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
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@
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@
51	0.002362	0.1545	bsu28450	sdhC	-14.17	0.043697	178 -- 219	14 -- 47	succinate dehydrogenase cytochrome b558 subunit	_____________177_________________________________________220\n_____________\|___________________________________________\|\n5'-AAA...UCGCA_______AAAC______UAAAGUAAU__CU_____________UUUAU...AGU-3'\n______________CUU_AUC____AGGGGG_________GU__GGGAACAGAGAGU\n______________\|\|\|_\|\|\|____\|\|:\|\|\|_________\|\|__\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________GAA_UAG____UCUCCC_________CA__CCCUUGUCUCUCA\n3'-UUU...GCCUA___C___ACUA_________________AC_____________UCGAA...AUA-5'\n_____________\|___________________________________________\|\n_____________48__________________________________________13\n	213 -- 219	14 -- 20	-33.4599 kcal/mol	9.41028 kcal/mol	9.88362 kcal/mol	177 220@LB@ \| \|@LB@5'-AAA...UCGCA AAAC UAAAGUAAU CU UUUAU...AGU-3'@LB@ CUU AUC AGGGGG GU GGGAACAGAGAGU@LB@ \|\|\| \|\|\| \|\|:\|\|\| \|\| \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ GAA UAG UCUCCC CA CCCUUGUCUCUCA@LB@3'-UUU...GCCUA C ACUA AC UCGAA...AUA-5'@LB@ \| \|@LB@ 48 13@LB@@LB@@LB@Energy -14.17 kcal/mol@LB@Hybridization Energy -33.4599 kcal/mol@LB@Unfolding Energy - mRNA 9.41028 kcal/mol@LB@Unfolding Energy - sRNA 9.88362 kcal/mol@LB@@LB@Position - mRNA 178 -- 219@LB@Position - sRNA 14 -- 47@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 14 -- 20@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@
177	0.01681	0.3152	bsu00910	ispF	-14.14	0.044127	219 -- 247	31 -- 51	2-D-methyl-D-erythritol 2 4-cyclodiphosphate synthase	_____________218____________________________248\n_____________\|______________________________\|\n5'-UCG...GACAA__________G__CAUCAAUUA________CCGUC...UUG-3'\n______________GGAUU_UGAU_UG_________GUGGAGGG\n______________\|\|\|\|:_\|\|\|\|_\|\|_________:\|:\|\|\|\|\|\n______________CCUAG_ACUA_AC_________UAUCUCCC\n3'-UUU...AAAAG_____A____G___________________CAACC...AUA-5'\n_____________\|______________________________\|\n_____________52_____________________________30\n	241 -- 247	31 -- 37	-21.3343 kcal/mol	6.22033 kcal/mol	0.970589 kcal/mol	218 248@LB@ \| \|@LB@5'-UCG...GACAA G CAUCAAUUA CCGUC...UUG-3'@LB@ GGAUU UGAU UG GUGGAGGG@LB@ \|\|\|\|: \|\|\|\| \|\| :\|:\|\|\|\|\|@LB@ CCUAG ACUA AC UAUCUCCC@LB@3'-UUU...AAAAG A G CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.14 kcal/mol@LB@Hybridization Energy -21.3343 kcal/mol@LB@Unfolding Energy - mRNA 6.22033 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 219 -- 247@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 31 -- 37@LB@
76	0.005654	0.2441	bsu14240	rok	-14.05	0.045854	178 -- 222	9 -- 42	repressor rok	_____________177______________________________________________223\n_____________\|________________________________________________\|\n5'-UUA...UUAAU______________ACAU__A_____GUUUAAUGAA____________UGCGC...UAU-3'\n______________UUUGAUAG_GGGGU____UG_GGAAU__________AGAGA__AGCUU\n______________\|:\|\|\|\|\|\|_\|\|\|\|\|____\|\|_\|\|\|\|:__________\|\|\|\|\|__\|\|\|\|\|\n______________AGACUAUC_CCCCA____AC_CCUUG__________UCUCU__UCGAA\n3'-UUU...GAACU________U___________C____________________CA_____GAGAGAUA-5'\n_____________\|________________________________________________\|\n_____________43_______________________________________________8\n	179 -- 185	35 -- 41	-31.6296 kcal/mol	7.67652 kcal/mol	9.89852 kcal/mol	177 223@LB@ \| \|@LB@5'-UUA...UUAAU ACAU A GUUUAAUGAA UGCGC...UAU-3'@LB@ UUUGAUAG GGGGU UG GGAAU AGAGA AGCUU@LB@ \|:\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|@LB@ AGACUAUC CCCCA AC CCUUG UCUCU UCGAA@LB@3'-UUU...GAACU U C CA GAGAGAUA-5'@LB@ \| \|@LB@ 43 8@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -31.6296 kcal/mol@LB@Unfolding Energy - mRNA 7.67652 kcal/mol@LB@Unfolding Energy - sRNA 9.89852 kcal/mol@LB@@LB@Position - mRNA 178 -- 222@LB@Position - sRNA 9 -- 42@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 35 -- 41@LB@
154	0.01388	0.2994	bsu23480	dacF	-14.01	0.046761	175 -- 192	31 -- 51	D-alanyl-D-alanine carboxypeptidase DacF	_____________174___________________193\n_____________\|_____________________\|\n5'-UGG...AAAAA_____A___A___________CUUUU...UUG-3'\n______________GGAUU_UGA____AUGGAGGG\n______________\|\|\|\|:_\|\|\|____\|\|:\|\|\|\|\|\n______________CCUAG_ACU____UAUCUCCC\n3'-UUU...AAAAG_____A___AGAC________CAACC...AUA-5'\n_____________\|_____________________\|\n_____________52____________________30\n	186 -- 192	31 -- 37	-18.482 kcal/mol	3.50235 kcal/mol	0.970589 kcal/mol	174 193@LB@ \| \|@LB@5'-UGG...AAAAA A A CUUUU...UUG-3'@LB@ GGAUU UGA AUGGAGGG@LB@ \|\|\|\|: \|\|\| \|\|:\|\|\|\|\|@LB@ CCUAG ACU UAUCUCCC@LB@3'-UUU...AAAAG A AGAC CAACC...AUA-5'@LB@ \| \|@LB@ 52 30@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -18.482 kcal/mol@LB@Unfolding Energy - mRNA 3.50235 kcal/mol@LB@Unfolding Energy - sRNA 0.970589 kcal/mol@LB@@LB@Position - mRNA 175 -- 192@LB@Position - sRNA 31 -- 51@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 31 -- 37@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@
167	0.01619	0.3152	bsu31500	yuxK	-13.98	0.047449	182 -- 199	26 -- 51	Evidence 4: Homologs of previously reported genes of unknown function	_____________181__________________________200\n_____________\|____________________________\|\n5'-UAC...UUAAA______________________AUA___AGUGA...ACG-3'\n______________GGAUC__________GGAGGGG___UGG\n______________\|\|\|\|\|__________:\|\|\|\|\|\|___\|\|\|\n______________CCUAG__________UCUCCCC___ACC\n3'-UUU...AAAAG_____AACUAGACUA_______A_____CCUUG...AUA-5'\n_____________\|____________________________\|\n_____________52___________________________25\n	187 -- 193	30 -- 36	-20.9361 kcal/mol	5.98517 kcal/mol	0.975822 kcal/mol	181 200@LB@ \| \|@LB@5'-UAC...UUAAA AUA AGUGA...ACG-3'@LB@ GGAUC GGAGGGG UGG@LB@ \|\|\|\|\| :\|\|\|\|\|\| \|\|\|@LB@ CCUAG UCUCCCC ACC@LB@3'-UUU...AAAAG AACUAGACUA A CCUUG...AUA-5'@LB@ \| \|@LB@ 52 25@LB@@LB@@LB@Energy -13.98 kcal/mol@LB@Hybridization Energy -20.9361 kcal/mol@LB@Unfolding Energy - mRNA 5.98517 kcal/mol@LB@Unfolding Energy - sRNA 0.975822 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 26 -- 51@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@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@

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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