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
163	0.004151	0.1159	pa3263	N/A	-13.17	0.032863	133 -- 150	104 -- 121	recombination associated protein RdgC	_____________132________________151\n_____________\|__________________\|\n5'-GUA...GCGAC______G___________GCCGC...CCU-3'\n______________GGACCG_GGUUGGCCUGA\n______________::\|\|\|\|_\|:\|\|:\|\|\|\|\|\|\n______________UUUGGC_CUAAUCGGACU\n3'-UUU...CAGUU______A___________ACUCC...GUU-5'\n_____________\|__________________\|\n_____________122________________103\n	144 -- 150	104 -- 110	-25.1519 kcal/mol	9.74439 kcal/mol	2.24203 kcal/mol	132 151@LB@ \| \|@LB@5'-GUA...GCGAC G GCCGC...CCU-3'@LB@ GGACCG GGUUGGCCUGA@LB@ ::\|\|\|\| \|:\|\|:\|\|\|\|\|\|@LB@ UUUGGC CUAAUCGGACU@LB@3'-UUU...CAGUU A ACUCC...GUU-5'@LB@ \| \|@LB@ 122 103@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -25.1519 kcal/mol@LB@Unfolding Energy - mRNA 9.74439 kcal/mol@LB@Unfolding Energy - sRNA 2.24203 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 104 -- 121@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 104 -- 110@LB@
165	0.004162	0.1159	pa1850	N/A	-12.78	0.041348	242 -- 255	104 -- 117	transcriptional regulator	_____________241____________256\n_____________\|______________\|\n5'-AUA...CCCGA______G_______ACGUG...AAC-3'\n______________CGUGAU_AGCCUGG\n______________\|\|\|\|\|\|_\|\|\|\|\|\|:\n______________GCACUA_UCGGACU\n3'-UUU...UUUUG______A_______ACUCC...GUU-5'\n_____________\|______________\|\n_____________118____________103\n	249 -- 255	104 -- 110	-19.8167 kcal/mol	4.81117 kcal/mol	2.2292 kcal/mol	241 256@LB@ \| \|@LB@5'-AUA...CCCGA G ACGUG...AAC-3'@LB@ CGUGAU AGCCUGG@LB@ \|\|\|\|\|\| \|\|\|\|\|\|:@LB@ GCACUA UCGGACU@LB@3'-UUU...UUUUG A ACUCC...GUU-5'@LB@ \| \|@LB@ 118 103@LB@@LB@@LB@Energy -12.78 kcal/mol@LB@Hybridization Energy -19.8167 kcal/mol@LB@Unfolding Energy - mRNA 4.81117 kcal/mol@LB@Unfolding Energy - sRNA 2.2292 kcal/mol@LB@@LB@Position - mRNA 242 -- 255@LB@Position - sRNA 104 -- 117@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 104 -- 110@LB@
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@
143	0.003113	0.1001	pa1811	N/A	-11.02	0.108661	233 -- 245	105 -- 120	solute-binding protein	_____________232______________246\n_____________\|________________\|\n5'-GAG...GGCCU________________CCCAG...UCA-3'\n______________GGCCGUGA___GCCUG\n______________::\|\|\|\|\|\|___\|\|\|\|\|\n______________UUGGCACU___CGGAC\n3'-UUU...AGUUU________AAU_____UACUC...GUU-5'\n_____________\|________________\|\n_____________121______________104\n	234 -- 240	113 -- 119	-18.7383 kcal/mol	5.48096 kcal/mol	2.24173 kcal/mol	232 246@LB@ \| \|@LB@5'-GAG...GGCCU CCCAG...UCA-3'@LB@ GGCCGUGA GCCUG@LB@ ::\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGGCACU CGGAC@LB@3'-UUU...AGUUU AAU UACUC...GUU-5'@LB@ \| \|@LB@ 121 104@LB@@LB@@LB@Energy -11.02 kcal/mol@LB@Hybridization Energy -18.7383 kcal/mol@LB@Unfolding Energy - mRNA 5.48096 kcal/mol@LB@Unfolding Energy - sRNA 2.24173 kcal/mol@LB@@LB@Position - mRNA 233 -- 245@LB@Position - sRNA 105 -- 120@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 113 -- 119@LB@
147	0.003398	0.1053	pa4657	N/A	-14.94	0.010704	152 -- 169	105 -- 123	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________151_________________170\n_____________\|___________________\|\n5'-UCU...GUACA_____________C_____UCCAG...AGG-3'\n______________AGAAACC_UGAUU_GCCUG\n______________\|:\|\|\|\|\|_\|\|\|\|\|_\|\|\|\|\|\n______________UUUUUGG_ACUAA_CGGAC\n3'-UUU...CCCAG_______C_____U_____UACUC...GUU-5'\n_____________\|___________________\|\n_____________124_________________104\n	152 -- 158	117 -- 123	-19.6832 kcal/mol	2.50735 kcal/mol	2.24275 kcal/mol	151 170@LB@ \| \|@LB@5'-UCU...GUACA C UCCAG...AGG-3'@LB@ AGAAACC UGAUU GCCUG@LB@ \|:\|\|\|\|\| \|\|\|\|\| \|\|\|\|\|@LB@ UUUUUGG ACUAA CGGAC@LB@3'-UUU...CCCAG C U UACUC...GUU-5'@LB@ \| \|@LB@ 124 104@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -19.6832 kcal/mol@LB@Unfolding Energy - mRNA 2.50735 kcal/mol@LB@Unfolding Energy - sRNA 2.24275 kcal/mol@LB@@LB@Position - mRNA 152 -- 169@LB@Position - sRNA 105 -- 123@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 117 -- 123@LB@
156	0.00379	0.1117	pa3495	nth	-14.09	0.018638	94 -- 117	105 -- 123	endonuclease III	_____________93_______________________118\n_____________\|________________________\|\n5'-UGG...CCCUG_________AUC___GAA______GCGGA...UCA-3'\n______________AAGAACCGU___GAU___AGCCUG\n______________\|\|:\|\|\|\|\|\|___\|\|\|___\|\|\|\|\|\|\n______________UUUUUGGCA___CUA___UCGGAC\n3'-UUU...CCCAG_______________A________UACUC...GUU-5'\n_____________\|________________________\|\n_____________124______________________104\n	96 -- 102	115 -- 121	-18.312 kcal/mol	1.98459 kcal/mol	2.24275 kcal/mol	93 118@LB@ \| \|@LB@5'-UGG...CCCUG AUC GAA GCGGA...UCA-3'@LB@ AAGAACCGU GAU AGCCUG@LB@ \|\|:\|\|\|\|\|\| \|\|\| \|\|\|\|\|\|@LB@ UUUUUGGCA CUA UCGGAC@LB@3'-UUU...CCCAG A UACUC...GUU-5'@LB@ \| \|@LB@ 124 104@LB@@LB@@LB@Energy -14.09 kcal/mol@LB@Hybridization Energy -18.312 kcal/mol@LB@Unfolding Energy - mRNA 1.98459 kcal/mol@LB@Unfolding Energy - sRNA 2.24275 kcal/mol@LB@@LB@Position - mRNA 94 -- 117@LB@Position - sRNA 105 -- 123@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 115 -- 121@LB@
166	0.004233	0.117	pa2585	uvrC	-12.59	0.046141	89 -- 105	106 -- 123	excinuclease ABC subunit C	_____________88_________________106\n_____________\|__________________\|\n5'-CGC...UCGCC___________A______AUCGC...UGG-3'\n______________GAAGACCGUGA_UA_CCU\n______________:\|\|:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UUUUUGGCACU_AU_GGA\n3'-UUU...CCCAG___________A__C___CUACU...GUU-5'\n_____________\|__________________\|\n_____________124________________105\n	93 -- 99	113 -- 119	-17.5883 kcal/mol	2.75927 kcal/mol	2.24138 kcal/mol	88 106@LB@ \| \|@LB@5'-CGC...UCGCC A AUCGC...UGG-3'@LB@ GAAGACCGUGA UA CCU@LB@ :\|\|:\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UUUUUGGCACU AU GGA@LB@3'-UUU...CCCAG A C CUACU...GUU-5'@LB@ \| \|@LB@ 124 105@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -17.5883 kcal/mol@LB@Unfolding Energy - mRNA 2.75927 kcal/mol@LB@Unfolding Energy - sRNA 2.24138 kcal/mol@LB@@LB@Position - mRNA 89 -- 105@LB@Position - sRNA 106 -- 123@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 113 -- 119@LB@
181	0.004727	0.1199	pa2509	catB	-12.44	0.050225	208 -- 226	106 -- 121	muconate cycloisomerase I	_____________207_________________227\n_____________\|___________________\|\n5'-GGC...GAGCC__________CCAA_____CGAGU...CCC-3'\n______________AAGCCGUGAU____AGCCU\n______________\|\|:\|\|\|\|\|\|\|____\|\|\|\|\|\n______________UUUGGCACUA____UCGGA\n3'-UUU...CAGUU__________A________CUACU...GUU-5'\n_____________\|___________________\|\n_____________122_________________105\n	211 -- 217	112 -- 118	-19.0549 kcal/mol	4.37421 kcal/mol	2.24058 kcal/mol	207 227@LB@ \| \|@LB@5'-GGC...GAGCC CCAA CGAGU...CCC-3'@LB@ AAGCCGUGAU AGCCU@LB@ \|\|:\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUGGCACUA UCGGA@LB@3'-UUU...CAGUU A CUACU...GUU-5'@LB@ \| \|@LB@ 122 105@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -19.0549 kcal/mol@LB@Unfolding Energy - mRNA 4.37421 kcal/mol@LB@Unfolding Energy - sRNA 2.24058 kcal/mol@LB@@LB@Position - mRNA 208 -- 226@LB@Position - sRNA 106 -- 121@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 112 -- 118@LB@
182	0.004765	0.1199	pa1522	N/A	-10.50	0.140829	28 -- 41	106 -- 119	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________27_____________42\n_____________\|______________\|\n5'-AUC...AGGAC_______CC_____CGCCG...CCG-3'\n______________GCCGUGG__AGCCU\n______________:\|\|\|\|\|:__\|\|\|\|\|\n______________UGGCACU__UCGGA\n3'-UUU...GUUUU_______AA_____CUACU...GUU-5'\n_____________\|______________\|\n_____________120____________105\n	28 -- 34	113 -- 119	-17.7026 kcal/mol	4.96349 kcal/mol	2.24014 kcal/mol	27 42@LB@ \| \|@LB@5'-AUC...AGGAC CC CGCCG...CCG-3'@LB@ GCCGUGG AGCCU@LB@ :\|\|\|\|\|: \|\|\|\|\|@LB@ UGGCACU UCGGA@LB@3'-UUU...GUUUU AA CUACU...GUU-5'@LB@ \| \|@LB@ 120 105@LB@@LB@@LB@Energy -10.50 kcal/mol@LB@Hybridization Energy -17.7026 kcal/mol@LB@Unfolding Energy - mRNA 4.96349 kcal/mol@LB@Unfolding Energy - sRNA 2.24014 kcal/mol@LB@@LB@Position - mRNA 28 -- 41@LB@Position - sRNA 106 -- 119@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 113 -- 119@LB@
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@

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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching