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
153	0.01377	0.2994	bsu37510	pbpG	-15.25	0.026855	95 -- 111	23 -- 38	penicillin-binding protein 2D	_____________94_________________112\n_____________\|__________________\|\n5'-UGU...AAAGU_______AU__C______AAAAG...UGU-3'\n______________AUAGAGG__GG__GGGGA\n______________\|\|\|\|\|\|\|__\|\|__\|\|\|\|\|\n______________UAUCUCC__CC__CCCCU\n3'-UUU...UAGAC___________AA_____UGUCU...AUA-5'\n_____________\|__________________\|\n_____________39_________________22\n	95 -- 101	32 -- 38	-18.2895 kcal/mol	2.3676 kcal/mol	0.66977 kcal/mol	94 112@LB@ \| \|@LB@5'-UGU...AAAGU AU C AAAAG...UGU-3'@LB@ AUAGAGG GG GGGGA@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|@LB@ UAUCUCC CC CCCCU@LB@3'-UUU...UAGAC AA UGUCU...AUA-5'@LB@ \| \|@LB@ 39 22@LB@@LB@@LB@Energy -15.25 kcal/mol@LB@Hybridization Energy -18.2895 kcal/mol@LB@Unfolding Energy - mRNA 2.3676 kcal/mol@LB@Unfolding Energy - sRNA 0.66977 kcal/mol@LB@@LB@Position - mRNA 95 -- 111@LB@Position - sRNA 23 -- 38@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 32 -- 38@LB@
124	0.01102	0.2883	bsu36860	atpE	-15.23	0.027175	263 -- 293	30 -- 52	ATP synthase subunit c	_____________262_______________________________294\n_____________\|_________________________________\|\n5'-AAA...GGUAA____________GUUUCACGUAC__________AUUGCCC-3'\n______________CGG__UUUGAUU___________GGUAGAGGGG\n______________\|\|\|__:\|\|\|\|\|:___________\|:\|\|\|\|\|\|\|\|\n______________GCC__GAACUAG___________CUAUCUCCCC\n3'-UUU...AAAAA___UA_______A____________________AACCC...AUA-5'\n_____________\|_________________________________\|\n_____________53________________________________29\n	287 -- 293	30 -- 36	-22.7251 kcal/mol	6.51858 kcal/mol	0.979974 kcal/mol	262 294@LB@ \| \|@LB@5'-AAA...GGUAA GUUUCACGUAC AUUGCCC-3'@LB@ CGG UUUGAUU GGUAGAGGGG@LB@ \|\|\| :\|\|\|\|\|: \|:\|\|\|\|\|\|\|\|@LB@ GCC GAACUAG CUAUCUCCCC@LB@3'-UUU...AAAAA UA A AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.23 kcal/mol@LB@Hybridization Energy -22.7251 kcal/mol@LB@Unfolding Energy - mRNA 6.51858 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 30 -- 36@LB@
181	0.0171	0.3152	bsu32040	yuiF	-15.17	0.027943	179 -- 194	29 -- 51	amino acid transporter YuiF	_____________178_____________________195\n_____________\|_______________________\|\n5'-ACA...CUAAA_______________________AUCAU...GGU-3'\n______________GGAUUUU_______UGGAGGGGU\n______________\|\|\|\|:\|\|_______\|:\|\|\|\|\|\|\|\n______________CCUAGAA_______AUCUCCCCA\n3'-UUU...AAAAG_______CUAGACU_________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	188 -- 194	29 -- 35	-21.3957 kcal/mol	5.25498 kcal/mol	0.974539 kcal/mol	178 195@LB@ \| \|@LB@5'-ACA...CUAAA AUCAU...GGU-3'@LB@ GGAUUUU UGGAGGGGU@LB@ \|\|\|\|:\|\| \|:\|\|\|\|\|\|\|@LB@ CCUAGAA AUCUCCCCA@LB@3'-UUU...AAAAG CUAGACU ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -15.17 kcal/mol@LB@Hybridization Energy -21.3957 kcal/mol@LB@Unfolding Energy - mRNA 5.25498 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 179 -- 194@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 29 -- 35@LB@
33	0.001178	0.119	bsu14840	ylaN	-15.06	0.029338	181 -- 208	8 -- 28	depletion of this protein in Bacillus subtilis results in defects in cell morphology; crystal structure of Staphylococcus protein shows homodimer; ligand binding protein	_____________180__________________________209\n_____________\|____________________________\|\n5'-GAU...UCGCC______________AUACUUU_______AGAGA...AUA-3'\n______________UGGGGAACGGAGGG_______UGGCUUC\n______________\|\|\|\|\|\|\|\|:\|\|\|:\|_______\|:\|\|\|\|\|\n______________ACCCCUUGUCUCUC_______AUCGAAG\n3'-UUU...CCCCA____________________________AGAGAUA-5'\n_____________\|____________________________\|\n_____________29___________________________7\n	202 -- 208	8 -- 14	-32.8109 kcal/mol	11.1547 kcal/mol	6.59627 kcal/mol	180 209@LB@ \| \|@LB@5'-GAU...UCGCC AUACUUU AGAGA...AUA-3'@LB@ UGGGGAACGGAGGG UGGCUUC@LB@ \|\|\|\|\|\|\|\|:\|\|\|:\| \|:\|\|\|\|\|@LB@ ACCCCUUGUCUCUC AUCGAAG@LB@3'-UUU...CCCCA AGAGAUA-5'@LB@ \| \|@LB@ 29 7@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -32.8109 kcal/mol@LB@Unfolding Energy - mRNA 11.1547 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 181 -- 208@LB@Position - sRNA 8 -- 28@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@LB@
138	0.01215	0.2883	bsu17940	yneI	-15.06	0.029368	176 -- 197	30 -- 52	plasmid maintenance protein CcdB	_____________175_____________________198\n_____________\|_______________________\|\n5'-GAA...AUCUG____AA_C____GU_________AAUAU...CGG-3'\n______________UGGA__U_GAUU___UGGAGGGG\n______________:\|\|\|__\|_\|\|\|:___\|:\|\|\|\|\|\|\n______________GCCU__A_CUAG___AUCUCCCC\n3'-UUU...AAAAA____AG_A____ACU________AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	191 -- 197	30 -- 36	-21.3361 kcal/mol	5.29839 kcal/mol	0.979974 kcal/mol	175 198@LB@ \| \|@LB@5'-GAA...AUCUG AA C GU AAUAU...CGG-3'@LB@ UGGA U GAUU UGGAGGGG@LB@ :\|\|\| \| \|\|\|: \|:\|\|\|\|\|\|@LB@ GCCU A CUAG AUCUCCCC@LB@3'-UUU...AAAAA AG A ACU AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.06 kcal/mol@LB@Hybridization Energy -21.3361 kcal/mol@LB@Unfolding Energy - mRNA 5.29839 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 176 -- 197@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 30 -- 36@LB@
70	0.004864	0.2318	bsu03720	gerKB	-15.05	0.029438	176 -- 191	30 -- 44	spore germination protein KB	_____________175_______________192\n_____________\|_________________\|\n5'-UUA...GAUUA___________AA____AAGUG...GCA-3'\n______________GGUCUGA_AGA__GGGG\n______________\|:\|\|\|\|\|_\|\|\|__\|\|\|\|\n______________CUAGACU_UCU__CCCC\n3'-UUU...UAGAA_______A_________AACCC...AUA-5'\n_____________\|_________________\|\n_____________45________________29\n	176 -- 182	38 -- 44	-18.3492 kcal/mol	2.32731 kcal/mol	0.969452 kcal/mol	175 192@LB@ \| \|@LB@5'-UUA...GAUUA AA AAGUG...GCA-3'@LB@ GGUCUGA AGA GGGG@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|@LB@ CUAGACU UCU CCCC@LB@3'-UUU...UAGAA A AACCC...AUA-5'@LB@ \| \|@LB@ 45 29@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -18.3492 kcal/mol@LB@Unfolding Energy - mRNA 2.32731 kcal/mol@LB@Unfolding Energy - sRNA 0.969452 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 30 -- 44@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@LB@
82	0.006245	0.254	bsu12400	yjnA	-14.90	0.031572	235 -- 273	19 -- 53	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; PubMedId: 15849754 16850406; Product type pm: membrane component'	_____________234_____________________________________274\n_____________\|_______________________________________\|\n5'-UUA...GUUUG_____GC___A___G___U__C___A__G__U_______CCUUA...UGC-3'\n______________UCGGA__CUU_GUC_GAU_GA_GGG_GU_GG_GGAGCGG\n______________\|\|\|\|\|__\|\|\|_:\|\|_\|\|\|_\|\|_\|\|\|_\|\|_\|\|_\|\|\|:\|:\|\n______________AGCCU__GAA_UAG_CUA_CU_CCC_CA_CC_CCUUGUC\n3'-UUU...AAAAA_____A____C___A___U_________A__________UCUCA...AUA-5'\n_____________\|_______________________________________\|\n_____________54______________________________________18\n	267 -- 273	19 -- 25	-33.8463 kcal/mol	12.0212 kcal/mol	6.92635 kcal/mol	234 274@LB@ \| \|@LB@5'-UUA...GUUUG GC A G U C A G U CCUUA...UGC-3'@LB@ UCGGA CUU GUC GAU GA GGG GU GG GGAGCGG@LB@ \|\|\|\|\| \|\|\| :\|\| \|\|\| \|\| \|\|\| \|\| \|\| \|\|\|:\|:\|@LB@ AGCCU GAA UAG CUA CU CCC CA CC CCUUGUC@LB@3'-UUU...AAAAA A C A U A UCUCA...AUA-5'@LB@ \| \|@LB@ 54 18@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -33.8463 kcal/mol@LB@Unfolding Energy - mRNA 12.0212 kcal/mol@LB@Unfolding Energy - sRNA 6.92635 kcal/mol@LB@@LB@Position - mRNA 235 -- 273@LB@Position - sRNA 19 -- 53@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 19 -- 25@LB@
16	0.0002979	0.06212	bsu28440	sdhA	-14.86	0.032148	176 -- 195	24 -- 44	succinate dehydrogenase flavoprotein subunit	_____________175___________________196\n_____________\|_____________________\|\n5'-GUG...UACUA____AC________AGA____CUAUC...CCA-3'\n______________GAUU___UAGAGGG___GGGG\n______________\|\|\|:___\|\|\|\|\|\|\|___\|\|\|\|\n______________CUAG___AUCUCCC___CCCC\n3'-UUU...UAGAA____ACU_______CAA____UUGUC...AUA-5'\n_____________\|_____________________\|\n_____________45____________________23\n	182 -- 188	31 -- 37	-20.465 kcal/mol	4.62868 kcal/mol	0.977523 kcal/mol	175 196@LB@ \| \|@LB@5'-GUG...UACUA AC AGA CUAUC...CCA-3'@LB@ GAUU UAGAGGG GGGG@LB@ \|\|\|: \|\|\|\|\|\|\| \|\|\|\|@LB@ CUAG AUCUCCC CCCC@LB@3'-UUU...UAGAA ACU CAA UUGUC...AUA-5'@LB@ \| \|@LB@ 45 23@LB@@LB@@LB@Energy -14.86 kcal/mol@LB@Hybridization Energy -20.465 kcal/mol@LB@Unfolding Energy - mRNA 4.62868 kcal/mol@LB@Unfolding Energy - sRNA 0.977523 kcal/mol@LB@@LB@Position - mRNA 176 -- 195@LB@Position - sRNA 24 -- 44@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
75	0.005596	0.2441	bsu19669	yoyF	-14.84	0.032440	230 -- 255	26 -- 52	Evidence 5: No homology to any previously reported sequences	_____________229_________________________256\n_____________\|___________________________\|\n5'-GUA...CUGGA____GAAA_________UCAUAA____AAAAA...GUC-3'\n______________CGGA____GAUUUGAUA_______UGG\n______________\|\|\|\|____\|\|\|:\|\|\|\|\|_______\|\|\|\n______________GCCU____CUAGACUAU_______ACC\n3'-UUU...AAAAA____AGAA_________CUCCCCA___CCUUG...AUA-5'\n_____________\|___________________________\|\n_____________53__________________________25\n	240 -- 246	36 -- 42	-17.4265 kcal/mol	1.6069 kcal/mol	0.980817 kcal/mol	229 256@LB@ \| \|@LB@5'-GUA...CUGGA GAAA UCAUAA AAAAA...GUC-3'@LB@ CGGA GAUUUGAUA UGG@LB@ \|\|\|\| \|\|\|:\|\|\|\|\| \|\|\|@LB@ GCCU CUAGACUAU ACC@LB@3'-UUU...AAAAA AGAA CUCCCCA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -17.4265 kcal/mol@LB@Unfolding Energy - mRNA 1.6069 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 36 -- 42@LB@
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@

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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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

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