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
93	0.001289	0.06355	pa4454	N/A	-9.11	0.266760	170 -- 178	75 -- 83	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________169_______179\n_____________\|_________\|\n5'-CCG...UUCAU_________UUUGA...UGG-3'\n______________UCUGACUGC\n______________\|\|:\|\|\|\|\|\|\n______________AGGCUGACG\n3'-UUU...UUCUC_________CACCC...GUU-5'\n_____________\|_________\|\n_____________84________74\n	172 -- 178	75 -- 81	-14.8179 kcal/mol	1.6159 kcal/mol	4.09544 kcal/mol	169 179@LB@ \| \|@LB@5'-CCG...UUCAU UUUGA...UGG-3'@LB@ UCUGACUGC@LB@ \|\|:\|\|\|\|\|\|@LB@ AGGCUGACG@LB@3'-UUU...UUCUC CACCC...GUU-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -14.8179 kcal/mol@LB@Unfolding Energy - mRNA 1.6159 kcal/mol@LB@Unfolding Energy - sRNA 4.09544 kcal/mol@LB@@LB@Position - mRNA 170 -- 178@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 75 -- 81@LB@
46	0.0003006	0.02946	pa4460	N/A	-9.10	0.267813	234 -- 244	75 -- 85	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________233_________245\n_____________\|___________\|\n5'-GCG...UUUUC___________CGCCC...UCC-3'\n______________GGUCUGACUGC\n______________:\|\|\|:\|\|\|\|\|\|\n______________UCAGGCUGACG\n3'-UUU...ACUUC___________CACCC...GUU-5'\n_____________\|___________\|\n_____________86__________74\n	238 -- 244	75 -- 81	-18.7561 kcal/mol	4.01129 kcal/mol	5.64974 kcal/mol	233 245@LB@ \| \|@LB@5'-GCG...UUUUC CGCCC...UCC-3'@LB@ GGUCUGACUGC@LB@ :\|\|\|:\|\|\|\|\|\|@LB@ UCAGGCUGACG@LB@3'-UUU...ACUUC CACCC...GUU-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -9.10 kcal/mol@LB@Hybridization Energy -18.7561 kcal/mol@LB@Unfolding Energy - mRNA 4.01129 kcal/mol@LB@Unfolding Energy - sRNA 5.64974 kcal/mol@LB@@LB@Position - mRNA 234 -- 244@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@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@
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@
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@
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@
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@
84	0.001042	0.05699	pa3121	leuC	-8.58	0.330521	182 -- 193	98 -- 110	3-isopropylmalate dehydratase large subunit	_____________181___________194\n_____________\|_____________\|\n5'-GCA...AAAUG_____________AAUCC...UGC-3'\n______________AG_CUGAUGAGGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________UC_GACUACUCCU\n3'-UUU...ACUAA__G__________CUAUU...GUU-5'\n_____________\|_____________\|\n_____________111___________97\n	187 -- 193	98 -- 104	-17.6185 kcal/mol	6.87469 kcal/mol	2.16105 kcal/mol	181 194@LB@ \| \|@LB@5'-GCA...AAAUG AAUCC...UGC-3'@LB@ AG CUGAUGAGGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ UC GACUACUCCU@LB@3'-UUU...ACUAA G CUAUU...GUU-5'@LB@ \| \|@LB@ 111 97@LB@@LB@@LB@Energy -8.58 kcal/mol@LB@Hybridization Energy -17.6185 kcal/mol@LB@Unfolding Energy - mRNA 6.87469 kcal/mol@LB@Unfolding Energy - sRNA 2.16105 kcal/mol@LB@@LB@Position - mRNA 182 -- 193@LB@Position - sRNA 98 -- 110@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 98 -- 104@LB@
126	0.002419	0.08825	pa0452	N/A	-8.57	0.332234	172 -- 209	83 -- 122	'Product name confidence: class 3 (Function proposed based on presence of conserved amino acid motif structural feature or limited sequence similarity to an experimentally studied gene)'	_____________171_______________________________________210\n_____________\|_________________________________________\|\n5'-AGU...UCCUG_______C_C___________A_________A____U____AUUUC...UGG-3'\n______________GAAGUCG_G__UGGCC_GAUG_AGGAGGUGG__UGA_GGGU\n______________:\|\|::\|\|_\|__\|:\|\|\|_\|\|\|\|_\|\|\|\|\|:\|::__\|\|\|_\|:\|\|\n______________UUUUGGC_C__AUCGG_CUAC_UCCUCUAUU__ACU_CUCA\n3'-UUU...CCAGU_______A_UA_____A______________AG___U____GGCUG...GUU-5'\n_____________\|_________________________________________\|\n_____________123_______________________________________82\n	193 -- 199	94 -- 100	-32.4047 kcal/mol	13.786 kcal/mol	10.0547 kcal/mol	171 210@LB@ \| \|@LB@5'-AGU...UCCUG C C A A U AUUUC...UGG-3'@LB@ GAAGUCG G UGGCC GAUG AGGAGGUGG UGA GGGU@LB@ :\|\|::\|\| \| \|:\|\|\| \|\|\|\| \|\|\|\|\|:\|:: \|\|\| \|:\|\|@LB@ UUUUGGC C AUCGG CUAC UCCUCUAUU ACU CUCA@LB@3'-UUU...CCAGU A UA A AG U GGCUG...GUU-5'@LB@ \| \|@LB@ 123 82@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -32.4047 kcal/mol@LB@Unfolding Energy - mRNA 13.786 kcal/mol@LB@Unfolding Energy - sRNA 10.0547 kcal/mol@LB@@LB@Position - mRNA 172 -- 209@LB@Position - sRNA 83 -- 122@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 94 -- 100@LB@
117	0.002052	0.07999	pa0290	N/A	-8.56	0.333144	143 -- 150	40 -- 47	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________142______151\n_____________\|________\|\n5'-CCU...UAUCG________CCUGC...AAC-3'\n______________UCGCGACC\n______________\|\|\|\|\|\|\|\|\n______________AGCGCUGG\n3'-UUU...ACUAG________UCAAC...GUU-5'\n_____________\|________\|\n_____________48_______39\n	144 -- 150	40 -- 46	-14.5279 kcal/mol	2.30284 kcal/mol	3.66533 kcal/mol	142 151@LB@ \| \|@LB@5'-CCU...UAUCG CCUGC...AAC-3'@LB@ UCGCGACC@LB@ \|\|\|\|\|\|\|\|@LB@ AGCGCUGG@LB@3'-UUU...ACUAG UCAAC...GUU-5'@LB@ \| \|@LB@ 48 39@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -14.5279 kcal/mol@LB@Unfolding Energy - mRNA 2.30284 kcal/mol@LB@Unfolding Energy - sRNA 3.66533 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 40 -- 47@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 40 -- 46@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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