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
148	0.003408	0.1053	pa1533	N/A	-10.12	0.169364	218 -- 231	101 -- 120	nucleoid-associated protein	_____________217__________________232\n_____________\|____________________\|\n5'-AGA...GGCAU____________________AGCAG...CCG-3'\n______________GGCCG______GCCUGAUGA\n______________::\|\|\|______\|\|\|\|\|\|\|\|\|\n______________UUGGC______CGGACUACU\n3'-UUU...AGUUU_____ACUAAU_________CCUCU...GUU-5'\n_____________\|____________________\|\n_____________121__________________100\n	225 -- 231	101 -- 107	-19.3791 kcal/mol	7.01958 kcal/mol	2.2437 kcal/mol	217 232@LB@ \| \|@LB@5'-AGA...GGCAU AGCAG...CCG-3'@LB@ GGCCG GCCUGAUGA@LB@ ::\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UUGGC CGGACUACU@LB@3'-UUU...AGUUU ACUAAU CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -10.12 kcal/mol@LB@Hybridization Energy -19.3791 kcal/mol@LB@Unfolding Energy - mRNA 7.01958 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 218 -- 231@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 101 -- 107@LB@
132	0.002652	0.0912	pa0364	N/A	-15.84	0.005742	174 -- 193	100 -- 122	oxidoreductase	_____________173_____________________194\n_____________\|_______________________\|\n5'-AUU...AGCCC_______CC______________UGCAU...UGG-3'\n______________GAAGCCG____UAGCCUGA_GAG\n______________:\|\|:\|\|\|____\|\|\|\|\|\|\|\|_\|\|\|\n______________UUUUGGC____AUCGGACU_CUC\n3'-UUU...CCAGU_______ACUA________A___CUCUA...GUU-5'\n_____________\|_______________________\|\n_____________123_____________________99\n	184 -- 190	104 -- 110	-22.8122 kcal/mol	4.73034 kcal/mol	2.24976 kcal/mol	173 194@LB@ \| \|@LB@5'-AUU...AGCCC CC UGCAU...UGG-3'@LB@ GAAGCCG UAGCCUGA GAG@LB@ :\|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|@LB@ UUUUGGC AUCGGACU CUC@LB@3'-UUU...CCAGU ACUA A CUCUA...GUU-5'@LB@ \| \|@LB@ 123 99@LB@@LB@@LB@Energy -15.84 kcal/mol@LB@Hybridization Energy -22.8122 kcal/mol@LB@Unfolding Energy - mRNA 4.73034 kcal/mol@LB@Unfolding Energy - sRNA 2.24976 kcal/mol@LB@@LB@Position - mRNA 174 -- 193@LB@Position - sRNA 100 -- 122@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 104 -- 110@LB@
138	0.002776	0.09245	pa0440	N/A	-11.93	0.067049	197 -- 216	104 -- 120	oxidoreductase	_____________196__________________217\n_____________\|____________________\|\n5'-CGA...GCUAC_________CGAUUC_____ACCAC...AGG-3'\n______________AACCGUGAU______CCUGA\n______________\|\|\|\|\|\|\|\|\|______\|\|\|\|\|\n______________UUGGCACUA______GGACU\n3'-UUU...AGUUU_________AUC________ACUCC...GUU-5'\n_____________\|____________________\|\n_____________121__________________103\n	199 -- 205	112 -- 118	-17.8806 kcal/mol	3.71535 kcal/mol	2.24182 kcal/mol	196 217@LB@ \| \|@LB@5'-CGA...GCUAC CGAUUC ACCAC...AGG-3'@LB@ AACCGUGAU CCUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGGCACUA GGACU@LB@3'-UUU...AGUUU AUC ACUCC...GUU-5'@LB@ \| \|@LB@ 121 103@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -17.8806 kcal/mol@LB@Unfolding Energy - mRNA 3.71535 kcal/mol@LB@Unfolding Energy - sRNA 2.24182 kcal/mol@LB@@LB@Position - mRNA 197 -- 216@LB@Position - sRNA 104 -- 120@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 112 -- 118@LB@
196	0.005339	0.1252	pa1085	flgJ	-8.97	0.282317	179 -- 193	98 -- 119	peptidoglycan hydrolase FlgJ	_____________178____________________194\n_____________\|______________________\|\n5'-GGU...ACCUG______________________CGACG...GCG-3'\n______________AUCGUGAUU_______UGAGGA\n______________\|:\|\|\|\|\|\|\|_______\|\|\|\|\|\|\n______________UGGCACUAA_______ACUCCU\n3'-UUU...GUUUU_________UCGGACU______CUAUU...GUU-5'\n_____________\|______________________\|\n_____________120____________________97\n	181 -- 187	111 -- 117	-15.6275 kcal/mol	4.40725 kcal/mol	2.25153 kcal/mol	178 194@LB@ \| \|@LB@5'-GGU...ACCUG CGACG...GCG-3'@LB@ AUCGUGAUU UGAGGA@LB@ \|:\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UGGCACUAA ACUCCU@LB@3'-UUU...GUUUU UCGGACU CUAUU...GUU-5'@LB@ \| \|@LB@ 120 97@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -15.6275 kcal/mol@LB@Unfolding Energy - mRNA 4.40725 kcal/mol@LB@Unfolding Energy - sRNA 2.25153 kcal/mol@LB@@LB@Position - mRNA 179 -- 193@LB@Position - sRNA 98 -- 119@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 111 -- 117@LB@
53	0.0004056	0.03518	pa1750	N/A	-9.05	0.272805	157 -- 194	32 -- 72	phospho-2-dehydro-3-deoxyheptonate aldolase	_____________156________________________________________195\n_____________\|__________________________________________\|\n5'-ACU...GCAGG___C___C____G_______GC___________U_A______ACCAC...CCC-3'\n______________GGG_CUC_CGGC__GCCGGC____C_CGUGACC_G_UUGAGU\n______________\|\|\|_\|\|\|_\|:\|\|__:\|\|\|\|\|____\|_\|\|:\|\|\|\|_\|_\|\|\|\|\|\|\n______________CCC_GAG_GUCG__UGGCCG____G_GCGCUGG_C_AACUCA\n3'-UUU...ACGCA___A___A____AA______ACUA_A_______U________CUGUA...GUU-5'\n_____________\|__________________________________________\|\n_____________73_________________________________________31\n	179 -- 185	40 -- 46	-44.8167 kcal/mol	16.8729 kcal/mol	18.8965 kcal/mol	156 195@LB@ \| \|@LB@5'-ACU...GCAGG C C G GC U A ACCAC...CCC-3'@LB@ GGG CUC CGGC GCCGGC C CGUGACC G UUGAGU@LB@ \|\|\| \|\|\| \|:\|\| :\|\|\|\|\| \| \|\|:\|\|\|\| \| \|\|\|\|\|\|@LB@ CCC GAG GUCG UGGCCG G GCGCUGG C AACUCA@LB@3'-UUU...ACGCA A A AA ACUA A U CUGUA...GUU-5'@LB@ \| \|@LB@ 73 31@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -44.8167 kcal/mol@LB@Unfolding Energy - mRNA 16.8729 kcal/mol@LB@Unfolding Energy - sRNA 18.8965 kcal/mol@LB@@LB@Position - mRNA 157 -- 194@LB@Position - sRNA 32 -- 72@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 40 -- 46@LB@
123	0.00223	0.08331	pa0552	pgk	-10.33	0.153234	163 -- 259	42 -- 119	phosphoglycerate kinase	_____________162________________________________________________________________________________________________________260\n_____________\|__________________________________________________________________________________________________________\|\n5'-CAC...GCGCC_________________CAACAAGUACCCA____CU___U___AUGACCGUGU_______________ACCUCGAC___AAA___AA__G__U_____________GGACC...GCG-3'\n______________GCCGU_____GCCUGAU_____________AGGA__GAU_GUC__________UGAAGA___UGACUG________CUC___GGU__GC_CG_GCUGAUC_CGCGA\n______________:\|\|\|\|_____\|\|\|\|\|\|\|_____________\|\|\|\|__\|\|\|_:\|\|__________\|\|\|\|\|\|___:\|\|\|\|\|________\|\|\|___:\|:__:\|_\|\|_\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UGGCA_____CGGACUA_____________UCCU__CUA_UAG__________ACUUCU___GCUGAC________GAG___UCG__UG_GC_CGACUAG_GCGCU\n3'-UUU...GUUUU_____CUAAU_______C_____________________U___________________CAG______GCACCCA____AG____AA_____________A_____GGUCA...GUU-5'\n_____________\|__________________________________________________________________________________________________________\|\n_____________120________________________________________________________________________________________________________41\n	248 -- 254	48 -- 54	-58.6651 kcal/mol	25.0123 kcal/mol	23.3319 kcal/mol	162 260@LB@ \| \|@LB@5'-CAC...GCGCC CAACAAGUACCCA CU U AUGACCGUGU ACCUCGAC AAA AA G U GGACC...GCG-3'@LB@ GCCGU GCCUGAU AGGA GAU GUC UGAAGA UGACUG CUC GGU GC CG GCUGAUC CGCGA@LB@ :\|\|\|\| \|\|\|\|\|\|\| \|\|\|\| \|\|\| :\|\| \|\|\|\|\|\| :\|\|\|\|\| \|\|\| :\|: :\| \|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UGGCA CGGACUA UCCU CUA UAG ACUUCU GCUGAC GAG UCG UG GC CGACUAG GCGCU@LB@3'-UUU...GUUUU CUAAU C U CAG GCACCCA AG AA A GGUCA...GUU-5'@LB@ \| \|@LB@ 120 41@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -58.6651 kcal/mol@LB@Unfolding Energy - mRNA 25.0123 kcal/mol@LB@Unfolding Energy - sRNA 23.3319 kcal/mol@LB@@LB@Position - mRNA 163 -- 259@LB@Position - sRNA 42 -- 119@LB@Position Seed - mRNA 248 -- 254@LB@Position Seed - sRNA 48 -- 54@LB@
118	0.002082	0.07999	pa5066	hisI	-12.42	0.050876	194 -- 221	100 -- 123	phosphoribosyl-AMP cyclohydrolase	_____________193__________________________222\n_____________\|____________________________\|\n5'-CGA...CGUGG_______A___AAGAC_____G______AUUCA...GGA-3'\n______________AAAGACC_UGA_____UGGCU_GAUGAG\n______________\|\|\|:\|\|\|_\|\|\|_____\|:\|\|:_\|\|\|\|\|\|\n______________UUUUUGG_ACU_____AUCGG_CUACUC\n3'-UUU...CCCAG_______C___A_________A______CUCUA...GUU-5'\n_____________\|____________________________\|\n_____________124__________________________99\n	194 -- 200	117 -- 123	-21.0853 kcal/mol	6.41847 kcal/mol	2.24995 kcal/mol	193 222@LB@ \| \|@LB@5'-CGA...CGUGG A AAGAC G AUUCA...GGA-3'@LB@ AAAGACC UGA UGGCU GAUGAG@LB@ \|\|\|:\|\|\| \|\|\| \|:\|\|: \|\|\|\|\|\|@LB@ UUUUUGG ACU AUCGG CUACUC@LB@3'-UUU...CCCAG C A A CUCUA...GUU-5'@LB@ \| \|@LB@ 124 99@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -21.0853 kcal/mol@LB@Unfolding Energy - mRNA 6.41847 kcal/mol@LB@Unfolding Energy - sRNA 2.24995 kcal/mol@LB@@LB@Position - mRNA 194 -- 221@LB@Position - sRNA 100 -- 123@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 117 -- 123@LB@
67	0.0007208	0.0493	pa0304	spuH	-8.66	0.319981	266 -- 281	40 -- 54	polyamine transporter PotI	_____________265______________282\n_____________\|________________\|\n5'-CAA...CCGAU_______C_G______UAUUC...CCA-3'\n______________GCUGAUC_U_GUGAUC\n______________\|\|\|\|\|\|\|_\|_\|:\|\|:\|\n______________CGACUAG_A_CGCUGG\n3'-UUU...AUGGC_________G______UCAAC...GUU-5'\n_____________\|________________\|\n_____________55_______________39\n	266 -- 272	48 -- 54	-20.1848 kcal/mol	3.44761 kcal/mol	8.07324 kcal/mol	265 282@LB@ \| \|@LB@5'-CAA...CCGAU C G UAUUC...CCA-3'@LB@ GCUGAUC U GUGAUC@LB@ \|\|\|\|\|\|\| \| \|:\|\|:\|@LB@ CGACUAG A CGCUGG@LB@3'-UUU...AUGGC G UCAAC...GUU-5'@LB@ \| \|@LB@ 55 39@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -20.1848 kcal/mol@LB@Unfolding Energy - mRNA 3.44761 kcal/mol@LB@Unfolding Energy - sRNA 8.07324 kcal/mol@LB@@LB@Position - mRNA 266 -- 281@LB@Position - sRNA 40 -- 54@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 48 -- 54@LB@
176	0.004483	0.1171	pa1774	crfX	-11.59	0.080592	153 -- 172	96 -- 117	Product name confidence: class 1: Function experimentally demonstrated in P. aeruginosa	_____________152______________________173\n_____________\|________________________\|\n5'-UGC...UCUGA_____________GA_________GGGCG...AGA-3'\n______________CGUGA____CCUG__GUGAGGAGA\n______________\|\|\|\|\|____\|\|\|\|__:\|\|\|\|\|\|\|\|\n______________GCACU____GGAC__UACUCCUCU\n3'-UUU...UUUUG_____AAUC_______________AUUAG...GUU-5'\n_____________\|________________________\|\n_____________118______________________95\n	166 -- 172	96 -- 102	-24.6679 kcal/mol	7.55062 kcal/mol	5.53547 kcal/mol	152 173@LB@ \| \|@LB@5'-UGC...UCUGA GA GGGCG...AGA-3'@LB@ CGUGA CCUG GUGAGGAGA@LB@ \|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|\|@LB@ GCACU GGAC UACUCCUCU@LB@3'-UUU...UUUUG AAUC AUUAG...GUU-5'@LB@ \| \|@LB@ 118 95@LB@@LB@@LB@Energy -11.59 kcal/mol@LB@Hybridization Energy -24.6679 kcal/mol@LB@Unfolding Energy - mRNA 7.55062 kcal/mol@LB@Unfolding Energy - sRNA 5.53547 kcal/mol@LB@@LB@Position - mRNA 153 -- 172@LB@Position - sRNA 96 -- 117@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 96 -- 102@LB@
64	0.000634	0.04553	pa1832	N/A	-15.82	0.005823	184 -- 249	39 -- 110	protease	_____________183________________________________________________________________________250\n_____________\|__________________________________________________________________________\|\n5'-GUA...UCAAC___A____________UG____U_____________CGAAUAUGCG______U_____CAG_____________UGCUG...GCC-3'\n______________AGU__GA_GAGGGGGU____UG_GGAGUUC_AUUGC___________GGCUU_CUGGC___GA_C_CGUGACCG\n______________\|\|:__\|\|_\|\|\|\|:\|:\|____\|\|_:\|\|\|\|:\|_\|:\|\|\|___________:\|\|\|\|_\|:\|\|\|___\|\|_\|_\|\|:\|\|\|\|:\n______________UCG__CU_CUCCUCUA____AC_UCUCAGG_UGACG___________UCGAA_GGCCG___CU_G_GCGCUGGU\n3'-UUU...ACUAA___GA__A________UUAG__U_______C_____CACCCAGAGAG_____U_____A____A_A________CAACU...GUU-5'\n_____________\|__________________________________________________________________________\|\n_____________111________________________________________________________________________38\n	243 -- 249	39 -- 45	-57.1706 kcal/mol	17.9919 kcal/mol	23.3669 kcal/mol	183 250@LB@ \| \|@LB@5'-GUA...UCAAC A UG U CGAAUAUGCG U CAG UGCUG...GCC-3'@LB@ AGU GA GAGGGGGU UG GGAGUUC AUUGC GGCUU CUGGC GA C CGUGACCG@LB@ \|\|: \|\| \|\|\|\|:\|:\| \|\| :\|\|\|\|:\| \|:\|\|\| :\|\|\|\| \|:\|\|\| \|\| \| \|\|:\|\|\|\|:@LB@ UCG CU CUCCUCUA AC UCUCAGG UGACG UCGAA GGCCG CU G GCGCUGGU@LB@3'-UUU...ACUAA GA A UUAG U C CACCCAGAGAG U A A A CAACU...GUU-5'@LB@ \| \|@LB@ 111 38@LB@@LB@@LB@Energy -15.82 kcal/mol@LB@Hybridization Energy -57.1706 kcal/mol@LB@Unfolding Energy - mRNA 17.9919 kcal/mol@LB@Unfolding Energy - sRNA 23.3669 kcal/mol@LB@@LB@Position - mRNA 184 -- 249@LB@Position - sRNA 39 -- 110@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 39 -- 45@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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