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
31	0.001131	0.119	bsu15020	coaD	-13.71	0.053189	186 -- 192	30 -- 36	phosphopantetheine adenylyltransferase	_____________185_____193\n_____________\|_______\|\n5'-UCC...UAAAA_______GUAGU...AUG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-14.3069 kcal/mol	0.46648 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCC...UAAAA GUAGU...AUG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -14.3069 kcal/mol@LB@Unfolding Energy - mRNA 0.46648 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 186 -- 192@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 30 -- 36@LB@
11	0.0001235	0.03747	bsu15610	sumT	-12.35	0.092299	189 -- 208	22 -- 34	uroporphyrinogen-iii C-methyltransferase	_____________188__________________209\n_____________\|____________________\|\n5'-GAA...AGAUC_____AAAUACGA_______AGUAU...AUG-3'\n______________GGGGG________UGGGGAA\n______________:\|\|\|\|________\|\|\|\|\|\|\|\n______________UCCCC________ACCCCUU\n3'-UUU...CUAUC_____A______________GUCUC...AUA-5'\n_____________\|____________________\|\n_____________35___________________21\n	202 -- 208	22 -- 28	-16.2617 kcal/mol	2.89451 kcal/mol	1.02154 kcal/mol	188 209@LB@ \| \|@LB@5'-GAA...AGAUC AAAUACGA AGUAU...AUG-3'@LB@ GGGGG UGGGGAA@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ UCCCC ACCCCUU@LB@3'-UUU...CUAUC A GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -16.2617 kcal/mol@LB@Unfolding Energy - mRNA 2.89451 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 189 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
144	0.01244	0.2883	bsu15720	def	-10.99	0.152648	175 -- 193	31 -- 50	peptide deformylase	_____________174___________________194\n_____________\|_____________________\|\n5'-GCG...UGUAA_____CAC_____________UAACA...AUG-3'\n______________GAUCU___GUCU__UGGAGGG\n______________\|\|\|\|\|___:\|\|\|__\|:\|\|\|\|\|\n______________CUAGA___UAGA__AUCUCCC\n3'-UUU...AAAGC_____AC_____CU_______CAACC...AUA-5'\n_____________\|_____________________\|\n_____________51____________________30\n	187 -- 193	31 -- 37	-18.0798 kcal/mol	6.12249 kcal/mol	0.970579 kcal/mol	174 194@LB@ \| \|@LB@5'-GCG...UGUAA CAC UAACA...AUG-3'@LB@ GAUCU GUCU UGGAGGG@LB@ \|\|\|\|\| :\|\|\| \|:\|\|\|\|\|@LB@ CUAGA UAGA AUCUCCC@LB@3'-UUU...AAAGC AC CU CAACC...AUA-5'@LB@ \| \|@LB@ 51 30@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -18.0798 kcal/mol@LB@Unfolding Energy - mRNA 6.12249 kcal/mol@LB@Unfolding Energy - sRNA 0.970579 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 31 -- 50@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 31 -- 37@LB@
196	0.01947	0.3269	bsu15810	spoVM	-12.63	0.082660	188 -- 194	30 -- 36	stage V sporulation protein M	_____________187_____195\n_____________\|_______\|\n5'-AAA...UUAUA_______ACAAA...GCC-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	188 -- 194	30 -- 36	-13.8815 kcal/mol	1.12038 kcal/mol	0.133643 kcal/mol	187 195@LB@ \| \|@LB@5'-AAA...UUAUA ACAAA...GCC-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.63 kcal/mol@LB@Hybridization Energy -13.8815 kcal/mol@LB@Unfolding Energy - mRNA 1.12038 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 188 -- 194@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
126	0.0111	0.2883	bsu16220	fliG	-14.68	0.034861	264 -- 293	1 -- 29	flagellar motor switch protein FliG	_____________263_____________________________294\n_____________\|_______________________________\|\n5'-GGG...UUUCC______U_____U_U__C_______G_____AAGCACU-3'\n______________UUGGGG__UAGA_G_GU_AGCUUCU_UCUAU\n______________\|\|\|\|\|\|__:\|\|\|_\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________AACCCC__GUCU_C_CA_UCGAAGA_AGAUA\n3'-UUU...UCCCC______UU______U__________G_____-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	281 -- 287	7 -- 13	-31.0613 kcal/mol	7.38869 kcal/mol	8.9939 kcal/mol	263 294@LB@ \| \|@LB@5'-GGG...UUUCC U U U C G AAGCACU-3'@LB@ UUGGGG UAGA G GU AGCUUCU UCUAU@LB@ \|\|\|\|\|\| :\|\|\| \| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ AACCCC GUCU C CA UCGAAGA AGAUA@LB@3'-UUU...UCCCC UU U G -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -14.68 kcal/mol@LB@Hybridization Energy -31.0613 kcal/mol@LB@Unfolding Energy - mRNA 7.38869 kcal/mol@LB@Unfolding Energy - sRNA 8.9939 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@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@
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@
86	0.006791	0.2588	bsu17010	ymcB	-10.99	0.152529	169 -- 190	33 -- 52	(dimethylallyl)adenosine tRNA methylthiotransferase MiaB	_____________168____________________191\n_____________\|______________________\|\n5'-AUC...AAGGG____AG__________AA____AAAAU...CGC-3'\n______________UGGA__UUUGGUUUGA__GGAG\n______________:\|\|\|__:\|\|\|:\|:\|\|\|__:\|\|\|\n______________GCCU__GAACUAGACU__UCUC\n3'-UUU...AAAAA____A___________A_____CCCAA...AUA-5'\n_____________\|______________________\|\n_____________53_____________________32\n	178 -- 184	38 -- 44	-16.81 kcal/mol	4.84464 kcal/mol	0.976367 kcal/mol	168 191@LB@ \| \|@LB@5'-AUC...AAGGG AG AA AAAAU...CGC-3'@LB@ UGGA UUUGGUUUGA GGAG@LB@ :\|\|\| :\|\|\|:\|:\|\|\| :\|\|\|@LB@ GCCU GAACUAGACU UCUC@LB@3'-UUU...AAAAA A A CCCAA...AUA-5'@LB@ \| \|@LB@ 53 32@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.81 kcal/mol@LB@Unfolding Energy - mRNA 4.84464 kcal/mol@LB@Unfolding Energy - sRNA 0.976367 kcal/mol@LB@@LB@Position - mRNA 169 -- 190@LB@Position - sRNA 33 -- 52@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 38 -- 44@LB@
83	0.006595	0.2588	bsu17210	pksN	-11.93	0.108023	61 -- 115	29 -- 70	polyketide synthase PksN	_____________60_______________________________________________________116\n_____________\|________________________________________________________\|\n5'-AGC...CAAGA____________GAAA__________AA__G_G__CAAAACAUC____A____A__AAAUC...UAU-3'\n______________GGUGGCGCUAGG_____UUGGAUUUU__GA_U_UG_________AUAG_AGGG_GU\n______________\|\|\|:\|\|\|\|:\|:\|_____\|:\|\|\|\|:\|\|__\|\|_\|_\|\|_________\|\|\|\|_\|\|\|\|_\|\|\n______________CCAUCGCGGUUC_____AGCCUAGAA__CU_A_AC_________UAUC_UCCC_CA\n3'-UUU...CGCCC____________AAAAA_______________G_______________________ACCCC...AUA-5'\n_____________\|________________________________________________________\|\n_____________71_______________________________________________________28\n	79 -- 85	45 -- 51	-37.7722 kcal/mol	10.06 kcal/mol	15.7778 kcal/mol	60 116@LB@ \| \|@LB@5'-AGC...CAAGA GAAA AA G G CAAAACAUC A A AAAUC...UAU-3'@LB@ GGUGGCGCUAGG UUGGAUUUU GA U UG AUAG AGGG GU@LB@ \|\|\|:\|\|\|\|:\|:\| \|:\|\|\|\|:\|\| \|\| \| \|\| \|\|\|\| \|\|\|\| \|\|@LB@ CCAUCGCGGUUC AGCCUAGAA CU A AC UAUC UCCC CA@LB@3'-UUU...CGCCC AAAAA G ACCCC...AUA-5'@LB@ \| \|@LB@ 71 28@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -37.7722 kcal/mol@LB@Unfolding Energy - mRNA 10.06 kcal/mol@LB@Unfolding Energy - sRNA 15.7778 kcal/mol@LB@@LB@Position - mRNA 61 -- 115@LB@Position - sRNA 29 -- 70@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 45 -- 51@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@

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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