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
151	0.003549	0.1073	pa4443	cysD	-8.92	0.288201	61 -- 67	74 -- 80	sulfate adenylyltransferase subunit 2		_____________60______68\n_____________\|_______\|\n5'-CUU...UCGCC_______AGGCU...ACU-3'\n______________GGCUGCG\n______________\|:\|\|\|\|\|\n______________CUGACGC\n3'-UUU...UCAGG_______ACCCA...GUU-5'\n_____________\|_______\|\n_____________81______73\n	61 -- 67	74 -- 80	-10.9675 kcal/mol	1.23954 kcal/mol	0.805988 kcal/mol	60 68@LB@ \| \|@LB@5'-CUU...UCGCC AGGCU...ACU-3'@LB@ GGCUGCG@LB@ \|:\|\|\|\|\|@LB@ CUGACGC@LB@3'-UUU...UCAGG ACCCA...GUU-5'@LB@ \| \|@LB@ 81 73@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -10.9675 kcal/mol@LB@Unfolding Energy - mRNA 1.23954 kcal/mol@LB@Unfolding Energy - sRNA 0.805988 kcal/mol@LB@@LB@Position - mRNA 61 -- 67@LB@Position - sRNA 74 -- 80@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 74 -- 80@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@
153	0.003576	0.1073	pa5013	ilvE	-11.20	0.098760	213 -- 229	103 -- 120	branched-chain amino acid aminotransferase		_____________212________________230\n_____________\|__________________\|\n5'-UCU...UGGCC_____________G____CUGGU...AUG-3'\n______________GAUCGUGAU_GGC_UGAU\n______________:\|:\|\|\|\|\|\|_:\|\|_\|\|\|\|\n______________UUGGCACUA_UCG_ACUA\n3'-UUU...AGUUU_________A___G____CUCCU...GUU-5'\n_____________\|__________________\|\n_____________121________________102\n	215 -- 221	112 -- 118	-19.7956 kcal/mol	6.35284 kcal/mol	2.24268 kcal/mol	212 230@LB@ \| \|@LB@5'-UCU...UGGCC G CUGGU...AUG-3'@LB@ GAUCGUGAU GGC UGAU@LB@ :\|:\|\|\|\|\|\| :\|\| \|\|\|\|@LB@ UUGGCACUA UCG ACUA@LB@3'-UUU...AGUUU A G CUCCU...GUU-5'@LB@ \| \|@LB@ 121 102@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.7956 kcal/mol@LB@Unfolding Energy - mRNA 6.35284 kcal/mol@LB@Unfolding Energy - sRNA 2.24268 kcal/mol@LB@@LB@Position - mRNA 213 -- 229@LB@Position - sRNA 103 -- 120@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 112 -- 118@LB@
154	0.003595	0.1073	pa3974	ladS	-15.87	0.005612	181 -- 233	43 -- 89	lost adherence sensor LadS		_____________180_________________________________________________________234\n_____________\|___________________________________________________________\|\n5'-CUU...CGUUC____________________CA__AUG_______________UUCUCUUUCU_______UUGCC...CCA-3'\n______________GAGGAG_C__ACUGCG_GGG__UC___CGGC__ACUGGCUGA__________UCUUGCG\n______________\|\|:\|\|\|_\|__\|\|\|\|\|\|_\|\|\|__\|\|___\|:\|\|__\|\|:\|\|\|\|\|\|__________\|\|\|:\|\|\|\n______________CUUCUC_G__UGACGC_CCC__AG___GUCG__UGGCCGACU__________AGAGCGC\n3'-UUU...UUAGA______A_GC______A___AG__A______AA__________________________UGGUC...GUU-5'\n_____________\|___________________________________________________________\|\n_____________90__________________________________________________________42\n	227 -- 233	43 -- 49	-49.9041 kcal/mol	15.1092 kcal/mol	18.9299 kcal/mol	180 234@LB@ \| \|@LB@5'-CUU...CGUUC CA AUG UUCUCUUUCU UUGCC...CCA-3'@LB@ GAGGAG C ACUGCG GGG UC CGGC ACUGGCUGA UCUUGCG@LB@ \|\|:\|\|\| \| \|\|\|\|\|\| \|\|\| \|\| \|:\|\| \|\|:\|\|\|\|\|\| \|\|\|:\|\|\|@LB@ CUUCUC G UGACGC CCC AG GUCG UGGCCGACU AGAGCGC@LB@3'-UUU...UUAGA A GC A AG A AA UGGUC...GUU-5'@LB@ \| \|@LB@ 90 42@LB@@LB@@LB@Energy -15.87 kcal/mol@LB@Hybridization Energy -49.9041 kcal/mol@LB@Unfolding Energy - mRNA 15.1092 kcal/mol@LB@Unfolding Energy - sRNA 18.9299 kcal/mol@LB@@LB@Position - mRNA 181 -- 233@LB@Position - sRNA 43 -- 89@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 43 -- 49@LB@
155	0.003654	0.1083	pa1551	N/A	-14.46	0.014645	185 -- 205	100 -- 119	ferredoxin		_____________184___________________206\n_____________\|_____________________\|\n5'-ACC...CCACU________AC__A________CAAAC...GGG-3'\n______________GCCGUGGU__GC_CUGAUGAG\n______________:\|\|\|\|\|:\|__\|\|_\|\|\|\|\|\|\|\|\n______________UGGCACUA__CG_GACUACUC\n3'-UUU...GUUUU________AU___________CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________120___________________99\n	199 -- 205	100 -- 106	-27.0785 kcal/mol	10.3705 kcal/mol	2.24903 kcal/mol	184 206@LB@ \| \|@LB@5'-ACC...CCACU AC A CAAAC...GGG-3'@LB@ GCCGUGGU GC CUGAUGAG@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|\|@LB@ UGGCACUA CG GACUACUC@LB@3'-UUU...GUUUU AU CUCUA...GUU-5'@LB@ \| \|@LB@ 120 99@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -27.0785 kcal/mol@LB@Unfolding Energy - mRNA 10.3705 kcal/mol@LB@Unfolding Energy - sRNA 2.24903 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 100 -- 119@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 100 -- 106@LB@
156	0.00379	0.1117	pa3495	nth	-14.09	0.018638	94 -- 117	105 -- 123	endonuclease III		_____________93_______________________118\n_____________\|________________________\|\n5'-UGG...CCCUG_________AUC___GAA______GCGGA...UCA-3'\n______________AAGAACCGU___GAU___AGCCUG\n______________\|\|:\|\|\|\|\|\|___\|\|\|___\|\|\|\|\|\|\n______________UUUUUGGCA___CUA___UCGGAC\n3'-UUU...CCCAG_______________A________UACUC...GUU-5'\n_____________\|________________________\|\n_____________124______________________104\n	96 -- 102	115 -- 121	-18.312 kcal/mol	1.98459 kcal/mol	2.24275 kcal/mol	93 118@LB@ \| \|@LB@5'-UGG...CCCUG AUC GAA GCGGA...UCA-3'@LB@ AAGAACCGU GAU AGCCUG@LB@ \|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUUUUGGCA CUA UCGGAC@LB@3'-UUU...CCCAG A UACUC...GUU-5'@LB@ \| \|@LB@ 124 104@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -18.312 kcal/mol@LB@Unfolding Energy - mRNA 1.98459 kcal/mol@LB@Unfolding Energy - sRNA 2.24275 kcal/mol@LB@@LB@Position - mRNA 94 -- 117@LB@Position - sRNA 105 -- 123@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 115 -- 121@LB@
157	0.003825	0.112	pa0687	N/A	-10.29	0.156397	189 -- 203	102 -- 118	type II secretion system protein	pa3102	_____________188_______________204\n_____________\|_________________\|\n5'-AGC...GUGAC___G__C__________CAGAC...GCG-3'\n______________CCG_GA___GCCUGAUG\n______________\|\|\|_\|\|___\|\|\|\|\|\|\|\|\n______________GGC_CU___CGGACUAC\n3'-UUU...UUUUU___A__AAU________UCCUC...GUU-5'\n_____________\|_________________\|\n_____________119_______________101\n	197 -- 203	102 -- 108	-18.3707 kcal/mol	5.84542 kcal/mol	2.2426 kcal/mol	188 204@LB@ \| \|@LB@5'-AGC...GUGAC G C CAGAC...GCG-3'@LB@ CCG GA GCCUGAUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GGC CU CGGACUAC@LB@3'-UUU...UUUUU A AAU UCCUC...GUU-5'@LB@ \| \|@LB@ 119 101@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -18.3707 kcal/mol@LB@Unfolding Energy - mRNA 5.84542 kcal/mol@LB@Unfolding Energy - sRNA 2.2426 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 102 -- 118@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 102 -- 108@LB@
158	0.003862	0.1123	pa4780	N/A	-10.69	0.128339	184 -- 207	98 -- 122	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________183________________________208\n_____________\|__________________________\|\n5'-AGG...CCCGA_______C_______A_C_____A__CACCC...UGG-3'\n______________GGAACCG_G__UAGC_C_GAUGA_GA\n______________::\|\|\|\|\|_\|__\|\|\|\|_\|_\|\|\|\|\|_\|\|\n______________UUUUGGC_C__AUCG_G_CUACU_CU\n3'-UUU...CCAGU_______A_UA______A_____C__CUAUU...GUU-5'\n_____________\|__________________________\|\n_____________123________________________97\n	184 -- 190	116 -- 122	-18.2775 kcal/mol	5.33909 kcal/mol	2.25226 kcal/mol	183 208@LB@ \| \|@LB@5'-AGG...CCCGA C A C A CACCC...UGG-3'@LB@ GGAACCG G UAGC C GAUGA GA@LB@ ::\|\|\|\|\| \| \|\|\|\| \| \|\|\|\|\| \|\|@LB@ UUUUGGC C AUCG G CUACU CU@LB@3'-UUU...CCAGU A UA A C CUAUU...GUU-5'@LB@ \| \|@LB@ 123 97@LB@@LB@@LB@Energy -10.69 kcal/mol@LB@Hybridization Energy -18.2775 kcal/mol@LB@Unfolding Energy - mRNA 5.33909 kcal/mol@LB@Unfolding Energy - sRNA 2.25226 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 98 -- 122@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 116 -- 122@LB@
159	0.003984	0.115	pa2627	N/A	-8.37	0.359084	22 -- 39	38 -- 59	high frequency lysogenization protein HflD		_____________21_____________________40\n_____________\|______________________\|\n5'-CGC...UGCGC_______A______________GACUG...CCC-3'\n______________UACCGGC_GA____GCGACCAG\n______________\|\|\|\|\|\|\|_\|\|____\|\|\|\|\|\|\|\|\n______________AUGGCCG_CU____CGCUGGUC\n3'-UUU...GUCGA_______A__AGAG________AACUC...GUU-5'\n_____________\|______________________\|\n_____________60_____________________37\n	33 -- 39	38 -- 44	-28.3931 kcal/mol	8.63241 kcal/mol	11.3994 kcal/mol	21 40@LB@ \| \|@LB@5'-CGC...UGCGC A GACUG...CCC-3'@LB@ UACCGGC GA GCGACCAG@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ AUGGCCG CU CGCUGGUC@LB@3'-UUU...GUCGA A AGAG AACUC...GUU-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -28.3931 kcal/mol@LB@Unfolding Energy - mRNA 8.63241 kcal/mol@LB@Unfolding Energy - sRNA 11.3994 kcal/mol@LB@@LB@Position - mRNA 22 -- 39@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 38 -- 44@LB@
160	0.004014	0.115	pa3736	hom	-12.18	0.058138	179 -- 203	72 -- 98	homoserine dehydrogenase		_____________178_________________________204\n_____________\|___________________________\|\n5'-GAA...GUCGU______GA__________CA_______AAACC...CCG-3'\n______________AGGUGA__UGGGGAGUUC____GCGUG\n______________\|\|:\|:\|__\|\|::\|\|\|\|:\|____\|\|\|\|\|\n______________UCUAUU__ACUUCUCAGG____CGCAC\n3'-UUU...ACUCC______AG__________CUGA_____CCAGA...GUU-5'\n_____________\|___________________________\|\n_____________99__________________________71\n	190 -- 196	81 -- 87	-26.8 kcal/mol	8.47001 kcal/mol	6.1492 kcal/mol	178 204@LB@ \| \|@LB@5'-GAA...GUCGU GA CA AAACC...CCG-3'@LB@ AGGUGA UGGGGAGUUC GCGUG@LB@ \|\|:\|:\| \|\|::\|\|\|\|:\| \|\|\|\|\|@LB@ UCUAUU ACUUCUCAGG CGCAC@LB@3'-UUU...ACUCC AG CUGA CCAGA...GUU-5'@LB@ \| \|@LB@ 99 71@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -26.8 kcal/mol@LB@Unfolding Energy - mRNA 8.47001 kcal/mol@LB@Unfolding Energy - sRNA 6.1492 kcal/mol@LB@@LB@Position - mRNA 179 -- 203@LB@Position - sRNA 72 -- 98@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 81 -- 87@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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