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	Additional homologs
176	0.01673	0.3152	bsu08790	thiC	-9.56	0.245346	273 -- 280	31 -- 38	phosphomethylpyrimidine synthase		_____________272______281\n_____________\|________\|\n5'-GGC...UAUAC________UUCUU...AAG-3'\n______________GUGGAGGG\n______________:\|:\|\|\|\|\|\n______________UAUCUCCC\n3'-UUU...UAGAC________CAACC...AUA-5'\n_____________\|________\|\n_____________39_______30\n	274 -- 280	31 -- 37	-12.4867 kcal/mol	2.26991 kcal/mol	0.65488 kcal/mol	272 281@LB@ \| \|@LB@5'-GGC...UAUAC UUCUU...AAG-3'@LB@ GUGGAGGG@LB@ :\|:\|\|\|\|\|@LB@ UAUCUCCC@LB@3'-UUU...UAGAC CAACC...AUA-5'@LB@ \| \|@LB@ 39 30@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -12.4867 kcal/mol@LB@Unfolding Energy - mRNA 2.26991 kcal/mol@LB@Unfolding Energy - sRNA 0.65488 kcal/mol@LB@@LB@Position - mRNA 273 -- 280@LB@Position - sRNA 31 -- 38@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 31 -- 37@LB@
9	8.212e-05	0.03044	bsu07800	treP	-22.21	0.000470	182 -- 210	21 -- 52	PTS system-trehalose-specific transporter subunit EIIBC		_____________181____________________________________211\n_____________\|______________________________________\|\n5'-UUA...AAAAA_____AC__________________GGCAUG_______UGAAC...UUG-3'\n______________CGGAU___________GGAGGGGUU______GGGGAAC\n______________\|\|\|\|\|___________:\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GCCUA___________UCUCCCCAA______CCCCUUG\n3'-UUU...AAAAA_____GAACUAGACUA______________________UCUCU...AUA-5'\n_____________\|______________________________________\|\n_____________53_____________________________________20\n	204 -- 210	21 -- 27	-29.9746 kcal/mol	4.99416 kcal/mol	2.77037 kcal/mol	181 211@LB@ \| \|@LB@5'-UUA...AAAAA AC GGCAUG UGAAC...UUG-3'@LB@ CGGAU GGAGGGGUU GGGGAAC@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ GCCUA UCUCCCCAA CCCCUUG@LB@3'-UUU...AAAAA GAACUAGACUA UCUCU...AUA-5'@LB@ \| \|@LB@ 53 20@LB@@LB@@LB@Energy -22.21 kcal/mol@LB@Hybridization Energy -29.9746 kcal/mol@LB@Unfolding Energy - mRNA 4.99416 kcal/mol@LB@Unfolding Energy - sRNA 2.77037 kcal/mol@LB@@LB@Position - mRNA 182 -- 210@LB@Position - sRNA 21 -- 52@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 21 -- 27@LB@
46	0.002102	0.1496	bsu35160	uvrA	-18.29	0.005742	210 -- 232	21 -- 44	UvrABC system protein A		_____________209______________________233\n_____________\|________________________\|\n5'-CAC...CUAUG____G________UGAA_______CAGGG...GUU-3'\n______________GAUC_GAUAGAGG_____GGGAGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|_____\|\|\|\|:\|\n______________CUAG_CUAUCUCC_____CCCUUG\n3'-UUU...UAGAA____A________CCAAC______UCUCU...AUA-5'\n_____________\|________________________\|\n_____________45_______________________20\n	216 -- 222	32 -- 38	-26.4443 kcal/mol	5.3846 kcal/mol	2.7671 kcal/mol	209 233@LB@ \| \|@LB@5'-CAC...CUAUG G UGAA CAGGG...GUU-3'@LB@ GAUC GAUAGAGG GGGAGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|:\|@LB@ CUAG CUAUCUCC CCCUUG@LB@3'-UUU...UAGAA A CCAAC UCUCU...AUA-5'@LB@ \| \|@LB@ 45 20@LB@@LB@@LB@Energy -18.29 kcal/mol@LB@Hybridization Energy -26.4443 kcal/mol@LB@Unfolding Energy - mRNA 5.3846 kcal/mol@LB@Unfolding Energy - sRNA 2.7671 kcal/mol@LB@@LB@Position - mRNA 210 -- 232@LB@Position - sRNA 21 -- 44@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 32 -- 38@LB@
107	0.009163	0.2778	bsu12780	xepA	-15.86	0.020153	79 -- 99	29 -- 48	phage-like element PBSX protein XepA		_____________78____________________100\n_____________\|_____________________\|\n5'-UUG...UCAAU__AG_______C______U__GAACA...UUU-3'\n______________UC__GAUCUGG_AGAGGG_GU\n______________\|\|__\|\|\|\|\|\|:_\|\|\|\|\|\|_\|\|\n______________AG__CUAGACU_UCUCCC_CA\n3'-UUU...AGCCU__AA_______A_________ACCCC...AUA-5'\n_____________\|_____________________\|\n_____________49____________________28\n	83 -- 89	38 -- 44	-22.9588 kcal/mol	6.12286 kcal/mol	0.974361 kcal/mol	78 100@LB@ \| \|@LB@5'-UUG...UCAAU AG C U GAACA...UUU-3'@LB@ UC GAUCUGG AGAGGG GU@LB@ \|\| \|\|\|\|\|\|: \|\|\|\|\|\| \|\|@LB@ AG CUAGACU UCUCCC CA@LB@3'-UUU...AGCCU AA A ACCCC...AUA-5'@LB@ \| \|@LB@ 49 28@LB@@LB@@LB@Energy -15.86 kcal/mol@LB@Hybridization Energy -22.9588 kcal/mol@LB@Unfolding Energy - mRNA 6.12286 kcal/mol@LB@Unfolding Energy - sRNA 0.974361 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 29 -- 48@LB@Position Seed - mRNA 83 -- 89@LB@Position Seed - sRNA 38 -- 44@LB@
189	0.01911	0.3269	bsu24290	xseB	-12.91	0.073825	187 -- 193	30 -- 36	exodeoxyribonuclease 7 small subunit		_____________186_____194\n_____________\|_______\|\n5'-CAU...AAAAG_______AAGAA...UAG-3'\n______________AGAGGGG\n______________\|\|\|\|\|\|\|\n______________UCUCCCC\n3'-UUU...GACUA_______AACCC...AUA-5'\n_____________\|_______\|\n_____________37______29\n	187 -- 193	30 -- 36	-14.0184 kcal/mol	0.973532 kcal/mol	0.133643 kcal/mol	186 194@LB@ \| \|@LB@5'-CAU...AAAAG AAGAA...UAG-3'@LB@ AGAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UCUCCCC@LB@3'-UUU...GACUA AACCC...AUA-5'@LB@ \| \|@LB@ 37 29@LB@@LB@@LB@Energy -12.91 kcal/mol@LB@Hybridization Energy -14.0184 kcal/mol@LB@Unfolding Energy - mRNA 0.973532 kcal/mol@LB@Unfolding Energy - sRNA 0.133643 kcal/mol@LB@@LB@Position - mRNA 187 -- 193@LB@Position - sRNA 30 -- 36@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 30 -- 36@LB@
71	0.005061	0.2378	bsu02170	ybfB	-12.87	0.075045	244 -- 269	24 -- 48	MFS transporter	bsu03530	_____________243__________________________270\n_____________\|____________________________\|\n5'-CUU...CACCU_____________UU__C____CA____GUGCG...AGC-3'\n______________UUUUGAUCU__UA__GG_GGUU__GGGG\n______________\|:\|\|\|\|\|\|\|__\|\|__\|\|_\|\|\|\|__\|\|\|\|\n______________AGAACUAGA__AU__CC_CCAA__CCCC\n3'-UUU...AGCCU_________CU__CU_____________UUGUC...AUA-5'\n_____________\|____________________________\|\n_____________49___________________________23\n	246 -- 252	40 -- 46	-21.3597 kcal/mol	7.5105 kcal/mol	0.978761 kcal/mol	243 270@LB@ \| \|@LB@5'-CUU...CACCU UU C CA GUGCG...AGC-3'@LB@ UUUUGAUCU UA GG GGUU GGGG@LB@ \|:\|\|\|\|\|\|\| \|\| \|\| \|\|\|\| \|\|\|\|@LB@ AGAACUAGA AU CC CCAA CCCC@LB@3'-UUU...AGCCU CU CU UUGUC...AUA-5'@LB@ \| \|@LB@ 49 23@LB@@LB@@LB@Energy -12.87 kcal/mol@LB@Hybridization Energy -21.3597 kcal/mol@LB@Unfolding Energy - mRNA 7.5105 kcal/mol@LB@Unfolding Energy - sRNA 0.978761 kcal/mol@LB@@LB@Position - mRNA 244 -- 269@LB@Position - sRNA 24 -- 48@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 40 -- 46@LB@
131	0.01151	0.2883	bsu03110	ycgH	-12.02	0.104581	161 -- 192	27 -- 50	transporter		_____________160______________________________193\n_____________\|________________________________\|\n5'-UUU...GGACA____ACA____AACCUUA____AA________AAUAA...UCG-3'\n______________GAUC___AUCU_______GAUA__AGGGGUUG\n______________\|\|\|\|___\|\|\|\|_______\|\|\|\|__\|\|\|\|\|\|\|\|\n______________CUAG___UAGA_______CUAU__UCCCCAAC\n3'-UUU...AAAGC____AAC_______________C_________CCCUU...AUA-5'\n_____________\|________________________________\|\n_____________51_______________________________26\n	186 -- 192	27 -- 33	-20.341 kcal/mol	7.34553 kcal/mol	0.975523 kcal/mol	160 193@LB@ \| \|@LB@5'-UUU...GGACA ACA AACCUUA AA AAUAA...UCG-3'@LB@ GAUC AUCU GAUA AGGGGUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\|@LB@ CUAG UAGA CUAU UCCCCAAC@LB@3'-UUU...AAAGC AAC C CCCUU...AUA-5'@LB@ \| \|@LB@ 51 26@LB@@LB@@LB@Energy -12.02 kcal/mol@LB@Hybridization Energy -20.341 kcal/mol@LB@Unfolding Energy - mRNA 7.34553 kcal/mol@LB@Unfolding Energy - sRNA 0.975523 kcal/mol@LB@@LB@Position - mRNA 161 -- 192@LB@Position - sRNA 27 -- 50@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 27 -- 33@LB@
105	0.009074	0.2778	bsu03220	ycgO	-6.59	0.539508	105 -- 111	67 -- 73	symporter		_____________104_____112\n_____________\|_______\|\n5'-GAA...CCUGC_______UCCAU...GUG-3'\n______________GGGGGUG\n______________\|\|\|\|\|\|:\n______________CCCCCAU\n3'-UUU...AACCG_______CGCGG...AUA-5'\n_____________\|_______\|\n_____________74______66\n	105 -- 111	67 -- 73	-12.2711 kcal/mol	3.65196 kcal/mol	2.02624 kcal/mol	104 112@LB@ \| \|@LB@5'-GAA...CCUGC UCCAU...GUG-3'@LB@ GGGGGUG@LB@ \|\|\|\|\|\|:@LB@ CCCCCAU@LB@3'-UUU...AACCG CGCGG...AUA-5'@LB@ \| \|@LB@ 74 66@LB@@LB@@LB@Energy -6.59 kcal/mol@LB@Hybridization Energy -12.2711 kcal/mol@LB@Unfolding Energy - mRNA 3.65196 kcal/mol@LB@Unfolding Energy - sRNA 2.02624 kcal/mol@LB@@LB@Position - mRNA 105 -- 111@LB@Position - sRNA 67 -- 73@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 67 -- 73@LB@
36	0.001585	0.1432	bsu03680	yclG	-9.13	0.280303	226 -- 251	29 -- 52	'Evidence 3: Function proposed based on presence of conserved amino acid motif structural feature or limited homology; Product type pe: enzyme'		_____________225________________________252\n_____________\|__________________________\|\n5'-UCA...UGCAG_______C___G_UCC_____AU___AAAAC...UUU-3'\n______________CGGAUUU_GGU_U___UAGAG__GGU\n______________\|\|\|\|\|:\|_\|:\|_\|___\|\|\|\|\|__\|\|\|\n______________GCCUAGA_CUA_A___AUCUC__CCA\n3'-UUU...AAAAA_______A___G_CU______C____ACCCC...AUA-5'\n_____________\|__________________________\|\n_____________53_________________________28\n	226 -- 232	46 -- 52	-18.2294 kcal/mol	8.1219 kcal/mol	0.980233 kcal/mol	225 252@LB@ \| \|@LB@5'-UCA...UGCAG C G UCC AU AAAAC...UUU-3'@LB@ CGGAUUU GGU U UAGAG GGU@LB@ \|\|\|\|\|:\| \|:\| \| \|\|\|\|\| \|\|\|@LB@ GCCUAGA CUA A AUCUC CCA@LB@3'-UUU...AAAAA A G CU C ACCCC...AUA-5'@LB@ \| \|@LB@ 53 28@LB@@LB@@LB@Energy -9.13 kcal/mol@LB@Hybridization Energy -18.2294 kcal/mol@LB@Unfolding Energy - mRNA 8.1219 kcal/mol@LB@Unfolding Energy - sRNA 0.980233 kcal/mol@LB@@LB@Position - mRNA 226 -- 251@LB@Position - sRNA 29 -- 52@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 46 -- 52@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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