Input and runtime details for job 7743500 (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 7743500 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:35:00 CET 2018
	CopraRNA Started		@ Fri Feb 16 21:27:12 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 06:56:30 CET 2018
	Post-Processing Finished		@ Sat Feb 17 06:56:38 CET 2018
	Job Completed		@ Sat Feb 17 06:57:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7743500&toolName=CopraRNA ( 30 days expiry )

Description of the job

PrrF1

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_002516 Pseudomonas aeruginosa PAO1

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
165	0.004162	0.1159	pa1850	N/A	-12.78	0.041348	242 -- 255	104 -- 117	transcriptional regulator		_____________241____________256\n_____________\|______________\|\n5'-AUA...CCCGA______G_______ACGUG...AAC-3'\n______________CGUGAU_AGCCUGG\n______________\|\|\|\|\|\|_\|\|\|\|\|\|:\n______________GCACUA_UCGGACU\n3'-UUU...UUUUG______A_______ACUCC...GUU-5'\n_____________\|______________\|\n_____________118____________103\n	249 -- 255	104 -- 110	-19.8167 kcal/mol	4.81117 kcal/mol	2.2292 kcal/mol	241 256@LB@ \| \|@LB@5'-AUA...CCCGA G ACGUG...AAC-3'@LB@ CGUGAU AGCCUGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|:@LB@ GCACUA UCGGACU@LB@3'-UUU...UUUUG A ACUCC...GUU-5'@LB@ \| \|@LB@ 118 103@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -19.8167 kcal/mol@LB@Unfolding Energy - mRNA 4.81117 kcal/mol@LB@Unfolding Energy - sRNA 2.2292 kcal/mol@LB@@LB@Position - mRNA 242 -- 255@LB@Position - sRNA 104 -- 117@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 104 -- 110@LB@
102	0.001679	0.07499	pa2657	N/A	-10.65	0.130856	243 -- 261	104 -- 121	two-component response regulator		_____________242_________________262\n_____________\|___________________\|\n5'-GGU...CCGAC______A___CC_______CCCGC...GCC-3'\n______________GAACUG_UGG__AGCCUGA\n______________:\|\|\|:\|_\|\|:__\|\|\|\|\|\|\|\n______________UUUGGC_ACU__UCGGACU\n3'-UUU...CAGUU__________AA_______ACUCC...GUU-5'\n_____________\|___________________\|\n_____________122_________________103\n	255 -- 261	104 -- 110	-18.2987 kcal/mol	5.4095 kcal/mol	2.24203 kcal/mol	242 262@LB@ \| \|@LB@5'-GGU...CCGAC A CC CCCGC...GCC-3'@LB@ GAACUG UGG AGCCUGA@LB@ :\|\|\|:\| \|\|: \|\|\|\|\|\|\|@LB@ UUUGGC ACU UCGGACU@LB@3'-UUU...CAGUU AA ACUCC...GUU-5'@LB@ \| \|@LB@ 122 103@LB@@LB@@LB@Energy -10.65 kcal/mol@LB@Hybridization Energy -18.2987 kcal/mol@LB@Unfolding Energy - mRNA 5.4095 kcal/mol@LB@Unfolding Energy - sRNA 2.24203 kcal/mol@LB@@LB@Position - mRNA 243 -- 261@LB@Position - sRNA 104 -- 121@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 104 -- 110@LB@
108	0.001802	0.07562	pa0365	N/A	-14.54	0.013920	243 -- 252	101 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________242________253\n_____________\|__________\|\n5'-GCC...GACGC__________AAGUC...CCG-3'\n______________AGCCUGAUGA\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	246 -- 252	101 -- 107	-17.5523 kcal/mol	0.900236 kcal/mol	2.11196 kcal/mol	242 253@LB@ \| \|@LB@5'-GCC...GACGC AAGUC...CCG-3'@LB@ AGCCUGAUGA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -14.54 kcal/mol@LB@Hybridization Energy -17.5523 kcal/mol@LB@Unfolding Energy - mRNA 0.900236 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 243 -- 252@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 101 -- 107@LB@
8	1.007e-05	0.004211	pa3621	fdxA	-18.47	0.000724	244 -- 255	71 -- 82	ferredoxin I		_____________243__________256\n_____________\|____________\|\n5'-CCU...AUACA____________AAGUC...UGG-3'\n______________CCGACUGCGUGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUGACGCACC\n3'-UUU...UCUCA____________CAGAG...GUU-5'\n_____________\|____________\|\n_____________83___________70\n	249 -- 255	71 -- 77	-26.3412 kcal/mol	3.76302 kcal/mol	4.10469 kcal/mol	243 256@LB@ \| \|@LB@5'-CCU...AUACA AAGUC...UGG-3'@LB@ CCGACUGCGUGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUGACGCACC@LB@3'-UUU...UCUCA CAGAG...GUU-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -26.3412 kcal/mol@LB@Unfolding Energy - mRNA 3.76302 kcal/mol@LB@Unfolding Energy - sRNA 4.10469 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 71 -- 77@LB@
103	0.001681	0.07499	pa3587	metR	-12.26	0.055812	244 -- 261	101 -- 121	transcriptional regulator MetR		_____________243___________________262\n_____________\|_____________________\|\n5'-CAG...GCGCG______AC_____________AAGCC...UGU-3'\n______________AAGCCG_____AGCCUGGUGG\n______________\|\|:\|\|\|_____\|\|\|\|\|\|:\|\|:\n______________UUUGGC_____UCGGACUACU\n3'-UUU...CAGUU______ACUAA__________CCUCU...GUU-5'\n_____________\|_____________________\|\n_____________122___________________100\n	255 -- 261	101 -- 107	-20.5431 kcal/mol	6.04584 kcal/mol	2.24386 kcal/mol	243 262@LB@ \| \|@LB@5'-CAG...GCGCG AC AAGCC...UGU-3'@LB@ AAGCCG AGCCUGGUGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|:\|\|:@LB@ UUUGGC UCGGACUACU@LB@3'-UUU...CAGUU ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 122 100@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -20.5431 kcal/mol@LB@Unfolding Energy - mRNA 6.04584 kcal/mol@LB@Unfolding Energy - sRNA 2.24386 kcal/mol@LB@@LB@Position - mRNA 244 -- 261@LB@Position - sRNA 101 -- 121@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 101 -- 107@LB@
152	0.003562	0.1073	pa3096	xcpY	-9.37	0.238148	248 -- 259	98 -- 110	type II secretion system protein L		_____________247___________260\n_____________\|_____________\|\n5'-ACC...GCGGG_____________ACUGG...GCG-3'\n______________GGCC_GAUGGGGA\n______________:\|\|\|_\|\|\|\|:\|\|\|\n______________UCGG_CUACUCCU\n3'-UUU...ACUAA____A________CUAUU...GUU-5'\n_____________\|_____________\|\n_____________111___________97\n	253 -- 259	98 -- 104	-17.5774 kcal/mol	6.04509 kcal/mol	2.16105 kcal/mol	247 260@LB@ \| \|@LB@5'-ACC...GCGGG ACUGG...GCG-3'@LB@ GGCC GAUGGGGA@LB@ :\|\|\| \|\|\|\|:\|\|\|@LB@ UCGG CUACUCCU@LB@3'-UUU...ACUAA A CUAUU...GUU-5'@LB@ \| \|@LB@ 111 97@LB@@LB@@LB@Energy -9.37 kcal/mol@LB@Hybridization Energy -17.5774 kcal/mol@LB@Unfolding Energy - mRNA 6.04509 kcal/mol@LB@Unfolding Energy - sRNA 2.16105 kcal/mol@LB@@LB@Position - mRNA 248 -- 259@LB@Position - sRNA 98 -- 110@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 98 -- 104@LB@
92	0.001266	0.06327	pa1307	N/A	-13.15	0.033214	250 -- 278	41 -- 65	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________249___________________________279\n_____________\|_____________________________\|\n5'-UGC...CGUCU_______C_____A_____GCAG______GGCGG...GCG-3'\n______________UCAGCUU_ACCGG_CUGAU____CGCGGC\n______________\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|\|\|\|____\|\|\|\|:\|\n______________AGUCGAA_UGGCC_GACUA____GCGCUG\n3'-UUU...CAGAG___________________GA________GUCAA...GUU-5'\n_____________\|_____________________________\|\n_____________66____________________________40\n	250 -- 256	59 -- 65	-34.6223 kcal/mol	8.37343 kcal/mol	13.1048 kcal/mol	249 279@LB@ \| \|@LB@5'-UGC...CGUCU C A GCAG GGCGG...GCG-3'@LB@ UCAGCUU ACCGG CUGAU CGCGGC@LB@ \|\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|@LB@ AGUCGAA UGGCC GACUA GCGCUG@LB@3'-UUU...CAGAG GA GUCAA...GUU-5'@LB@ \| \|@LB@ 66 40@LB@@LB@@LB@Energy -13.15 kcal/mol@LB@Hybridization Energy -34.6223 kcal/mol@LB@Unfolding Energy - mRNA 8.37343 kcal/mol@LB@Unfolding Energy - sRNA 13.1048 kcal/mol@LB@@LB@Position - mRNA 250 -- 278@LB@Position - sRNA 41 -- 65@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 59 -- 65@LB@
174	0.00444	0.1171	pa4756	carB	-14.46	0.014655	252 -- 264	107 -- 119	carbamoyl phosphate synthase large subunit		_____________251___________265\n_____________\|_____________\|\n5'-GGU...GCCCC_____________AGGCC...CCU-3'\n______________AUCGUGAUUGGCC\n______________\|:\|\|\|\|\|\|\|:\|\|\|\n______________UGGCACUAAUCGG\n3'-UUU...GUUUU_____________ACUAC...GUU-5'\n_____________\|_____________\|\n_____________120___________106\n	258 -- 264	107 -- 113	-20.5807 kcal/mol	3.88907 kcal/mol	2.23484 kcal/mol	251 265@LB@ \| \|@LB@5'-GGU...GCCCC AGGCC...CCU-3'@LB@ AUCGUGAUUGGCC@LB@ \|:\|\|\|\|\|\|\|:\|\|\|@LB@ UGGCACUAAUCGG@LB@3'-UUU...GUUUU ACUAC...GUU-5'@LB@ \| \|@LB@ 120 106@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -20.5807 kcal/mol@LB@Unfolding Energy - mRNA 3.88907 kcal/mol@LB@Unfolding Energy - sRNA 2.23484 kcal/mol@LB@@LB@Position - mRNA 252 -- 264@LB@Position - sRNA 107 -- 119@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 107 -- 113@LB@
9	1.098e-05	0.004211	pa0119	N/A	-18.72	0.000584	256 -- 296	78 -- 118	C4-dicarboxylate transporter DctA	pa5479 pa1183	_____________255________________________________________297\n_____________\|__________________________________________\|\n5'-GCC...GCAAG__________________UA__C________C__________AUUC-3'\n______________UCGUGAUUGGCCUGGUGA__GG_GUGAUCUG_GGGGU_CGGC\n______________:\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|__:\|_:\|:\|\|\|\|\|_:\|:\|\|_\|\|:\|\n______________GGCACUAAUCGGACUACU__UC_UAUUAGAC_UCUCA_GCUG\n3'-UUU...UUUUU__________________CC___________U_____G____ACGCA...GUU-5'\n_____________\|__________________________________________\|\n_____________119________________________________________77\n	267 -- 273	101 -- 107	-51.6638 kcal/mol	20.8263 kcal/mol	12.1236 kcal/mol	255 297@LB@ \| \|@LB@5'-GCC...GCAAG UA C C AUUC-3'@LB@ UCGUGAUUGGCCUGGUGA GG GUGAUCUG GGGGU CGGC@LB@ :\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|\| :\| :\|:\|\|\|\|\| :\|:\|\| \|\|:\|@LB@ GGCACUAAUCGGACUACU UC UAUUAGAC UCUCA GCUG@LB@3'-UUU...UUUUU CC U G ACGCA...GUU-5'@LB@ \| \|@LB@ 119 77@LB@@LB@@LB@Energy -18.72 kcal/mol@LB@Hybridization Energy -51.6638 kcal/mol@LB@Unfolding Energy - mRNA 20.8263 kcal/mol@LB@Unfolding Energy - sRNA 12.1236 kcal/mol@LB@@LB@Position - mRNA 256 -- 296@LB@Position - sRNA 78 -- 118@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 101 -- 107@LB@
113	0.001932	0.07857	pa1964	N/A	-9.53	0.221537	258 -- 274	103 -- 120	ABC-F family ATPase		_____________257________________275\n_____________\|__________________\|\n5'-GCA...ACGGC_____CUAC_________CGGCG...CGA-3'\n______________AACCG_____GGCCUGAU\n______________\|\|\|\|\|_____:\|\|\|\|\|\|\|\n______________UUGGC_____UCGGACUA\n3'-UUU...AGUUU_____ACUAA________CUCCU...GUU-5'\n_____________\|__________________\|\n_____________121________________102\n	268 -- 274	103 -- 109	-16.8873 kcal/mol	5.11311 kcal/mol	2.24268 kcal/mol	257 275@LB@ \| \|@LB@5'-GCA...ACGGC CUAC CGGCG...CGA-3'@LB@ AACCG GGCCUGAU@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|@LB@ UUGGC UCGGACUA@LB@3'-UUU...AGUUU ACUAA CUCCU...GUU-5'@LB@ \| \|@LB@ 121 102@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -16.8873 kcal/mol@LB@Unfolding Energy - mRNA 5.11311 kcal/mol@LB@Unfolding Energy - sRNA 2.24268 kcal/mol@LB@@LB@Position - mRNA 258 -- 274@LB@Position - sRNA 103 -- 120@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 103 -- 109@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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