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
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@
38	0.001645	0.1432	bsu19540	yodB	-7.66	0.420262	259 -- 271	37 -- 51	ArsR family transcriptional regulator	_____________258_____________272\n_____________\|_______________\|\n5'-GAG...ACGAU___AC__________CAUCC...AAC-3'\n______________GGA____GGUCUGAU\n______________\|\|\|____\|:\|\|\|\|\|\|\n______________CCU____CUAGACUA\n3'-UUU...AAAAG___AGAA________UCUCC...AUA-5'\n_____________\|_______________\|\n_____________52______________36\n	265 -- 271	37 -- 43	-11.6813 kcal/mol	3.05786 kcal/mol	0.959935 kcal/mol	258 272@LB@ \| \|@LB@5'-GAG...ACGAU AC CAUCC...AAC-3'@LB@ GGA GGUCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|@LB@ CCU CUAGACUA@LB@3'-UUU...AAAAG AGAA UCUCC...AUA-5'@LB@ \| \|@LB@ 52 36@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -11.6813 kcal/mol@LB@Unfolding Energy - mRNA 3.05786 kcal/mol@LB@Unfolding Energy - sRNA 0.959935 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 37 -- 51@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 37 -- 43@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@
149	0.01325	0.2966	bsu07610	citM	-7.43	0.445360	149 -- 162	15 -- 27	Mg(2+)/citrate complex secondary transporter	_____________148____________163\n_____________\|______________\|\n5'-AUU...AAAAA_______A______AAAAA...UUG-3'\n______________GGGGAGU_AGGGAG\n______________\|\|\|\|\|::_\|\|:\|\|\|\n______________CCCCUUG_UCUCUC\n3'-UUU...CCCAA______________AUCGA...AUA-5'\n_____________\|______________\|\n_____________28_____________14\n	149 -- 155	21 -- 27	-17.4184 kcal/mol	3.9771 kcal/mol	6.01129 kcal/mol	148 163@LB@ \| \|@LB@5'-AUU...AAAAA A AAAAA...UUG-3'@LB@ GGGGAGU AGGGAG@LB@ \|\|\|\|\|:: \|\|:\|\|\|@LB@ CCCCUUG UCUCUC@LB@3'-UUU...CCCAA AUCGA...AUA-5'@LB@ \| \|@LB@ 28 14@LB@@LB@@LB@Energy -7.43 kcal/mol@LB@Hybridization Energy -17.4184 kcal/mol@LB@Unfolding Energy - mRNA 3.9771 kcal/mol@LB@Unfolding Energy - sRNA 6.01129 kcal/mol@LB@@LB@Position - mRNA 149 -- 162@LB@Position - sRNA 15 -- 27@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 21 -- 27@LB@
69	0.004753	0.2298	bsu24850	glcK	-6.97	0.496286	33 -- 46	15 -- 29	glucokinase	_____________32______________47\n_____________\|_______________\|\n5'-GCU...UUAUU____A__________CUUGA...UUC-3'\n______________UUGG__GACAGAGAG\n______________\|\|\|\|__:\|\|\|\|\|\|\|\|\n______________AACC__UUGUCUCUC\n3'-UUU...UCCCC____CC_________AUCGA...AUA-5'\n_____________\|_______________\|\n_____________30______________14\n	40 -- 46	15 -- 21	-16.6304 kcal/mol	3.64593 kcal/mol	6.01316 kcal/mol	32 47@LB@ \| \|@LB@5'-GCU...UUAUU A CUUGA...UUC-3'@LB@ UUGG GACAGAGAG@LB@ \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ AACC UUGUCUCUC@LB@3'-UUU...UCCCC CC AUCGA...AUA-5'@LB@ \| \|@LB@ 30 14@LB@@LB@@LB@Energy -6.97 kcal/mol@LB@Hybridization Energy -16.6304 kcal/mol@LB@Unfolding Energy - mRNA 3.64593 kcal/mol@LB@Unfolding Energy - sRNA 6.01316 kcal/mol@LB@@LB@Position - mRNA 33 -- 46@LB@Position - sRNA 15 -- 29@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 15 -- 21@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@
140	0.01224	0.2883	bsu36480	ywoD	-6.33	0.569704	31 -- 37	66 -- 72	MFS transporter	_____________30______38\n_____________\|_______\|\n5'-AUU...AUAUC_______AAAGC...AUA-3'\n______________GGGGUGG\n______________\|\|\|\|\|:\|\n______________CCCCAUC\n3'-UUU...ACCGC_______GCGGU...AUA-5'\n_____________\|_______\|\n_____________73______65\n	31 -- 37	66 -- 72	-11.1749 kcal/mol	4.83937 kcal/mol	0.00366414 kcal/mol	30 38@LB@ \| \|@LB@5'-AUU...AUAUC AAAGC...AUA-3'@LB@ GGGGUGG@LB@ \|\|\|\|\|:\|@LB@ CCCCAUC@LB@3'-UUU...ACCGC GCGGU...AUA-5'@LB@ \| \|@LB@ 73 65@LB@@LB@@LB@Energy -6.33 kcal/mol@LB@Hybridization Energy -11.1749 kcal/mol@LB@Unfolding Energy - mRNA 4.83937 kcal/mol@LB@Unfolding Energy - sRNA 0.00366414 kcal/mol@LB@@LB@Position - mRNA 31 -- 37@LB@Position - sRNA 66 -- 72@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 66 -- 72@LB@
110	0.009311	0.2778	bsu18230	yngG	-6.09	0.597733	269 -- 285	32 -- 53	hydroxymethylglutaryl-CoA lyase YngG	_____________268____________________286\n_____________\|______________________\|\n5'-AAA...CCCGU_______GCAAC__________AUAAA...GGA-3'\n______________UUGGAUC__________AGAGG\n______________\|:\|\|\|\|\|__________\|\|\|\|\|\n______________AGCCUAG__________UCUCC\n3'-UUU...AAAAA_______AACUAGACUA_____CCAAC...AUA-5'\n_____________\|______________________\|\n_____________54_____________________31\n	269 -- 275	47 -- 53	-12.5955 kcal/mol	5.52332 kcal/mol	0.981755 kcal/mol	268 286@LB@ \| \|@LB@5'-AAA...CCCGU GCAAC AUAAA...GGA-3'@LB@ UUGGAUC AGAGG@LB@ \|:\|\|\|\|\| \|\|\|\|\|@LB@ AGCCUAG UCUCC@LB@3'-UUU...AAAAA AACUAGACUA CCAAC...AUA-5'@LB@ \| \|@LB@ 54 31@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -12.5955 kcal/mol@LB@Unfolding Energy - mRNA 5.52332 kcal/mol@LB@Unfolding Energy - sRNA 0.981755 kcal/mol@LB@@LB@Position - mRNA 269 -- 285@LB@Position - sRNA 32 -- 53@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 47 -- 53@LB@
93	0.007837	0.2778	bsu33430	yvgQ	-5.79	0.632053	172 -- 180	38 -- 46	sulfite reductase [NADPH] hemoprotein beta-component	_____________171_______181\n_____________\|_________\|\n5'-GCU...GUAUA_________CUUGA...UGA-3'\n______________UUGAUUUGA\n______________\|\|\|\|\|:\|\|\|\n______________AACUAGACU\n3'-UUU...CCUAG_________AUCUC...AUA-5'\n_____________\|_________\|\n_____________47________37\n	174 -- 180	38 -- 44	-9.05403 kcal/mol	2.31378 kcal/mol	0.946105 kcal/mol	171 181@LB@ \| \|@LB@5'-GCU...GUAUA CUUGA...UGA-3'@LB@ UUGAUUUGA@LB@ \|\|\|\|\|:\|\|\|@LB@ AACUAGACU@LB@3'-UUU...CCUAG AUCUC...AUA-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -5.79 kcal/mol@LB@Hybridization Energy -9.05403 kcal/mol@LB@Unfolding Energy - mRNA 2.31378 kcal/mol@LB@Unfolding Energy - sRNA 0.946105 kcal/mol@LB@@LB@Position - mRNA 172 -- 180@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 38 -- 44@LB@
22	0.0004167	0.06318	bsu07570	yflS	-5.44	0.672400	163 -- 208	8 -- 27	malate transporter YflS	_____________162____________________________________________209\n_____________\|______________________________________________\|\n5'-AUG...GAAAA_____U____AAACAAGUAUAUAG___GAGACCUAUUUA_______AGAAA...CUC-3'\n______________GGGGA_CGGA______________GAG____________UGGCUUC\n______________\|\|\|\|\|_\|:\|\|______________\|\|\|____________\|:\|\|\|\|\|\n______________CCCCU_GUCU______________CUC____________AUCGAAG\n3'-UUU...CCCAA_____U________________________________________AGAGAUA-5'\n_____________\|______________________________________________\|\n_____________28_____________________________________________7\n	202 -- 208	8 -- 14	-21.2785 kcal/mol	9.2406 kcal/mol	6.59627 kcal/mol	162 209@LB@ \| \|@LB@5'-AUG...GAAAA U AAACAAGUAUAUAG GAGACCUAUUUA AGAAA...CUC-3'@LB@ GGGGA CGGA GAG UGGCUUC@LB@ \|\|\|\|\| \|:\|\| \|\|\| \|:\|\|\|\|\|@LB@ CCCCU GUCU CUC AUCGAAG@LB@3'-UUU...CCCAA U AGAGAUA-5'@LB@ \| \|@LB@ 28 7@LB@@LB@@LB@Energy -5.44 kcal/mol@LB@Hybridization Energy -21.2785 kcal/mol@LB@Unfolding Energy - mRNA 9.2406 kcal/mol@LB@Unfolding Energy - sRNA 6.59627 kcal/mol@LB@@LB@Position - mRNA 163 -- 208@LB@Position - sRNA 8 -- 27@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 8 -- 14@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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