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
79	0.0008761	0.05078	pa2577	N/A	-12.88	0.038908	242 -- 256	40 -- 55	transcriptional regulator		_____________241______________257\n_____________\|________________\|\n5'-CCA...CUCAU________________GUCCC...CGA-3'\n______________GGCUGA_CUCGCGACU\n______________\|\|\|\|\|\|_\|\|\|\|\|\|\|\|:\n______________CCGACU_GAGCGCUGG\n3'-UUU...AAUGG______A_________UCAAC...GUU-5'\n_____________\|________________\|\n_____________56_______________39\n	250 -- 256	40 -- 46	-27.0793 kcal/mol	6.12113 kcal/mol	8.07531 kcal/mol	241 257@LB@ \| \|@LB@5'-CCA...CUCAU GUCCC...CGA-3'@LB@ GGCUGA CUCGCGACU@LB@ \|\|\|\|\|\| \|\|\|\|\|\|\|\|:@LB@ CCGACU GAGCGCUGG@LB@3'-UUU...AAUGG A UCAAC...GUU-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -27.0793 kcal/mol@LB@Unfolding Energy - mRNA 6.12113 kcal/mol@LB@Unfolding Energy - sRNA 8.07531 kcal/mol@LB@@LB@Position - mRNA 242 -- 256@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 40 -- 46@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@
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@
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@
175	0.004467	0.1171	pa2047	N/A	-7.63	0.467709	171 -- 177	103 -- 109	transcriptional regulator		_____________170_____178\n_____________\|_______\|\n5'-CCC...UGCUU_______CCUGC...CCG-3'\n______________GCCUGAU\n______________\|\|\|\|\|\|\|\n______________CGGACUA\n3'-UUU...CUAAU_______CUCCU...GUU-5'\n_____________\|_______\|\n_____________110_____102\n	171 -- 177	103 -- 109	-11.5321 kcal/mol	1.79595 kcal/mol	2.10421 kcal/mol	170 178@LB@ \| \|@LB@5'-CCC...UGCUU CCUGC...CCG-3'@LB@ GCCUGAU@LB@ \|\|\|\|\|\|\|@LB@ CGGACUA@LB@3'-UUU...CUAAU CUCCU...GUU-5'@LB@ \| \|@LB@ 110 102@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.5321 kcal/mol@LB@Unfolding Energy - mRNA 1.79595 kcal/mol@LB@Unfolding Energy - sRNA 2.10421 kcal/mol@LB@@LB@Position - mRNA 171 -- 177@LB@Position - sRNA 103 -- 109@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 103 -- 109@LB@
145	0.003161	0.1002	pa4147	acoR	-9.16	0.260996	230 -- 255	98 -- 121	transcriptional regulator AcoR	pa4021	_____________229_________________________256\n_____________\|___________________________\|\n5'-UAG...CAUGU________UC_____G__UCC______ACGCC...UCG-3'\n______________GGACUGUG___AGCC_UG___UGAGGA\n______________::\|\|:\|\|\|___\|\|\|\|_\|\|___\|\|\|\|\|\|\n______________UUUGGCAC___UCGG_AC___ACUCCU\n3'-UUU...CAGUU________UAA_______U________CUAUU...GUU-5'\n_____________\|___________________________\|\n_____________122_________________________97\n	231 -- 237	114 -- 120	-22.6885 kcal/mol	11.2814 kcal/mol	2.25186 kcal/mol	229 256@LB@ \| \|@LB@5'-UAG...CAUGU UC G UCC ACGCC...UCG-3'@LB@ GGACUGUG AGCC UG UGAGGA@LB@ ::\|\|:\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|@LB@ UUUGGCAC UCGG AC ACUCCU@LB@3'-UUU...CAGUU UAA U CUAUU...GUU-5'@LB@ \| \|@LB@ 122 97@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -22.6885 kcal/mol@LB@Unfolding Energy - mRNA 11.2814 kcal/mol@LB@Unfolding Energy - sRNA 2.25186 kcal/mol@LB@@LB@Position - mRNA 230 -- 255@LB@Position - sRNA 98 -- 121@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 114 -- 120@LB@
103	0.001681	0.07499	pa3587	metR	-12.26	0.055812	244 -- 261	101 -- 121	transcriptional regulator MetR		_____________243___________________262\n_____________\|_____________________\|\n5'-CAG...GCGCG______AC_____________AAGCC...UGU-3'\n______________AAGCCG_____AGCCUGGUGG\n______________\|\|:\|\|\|_____\|\|\|\|\|\|:\|\|:\n______________UUUGGC_____UCGGACUACU\n3'-UUU...CAGUU______ACUAA__________CCUCU...GUU-5'\n_____________\|_____________________\|\n_____________122___________________100\n	255 -- 261	101 -- 107	-20.5431 kcal/mol	6.04584 kcal/mol	2.24386 kcal/mol	243 262@LB@ \| \|@LB@5'-CAG...GCGCG AC AAGCC...UGU-3'@LB@ AAGCCG AGCCUGGUGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|:\|\|:@LB@ UUUGGC UCGGACUACU@LB@3'-UUU...CAGUU ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 122 100@LB@@LB@@LB@Energy -12.26 kcal/mol@LB@Hybridization Energy -20.5431 kcal/mol@LB@Unfolding Energy - mRNA 6.04584 kcal/mol@LB@Unfolding Energy - sRNA 2.24386 kcal/mol@LB@@LB@Position - mRNA 244 -- 261@LB@Position - sRNA 101 -- 121@LB@Position Seed - mRNA 255 -- 261@LB@Position Seed - sRNA 101 -- 107@LB@
129	0.002597	0.0912	pa2983	N/A	-10.36	0.150975	196 -- 207	70 -- 82	translocation protein TolQ		_____________195___________208\n_____________\|_____________\|\n5'-AGC...AUAUG_____________AACUG...UGC-3'\n______________CC_ACUGUGUGGG\n______________\|\|_\|\|\|\|:\|\|\|\|\|\n______________GG_UGACGCACCC\n3'-UUU...UCUCA__C__________AGAGA...GUU-5'\n_____________\|_____________\|\n_____________83____________69\n	201 -- 207	70 -- 76	-20.9892 kcal/mol	6.52553 kcal/mol	4.10497 kcal/mol	195 208@LB@ \| \|@LB@5'-AGC...AUAUG AACUG...UGC-3'@LB@ CC ACUGUGUGGG@LB@ \|\| \|\|\|\|:\|\|\|\|\|@LB@ GG UGACGCACCC@LB@3'-UUU...UCUCA C AGAGA...GUU-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -20.9892 kcal/mol@LB@Unfolding Energy - mRNA 6.52553 kcal/mol@LB@Unfolding Energy - sRNA 4.10497 kcal/mol@LB@@LB@Position - mRNA 196 -- 207@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 70 -- 76@LB@
19	3.906e-05	0.009449	pa0443	N/A	-14.62	0.013168	152 -- 204	75 -- 119	transporter		_____________151______________________________________________________205\n_____________\|________________________________________________________\|\n5'-UUG...CGGCC____C________C______C_______CUAAAAGAAU_________G__CA____AACAG...UCG-3'\n______________AUCG__AUUAGCC_GAUGAG_GA_AUAA__________UCUGGAGAG_CC___UGC\n______________\|:\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\|_\|\|_\|\|\|\|__________\|\|\|\|:\|\|\|\|_\|\|___\|\|\|\n______________UGGC__UAAUCGG_CUACUC_CU_UAUU__________AGACUUCUC_GG___ACG\n3'-UUU...GUUUU____AC_______A_________C_______________________A__CUG___CACCC...GUU-5'\n_____________\|________________________________________________________\|\n_____________120______________________________________________________74\n	190 -- 196	84 -- 90	-39.3471 kcal/mol	12.5408 kcal/mol	12.1884 kcal/mol	151 205@LB@ \| \|@LB@5'-UUG...CGGCC C C C CUAAAAGAAU G CA AACAG...UCG-3'@LB@ AUCG AUUAGCC GAUGAG GA AUAA UCUGGAGAG CC UGC@LB@ \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|:\|\|\|\| \|\| \|\|\|@LB@ UGGC UAAUCGG CUACUC CU UAUU AGACUUCUC GG ACG@LB@3'-UUU...GUUUU AC A C A CUG CACCC...GUU-5'@LB@ \| \|@LB@ 120 74@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -39.3471 kcal/mol@LB@Unfolding Energy - mRNA 12.5408 kcal/mol@LB@Unfolding Energy - sRNA 12.1884 kcal/mol@LB@@LB@Position - mRNA 152 -- 204@LB@Position - sRNA 75 -- 119@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 84 -- 90@LB@
11	1.195e-05	0.004211	pa3638	N/A	-14.67	0.012752	102 -- 115	100 -- 120	tRNA(Ile)-lysidine synthase		_____________101___________________116\n_____________\|_____________________\|\n5'-GCG...GUUAC_____________________CUACG...CCA-3'\n______________GACC_______GCCUGAUGAG\n______________:\|\|\|_______\|\|\|\|\|\|\|\|\|\|\n______________UUGG_______CGGACUACUC\n3'-UUU...AGUUU____CACUAAU__________CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________121___________________99\n	109 -- 115	100 -- 106	-19.8992 kcal/mol	2.98005 kcal/mol	2.24919 kcal/mol	101 116@LB@ \| \|@LB@5'-GCG...GUUAC CUACG...CCA-3'@LB@ GACC GCCUGAUGAG@LB@ :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUGG CGGACUACUC@LB@3'-UUU...AGUUU CACUAAU CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -14.67 kcal/mol@LB@Hybridization Energy -19.8992 kcal/mol@LB@Unfolding Energy - mRNA 2.98005 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 102 -- 115@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 109 -- 115@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)

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