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
194	0.005258	0.1243	pa3808	N/A	-13.66	0.024437	189 -- 216	98 -- 123	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________188__________________________217\n_____________\|____________________________\|\n5'-CGC...UAGUA_____G____CAAUG_______AAU___CCGAU...GGC-3'\n______________GAGGA_CGUG_____AGCCUGA___GGA\n______________:\|::\|_\|\|\|\|_____\|\|\|\|\|\|\|___\|\|\|\n______________UUUUU_GCAC_____UCGGACU___CCU\n3'-UUU...CCCAG_____G____UAA_________ACU___CUAUU...GUU-5'\n_____________\|____________________________\|\n_____________124__________________________97\n	204 -- 210	104 -- 110	-22.3129 kcal/mol	6.40825 kcal/mol	2.25245 kcal/mol	188 217@LB@ \| \|@LB@5'-CGC...UAGUA G CAAUG AAU CCGAU...GGC-3'@LB@ GAGGA CGUG AGCCUGA GGA@LB@ :\|::\| \|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UUUUU GCAC UCGGACU CCU@LB@3'-UUU...CCCAG G UAA ACU CUAUU...GUU-5'@LB@ \| \|@LB@ 124 97@LB@@LB@@LB@Energy -13.66 kcal/mol@LB@Hybridization Energy -22.3129 kcal/mol@LB@Unfolding Energy - mRNA 6.40825 kcal/mol@LB@Unfolding Energy - sRNA 2.25245 kcal/mol@LB@@LB@Position - mRNA 189 -- 216@LB@Position - sRNA 98 -- 123@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 104 -- 110@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@
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@
25	6.377e-05	0.01172	pa4235	bfrA	-17.70	0.001383	58 -- 83	99 -- 122	bacterioferritin	_____________57__________________________84\n_____________\|___________________________\|\n5'-CCU...GGCCU_______GAC_________________CCCCC...AGG-3'\n______________GAAGCUG___UGA_UGGCCUGAUGAGG\n______________:\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\|\|\|\|\|\|\n______________UUUUGGC___ACU_AUCGGACUACUCC\n3'-UUU...CCAGU_____________A_____________UCUAU...GUU-5'\n_____________\|___________________________\|\n_____________123_________________________98\n	77 -- 83	99 -- 105	-30.6433 kcal/mol	10.6928 kcal/mol	2.25034 kcal/mol	57 84@LB@ \| \|@LB@5'-CCU...GGCCU GAC CCCCC...AGG-3'@LB@ GAAGCUG UGA UGGCCUGAUGAGG@LB@ :\|\|:\|:\| \|\|\| \|:\|\|\|\|\|\|\|\|\|\|\|@LB@ UUUUGGC ACU AUCGGACUACUCC@LB@3'-UUU...CCAGU A UCUAU...GUU-5'@LB@ \| \|@LB@ 123 98@LB@@LB@@LB@Energy -17.70 kcal/mol@LB@Hybridization Energy -30.6433 kcal/mol@LB@Unfolding Energy - mRNA 10.6928 kcal/mol@LB@Unfolding Energy - sRNA 2.25034 kcal/mol@LB@@LB@Position - mRNA 58 -- 83@LB@Position - sRNA 99 -- 122@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 99 -- 105@LB@
43	0.0002634	0.02815	pa2831	N/A	-19.04	0.000437	175 -- 195	99 -- 118	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________174___________________196\n_____________\|_____________________\|\n5'-CUG...CGGGU________UC___C_______UUCCC...GCC-3'\n______________CCGUGAUU__GCC_GAUGAGG\n______________\|\|\|\|\|\|\|\|__\|\|\|_\|\|\|\|\|\|\|\n______________GGCACUAA__CGG_CUACUCC\n3'-UUU...UUUUU________U____A_______UCUAU...GUU-5'\n_____________\|_____________________\|\n_____________119___________________98\n	189 -- 195	99 -- 105	-28.8067 kcal/mol	7.51614 kcal/mol	2.24947 kcal/mol	174 196@LB@ \| \|@LB@5'-CUG...CGGGU UC C UUCCC...GCC-3'@LB@ CCGUGAUU GCC GAUGAGG@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ GGCACUAA CGG CUACUCC@LB@3'-UUU...UUUUU U A UCUAU...GUU-5'@LB@ \| \|@LB@ 119 98@LB@@LB@@LB@Energy -19.04 kcal/mol@LB@Hybridization Energy -28.8067 kcal/mol@LB@Unfolding Energy - mRNA 7.51614 kcal/mol@LB@Unfolding Energy - sRNA 2.24947 kcal/mol@LB@@LB@Position - mRNA 175 -- 195@LB@Position - sRNA 99 -- 118@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 99 -- 105@LB@
75	0.0008154	0.04991	pa4367	bifA	-16.44	0.003694	124 -- 142	99 -- 118	protein BifA	_____________123__________________143\n_____________\|____________________\|\n5'-CGA...UUCGC_____________CU_____UAAAC...UCG-3'\n______________UCGUGAU_AGCCU__UGAGG\n______________:\|\|\|\|\|\|_\|\|\|\|\|__\|\|\|\|\|\n______________GGCACUA_UCGGA__ACUCC\n3'-UUU...UUUUU_______A_____CU_____UCUAU...GUU-5'\n_____________\|____________________\|\n_____________119__________________98\n	124 -- 130	112 -- 118	-25.0523 kcal/mol	6.36496 kcal/mol	2.24947 kcal/mol	123 143@LB@ \| \|@LB@5'-CGA...UUCGC CU UAAAC...UCG-3'@LB@ UCGUGAU AGCCU UGAGG@LB@ :\|\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|@LB@ GGCACUA UCGGA ACUCC@LB@3'-UUU...UUUUU A CU UCUAU...GUU-5'@LB@ \| \|@LB@ 119 98@LB@@LB@@LB@Energy -16.44 kcal/mol@LB@Hybridization Energy -25.0523 kcal/mol@LB@Unfolding Energy - mRNA 6.36496 kcal/mol@LB@Unfolding Energy - sRNA 2.24947 kcal/mol@LB@@LB@Position - mRNA 124 -- 142@LB@Position - sRNA 99 -- 118@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 112 -- 118@LB@
100	0.001607	0.07384	pa0607	rpe	-12.76	0.041806	177 -- 194	99 -- 118	ribulose-phosphate 3-epimerase	_____________176__________________195\n_____________\|____________________\|\n5'-CCG...GCCUU_______CC____U______UGCGC...UUC-3'\n______________CCGUGAU___CCU__UGAGG\n______________\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|\|\n______________GGCACUA___GGA__ACUCC\n3'-UUU...UUUUU_______AUC___CU_____UCUAU...GUU-5'\n_____________\|____________________\|\n_____________119__________________98\n	177 -- 183	112 -- 118	-19.2108 kcal/mol	4.20353 kcal/mol	2.24947 kcal/mol	176 195@LB@ \| \|@LB@5'-CCG...GCCUU CC U UGCGC...UUC-3'@LB@ CCGUGAU CCU UGAGG@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ GGCACUA GGA ACUCC@LB@3'-UUU...UUUUU AUC CU UCUAU...GUU-5'@LB@ \| \|@LB@ 119 98@LB@@LB@@LB@Energy -12.76 kcal/mol@LB@Hybridization Energy -19.2108 kcal/mol@LB@Unfolding Energy - mRNA 4.20353 kcal/mol@LB@Unfolding Energy - sRNA 2.24947 kcal/mol@LB@@LB@Position - mRNA 177 -- 194@LB@Position - sRNA 99 -- 118@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 112 -- 118@LB@
110	0.00181	0.07562	pa2449	N/A	-19.06	0.000430	48 -- 69	99 -- 122	transcriptional regulator	_____________47_______________________70\n_____________\|________________________\|\n5'-UGC...UGACC___________________C____GCGAC...UGG-3'\n______________GAAACCGUGAU_GGCC_GA_GAGG\n______________:\|\|\|\|\|\|\|\|\|\|_:\|\|\|_\|\|_\|\|\|\|\n______________UUUUGGCACUA_UCGG_CU_CUCC\n3'-UUU...CCAGU___________A____A__A____UCUAU...GUU-5'\n_____________\|________________________\|\n_____________123______________________98\n	52 -- 58	112 -- 118	-29.2814 kcal/mol	7.97339 kcal/mol	2.25034 kcal/mol	47 70@LB@ \| \|@LB@5'-UGC...UGACC C GCGAC...UGG-3'@LB@ GAAACCGUGAU GGCC GA GAGG@LB@ :\|\|\|\|\|\|\|\|\|\| :\|\|\| \|\| \|\|\|\|@LB@ UUUUGGCACUA UCGG CU CUCC@LB@3'-UUU...CCAGU A A A UCUAU...GUU-5'@LB@ \| \|@LB@ 123 98@LB@@LB@@LB@Energy -19.06 kcal/mol@LB@Hybridization Energy -29.2814 kcal/mol@LB@Unfolding Energy - mRNA 7.97339 kcal/mol@LB@Unfolding Energy - sRNA 2.25034 kcal/mol@LB@@LB@Position - mRNA 48 -- 69@LB@Position - sRNA 99 -- 122@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 112 -- 118@LB@
130	0.002619	0.0912	pa1320	cyoD	-12.20	0.057664	172 -- 192	99 -- 119	cytochrome o ubiquinol oxidase subunit IV	_____________171____________________193\n_____________\|______________________\|\n5'-UUC...UCUUC_____C_UC_____________GCCCU...CGU-3'\n______________ACCGU_G__UA_CCUGAUGGGG\n______________\|\|\|\|\|_\|__\|\|_\|\|\|\|\|\|\|:\|\|\n______________UGGCA_C__AU_GGACUACUCC\n3'-UUU...GUUUU_______UA__C__________UCUAU...GUU-5'\n_____________\|______________________\|\n_____________120____________________98\n	186 -- 192	99 -- 105	-23.5184 kcal/mol	9.07359 kcal/mol	2.24961 kcal/mol	171 193@LB@ \| \|@LB@5'-UUC...UCUUC C UC GCCCU...CGU-3'@LB@ ACCGU G UA CCUGAUGGGG@LB@ \|\|\|\|\| \| \|\| \|\|\|\|\|\|\|:\|\|@LB@ UGGCA C AU GGACUACUCC@LB@3'-UUU...GUUUU UA C UCUAU...GUU-5'@LB@ \| \|@LB@ 120 98@LB@@LB@@LB@Energy -12.20 kcal/mol@LB@Hybridization Energy -23.5184 kcal/mol@LB@Unfolding Energy - mRNA 9.07359 kcal/mol@LB@Unfolding Energy - sRNA 2.24961 kcal/mol@LB@@LB@Position - mRNA 172 -- 192@LB@Position - sRNA 99 -- 119@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 99 -- 105@LB@
192	0.005234	0.1243	pa1840	N/A	-6.31	0.681723	125 -- 149	99 -- 122	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________124_________________________150\n_____________\|___________________________\|\n5'-GCA...GCGCC_______GC_______G_____G____UCUUG...ACG-3'\n______________GAGAUCG__GA__GGC_CUGGU_GAGG\n______________:\|:\|:\|\|__\|\|__:\|\|_\|\|\|:\|_\|\|\|\|\n______________UUUUGGC__CU__UCG_GACUA_CUCC\n3'-UUU...CCAGU_______A___AA______________UCUAU...GUU-5'\n_____________\|___________________________\|\n_____________123_________________________98\n	125 -- 131	116 -- 122	-20.2979 kcal/mol	11.7389 kcal/mol	2.25034 kcal/mol	124 150@LB@ \| \|@LB@5'-GCA...GCGCC GC G G UCUUG...ACG-3'@LB@ GAGAUCG GA GGC CUGGU GAGG@LB@ :\|:\|:\|\| \|\| :\|\| \|\|\|:\| \|\|\|\|@LB@ UUUUGGC CU UCG GACUA CUCC@LB@3'-UUU...CCAGU A AA UCUAU...GUU-5'@LB@ \| \|@LB@ 123 98@LB@@LB@@LB@Energy -6.31 kcal/mol@LB@Hybridization Energy -20.2979 kcal/mol@LB@Unfolding Energy - mRNA 11.7389 kcal/mol@LB@Unfolding Energy - sRNA 2.25034 kcal/mol@LB@@LB@Position - mRNA 125 -- 149@LB@Position - sRNA 99 -- 122@LB@Position Seed - mRNA 125 -- 131@LB@Position Seed - sRNA 116 -- 122@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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