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: https://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
1	0	0	pa3775	N/A	-6.65	0.627514	32 -- 38	50 -- 56	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________31______39\n_____________\|_______\|\n5'-CGA...CGGCA_______AGCCG...UGU-3'\n______________CGGCUGA\n______________\|\|\|\|\|\|\|\n______________GCCGACU\n3'-UUU...GAAUG_______AGAGC...GUU-5'\n_____________\|_______\|\n_____________57______49\n	32 -- 38	50 -- 56	-12.177 kcal/mol	0.20262 kcal/mol	5.33178 kcal/mol	31 39@LB@ \| \|@LB@5'-CGA...CGGCA AGCCG...UGU-3'@LB@ CGGCUGA@LB@ \|\|\|\|\|\|\|@LB@ GCCGACU@LB@3'-UUU...GAAUG AGAGC...GUU-5'@LB@ \| \|@LB@ 57 49@LB@@LB@@LB@Energy -6.65 kcal/mol@LB@Hybridization Energy -12.177 kcal/mol@LB@Unfolding Energy - mRNA 0.20262 kcal/mol@LB@Unfolding Energy - sRNA 5.33178 kcal/mol@LB@@LB@Position - mRNA 32 -- 38@LB@Position - sRNA 50 -- 56@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 50 -- 56@LB@
2	9.847e-10	2.263e-06	pa5490	cc4	-23.49	0.000003	181 -- 254	56 -- 120	cytochrome C4		_____________180___________________________________________________________________________255\n_____________\|_____________________________________________________________________________\|\n5'-ACC...CCCUU______AAUUG______________ACAAACU____CGU___________U__ACCC_______GAC___C______CAUGC...UAU-3'\n______________AGCCGU_____GAUUAG_CUGAUGA________UCU___GAGUCUG_CUG_UG____UGGGUCU___CGG_CUUGCC\n______________\|:\|\|\|\|_____\|\|\|\|\|\|_\|\|\|\|\|\|\|________\|\|\|___\|\|\|\|\|:\|_\|\|\|_:\|____\|\|\|\|\|\|\|___\|:\|_\|\|\|:\|\|\n______________UUGGCA_____CUAAUC_GACUACU________AGA___CUCAGGC_GAC_GC____ACCCAGA___GUC_GAAUGG\n3'-UUU...AGUUU_________________G_______CCUCUAUU___CUU_______U_________________GA___________CCGAC...GUU-5'\n_____________\|_____________________________________________________________________________\|\n_____________121___________________________________________________________________________55\n	235 -- 241	67 -- 73	-59.1342 kcal/mol	19.5582 kcal/mol	16.0942 kcal/mol	180 255@LB@ \| \|@LB@5'-ACC...CCCUU AAUUG ACAAACU CGU U ACCC GAC C CAUGC...UAU-3'@LB@ AGCCGU GAUUAG CUGAUGA UCU GAGUCUG CUG UG UGGGUCU CGG CUUGCC@LB@ \|:\|\|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|:\| \|\|\| :\| \|\|\|\|\|\|\| \|:\| \|\|\|:\|\|@LB@ UUGGCA CUAAUC GACUACU AGA CUCAGGC GAC GC ACCCAGA GUC GAAUGG@LB@3'-UUU...AGUUU G CCUCUAUU CUU U GA CCGAC...GUU-5'@LB@ \| \|@LB@ 121 55@LB@@LB@@LB@Energy -23.49 kcal/mol@LB@Hybridization Energy -59.1342 kcal/mol@LB@Unfolding Energy - mRNA 19.5582 kcal/mol@LB@Unfolding Energy - sRNA 16.0942 kcal/mol@LB@@LB@Position - mRNA 181 -- 254@LB@Position - sRNA 56 -- 120@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 67 -- 73@LB@
3	1.464e-07	0.0002243	pa3814	iscS	-11.38	0.090161	182 -- 237	39 -- 110	cysteine desulfurase		_____________181___________________________________________________________________________238\n_____________\|_____________________________________________________________________________\|\n5'-CAC...GCGCC______U_______UUAC_____U__AAUUG________________AC____A_______________________CUCCC...UCG-3'\n______________AGCCUG___AGGAG_____CUGA_GA_____CCGA_________UCU__CUCG__UUAC_______UC_CGCGACCA\n______________\|\|\|\|\|\|___\|\|\|\|\|_____\|\|\|\|_\|\|_____\|\|\|\|_________\|\|\|__\|\|\|:__\|\|\|\|_______\|\|_\|\|\|\|\|\|\|\|\n______________UCGGAC___UCCUC_____GACU_CU_____GGCU_________AGA__GAGU__AAUG_______AG_GCGCUGGU\n3'-UUU...ACUAA______UAC_____UAUUA____U__CA_______GACGCACCC_________CG____GCCGACU__A________CAACU...GUU-5'\n_____________\|_____________________________________________________________________________\|\n_____________111___________________________________________________________________________38\n	231 -- 237	39 -- 45	-44.4171 kcal/mol	9.67698 kcal/mol	23.3669 kcal/mol	181 238@LB@ \| \|@LB@5'-CAC...GCGCC U UUAC U AAUUG AC A CUCCC...UCG-3'@LB@ AGCCUG AGGAG CUGA GA CCGA UCU CUCG UUAC UC CGCGACCA@LB@ \|\|\|\|\|\| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\| \|\|\| \|\|\|: \|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ UCGGAC UCCUC GACU CU GGCU AGA GAGU AAUG AG GCGCUGGU@LB@3'-UUU...ACUAA UAC UAUUA U CA GACGCACCC CG GCCGACU A CAACU...GUU-5'@LB@ \| \|@LB@ 111 38@LB@@LB@@LB@Energy -11.38 kcal/mol@LB@Hybridization Energy -44.4171 kcal/mol@LB@Unfolding Energy - mRNA 9.67698 kcal/mol@LB@Unfolding Energy - sRNA 23.3669 kcal/mol@LB@@LB@Position - mRNA 182 -- 237@LB@Position - sRNA 39 -- 110@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 39 -- 45@LB@
4	5.154e-07	0.0005922	pa1581	sdhC	-15.05	0.009907	206 -- 221	108 -- 123	succinate dehydrogenase subunit C		_____________205______________222\n_____________\|________________\|\n5'-ACG...GUGAA___________A____AAACG...CUG-3'\n______________AAAAGCCGUGA_UAGC\n______________\|\|\|\|:\|\|\|\|\|\|_\|\|\|\|\n______________UUUUUGGCACU_AUCG\n3'-UUU...CCCAG___________A____GACUA...GUU-5'\n_____________\|________________\|\n_____________124______________107\n	210 -- 216	113 -- 119	-19.67 kcal/mol	2.45872 kcal/mol	2.16544 kcal/mol	205 222@LB@ \| \|@LB@5'-ACG...GUGAA A AAACG...CUG-3'@LB@ AAAAGCCGUGA UAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UUUUUGGCACU AUCG@LB@3'-UUU...CCCAG A GACUA...GUU-5'@LB@ \| \|@LB@ 124 107@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -19.67 kcal/mol@LB@Unfolding Energy - mRNA 2.45872 kcal/mol@LB@Unfolding Energy - sRNA 2.16544 kcal/mol@LB@@LB@Position - mRNA 206 -- 221@LB@Position - sRNA 108 -- 123@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 113 -- 119@LB@
5	7.253e-07	0.0006667	pa5351	rubA1	-17.51	0.001615	172 -- 222	71 -- 121	rubredoxin		_____________171___________________________________________________223\n_____________\|_____________________________________________________\|\n5'-CGG...GCGCU__________AAC__GCCC____UAAACAA_______AG_____AA_______UGUGU...UGC-3'\n______________GAACCGUGGU___CC____GAGG________UGAAGA___UGGC__UGCGUGG\n______________:\|\|\|\|\|\|\|:\|___\|\|____\|\|\|\|________\|\|\|\|\|\|___:\|:\|__\|\|\|\|\|\|\|\n______________UUUGGCACUA___GG____CUCC________ACUUCU___GCUG__ACGCACC\n3'-UUU...CAGUU__________AUC__ACUA____UCUAUUAG______CAG_____________CAGAG...GUU-5'\n_____________\|_____________________________________________________\|\n_____________122___________________________________________________70\n	216 -- 222	71 -- 77	-42.807 kcal/mol	11.4444 kcal/mol	13.8582 kcal/mol	171 223@LB@ \| \|@LB@5'-CGG...GCGCU AAC GCCC UAAACAA AG AA UGUGU...UGC-3'@LB@ GAACCGUGGU CC GAGG UGAAGA UGGC UGCGUGG@LB@ :\|\|\|\|\|\|\|:\| \|\| \|\|\|\| \|\|\|\|\|\| :\|:\| \|\|\|\|\|\|\|@LB@ UUUGGCACUA GG CUCC ACUUCU GCUG ACGCACC@LB@3'-UUU...CAGUU AUC ACUA UCUAUUAG CAG CAGAG...GUU-5'@LB@ \| \|@LB@ 122 70@LB@@LB@@LB@Energy -17.51 kcal/mol@LB@Hybridization Energy -42.807 kcal/mol@LB@Unfolding Energy - mRNA 11.4444 kcal/mol@LB@Unfolding Energy - sRNA 13.8582 kcal/mol@LB@@LB@Position - mRNA 172 -- 222@LB@Position - sRNA 71 -- 121@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 71 -- 77@LB@
6	4.972e-06	0.003808	pa1336	N/A	-12.31	0.054230	242 -- 253	107 -- 120	two-component sensor		_____________241____________254\n_____________\|______________\|\n5'-GUC...UCACU______________CCGCC...UGA-3'\n______________GACCGUGA__AGCC\n______________:\|\|\|\|\|\|\|__\|\|\|\|\n______________UUGGCACU__UCGG\n3'-UUU...AGUUU________AA____ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	243 -- 249	113 -- 119	-17.7907 kcal/mol	3.25304 kcal/mol	2.2351 kcal/mol	241 254@LB@ \| \|@LB@5'-GUC...UCACU CCGCC...UGA-3'@LB@ GACCGUGA AGCC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UUGGCACU UCGG@LB@3'-UUU...AGUUU AA ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -17.7907 kcal/mol@LB@Unfolding Energy - mRNA 3.25304 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 113 -- 119@LB@
7	9.272e-06	0.004211	pa1571	N/A	-18.24	0.000884	168 -- 194	96 -- 121	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________167_________________________195\n_____________\|___________________________\|\n5'-CGG...UCCCU______CC___AAA_____________CGGGC...AGA-3'\n______________AGACUG__GAU___CCUGAUGAGGAGA\n______________\|:\|\|:\|__\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________UUUGGC__CUA___GGACUACUCCUCU\n3'-UUU...CAGUU______A____AUC_____________AUUAG...GUU-5'\n_____________\|___________________________\|\n_____________122_________________________95\n	188 -- 194	96 -- 102	-30.1565 kcal/mol	6.37386 kcal/mol	5.54718 kcal/mol	167 195@LB@ \| \|@LB@5'-CGG...UCCCU CC AAA CGGGC...AGA-3'@LB@ AGACUG GAU CCUGAUGAGGAGA@LB@ \|:\|\|:\| \|\|\| \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUGGC CUA GGACUACUCCUCU@LB@3'-UUU...CAGUU A AUC AUUAG...GUU-5'@LB@ \| \|@LB@ 122 95@LB@@LB@@LB@Energy -18.24 kcal/mol@LB@Hybridization Energy -30.1565 kcal/mol@LB@Unfolding Energy - mRNA 6.37386 kcal/mol@LB@Unfolding Energy - sRNA 5.54718 kcal/mol@LB@@LB@Position - mRNA 168 -- 194@LB@Position - sRNA 96 -- 121@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 96 -- 102@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@
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@
10	1.1e-05	0.004211	pa5300	cycB	-16.80	0.002828	155 -- 174	99 -- 117	cytochrome C5		_____________154__________________175\n_____________\|____________________\|\n5'-GGG...CCGGG______A____AC_______GUGUA...GCA-3'\n______________UGUGAU_AGCC__GAUGAGG\n______________:\|\|\|\|\|_\|\|\|\|__\|\|\|\|\|\|\|\n______________GCACUA_UCGG__CUACUCC\n3'-UUU...UUUUG______A____A________UCUAU...GUU-5'\n_____________\|____________________\|\n_____________118__________________98\n	168 -- 174	99 -- 105	-24.2788 kcal/mol	5.2486 kcal/mol	2.23779 kcal/mol	154 175@LB@ \| \|@LB@5'-GGG...CCGGG A AC GUGUA...GCA-3'@LB@ UGUGAU AGCC GAUGAGG@LB@ :\|\|\|\|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ GCACUA UCGG CUACUCC@LB@3'-UUU...UUUUG A A UCUAU...GUU-5'@LB@ \| \|@LB@ 118 98@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -24.2788 kcal/mol@LB@Unfolding Energy - mRNA 5.2486 kcal/mol@LB@Unfolding Energy - sRNA 2.23779 kcal/mol@LB@@LB@Position - mRNA 155 -- 174@LB@Position - sRNA 99 -- 117@LB@Position Seed - mRNA 168 -- 174@LB@Position Seed - sRNA 99 -- 105@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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service.

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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