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
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@
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@
11	1.195e-05	0.004211	pa3638	N/A	-14.67	0.012752	102 -- 115	100 -- 120	tRNA(Ile)-lysidine synthase		_____________101___________________116\n_____________\|_____________________\|\n5'-GCG...GUUAC_____________________CUACG...CCA-3'\n______________GACC_______GCCUGAUGAG\n______________:\|\|\|_______\|\|\|\|\|\|\|\|\|\|\n______________UUGG_______CGGACUACUC\n3'-UUU...AGUUU____CACUAAU__________CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________121___________________99\n	109 -- 115	100 -- 106	-19.8992 kcal/mol	2.98005 kcal/mol	2.24919 kcal/mol	101 116@LB@ \| \|@LB@5'-GCG...GUUAC CUACG...CCA-3'@LB@ GACC GCCUGAUGAG@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUGG CGGACUACUC@LB@3'-UUU...AGUUU CACUAAU CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -14.67 kcal/mol@LB@Hybridization Energy -19.8992 kcal/mol@LB@Unfolding Energy - mRNA 2.98005 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 100 -- 106@LB@
12	1.22e-05	0.004211	pa3312	N/A	-10.60	0.134070	231 -- 250	100 -- 119	3-hydroxyisobutyrate dehydrogenase		_____________230__________________251\n_____________\|____________________\|\n5'-CGG...CCUUC____GUCUC___________CGUGC...UGU-3'\n______________GCCG_____GGCCUGAUGGG\n______________:\|\|\|_____:\|\|\|\|\|\|\|\|:\|\n______________UGGC_____UCGGACUACUC\n3'-UUU...GUUUU____ACUAA___________CUCUA...GUU-5'\n_____________\|____________________\|\n_____________120__________________99\n	244 -- 250	100 -- 106	-24.2186 kcal/mol	11.3713 kcal/mol	2.24903 kcal/mol	230 251@LB@ \| \|@LB@5'-CGG...CCUUC GUCUC CGUGC...UGU-3'@LB@ GCCG GGCCUGAUGGG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UGGC UCGGACUACUC@LB@3'-UUU...GUUUU ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 120 99@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -24.2186 kcal/mol@LB@Unfolding Energy - mRNA 11.3713 kcal/mol@LB@Unfolding Energy - sRNA 2.24903 kcal/mol@LB@@LB@Position - mRNA 231 -- 250@LB@Position - sRNA 100 -- 119@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 100 -- 106@LB@
13	1.26e-05	0.004211	pa3276	N/A	-14.47	0.014594	182 -- 242	38 -- 108	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________181______________________________________________________________________243\n_____________\|________________________________________________________________________\|\n5'-CUU...UCCGU____UUCU____UACCC___U_________AUCCAUC_____A_______________C_____________CCGGG...ACA-3'\n______________UCUG____GGAG_____CUG_GGAGUCUGA________GUCU__________UGGCUG_AUC_CGCGACUGG\n______________:\|\|\|____\|\|\|\|_____\|\|\|_:\|\|\|\|\|:\|\|________\|\|\|\|__________:\|\|\|\|\|_\|\|\|_\|\|\|\|\|\|::\|\n______________GGAC____CCUC_____GAC_UCUCAGGCU________CAGA__________GCCGAC_UAG_GCGCUGGUC\n3'-UUU...UAAUC____UACU____UAUUA___U_________GACGCACC____GAGUCGAAUG__________A_________AACUC...GUU-5'\n_____________\|________________________________________________________________________\|\n_____________109______________________________________________________________________37\n	236 -- 242	38 -- 44	-54.8405 kcal/mol	17.042 kcal/mol	23.3354 kcal/mol	181 243@LB@ \| \|@LB@5'-CUU...UCCGU UUCU UACCC U AUCCAUC A C CCGGG...ACA-3'@LB@ UCUG GGAG CUG GGAGUCUGA GUCU UGGCUG AUC CGCGACUGG@LB@ :\|\|\| \|\|\|\| \|\|\| :\|\|\|\|\|:\|\| \|\|\|\| :\|\|\|\|\| \|\|\| \|\|\|\|\|\|::\|@LB@ GGAC CCUC GAC UCUCAGGCU CAGA GCCGAC UAG GCGCUGGUC@LB@3'-UUU...UAAUC UACU UAUUA U GACGCACC GAGUCGAAUG A AACUC...GUU-5'@LB@ \| \|@LB@ 109 37@LB@@LB@@LB@Energy -14.47 kcal/mol@LB@Hybridization Energy -54.8405 kcal/mol@LB@Unfolding Energy - mRNA 17.042 kcal/mol@LB@Unfolding Energy - sRNA 23.3354 kcal/mol@LB@@LB@Position - mRNA 182 -- 242@LB@Position - sRNA 38 -- 108@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 38 -- 44@LB@
14	1.283e-05	0.004211	pa2953	N/A	-15.00	0.010274	173 -- 195	95 -- 119	electron transfer flavoprotein-ubiquinone oxidoreductase		_____________172________________________196\n_____________\|__________________________\|\n5'-CGG...CAGAU_____________U___GU_______CGAUA...CCG-3'\n______________ACCGUGA___GCC_UGA__AGGAGAU\n______________\|\|\|\|\|\|\|___\|\|\|_\|\|\|__\|\|\|\|\|\|\|\n______________UGGCACU___CGG_ACU__UCCUCUA\n3'-UUU...GUUUU_______AAU_______AC_______UUAGA...GUU-5'\n_____________\|__________________________\|\n_____________120________________________94\n	189 -- 195	95 -- 101	-27.294 kcal/mol	6.46266 kcal/mol	5.83995 kcal/mol	172 196@LB@ \| \|@LB@5'-CGG...CAGAU U GU CGAUA...CCG-3'@LB@ ACCGUGA GCC UGA AGGAGAU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ UGGCACU CGG ACU UCCUCUA@LB@3'-UUU...GUUUU AAU AC UUAGA...GUU-5'@LB@ \| \|@LB@ 120 94@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -27.294 kcal/mol@LB@Unfolding Energy - mRNA 6.46266 kcal/mol@LB@Unfolding Energy - sRNA 5.83995 kcal/mol@LB@@LB@Position - mRNA 173 -- 195@LB@Position - sRNA 95 -- 119@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 95 -- 101@LB@
16	3.003e-05	0.008352	pa2689	N/A	-17.00	0.002414	189 -- 205	100 -- 117	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________188________________206\n_____________\|__________________\|\n5'-CGG...CAUAA__A__A____________AACCU...UGG-3'\n______________CG_GA__AGCCUGAUGAG\n______________\|\|_\|\|__\|\|\|\|\|\|\|\|\|\|\|\n______________GC_CU__UCGGACUACUC\n3'-UUU...UUUUG__A__AA___________CUCUA...GUU-5'\n_____________\|__________________\|\n_____________118________________99\n	199 -- 205	100 -- 106	-22.2469 kcal/mol	3.0121 kcal/mol	2.23711 kcal/mol	188 206@LB@ \| \|@LB@5'-CGG...CAUAA A A AACCU...UGG-3'@LB@ CG GA AGCCUGAUGAG@LB@ \|\| \|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ GC CU UCGGACUACUC@LB@3'-UUU...UUUUG A AA CUCUA...GUU-5'@LB@ \| \|@LB@ 118 99@LB@@LB@@LB@Energy -17.00 kcal/mol@LB@Hybridization Energy -22.2469 kcal/mol@LB@Unfolding Energy - mRNA 3.0121 kcal/mol@LB@Unfolding Energy - sRNA 2.23711 kcal/mol@LB@@LB@Position - mRNA 189 -- 205@LB@Position - sRNA 100 -- 117@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 100 -- 106@LB@
17	3.089e-05	0.008352	pa5396	N/A	-7.92	0.424136	180 -- 186	104 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________179_____187\n_____________\|_______\|\n5'-CGC...CGCCC_______AAGGG...GCC-3'\n______________AGCCUGA\n______________\|\|\|\|\|\|\|\n______________UCGGACU\n3'-UUU...ACUAA_______ACUCC...GUU-5'\n_____________\|_______\|\n_____________111_____103\n	180 -- 186	104 -- 110	-11.2317 kcal/mol	1.21017 kcal/mol	2.10482 kcal/mol	179 187@LB@ \| \|@LB@5'-CGC...CGCCC AAGGG...GCC-3'@LB@ AGCCUGA@LB@ \|\|\|\|\|\|\|@LB@ UCGGACU@LB@3'-UUU...ACUAA ACUCC...GUU-5'@LB@ \| \|@LB@ 111 103@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -11.2317 kcal/mol@LB@Unfolding Energy - mRNA 1.21017 kcal/mol@LB@Unfolding Energy - sRNA 2.10482 kcal/mol@LB@@LB@Position - mRNA 180 -- 186@LB@Position - sRNA 104 -- 110@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 104 -- 110@LB@
19	3.906e-05	0.009449	pa0443	N/A	-14.62	0.013168	152 -- 204	75 -- 119	transporter		_____________151______________________________________________________205\n_____________\|________________________________________________________\|\n5'-UUG...CGGCC____C________C______C_______CUAAAAGAAU_________G__CA____AACAG...UCG-3'\n______________AUCG__AUUAGCC_GAUGAG_GA_AUAA__________UCUGGAGAG_CC___UGC\n______________\|:\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\|_\|\|_\|\|\|\|__________\|\|\|\|:\|\|\|\|_\|\|___\|\|\|\n______________UGGC__UAAUCGG_CUACUC_CU_UAUU__________AGACUUCUC_GG___ACG\n3'-UUU...GUUUU____AC_______A_________C_______________________A__CUG___CACCC...GUU-5'\n_____________\|________________________________________________________\|\n_____________120______________________________________________________74\n	190 -- 196	84 -- 90	-39.3471 kcal/mol	12.5408 kcal/mol	12.1884 kcal/mol	151 205@LB@ \| \|@LB@5'-UUG...CGGCC C C C CUAAAAGAAU G CA AACAG...UCG-3'@LB@ AUCG AUUAGCC GAUGAG GA AUAA UCUGGAGAG CC UGC@LB@ \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|:\|\|\|\| \|\| \|\|\|@LB@ UGGC UAAUCGG CUACUC CU UAUU AGACUUCUC GG ACG@LB@3'-UUU...GUUUU AC A C A CUG CACCC...GUU-5'@LB@ \| \|@LB@ 120 74@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -39.3471 kcal/mol@LB@Unfolding Energy - mRNA 12.5408 kcal/mol@LB@Unfolding Energy - sRNA 12.1884 kcal/mol@LB@@LB@Position - mRNA 152 -- 204@LB@Position - sRNA 75 -- 119@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 84 -- 90@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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