________________________27\n	204 -- 210	28 -- 34	-21.1469 kcal/mol	9.22099 kcal/mol	0.985925 kcal/mol	178 211@LB@ \| \|@LB@5'-GUC...UUCAA AAG G CACAUCAUUU UUUUU...UCG-3'@LB@ UCGGA GA CUG GAGGGGUU@LB@ \|\|\|\|\| \|\| \|\|\| \|\|\|\|\|\|\|\|@LB@ AGCCU CU GAC CUCCCCAA@LB@3'-UUU...AAAAA AGAA A UAU CCCCU...AUA-5'@LB@ \| \|@LB@ 54 27@LB@@LB@@LB@Energy -10.94 kcal/mol@LB@Hybridization Energy -21.1469 kcal/mol@LB@Unfolding Energy - mRNA 9.22099 kcal/mol@LB@Unfolding Energy - sRNA 0.985925 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 28 -- 53@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 28 -- 34@LB@
39	0.001675	0.1432	bsu23240	ypzK	-16.45	0.015090	173 -- 197	28 -- 52	riboflavin biosynthesis protein RibT	_____________172_________________________198\n_____________\|___________________________\|\n5'-GCG...CAGAC____CA______AU_____________UUUAU...UUA-3'\n______________UGGA__UUUUGG____AUAGAGGGGUU\n______________:\|\|\|__\|:\|\|\|:____\|\|\|\|\|\|\|\|\|\|\|\n______________GCCU__AGAACU____UAUCUCCCCAA\n3'-UUU...AAAAA____________AGAC___________CCCCU...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________27\n	191 -- 197	28 -- 34	-23.4842 kcal/mol	6.04944 kcal/mol	0.980555 kcal/mol	172 198@LB@ \| \|@LB@5'-GCG...CAGAC CA AU UUUAU...UUA-3'@LB@ UGGA UUUUGG AUAGAGGGGUU@LB@ :\|\|\| \|:\|\|\|: \|\|\|\|\|\|\|\|\|\|\|@LB@ GCCU AGAACU UAUCUCCCCAA@LB@3'-UUU...AAAAA AGAC CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -16.45 kcal/mol@LB@Hybridization Energy -23.4842 kcal/mol@LB@Unfolding Energy - mRNA 6.04944 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 173 -- 197@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 191 -- 197@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@
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@
73	0.005255	0.2402	bsu21750	scuA	-12.63	0.082513	190 -- 220	28 -- 51	SCO1 protein	_____________189_____________________________221\n_____________\|_______________________________\|\n5'-GGG...GGAAA____GGAU___A___A__UUAUCA_______AACGG...AGC-3'\n______________GGAU____GUC_UGA_GG______AGGGGUU\n______________\|\|\|\|____:\|\|_\|\|\|_:\|______\|\|\|\|\|\|\|\n______________CCUA____UAG_ACU_UC______UCCCCAA\n3'-UUU...AAAAG____GAAC_______A_______________CCCCU...AUA-5'\n_____________\|_______________________________\|\n_____________52______________________________27\n	214 -- 220	28 -- 34	-18.667 kcal/mol	5.06013 kcal/mol	0.974859 kcal/mol	189 221@LB@ \| \|@LB@5'-GGG...GGAAA GGAU A A UUAUCA AACGG...AGC-3'@LB@ GGAU GUC UGA GG AGGGGUU@LB@ \|\|\|\| :\|\| \|\|\| :\| \|\|\|\|\|\|\|@LB@ CCUA UAG ACU UC UCCCCAA@LB@3'-UUU...AAAAG GAAC A CCCCU...AUA-5'@LB@ \| \|@LB@ 52 27@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -18.667 kcal/mol@LB@Unfolding Energy - mRNA 5.06013 kcal/mol@LB@Unfolding Energy - sRNA 0.974859 kcal/mol@LB@@LB@Position - mRNA 190 -- 220@LB@Position - sRNA 28 -- 51@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 28 -- 34@LB@
80	0.005932	0.2448	bsu24430	spoIIIAA	-11.72	0.117179	88 -- 116	28 -- 52	stage III sporulation protein AA	_____________87______________________________117\n_____________\|_______________________________\|\n5'-GUC...UUUUA___GUGUU_______________C___U___CAUAA...GGA-3'\n______________CGG_____GUCUUGAUUU__UGG_GGG_GUU\n______________\|\|\|_____:\|\|\|\|\|\|\|:\|__\|:\|_\|\|\|_\|\|\|\n______________GCC_____UAGAACUAGA__AUC_CCC_CAA\n3'-UUU...AAAAA__________________CU___U_______CCCCU...AUA-5'\n_____________\|_______________________________\|\n_____________53______________________________27\n	99 -- 105	40 -- 46	-20.9874 kcal/mol	8.2899 kcal/mol	0.980555 kcal/mol	87 117@LB@ \| \|@LB@5'-GUC...UUUUA GUGUU C U CAUAA...GGA-3'@LB@ CGG GUCUUGAUUU UGG GGG GUU@LB@ \|\|\| :\|\|\|\|\|\|\|:\| \|:\| \|\|\| \|\|\|@LB@ GCC UAGAACUAGA AUC CCC CAA@LB@3'-UUU...AAAAA CU U CCCCU...AUA-5'@LB@ \| \|@LB@ 53 27@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -20.9874 kcal/mol@LB@Unfolding Energy - mRNA 8.2899 kcal/mol@LB@Unfolding Energy - sRNA 0.980555 kcal/mol@LB@@LB@Position - mRNA 88 -- 116@LB@Position - sRNA 28 -- 52@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 40 -- 46@LB@
97	0.008118	0.2778	bsu16450	cheC	-9.97	0.215069	178 -- 195	28 -- 47	Chey-P phosphatase CheC	_____________177__________________196\n_____________\|____________________\|\n5'-CGA...UCAAG___A________A_______AUGAC...UGU-3'\n______________CUU_AUCU__UA_AGGGGUU\n______________\|\|\|_\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________GAA_UAGA__AU_UCCCCAA\n3'-UUU...GCCUA___C____CU__C_______CCCCU...AUA-5'\n_____________\|____________________\|\n_____________48___________________27\n	189 -- 195	28 -- 34	-14.5799 kcal/mol	3.63028 kcal/mol	0.974663 kcal/mol	177 196@LB@ \| \|@LB@5'-CGA...UCAAG A A AUGAC...UGU-3'@LB@ CUU AUCU UA AGGGGUU@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ GAA UAGA AU UCCCCAA@LB@3'-UUU...GCCUA C CU C CCCCU...AUA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -14.5799 kcal/mol@LB@Unfolding Energy - mRNA 3.63028 kcal/mol@LB@Unfolding Energy - sRNA 0.974663 kcal/mol@LB@@LB@Position - mRNA 178 -- 195@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 28 -- 34@LB@
122	0.01077	0.2883	bsu18910	rapK	-11.72	0.116857	189 -- 197	28 -- 36	response regulator aspartate phosphatase K	_____________188_______198\n_____________\|_________\|\n5'-UAU...CAGAA_________UAAAU...CAG-3'\n______________AGAGGGGUU\n______________\|\|\|\|\|\|\|\|\|\n______________UCUCCCCAA\n3'-UUU...GACUA_________CCCCU...AUA-5'\n_____________\|_________\|\n_____________37________27\n	191 -- 197	28 -- 34	-15.633 kcal/mol	3.77416 kcal/mol	0.134381 kcal/mol	188 198@LB@ \| \|@LB@5'-UAU...CAGAA UAAAU...CAG-3'@LB@ AGAGGGGUU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCUCCCCAA@LB@3'-UUU...GACUA CCCCU...AUA-5'@LB@ \| \|@LB@ 37 27@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -15.633 kcal/mol@LB@Unfolding Energy - mRNA 3.77416 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@

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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