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
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@
118	0.01022	0.2883	bsu19370	sucA	-9.59	0.243554	183 -- 190	23 -- 30	2-oxoglutarate dehydrogenase subunit E1	_____________182______191\n_____________\|________\|\n5'-UUU...UUUAA________UAAUA...AUC-3'\n______________GUUGGGGG\n______________\|\|\|\|\|\|\|:\n______________CAACCCCU\n3'-UUU...CUCCC________UGUCU...AUA-5'\n_____________\|________\|\n_____________31_______22\n	184 -- 190	23 -- 29	-13.0923 kcal/mol	3.48895 kcal/mol	0.018115 kcal/mol	182 191@LB@ \| \|@LB@5'-UUU...UUUAA UAAUA...AUC-3'@LB@ GUUGGGGG@LB@ \|\|\|\|\|\|\|:@LB@ CAACCCCU@LB@3'-UUU...CUCCC UGUCU...AUA-5'@LB@ \| \|@LB@ 31 22@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0923 kcal/mol@LB@Unfolding Energy - mRNA 3.48895 kcal/mol@LB@Unfolding Energy - sRNA 0.018115 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 23 -- 30@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 23 -- 29@LB@
72	0.005249	0.2402	bsu31470	kapD	-7.49	0.439018	141 -- 147	21 -- 27	3'-5' exonuclease KapD	_____________140_____148\n_____________\|_______\|\n5'-UUU...GAGAA_______UGAUA...GAA-3'\n______________GGGGAAU\n______________\|\|\|\|\|\|:\n______________CCCCUUG\n3'-UUU...CCCAA_______UCUCU...AUA-5'\n_____________\|_______\|\n_____________28______20\n	141 -- 147	21 -- 27	-11.5159 kcal/mol	2.2254 kcal/mol	1.80207 kcal/mol	140 148@LB@ \| \|@LB@5'-UUU...GAGAA UGAUA...GAA-3'@LB@ GGGGAAU@LB@ \|\|\|\|\|\|:@LB@ CCCCUUG@LB@3'-UUU...CCCAA UCUCU...AUA-5'@LB@ \| \|@LB@ 28 20@LB@@LB@@LB@Energy -7.49 kcal/mol@LB@Hybridization Energy -11.5159 kcal/mol@LB@Unfolding Energy - mRNA 2.2254 kcal/mol@LB@Unfolding Energy - sRNA 1.80207 kcal/mol@LB@@LB@Position - mRNA 141 -- 147@LB@Position - sRNA 21 -- 27@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 21 -- 27@LB@
21	0.0003947	0.0627	bsu28260	leuC	-16.01	0.018761	166 -- 191	26 -- 52	3-isopropylmalate dehydratase large subunit	_____________165___________________________192\n_____________\|_____________________________\|\n5'-GAA...UUAAG________A_C___A_________A____AAAUA...UUC-3'\n______________CGG_UCUU_G_UCU_GGUAGAGGG___GG\n______________\|\|\|_\|\|\|\|_\|_\|\|\|_\|:\|\|\|\|\|\|\|___\|\|\n______________GCC_AGAA_C_AGA_CUAUCUCCC___CC\n3'-UUU...AAAAA___U______U_____________CAA__CCUUG...AUA-5'\n_____________\|_____________________________\|\n_____________53____________________________25\n	182 -- 188	31 -- 37	-26.3594 kcal/mol	9.36849 kcal/mol	0.980817 kcal/mol	165 192@LB@ \| \|@LB@5'-GAA...UUAAG A C A A AAAUA...UUC-3'@LB@ CGG UCUU G UCU GGUAGAGGG GG@LB@ \|\|\| \|\|\|\| \| \|\|\| \|:\|\|\|\|\|\|\| \|\|@LB@ GCC AGAA C AGA CUAUCUCCC CC@LB@3'-UUU...AAAAA U U CAA CCUUG...AUA-5'@LB@ \| \|@LB@ 53 25@LB@@LB@@LB@Energy -16.01 kcal/mol@LB@Hybridization Energy -26.3594 kcal/mol@LB@Unfolding Energy - mRNA 9.36849 kcal/mol@LB@Unfolding Energy - sRNA 0.980817 kcal/mol@LB@@LB@Position - mRNA 166 -- 191@LB@Position - sRNA 26 -- 52@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 31 -- 37@LB@
117	0.0101	0.2881	bsu39670	iolJ	-13.86	0.049938	182 -- 196	29 -- 51	6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase	_____________181_____________________197\n_____________\|_______________________\|\n5'-CCG...GUAAU____AAA________________GAAUA...CGA-3'\n______________GGAU___________GGAGGGGU\n______________\|\|\|\|___________:\|\|\|\|\|\|\|\n______________CCUA___________UCUCCCCA\n3'-UUU...AAAAG____GAACUAGACUA________ACCCC...AUA-5'\n_____________\|_______________________\|\n_____________52______________________28\n	190 -- 196	29 -- 35	-16.9006 kcal/mol	2.07053 kcal/mol	0.974539 kcal/mol	181 197@LB@ \| \|@LB@5'-CCG...GUAAU AAA GAAUA...CGA-3'@LB@ GGAU GGAGGGGU@LB@ \|\|\|\| :\|\|\|\|\|\|\|@LB@ CCUA UCUCCCCA@LB@3'-UUU...AAAAG GAACUAGACUA ACCCC...AUA-5'@LB@ \| \|@LB@ 52 28@LB@@LB@@LB@Energy -13.86 kcal/mol@LB@Hybridization Energy -16.9006 kcal/mol@LB@Unfolding Energy - mRNA 2.07053 kcal/mol@LB@Unfolding Energy - sRNA 0.974539 kcal/mol@LB@@LB@Position - mRNA 182 -- 196@LB@Position - sRNA 29 -- 51@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 29 -- 35@LB@
95	0.007929	0.2778	bsu40080	gntZ	-7.93	0.392252	74 -- 93	34 -- 54	6-phosphogluconate dehydrogenase	_____________73____________________94\n_____________\|_____________________\|\n5'-ACU...AAUAC________AAGCA____A___AACAU...ACA-3'\n______________UUCGGAUU______UGA_AGA\n______________\|\|\|\|\|\|\|:______\|\|\|_\|\|\|\n______________AAGCCUAG______ACU_UCU\n3'-UUU...CAAAA________AACUAG___A___CCCCA...AUA-5'\n_____________\|_____________________\|\n_____________55____________________33\n	75 -- 81	47 -- 53	-13.3211 kcal/mol	3.78785 kcal/mol	1.60142 kcal/mol	73 94@LB@ \| \|@LB@5'-ACU...AAUAC AAGCA A AACAU...ACA-3'@LB@ UUCGGAUU UGA AGA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\|@LB@ AAGCCUAG ACU UCU@LB@3'-UUU...CAAAA AACUAG A CCCCA...AUA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -7.93 kcal/mol@LB@Hybridization Energy -13.3211 kcal/mol@LB@Unfolding Energy - mRNA 3.78785 kcal/mol@LB@Unfolding Energy - sRNA 1.60142 kcal/mol@LB@@LB@Position - mRNA 74 -- 93@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 75 -- 81@LB@Position Seed - sRNA 47 -- 53@LB@
17	0.0003284	0.06216	bsu08690	ygaD	-15.59	0.022949	198 -- 218	30 -- 49	ABC transporter ATP-binding protein	_____________197___________________219\n_____________\|_____________________\|\n5'-UGA...CACAC___A____AAA__G_______GAAUC...UCG-3'\n______________AUC_UGAU___GA_AGAGGGG\n______________\|\|\|_\|\|\|\|___\|\|_\|\|\|\|\|\|\|\n______________UAG_ACUA___CU_UCUCCCC\n3'-UUU...AAGCC___A____GA___A_______AACCC...AUA-5'\n_____________\|_____________________\|\n_____________50____________________29\n	212 -- 218	30 -- 36	-19.3788 kcal/mol	2.8161 kcal/mol	0.974265 kcal/mol	197 219@LB@ \| \|@LB@5'-UGA...CACAC A AAA G GAAUC...UCG-3'@LB@ AUC UGAU GA AGAGGGG@LB@ \|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UAG ACUA CU UCUCCCC@LB@3'-UUU...AAGCC A GA A AACCC...AUA-5'@LB@ \| \|@LB@ 50 29@LB@@LB@@LB@Energy -15.59 kcal/mol@LB@Hybridization Energy -19.3788 kcal/mol@LB@Unfolding Energy - mRNA 2.8161 kcal/mol@LB@Unfolding Energy - sRNA 0.974265 kcal/mol@LB@@LB@Position - mRNA 198 -- 218@LB@Position - sRNA 30 -- 49@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 30 -- 36@LB@
27	0.0005687	0.07027	bsu32550	yurJ	-13.20	0.065709	183 -- 191	31 -- 39	ABC transporter ATP-binding protein	_____________182_______192\n_____________\|_________\|\n5'-AAC...CAAAA_________ACUUU...UGC-3'\n______________GAUAGGGGG\n______________\|\|\|\|\|:\|\|\|\n______________CUAUCUCCC\n3'-UUU...CUAGA_________CAACC...AUA-5'\n_____________\|_________\|\n_____________40________30\n	185 -- 191	31 -- 37	-15.8488 kcal/mol	1.87568 kcal/mol	0.774822 kcal/mol	182 192@LB@ \| \|@LB@5'-AAC...CAAAA ACUUU...UGC-3'@LB@ GAUAGGGGG@LB@ \|\|\|\|\|:\|\|\|@LB@ CUAUCUCCC@LB@3'-UUU...CUAGA CAACC...AUA-5'@LB@ \| \|@LB@ 40 30@LB@@LB@@LB@Energy -13.20 kcal/mol@LB@Hybridization Energy -15.8488 kcal/mol@LB@Unfolding Energy - mRNA 1.87568 kcal/mol@LB@Unfolding Energy - sRNA 0.774822 kcal/mol@LB@@LB@Position - mRNA 183 -- 191@LB@Position - sRNA 31 -- 39@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 31 -- 37@LB@
53	0.002724	0.1697	bsu06970	yesO	-13.13	0.067695	188 -- 199	26 -- 36	ABC transporter substrate-binding protein	_____________187__________200\n_____________\|____________\|\n5'-CGA...AUUAA_______A____UUUGA...UUA-3'\n______________AGGGGGG_UUGG\n______________\|\|:\|\|\|\|_\|\|\|\|\n______________UCUCCCC_AACC\n3'-UUU...GACUA____________CCUUG...AUA-5'\n_____________\|____________\|\n_____________37___________25\n	188 -- 194	30 -- 36	-17.5942 kcal/mol	4.33325 kcal/mol	0.135623 kcal/mol	187 200@LB@ \| \|@LB@5'-CGA...AUUAA A UUUGA...UUA-3'@LB@ AGGGGGG UUGG@LB@ \|\|:\|\|\|\| \|\|\|\|@LB@ UCUCCCC AACC@LB@3'-UUU...GACUA CCUUG...AUA-5'@LB@ \| \|@LB@ 37 25@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -17.5942 kcal/mol@LB@Unfolding Energy - mRNA 4.33325 kcal/mol@LB@Unfolding Energy - sRNA 0.135623 kcal/mol@LB@@LB@Position - mRNA 188 -- 199@LB@Position - sRNA 26 -- 36@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 30 -- 36@LB@
128	0.01143	0.2883	bsu29690	acuA	-15.81	0.020690	248 -- 269	30 -- 52	acetoin utilization protein AcuA	_____________247_____________________270\n_____________\|_______________________\|\n5'-UAU...GCAAC___C____UA_________A___CCUGU...AUG-3'\n______________CGG_UCUU___CUGAUAGA_GGG\n______________\|\|\|_\|\|\|\|___\|\|\|\|\|\|\|\|_\|\|\|\n______________GCC_AGAA___GACUAUCU_CCC\n3'-UUU...AAAAA___U____CUA________C___AACCC...AUA-5'\n_____________\|_______________________\|\n_____________53______________________29\n	259 -- 265	34 -- 40	-22.8929 kcal/mol	6.10629 kcal/mol	0.979974 kcal/mol	247 270@LB@ \| \|@LB@5'-UAU...GCAAC C UA A CCUGU...AUG-3'@LB@ CGG UCUU CUGAUAGA GGG@LB@ \|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ GCC AGAA GACUAUCU CCC@LB@3'-UUU...AAAAA U CUA C AACCC...AUA-5'@LB@ \| \|@LB@ 53 29@LB@@LB@@LB@Energy -15.81 kcal/mol@LB@Hybridization Energy -22.8929 kcal/mol@LB@Unfolding Energy - mRNA 6.10629 kcal/mol@LB@Unfolding Energy - sRNA 0.979974 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 30 -- 52@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 34 -- 40@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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