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
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@
129	0.01144	0.2883	bsu36230	ywqF	-11.45	0.129133	185 -- 195	31 -- 41	UDP-glucose 6-dehydrogenase YwqF	_____________184_________196\n_____________\|___________\|\n5'-UUU...UUUAA___U_______AAACA...CUC-3'\n______________CUG_UGGAGGG\n______________\|\|\|_\|:\|\|\|\|\|\n______________GAC_AUCUCCC\n3'-UUU...AACUA___U_______CAACC...AUA-5'\n_____________\|___________\|\n_____________42__________30\n	189 -- 195	31 -- 37	-16.042 kcal/mol	3.66073 kcal/mol	0.928126 kcal/mol	184 196@LB@ \| \|@LB@5'-UUU...UUUAA U AAACA...CUC-3'@LB@ CUG UGGAGGG@LB@ \|\|\| \|:\|\|\|\|\|@LB@ GAC AUCUCCC@LB@3'-UUU...AACUA U CAACC...AUA-5'@LB@ \| \|@LB@ 42 30@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -16.042 kcal/mol@LB@Unfolding Energy - mRNA 3.66073 kcal/mol@LB@Unfolding Energy - sRNA 0.928126 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 31 -- 41@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 31 -- 37@LB@
132	0.01159	0.2883	bsu33140	yvqJ	-14.19	0.043338	185 -- 204	31 -- 52	MFS transporter	_____________184____________________205\n_____________\|______________________\|\n5'-GAC...GGCAA____GG___C_________U__UGAAU...UUA-3'\n______________CGGG____G_UCUGAUGGA_GG\n______________\|\|\|:____\|_\|\|\|\|\|\|:\|\|_\|\|\n______________GCCU____C_AGACUAUCU_CC\n3'-UUU...AAAAA____AGAA_U_________C__CAACC...AUA-5'\n_____________\|______________________\|\n_____________53_____________________30\n	195 -- 201	34 -- 40	-19.4408 kcal/mol	4.27934 kcal/mol	0.976414 kcal/mol	184 205@LB@ \| \|@LB@5'-GAC...GGCAA GG C U UGAAU...UUA-3'@LB@ CGGG G UCUGAUGGA GG@LB@ \|\|\|: \| \|\|\|\|\|\|:\|\| \|\|@LB@ GCCU C AGACUAUCU CC@LB@3'-UUU...AAAAA AGAA U C CAACC...AUA-5'@LB@ \| \|@LB@ 53 30@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -19.4408 kcal/mol@LB@Unfolding Energy - mRNA 4.27934 kcal/mol@LB@Unfolding Energy - sRNA 0.976414 kcal/mol@LB@@LB@Position - mRNA 185 -- 204@LB@Position - sRNA 31 -- 52@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 34 -- 40@LB@
163	0.01533	0.3122	bsu19639	yoyE	-15.95	0.019304	185 -- 198	25 -- 39	Evidence 4: Homologs of previously reported genes of unknown function	_____________184_____________199\n_____________\|_______________\|\n5'-UCA...CGCAG__A____________ACAUG...AAU-3'\n______________GA_GGAGGGGU_GGG\n______________\|\|_:\|\|\|\|\|\|\|_\|\|\|\n______________CU_UCUCCCCA_CCC\n3'-UUU...CUAGA__A________A___CUUGU...AUA-5'\n_____________\|_______________\|\n_____________40______________24\n	189 -- 195	29 -- 35	-22.4813 kcal/mol	5.74668 kcal/mol	0.783603 kcal/mol	184 199@LB@ \| \|@LB@5'-UCA...CGCAG A ACAUG...AAU-3'@LB@ GA GGAGGGGU GGG@LB@ \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CU UCUCCCCA CCC@LB@3'-UUU...CUAGA A A CUUGU...AUA-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -22.4813 kcal/mol@LB@Unfolding Energy - mRNA 5.74668 kcal/mol@LB@Unfolding Energy - sRNA 0.783603 kcal/mol@LB@@LB@Position - mRNA 185 -- 198@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 29 -- 35@LB@
165	0.01546	0.3127	bsu02230	purT	-12.11	0.100898	185 -- 195	30 -- 39	phosphoribosylglycinamide formyltransferase	_____________184_________196\n_____________\|___________\|\n5'-GAU...GAACA___A_______CAAAG...UUG-3'\n______________GAU_GGAGGGG\n______________\|\|\|_:\|\|\|\|\|\|\n______________CUA_UCUCCCC\n3'-UUU...CUAGA___________AACCC...AUA-5'\n_____________\|___________\|\n_____________40__________29\n	189 -- 195	30 -- 36	-15.5568 kcal/mol	2.66346 kcal/mol	0.779184 kcal/mol	184 196@LB@ \| \|@LB@5'-GAU...GAACA A CAAAG...UUG-3'@LB@ GAU GGAGGGG@LB@ \|\|\| :\|\|\|\|\|\|@LB@ CUA UCUCCCC@LB@3'-UUU...CUAGA AACCC...AUA-5'@LB@ \| \|@LB@ 40 29@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.5568 kcal/mol@LB@Unfolding Energy - mRNA 2.66346 kcal/mol@LB@Unfolding Energy - sRNA 0.779184 kcal/mol@LB@@LB@Position - mRNA 185 -- 195@LB@Position - sRNA 30 -- 39@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 30 -- 36@LB@
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@
41	0.001775	0.1444	bsu36710	fdhD	-11.37	0.133163	186 -- 192	30 -- 36	protein FdhD	_____________185_____193\n_____________\|_______\|\n5'-UCG...AUUGC_______AAGAG...CAG-3'\n______________GGAGGGG\n______________:\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	186 -- 192	30 -- 36	-13.1021 kcal/mol	1.59974 kcal/mol	0.133643 kcal/mol	185 193@LB@ \| \|@LB@5'-UCG...AUUGC AAGAG...CAG-3'@LB@ GGAGGGG@LB@ :\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -13.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.59974 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@
54	0.002747	0.1697	bsu35790	yvyI	-14.15	0.043919	186 -- 197	25 -- 36	mannose-6-phosphate isomerase YvyI	_____________185__________198\n_____________\|____________\|\n5'-UCU...ACAGG________AC__AUCAU...AAU-3'\n______________GGAGGGGU__GG\n______________:\|\|\|\|\|\|\|__\|\|\n______________UCUCCCCA__CC\n3'-UUU...GACUA________AC__CUUGU...AUA-5'\n_____________\|____________\|\n_____________37___________24\n	187 -- 193	29 -- 35	-17.2174 kcal/mol	2.92719 kcal/mol	0.135926 kcal/mol	185 198@LB@ \| \|@LB@5'-UCU...ACAGG AC AUCAU...AAU-3'@LB@ GGAGGGGU GG@LB@ :\|\|\|\|\|\|\| \|\|@LB@ UCUCCCCA CC@LB@3'-UUU...GACUA AC CUUGU...AUA-5'@LB@ \| \|@LB@ 37 24@LB@@LB@@LB@Energy -14.15 kcal/mol@LB@Hybridization Energy -17.2174 kcal/mol@LB@Unfolding Energy - mRNA 2.92719 kcal/mol@LB@Unfolding Energy - sRNA 0.135926 kcal/mol@LB@@LB@Position - mRNA 186 -- 197@LB@Position - sRNA 25 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 29 -- 35@LB@
169	0.01639	0.3152	bsu07850	yfkM	-11.33	0.135062	186 -- 208	22 -- 34	general stress protein 18	_____________185_____________________209\n_____________\|_______________________\|\n5'-UGU...AAAGC___A___UAUGAAUCA_______AAAAA...CUG-3'\n______________GGG_GGU_________UGGGGAA\n______________:\|\|_\|\|\|_________\|\|\|\|\|\|\|\n______________UCC_CCA_________ACCCCUU\n3'-UUU...CUAUC_______________________GUCUC...AUA-5'\n_____________\|_______________________\|\n_____________35______________________21\n	202 -- 208	22 -- 28	-15.0114 kcal/mol	2.66027 kcal/mol	1.02154 kcal/mol	185 209@LB@ \| \|@LB@5'-UGU...AAAGC A UAUGAAUCA AAAAA...CUG-3'@LB@ GGG GGU UGGGGAA@LB@ :\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UCC CCA ACCCCUU@LB@3'-UUU...CUAUC GUCUC...AUA-5'@LB@ \| \|@LB@ 35 21@LB@@LB@@LB@Energy -11.33 kcal/mol@LB@Hybridization Energy -15.0114 kcal/mol@LB@Unfolding Energy - mRNA 2.66027 kcal/mol@LB@Unfolding Energy - sRNA 1.02154 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 22 -- 34@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 22 -- 28@LB@
1	3.729e-08	0.0001244	bsu14890	ctaC	-17.27	0.009980	187 -- 199	23 -- 34	cytochrome c oxidase subunit 2	_____________186___________200\n_____________\|_____________\|\n5'-CGA...AGAAA__________U__AAUGG...GCG-3'\n______________AGGGGUUGGG_GA\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\n______________UCCCCAACCC_CU\n3'-UUU...CUAUC_____________UGUCU...AUA-5'\n_____________\|_____________\|\n_____________35____________22\n	190 -- 196	25 -- 31	-21.5157 kcal/mol	4.12609 kcal/mol	0.123213 kcal/mol	186 200@LB@ \| \|@LB@5'-CGA...AGAAA U AAUGG...GCG-3'@LB@ AGGGGUUGGG GA@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ UCCCCAACCC CU@LB@3'-UUU...CUAUC UGUCU...AUA-5'@LB@ \| \|@LB@ 35 22@LB@@LB@@LB@Energy -17.27 kcal/mol@LB@Hybridization Energy -21.5157 kcal/mol@LB@Unfolding Energy - mRNA 4.12609 kcal/mol@LB@Unfolding Energy - sRNA 0.123213 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 23 -- 34@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 25 -- 31@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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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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