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
4	5.154e-07	0.0005922	pa1581	sdhC	-15.05	0.009907	206 -- 221	108 -- 123	succinate dehydrogenase subunit C		_____________205______________222\n_____________\|________________\|\n5'-ACG...GUGAA___________A____AAACG...CUG-3'\n______________AAAAGCCGUGA_UAGC\n______________\|\|\|\|:\|\|\|\|\|\|_\|\|\|\|\n______________UUUUUGGCACU_AUCG\n3'-UUU...CCCAG___________A____GACUA...GUU-5'\n_____________\|________________\|\n_____________124______________107\n	210 -- 216	113 -- 119	-19.67 kcal/mol	2.45872 kcal/mol	2.16544 kcal/mol	205 222@LB@ \| \|@LB@5'-ACG...GUGAA A AAACG...CUG-3'@LB@ AAAAGCCGUGA UAGC@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ UUUUUGGCACU AUCG@LB@3'-UUU...CCCAG A GACUA...GUU-5'@LB@ \| \|@LB@ 124 107@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -19.67 kcal/mol@LB@Unfolding Energy - mRNA 2.45872 kcal/mol@LB@Unfolding Energy - sRNA 2.16544 kcal/mol@LB@@LB@Position - mRNA 206 -- 221@LB@Position - sRNA 108 -- 123@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 113 -- 119@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@
76	0.0008254	0.04991	pa0029	N/A	-13.54	0.026240	35 -- 51	100 -- 123	sulfate transporter		_____________34_______________________52\n_____________\|________________________\|\n5'-GCU...ACAUG________________________CGACG...UGG-3'\n______________GAGAACC_______GCCUGAUGAG\n______________:\|:\|\|\|\|_______\|\|\|\|\|\|\|\|\|\|\n______________UUUUUGG_______CGGACUACUC\n3'-UUU...CCCAG_______CACUAAU__________CUCUA...GUU-5'\n_____________\|________________________\|\n_____________124______________________99\n	45 -- 51	100 -- 106	-21.4793 kcal/mol	5.69273 kcal/mol	2.24995 kcal/mol	34 52@LB@ \| \|@LB@5'-GCU...ACAUG CGACG...UGG-3'@LB@ GAGAACC GCCUGAUGAG@LB@ :\|:\|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ UUUUUGG CGGACUACUC@LB@3'-UUU...CCCAG CACUAAU CUCUA...GUU-5'@LB@ \| \|@LB@ 124 99@LB@@LB@@LB@Energy -13.54 kcal/mol@LB@Hybridization Energy -21.4793 kcal/mol@LB@Unfolding Energy - mRNA 5.69273 kcal/mol@LB@Unfolding Energy - sRNA 2.24995 kcal/mol@LB@@LB@Position - mRNA 35 -- 51@LB@Position - sRNA 100 -- 123@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 100 -- 106@LB@
77	0.0008517	0.05078	pa4366	sodB	-3.26	0.982782	263 -- 269	117 -- 123	superoxide dismutase		_____________262_____270\n_____________\|_______\|\n5'-GAC...UCCGC_______CUGGA...ACA-3'\n______________AGAAACC\n______________\|:\|\|\|\|\|\n______________UUUUUGG\n3'-UUU...CCCAG_______CACUA...GUU-5'\n_____________\|_______\|\n_____________124_____116\n	263 -- 269	117 -- 123	-5.6152 kcal/mol	1.17222 kcal/mol	1.17573 kcal/mol	262 270@LB@ \| \|@LB@5'-GAC...UCCGC CUGGA...ACA-3'@LB@ AGAAACC@LB@ \|:\|\|\|\|\|@LB@ UUUUUGG@LB@3'-UUU...CCCAG CACUA...GUU-5'@LB@ \| \|@LB@ 124 116@LB@@LB@@LB@Energy -3.26 kcal/mol@LB@Hybridization Energy -5.6152 kcal/mol@LB@Unfolding Energy - mRNA 1.17222 kcal/mol@LB@Unfolding Energy - sRNA 1.17573 kcal/mol@LB@@LB@Position - mRNA 263 -- 269@LB@Position - sRNA 117 -- 123@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 117 -- 123@LB@
127	0.002525	0.0912	pa3976	thiE	-9.31	0.244259	189 -- 204	101 -- 123	thiamine-phosphate pyrophosphorylase		_____________188_____________________205\n_____________\|_______________________\|\n5'-GCC...UCACU_______________________AACUG...GCC-3'\n______________GAGAGCC______AGCC_GAUGA\n______________:\|:\|:\|\|______\|\|\|\|_\|\|\|\|\|\n______________UUUUUGG______UCGG_CUACU\n3'-UUU...CCCAG_______CACUAA____A_____CCUCU...GUU-5'\n_____________\|_______________________\|\n_____________124_____________________100\n	189 -- 195	117 -- 123	-15.9836 kcal/mol	4.42969 kcal/mol	2.24445 kcal/mol	188 205@LB@ \| \|@LB@5'-GCC...UCACU AACUG...GCC-3'@LB@ GAGAGCC AGCC GAUGA@LB@ :\|:\|:\|\| \|\|\|\| \|\|\|\|\|@LB@ UUUUUGG UCGG CUACU@LB@3'-UUU...CCCAG CACUAA A CCUCU...GUU-5'@LB@ \| \|@LB@ 124 100@LB@@LB@@LB@Energy -9.31 kcal/mol@LB@Hybridization Energy -15.9836 kcal/mol@LB@Unfolding Energy - mRNA 4.42969 kcal/mol@LB@Unfolding Energy - sRNA 2.24445 kcal/mol@LB@@LB@Position - mRNA 189 -- 204@LB@Position - sRNA 101 -- 123@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 117 -- 123@LB@
81	0.0009408	0.05338	pa2962	tmk	-12.93	0.037833	94 -- 116	34 -- 55	thymidylate kinase		_____________93________________________117\n_____________\|_________________________\|\n5'-CGC...AACAA______________GUA________AGCGU...AGG-3'\n______________GGC_GGUC_CGCGA___CCAGUUGA\n______________\|\|\|_\|:\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________CCG_CUAG_GCGCU___GGUCAACU\n3'-UUU...AAUGG___A____A________________CACUG...GUU-5'\n_____________\|_________________________\|\n_____________56________________________33\n	110 -- 116	34 -- 40	-28.5201 kcal/mol	7.46572 kcal/mol	8.1291 kcal/mol	93 117@LB@ \| \|@LB@5'-CGC...AACAA GUA AGCGU...AGG-3'@LB@ GGC GGUC CGCGA CCAGUUGA@LB@ \|\|\| \|:\|\| \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CCG CUAG GCGCU GGUCAACU@LB@3'-UUU...AAUGG A A CACUG...GUU-5'@LB@ \| \|@LB@ 56 33@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -28.5201 kcal/mol@LB@Unfolding Energy - mRNA 7.46572 kcal/mol@LB@Unfolding Energy - sRNA 8.1291 kcal/mol@LB@@LB@Position - mRNA 94 -- 116@LB@Position - sRNA 34 -- 55@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 34 -- 40@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@
115	0.001984	0.07883	pa3002	mfd	-15.72	0.006234	203 -- 232	53 -- 84	transcription-repair coupling factor		_____________202_______________________________233\n_____________\|_________________________________\|\n5'-GAU...CCCGU_____U_______C______C____C_______CAGCG...CCG-3'\n______________GUCCG_ACUGCGU____UUC_CAGC_UGCCGGC\n______________\|\|\|\|\|_\|\|\|\|\|\|\|____:\|\|_\|\|\|\|_\|:\|\|\|\|\|\n______________CAGGC_UGACGCA____GAG_GUCG_AUGGCCG\n3'-UUU...CUUCU_____________CCCA___A____A_______ACUAG...GUU-5'\n_____________\|_________________________________\|\n_____________85________________________________52\n	226 -- 232	53 -- 59	-40.2071 kcal/mol	10.3261 kcal/mol	14.162 kcal/mol	202 233@LB@ \| \|@LB@5'-GAU...CCCGU U C C C CAGCG...CCG-3'@LB@ GUCCG ACUGCGU UUC CAGC UGCCGGC@LB@ \|\|\|\|\| \|\|\|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|@LB@ CAGGC UGACGCA GAG GUCG AUGGCCG@LB@3'-UUU...CUUCU CCCA A A ACUAG...GUU-5'@LB@ \| \|@LB@ 85 52@LB@@LB@@LB@Energy -15.72 kcal/mol@LB@Hybridization Energy -40.2071 kcal/mol@LB@Unfolding Energy - mRNA 10.3261 kcal/mol@LB@Unfolding Energy - sRNA 14.162 kcal/mol@LB@@LB@Position - mRNA 203 -- 232@LB@Position - sRNA 53 -- 84@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 53 -- 59@LB@
57	0.0004766	0.03843	pa1413	N/A	-13.23	0.031643	209 -- 220	33 -- 44	transcriptional regulator	pa0708 pa4203	_____________208__________221\n_____________\|____________\|\n5'-GGU...GAGUU____________GAUUU...CGA-3'\n______________CGGCCAGUUGAG\n______________\|\|:\|\|\|\|\|\|\|\|\|\n______________GCUGGUCAACUC\n3'-UUU...AGAGC____________ACUGU...GUU-5'\n_____________\|____________\|\n_____________45___________32\n	214 -- 220	33 -- 39	-19.8607 kcal/mol	4.38796 kcal/mol	2.24787 kcal/mol	208 221@LB@ \| \|@LB@5'-GGU...GAGUU GAUUU...CGA-3'@LB@ CGGCCAGUUGAG@LB@ \|\|:\|\|\|\|\|\|\|\|\|@LB@ GCUGGUCAACUC@LB@3'-UUU...AGAGC ACUGU...GUU-5'@LB@ \| \|@LB@ 45 32@LB@@LB@@LB@Energy -13.23 kcal/mol@LB@Hybridization Energy -19.8607 kcal/mol@LB@Unfolding Energy - mRNA 4.38796 kcal/mol@LB@Unfolding Energy - sRNA 2.24787 kcal/mol@LB@@LB@Position - mRNA 209 -- 220@LB@Position - sRNA 33 -- 44@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 33 -- 39@LB@
71	0.000767	0.0493	pa3381	N/A	-11.39	0.089379	127 -- 140	103 -- 116	transcriptional regulator		_____________126____________141\n_____________\|______________\|\n5'-UCC...UCGUG_____G________CGACG...CCG-3'\n______________GUGGU_AGCCUGAU\n______________\|\|\|:\|_\|\|\|\|\|\|\|\|\n______________CACUA_UCGGACUA\n3'-UUU...UUUGG_____A________CUCCU...GUU-5'\n_____________\|______________\|\n_____________117____________102\n	134 -- 140	103 -- 109	-18.8905 kcal/mol	5.35984 kcal/mol	2.14311 kcal/mol	126 141@LB@ \| \|@LB@5'-UCC...UCGUG G CGACG...CCG-3'@LB@ GUGGU AGCCUGAU@LB@ \|\|\|:\| \|\|\|\|\|\|\|\|@LB@ CACUA UCGGACUA@LB@3'-UUU...UUUGG A CUCCU...GUU-5'@LB@ \| \|@LB@ 117 102@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -18.8905 kcal/mol@LB@Unfolding Energy - mRNA 5.35984 kcal/mol@LB@Unfolding Energy - sRNA 2.14311 kcal/mol@LB@@LB@Position - mRNA 127 -- 140@LB@Position - sRNA 103 -- 116@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 103 -- 109@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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