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
131	0.002644	0.0912	pa4772	N/A	-11.20	0.098904	193 -- 209	105 -- 123	ferredoxin		_____________192__________________210\n_____________\|____________________\|\n5'-CCG...CCGAG________A___________CCGAU...ACG-3'\n______________GAAAGCCG_UGA___GCCUG\n______________:\|\|\|:\|\|\|_\|\|\|___\|\|\|\|\|\n______________UUUUUGGC_ACU___CGGAC\n3'-UUU...CCCAG____________AAU_____UACUC...GUU-5'\n_____________\|____________________\|\n_____________124__________________104\n	194 -- 200	116 -- 122	-17.7993 kcal/mol	4.35882 kcal/mol	2.24275 kcal/mol	192 210@LB@ \| \|@LB@5'-CCG...CCGAG A CCGAU...ACG-3'@LB@ GAAAGCCG UGA GCCUG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUUGGC ACU CGGAC@LB@3'-UUU...CCCAG AAU UACUC...GUU-5'@LB@ \| \|@LB@ 124 104@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.7993 kcal/mol@LB@Unfolding Energy - mRNA 4.35882 kcal/mol@LB@Unfolding Energy - sRNA 2.24275 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 105 -- 123@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 116 -- 122@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@
133	0.002661	0.0912	pa2511	N/A	-14.22	0.017134	181 -- 210	98 -- 119	transcriptional regulator		_____________180____________________________211\n_____________\|______________________________\|\n5'-CGG...GCCUU______UCGAGU___GAACCA_________CCCAU...CGC-3'\n______________GCCGUG______GCC______UGAUGAGGA\n______________:\|\|\|\|\|______\|\|\|______\|\|\|\|\|\|\|\|\|\n______________UGGCAC______CGG______ACUACUCCU\n3'-UUU...GUUUU______UAAU____________________CUAUU...GUU-5'\n_____________\|______________________________\|\n_____________120____________________________97\n	204 -- 210	98 -- 104	-24.6889 kcal/mol	8.22136 kcal/mol	2.25153 kcal/mol	180 211@LB@ \| \|@LB@5'-CGG...GCCUU UCGAGU GAACCA CCCAU...CGC-3'@LB@ GCCGUG GCC UGAUGAGGA@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\|\|@LB@ UGGCAC CGG ACUACUCCU@LB@3'-UUU...GUUUU UAAU CUAUU...GUU-5'@LB@ \| \|@LB@ 120 97@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -24.6889 kcal/mol@LB@Unfolding Energy - mRNA 8.22136 kcal/mol@LB@Unfolding Energy - sRNA 2.25153 kcal/mol@LB@@LB@Position - mRNA 181 -- 210@LB@Position - sRNA 98 -- 119@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 98 -- 104@LB@
134	0.002678	0.0912	pa1421	gbuA	-12.45	0.050008	184 -- 195	107 -- 120	guanidinobutyrase		_____________183____________196\n_____________\|______________\|\n5'-UCC...ACAAC______________ACCCC...CCG-3'\n______________GACCGUGA__GGCC\n______________:\|\|\|\|\|\|\|__:\|\|\|\n______________UUGGCACU__UCGG\n3'-UUU...AGUUU________AA____ACUAC...GUU-5'\n_____________\|______________\|\n_____________121____________106\n	185 -- 191	113 -- 119	-18.3112 kcal/mol	3.63401 kcal/mol	2.2351 kcal/mol	183 196@LB@ \| \|@LB@5'-UCC...ACAAC ACCCC...CCG-3'@LB@ GACCGUGA GGCC@LB@ :\|\|\|\|\|\|\| :\|\|\|@LB@ UUGGCACU UCGG@LB@3'-UUU...AGUUU AA ACUAC...GUU-5'@LB@ \| \|@LB@ 121 106@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -18.3112 kcal/mol@LB@Unfolding Energy - mRNA 3.63401 kcal/mol@LB@Unfolding Energy - sRNA 2.2351 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 107 -- 120@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 113 -- 119@LB@
135	0.002679	0.0912	pa0035	trpA	-9.18	0.258333	240 -- 261	101 -- 123	tryptophan synthase subunit alpha		_____________239_____________________262\n_____________\|_______________________\|\n5'-GAC...AGCAG________C_CCGC_________CCUUC...CCC-3'\n______________GAAAACCG_G_____CCUGGUGA\n______________:\|\|\|\|\|\|\|_\|_____\|\|\|\|:\|\|\|\n______________UUUUUGGC_C_____GGACUACU\n3'-UUU...CCCAG________A_UAAUC________CCUCU...GUU-5'\n_____________\|_______________________\|\n_____________124_____________________100\n	255 -- 261	101 -- 107	-19.6747 kcal/mol	8.2509 kcal/mol	2.24445 kcal/mol	239 262@LB@ \| \|@LB@5'-GAC...AGCAG C CCGC CCUUC...CCC-3'@LB@ GAAAACCG G CCUGGUGA@LB@ :\|\|\|\|\|\|\| \| \|\|\|\|:\|\|\|@LB@ UUUUUGGC C GGACUACU@LB@3'-UUU...CCCAG A UAAUC CCUCU...GUU-5'@LB@ \| \|@LB@ 124 100@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -19.6747 kcal/mol@LB@Unfolding Energy - mRNA 8.2509 kcal/mol@LB@Unfolding Energy - sRNA 2.24445 kcal/mol@LB@@LB@Position - mRNA 240 -- 261@LB@Position - sRNA 101 -- 123@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 101 -- 107@LB@
136	0.00271	0.09122	pa0516	nirF	-12.42	0.050980	176 -- 250	51 -- 109	heme d1 biosynthesis protein NirF	pa0519 pa0509	_____________175___________________________________________________________________________251\n_____________\|_____________________________________________________________________________\|\n5'-UCC...GGACC_______C_A___________GCCCCA____CCU_C____C___C___CC_CU___C____CCCU___C________UAGCC...UCG-3'\n______________GCCUGAU_G_AGGAGA_GAUC______UGAA___G_GUCC__CU_GCG__G__UCU_CUCA____GCU_GCCGGCUG\n______________\|\|\|\|\|\|\|_\|_\|\|\|\|\|\|_:\|\|\|______\|\|\|\|___\|_\|\|\|\|__\|\|_\|\|\|__\|__\|\|\|_\|\|\|\|____\|\|\|_:\|\|\|\|\|\|\|\n______________CGGACUA_C_UCCUCU_UUAG______ACUU___C_CAGG__GA_CGC__C__AGA_GAGU____CGA_UGGCCGAC\n3'-UUU...CUAAU________________A__________________U____CU______A__CC_______________A________UAGAG...GUU-5'\n_____________\|_____________________________________________________________________________\|\n_____________110___________________________________________________________________________50\n	244 -- 250	51 -- 57	-56.426 kcal/mol	22.2414 kcal/mol	21.7733 kcal/mol	175 251@LB@ \| \|@LB@5'-UCC...GGACC C A GCCCCA CCU C C C CC CU C CCCU C UAGCC...UCG-3'@LB@ GCCUGAU G AGGAGA GAUC UGAA G GUCC CU GCG G UCU CUCA GCU GCCGGCUG@LB@ \|\|\|\|\|\|\| \| \|\|\|\|\|\| :\|\|\| \|\|\|\| \| \|\|\|\| \|\| \|\|\| \| \|\|\| \|\|\|\| \|\|\| :\|\|\|\|\|\|\|@LB@ CGGACUA C UCCUCU UUAG ACUU C CAGG GA CGC C AGA GAGU CGA UGGCCGAC@LB@3'-UUU...CUAAU A U CU A CC A UAGAG...GUU-5'@LB@ \| \|@LB@ 110 50@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -56.426 kcal/mol@LB@Unfolding Energy - mRNA 22.2414 kcal/mol@LB@Unfolding Energy - sRNA 21.7733 kcal/mol@LB@@LB@Position - mRNA 176 -- 250@LB@Position - sRNA 51 -- 109@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 51 -- 57@LB@
137	0.002719	0.09122	pa5476	citA	-9.77	0.199491	137 -- 148	71 -- 82	citrate transporter	pa0703 pa4343	_____________136__________149\n_____________\|____________\|\n5'-UCG...CGUAC___C________CCAUC...CCG-3'\n______________CCG_CUGCGUGG\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________GGC_GACGCACC\n3'-UUU...UCUCA___U________CAGAG...GUU-5'\n_____________\|____________\|\n_____________83___________70\n	142 -- 148	71 -- 77	-20.5392 kcal/mol	6.66778 kcal/mol	4.10469 kcal/mol	136 149@LB@ \| \|@LB@5'-UCG...CGUAC C CCAUC...CCG-3'@LB@ CCG CUGCGUGG@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ GGC GACGCACC@LB@3'-UUU...UCUCA U CAGAG...GUU-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -20.5392 kcal/mol@LB@Unfolding Energy - mRNA 6.66778 kcal/mol@LB@Unfolding Energy - sRNA 4.10469 kcal/mol@LB@@LB@Position - mRNA 137 -- 148@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@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@
139	0.002816	0.0931	pa1173	napB	-8.92	0.288683	179 -- 194	100 -- 120	cytochrome C protein NapB		_____________178___________________195\n_____________\|_____________________\|\n5'-GCG...UGCUC_________________G___CGCGC...ACG-3'\n______________AACC_____UGGCCUGA_GAG\n______________\|\|\|\|_____\|:\|\|\|\|\|\|_\|\|\|\n______________UUGG_____AUCGGACU_CUC\n3'-UUU...AGUUU____CACUA________A___CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________121___________________99\n	184 -- 190	104 -- 110	-18.0021 kcal/mol	6.83795 kcal/mol	2.24919 kcal/mol	178 195@LB@ \| \|@LB@5'-GCG...UGCUC G CGCGC...ACG-3'@LB@ AACC UGGCCUGA GAG@LB@ \|\|\|\| \|:\|\|\|\|\|\| \|\|\|@LB@ UUGG AUCGGACU CUC@LB@3'-UUU...AGUUU CACUA A CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -8.92 kcal/mol@LB@Hybridization Energy -18.0021 kcal/mol@LB@Unfolding Energy - mRNA 6.83795 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 179 -- 194@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 104 -- 110@LB@
140	0.002911	0.09555	pa4656	N/A	-13.59	0.025440	215 -- 238	100 -- 120	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________214______________________239\n_____________\|________________________\|\n5'-GCC...CUCUU_____GC___ACC___________UCGCC...GGC-3'\n______________GACCG__GGU___GGCCUGAUGGG\n______________:\|\|\|\|__\|:\|___:\|\|\|\|\|\|\|\|:\|\n______________UUGGC__CUA___UCGGACUACUC\n3'-UUU...AGUUU_____A____A_____________CUCUA...GUU-5'\n_____________\|________________________\|\n_____________121______________________99\n	232 -- 238	100 -- 106	-25.6163 kcal/mol	9.78003 kcal/mol	2.24919 kcal/mol	214 239@LB@ \| \|@LB@5'-GCC...CUCUU GC ACC UCGCC...GGC-3'@LB@ GACCG GGU GGCCUGAUGGG@LB@ :\|\|\|\| \|:\| :\|\|\|\|\|\|\|\|:\|@LB@ UUGGC CUA UCGGACUACUC@LB@3'-UUU...AGUUU A A CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -25.6163 kcal/mol@LB@Unfolding Energy - mRNA 9.78003 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 215 -- 238@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 100 -- 106@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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