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
188	0.00503	0.1227	pa1766	N/A	-13.35	0.029524	230 -- 250	100 -- 120	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________229___________________251\n_____________\|_____________________\|\n5'-CGA...GACCU_____C__AA___G_______CAUCA...ACC-3'\n______________GACCG_GA__GGC_UGAUGGG\n______________:\|\|\|\|_\|\|__:\|\|_\|\|\|\|\|:\|\n______________UUGGC_CU__UCG_ACUACUC\n3'-UUU...AGUUU_____A__AA___G_______CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________121___________________99\n	244 -- 250	100 -- 106	-24.1459 kcal/mol	8.55357 kcal/mol	2.24919 kcal/mol	229 251@LB@ \| \|@LB@5'-CGA...GACCU C AA G CAUCA...ACC-3'@LB@ GACCG GA GGC UGAUGGG@LB@ :\|\|\|\| \|\| :\|\| \|\|\|\|\|:\|@LB@ UUGGC CU UCG ACUACUC@LB@3'-UUU...AGUUU A AA G CUCUA...GUU-5'@LB@ \| \|@LB@ 121 99@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -24.1459 kcal/mol@LB@Unfolding Energy - mRNA 8.55357 kcal/mol@LB@Unfolding Energy - sRNA 2.24919 kcal/mol@LB@@LB@Position - mRNA 230 -- 250@LB@Position - sRNA 100 -- 120@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 100 -- 106@LB@
12	1.22e-05	0.004211	pa3312	N/A	-10.60	0.134070	231 -- 250	100 -- 119	3-hydroxyisobutyrate dehydrogenase	_____________230__________________251\n_____________\|____________________\|\n5'-CGG...CCUUC____GUCUC___________CGUGC...UGU-3'\n______________GCCG_____GGCCUGAUGGG\n______________:\|\|\|_____:\|\|\|\|\|\|\|\|:\|\n______________UGGC_____UCGGACUACUC\n3'-UUU...GUUUU____ACUAA___________CUCUA...GUU-5'\n_____________\|____________________\|\n_____________120__________________99\n	244 -- 250	100 -- 106	-24.2186 kcal/mol	11.3713 kcal/mol	2.24903 kcal/mol	230 251@LB@ \| \|@LB@5'-CGG...CCUUC GUCUC CGUGC...UGU-3'@LB@ GCCG GGCCUGAUGGG@LB@ :\|\|\| :\|\|\|\|\|\|\|\|:\|@LB@ UGGC UCGGACUACUC@LB@3'-UUU...GUUUU ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 120 99@LB@@LB@@LB@Energy -10.60 kcal/mol@LB@Hybridization Energy -24.2186 kcal/mol@LB@Unfolding Energy - mRNA 11.3713 kcal/mol@LB@Unfolding Energy - sRNA 2.24903 kcal/mol@LB@@LB@Position - mRNA 231 -- 250@LB@Position - sRNA 100 -- 119@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 100 -- 106@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@
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@
45	0.0002969	0.02946	pa0151	N/A	-17.56	0.001552	238 -- 273	39 -- 82	TonB-dependent receptor	_____________237___________________________________________274\n_____________\|_____________________________________________\|\n5'-GCU...UCUCC___CC__________________C________________C____CCGUG...GCU-3'\n______________CCG__CUGU_____UC_CUCAGC___UCGGCUG_UCUCGC_GCCA\n______________\|\|\|__\|\|\|:_____\|\|_\|\|\|\|\|\|___:\|\|\|\|\|\|_\|\|\|\|\|\|_:\|\|\|\n______________GGC__GACG_____AG_GAGUCG___GGCCGAC_AGAGCG_UGGU\n3'-UUU...UCUCA___U_____CACCC__A______AAU_______U______C____CAACU...GUU-5'\n_____________\|_____________________________________________\|\n_____________83____________________________________________38\n	256 -- 262	51 -- 57	-45.5625 kcal/mol	9.11749 kcal/mol	18.8872 kcal/mol	237 274@LB@ \| \|@LB@5'-GCU...UCUCC CC C C CCGUG...GCU-3'@LB@ CCG CUGU UC CUCAGC UCGGCUG UCUCGC GCCA@LB@ \|\|\| \|\|\|: \|\| \|\|\|\|\|\| :\|\|\|\|\|\| \|\|\|\|\|\| :\|\|\|@LB@ GGC GACG AG GAGUCG GGCCGAC AGAGCG UGGU@LB@3'-UUU...UCUCA U CACCC A AAU U C CAACU...GUU-5'@LB@ \| \|@LB@ 83 38@LB@@LB@@LB@Energy -17.56 kcal/mol@LB@Hybridization Energy -45.5625 kcal/mol@LB@Unfolding Energy - mRNA 9.11749 kcal/mol@LB@Unfolding Energy - sRNA 18.8872 kcal/mol@LB@@LB@Position - mRNA 238 -- 273@LB@Position - sRNA 39 -- 82@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 51 -- 57@LB@
18	3.753e-05	0.009449	pa5036	gltB	-9.24	0.251750	240 -- 259	103 -- 120	glutamate synthase subunit alpha	_____________239__________________260\n_____________\|____________________\|\n5'-GAA...AGGAU_____CG__U__________CGCCC...AAA-3'\n______________AACUG__GA_UUGGCCUGAU\n______________\|\|\|:\|__\|\|_\|\|:\|\|\|\|\|\|\|\n______________UUGGC__CU_AAUCGGACUA\n3'-UUU...AGUUU_____A______________CUCCU...GUU-5'\n_____________\|____________________\|\n_____________121__________________102\n	253 -- 259	103 -- 109	-18.8705 kcal/mol	7.38825 kcal/mol	2.24268 kcal/mol	239 260@LB@ \| \|@LB@5'-GAA...AGGAU CG U CGCCC...AAA-3'@LB@ AACUG GA UUGGCCUGAU@LB@ \|\|\|:\| \|\| \|\|:\|\|\|\|\|\|\|@LB@ UUGGC CU AAUCGGACUA@LB@3'-UUU...AGUUU A CUCCU...GUU-5'@LB@ \| \|@LB@ 121 102@LB@@LB@@LB@Energy -9.24 kcal/mol@LB@Hybridization Energy -18.8705 kcal/mol@LB@Unfolding Energy - mRNA 7.38825 kcal/mol@LB@Unfolding Energy - sRNA 2.24268 kcal/mol@LB@@LB@Position - mRNA 240 -- 259@LB@Position - sRNA 103 -- 120@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 103 -- 109@LB@
69	0.0007462	0.0493	pa0882	N/A	-13.09	0.034380	240 -- 255	104 -- 119	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________239______________256\n_____________\|________________\|\n5'-CAA...GCAUC________C_______AGCAC...AUC-3'\n______________ACCGUGGU_AGCCUGG\n______________\|\|\|\|\|\|:\|_\|\|\|\|\|\|:\n______________UGGCACUA_UCGGACU\n3'-UUU...GUUUU________A_______ACUCC...GUU-5'\n_____________\|________________\|\n_____________120______________103\n	249 -- 255	104 -- 110	-23.473 kcal/mol	8.14152 kcal/mol	2.24159 kcal/mol	239 256@LB@ \| \|@LB@5'-CAA...GCAUC C AGCAC...AUC-3'@LB@ ACCGUGGU AGCCUGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|\|:@LB@ UGGCACUA UCGGACU@LB@3'-UUU...GUUUU A ACUCC...GUU-5'@LB@ \| \|@LB@ 120 103@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -23.473 kcal/mol@LB@Unfolding Energy - mRNA 8.14152 kcal/mol@LB@Unfolding Energy - sRNA 2.24159 kcal/mol@LB@@LB@Position - mRNA 240 -- 255@LB@Position - sRNA 104 -- 119@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 104 -- 110@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@
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@
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@

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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