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
182	0.01724	0.3161	bsu22340	nth	-14.82	0.032761	30 -- 59	25 -- 52	endonuclease III	_____________29______________________________60\n_____________\|_______________________________\|\n5'-CAG...UUGAC______________A_____AGAAAAA____CUUAA...UAG-3'\n______________CGGAUUUUG_UUUG_AUGGA_______UGGG\n______________\|\|\|\|\|:\|\|\|_\|:\|\|_\|\|:\|\|_______\|\|\|\|\n______________GCCUAGAAC_AGAC_UAUCU_______ACCC\n3'-UUU...AAAAA_________U__________CCCCA______CUUGU...AUA-5'\n_____________\|_______________________________\|\n_____________53______________________________24\n	32 -- 38	44 -- 50	-22.2299 kcal/mol	6.43208 kcal/mol	0.980838 kcal/mol	29 60@LB@ \| \|@LB@5'-CAG...UUGAC A AGAAAAA CUUAA...UAG-3'@LB@ CGGAUUUUG UUUG AUGGA UGGG@LB@ \|\|\|\|\|:\|\|\| \|:\|\| \|\|:\|\| \|\|\|\|@LB@ GCCUAGAAC AGAC UAUCU ACCC@LB@3'-UUU...AAAAA U CCCCA CUUGU...AUA-5'@LB@ \| \|@LB@ 53 24@LB@@LB@@LB@Energy -14.82 kcal/mol@LB@Hybridization Energy -22.2299 kcal/mol@LB@Unfolding Energy - mRNA 6.43208 kcal/mol@LB@Unfolding Energy - sRNA 0.980838 kcal/mol@LB@@LB@Position - mRNA 30 -- 59@LB@Position - sRNA 25 -- 52@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 44 -- 50@LB@
134	0.01184	0.2883	bsu01450	cbiO	-8.85	0.304208	221 -- 231	32 -- 43	energy-coupling factor transporter ATP-binding protein EcfA1	_____________220__________232\n_____________\|____________\|\n5'-AUA...UUGAU____________AUAUC...AUG-3'\n______________AUC_GGUAGAGG\n______________\|\|\|_\|:\|\|\|\|\|\|\n______________UAG_CUAUCUCC\n3'-UUU...AGAAC___A________CCAAC...AUA-5'\n_____________\|____________\|\n_____________44___________31\n	225 -- 231	32 -- 38	-12.7681 kcal/mol	2.95776 kcal/mol	0.959872 kcal/mol	220 232@LB@ \| \|@LB@5'-AUA...UUGAU AUAUC...AUG-3'@LB@ AUC GGUAGAGG@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ UAG CUAUCUCC@LB@3'-UUU...AGAAC A CCAAC...AUA-5'@LB@ \| \|@LB@ 44 31@LB@@LB@@LB@Energy -8.85 kcal/mol@LB@Hybridization Energy -12.7681 kcal/mol@LB@Unfolding Energy - mRNA 2.95776 kcal/mol@LB@Unfolding Energy - sRNA 0.959872 kcal/mol@LB@@LB@Position - mRNA 221 -- 231@LB@Position - sRNA 32 -- 43@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 32 -- 38@LB@
186	0.01872	0.3269	bsu09880	yhaR	-10.74	0.166509	137 -- 152	16 -- 29	enoyl-CoA hydratase/isomerase YhaR	_____________136______________153\n_____________\|________________\|\n5'-CAG...UUUAU_______UG_______AUGUA...AAU-3'\n______________UUGGGGA__GCGGGGA\n______________\|\|\|\|\|\|\|__:\|:\|:\|\|\n______________AACCCCU__UGUCUCU\n3'-UUU...UCCCC________________CAUCG...AUA-5'\n_____________\|________________\|\n_____________30_______________15\n	146 -- 152	16 -- 22	-19.1675 kcal/mol	2.41685 kcal/mol	6.01276 kcal/mol	136 153@LB@ \| \|@LB@5'-CAG...UUUAU UG AUGUA...AAU-3'@LB@ UUGGGGA GCGGGGA@LB@ \|\|\|\|\|\|\| :\|:\|:\|\|@LB@ AACCCCU UGUCUCU@LB@3'-UUU...UCCCC CAUCG...AUA-5'@LB@ \| \|@LB@ 30 15@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -19.1675 kcal/mol@LB@Unfolding Energy - mRNA 2.41685 kcal/mol@LB@Unfolding Energy - sRNA 6.01276 kcal/mol@LB@@LB@Position - mRNA 137 -- 152@LB@Position - sRNA 16 -- 29@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 16 -- 22@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@
18	0.00036	0.06216	bsu24510	yqhO	-21.34	0.000873	175 -- 205	13 -- 44	Evidence 4: Homologs of previously reported genes of unknown function	_____________174_______________________________206\n_____________\|_________________________________\|\n5'-UAU...UAAAC____G__________GA____________U___UAUUG...GAG-3'\n______________GAUC_GAUGGAGGGG___GGGAAU_GAGA_GUA\n______________\|\|\|\|_\|\|\|:\|\|\|\|\|\|___\|\|\|\|\|:_\|\|\|\|_\|\|\|\n______________CUAG_CUAUCUCCCC___CCCUUG_CUCU_CAU\n3'-UUU...UAGAA____A__________AAC______U________CGAAG...AUA-5'\n_____________\|_________________________________\|\n_____________45________________________________12\n	183 -- 189	30 -- 36	-39.4543 kcal/mol	8.17177 kcal/mol	9.94171 kcal/mol	174 206@LB@ \| \|@LB@5'-UAU...UAAAC G GA U UAUUG...GAG-3'@LB@ GAUC GAUGGAGGGG GGGAAU GAGA GUA@LB@ \|\|\|\| \|\|\|:\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\| \|\|\|@LB@ CUAG CUAUCUCCCC CCCUUG CUCU CAU@LB@3'-UUU...UAGAA A AAC U CGAAG...AUA-5'@LB@ \| \|@LB@ 45 12@LB@@LB@@LB@Energy -21.34 kcal/mol@LB@Hybridization Energy -39.4543 kcal/mol@LB@Unfolding Energy - mRNA 8.17177 kcal/mol@LB@Unfolding Energy - sRNA 9.94171 kcal/mol@LB@@LB@Position - mRNA 175 -- 205@LB@Position - sRNA 13 -- 44@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 30 -- 36@LB@
37	0.00164	0.1432	bsu32390	yunF	-13.99	0.047070	211 -- 231	31 -- 53	Evidence 4: Homologs of previously reported genes of unknown function	_____________210_____________________232\n_____________\|_______________________\|\n5'-UGU...UUAUA___________CGG_________AUCAU...UUC-3'\n______________UCGGA_C_UGA___GAUGGGGGG\n______________\|\|\|\|\|_\|_\|\|\|___\|\|\|:\|:\|\|\|\n______________AGCCU_G_ACU___CUAUCUCCC\n3'-UUU...AAAAA_____A_A___AGA_________CAACC...AUA-5'\n_____________\|_______________________\|\n_____________54______________________30\n	225 -- 231	31 -- 37	-23.274 kcal/mol	8.29838 kcal/mol	0.981784 kcal/mol	210 232@LB@ \| \|@LB@5'-UGU...UUAUA CGG AUCAU...UUC-3'@LB@ UCGGA C UGA GAUGGGGGG@LB@ \|\|\|\|\| \| \|\|\| \|\|\|:\|:\|\|\|@LB@ AGCCU G ACU CUAUCUCCC@LB@3'-UUU...AAAAA A A AGA CAACC...AUA-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -13.99 kcal/mol@LB@Hybridization Energy -23.274 kcal/mol@LB@Unfolding Energy - mRNA 8.29838 kcal/mol@LB@Unfolding Energy - sRNA 0.981784 kcal/mol@LB@@LB@Position - mRNA 211 -- 231@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 31 -- 37@LB@
44	0.001968	0.1492	bsu14940	ylbA	-14.48	0.038144	221 -- 240	24 -- 52	Evidence 4: Homologs of previously reported genes of unknown function	_____________220___________________________241\n_____________\|_____________________________\|\n5'-CAU...GAAAG_________________________AA__CUGAG...AAU-3'\n______________CGGA_CUUGA________AGGGGUU__GG\n______________\|\|\|\|_\|\|\|\|\|________\|\|\|\|\|\|\|__\|\|\n______________GCCU_GAACU________UCCCCAA__CC\n3'-UUU...AAAAA____A_____AGACUAUC_______CC__UUGUC...AUA-5'\n_____________\|_____________________________\|\n_____________53____________________________23\n	230 -- 236	28 -- 34	-22.4266 kcal/mol	6.96942 kcal/mol	0.980851 kcal/mol	220 241@LB@ \| \|@LB@5'-CAU...GAAAG AA CUGAG...AAU-3'@LB@ CGGA CUUGA AGGGGUU GG@LB@ \|\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GCCU GAACU UCCCCAA CC@LB@3'-UUU...AAAAA A AGACUAUC CC UUGUC...AUA-5'@LB@ \| \|@LB@ 53 23@LB@@LB@@LB@Energy -14.48 kcal/mol@LB@Hybridization Energy -22.4266 kcal/mol@LB@Unfolding Energy - mRNA 6.96942 kcal/mol@LB@Unfolding Energy - sRNA 0.980851 kcal/mol@LB@@LB@Position - mRNA 221 -- 240@LB@Position - sRNA 24 -- 52@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 28 -- 34@LB@
56	0.002918	0.1738	bsu04390	ydbA	-13.95	0.047884	245 -- 258	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________244_____________259\n_____________\|_______________\|\n5'-UUC...AAAGA_______AAA_____AAAAA...GCC-3'\n______________GAUAGAG____UGGG\n______________\|\|\|\|\|\|\|____\|\|\|\|\n______________CUAUCUC____ACCC\n3'-UUU...CUAGA_______CCCA____CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	245 -- 251	33 -- 39	-15.533 kcal/mol	0.795684 kcal/mol	0.783603 kcal/mol	244 259@LB@ \| \|@LB@5'-UUC...AAAGA AAA AAAAA...GCC-3'@LB@ GAUAGAG UGGG@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ CUAUCUC ACCC@LB@3'-UUU...CUAGA CCCA CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -15.533 kcal/mol@LB@Unfolding Energy - mRNA 0.795684 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 245 -- 258@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 33 -- 39@LB@
99	0.00842	0.2778	bsu19470	yojF	-13.80	0.051174	184 -- 193	30 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________183________194\n_____________\|__________\|\n5'-GAA...AAGAA__A_______AGCAA...CAG-3'\n______________GA_AGAGGGG\n______________\|\|_\|\|\|\|\|\|\|\n______________CU_UCUCCCC\n3'-UUU...CUAGA__A_______AACCC...AUA-5'\n_____________\|__________\|\n_____________40_________29\n	187 -- 193	30 -- 36	-15.454 kcal/mol	0.87683 kcal/mol	0.779184 kcal/mol	183 194@LB@ \| \|@LB@5'-GAA...AAGAA A AGCAA...CAG-3'@LB@ GA AGAGGGG@LB@ \|\| \|\|\|\|\|\|\|@LB@ CU UCUCCCC@LB@3'-UUU...CUAGA A AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -15.454 kcal/mol@LB@Unfolding Energy - mRNA 0.87683 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 184 -- 193@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
136	0.01205	0.2883	bsu35319	yvzG	-14.21	0.042782	258 -- 272	27 -- 43	Evidence 4: Homologs of previously reported genes of unknown function	_____________257_______________273\n_____________\|_________________\|\n5'-AAG...UUACC_________________UGUUA...AUU-3'\n______________AUC_GA_AGAGGGGUUG\n______________\|\|\|_\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UAG_CU_UCUCCCCAAC\n3'-UUU...AGAAC___A__A__________CCCUU...AUA-5'\n_____________\|_________________\|\n_____________44________________26\n	266 -- 272	27 -- 33	-20.1473 kcal/mol	4.96591 kcal/mol	0.966729 kcal/mol	257 273@LB@ \| \|@LB@5'-AAG...UUACC UGUUA...AUU-3'@LB@ AUC GA AGAGGGGUUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UAG CU UCUCCCCAAC@LB@3'-UUU...AGAAC A A CCCUU...AUA-5'@LB@ \| \|@LB@ 44 26@LB@@LB@@LB@Energy -14.21 kcal/mol@LB@Hybridization Energy -20.1473 kcal/mol@LB@Unfolding Energy - mRNA 4.96591 kcal/mol@LB@Unfolding Energy - sRNA 0.966729 kcal/mol@LB@@LB@Position - mRNA 258 -- 272@LB@Position - sRNA 27 -- 43@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 27 -- 33@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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