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
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@
180	0.004705	0.1199	pa3616	N/A	-16.34	0.003989	120 -- 132	35 -- 47	recombination regulator RecX		_____________119___________133\n_____________\|_____________\|\n5'-GUC...ACCAU_____________CUGGC...UGC-3'\n______________UCGCGACCAGUUG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGCGCUGGUCAAC\n3'-UUU...ACUAG_____________UCACU...GUU-5'\n_____________\|_____________\|\n_____________48____________34\n	126 -- 132	35 -- 41	-23.7921 kcal/mol	3.77419 kcal/mol	3.68501 kcal/mol	119 133@LB@ \| \|@LB@5'-GUC...ACCAU CUGGC...UGC-3'@LB@ UCGCGACCAGUUG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGCGCUGGUCAAC@LB@3'-UUU...ACUAG UCACU...GUU-5'@LB@ \| \|@LB@ 48 34@LB@@LB@@LB@Energy -16.34 kcal/mol@LB@Hybridization Energy -23.7921 kcal/mol@LB@Unfolding Energy - mRNA 3.77419 kcal/mol@LB@Unfolding Energy - sRNA 3.68501 kcal/mol@LB@@LB@Position - mRNA 120 -- 132@LB@Position - sRNA 35 -- 47@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 35 -- 41@LB@
52	0.0004019	0.03518	pa4012	N/A	-10.34	0.152385	122 -- 132	100 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________121_________133\n_____________\|___________\|\n5'-CAU...CGAUG___________CGUUG...GCU-3'\n______________AGCCUGAUGGG\n______________\|\|\|\|\|\|\|\|\|:\|\n______________UCGGACUACUC\n3'-UUU...ACUAA___________CUCUA...GUU-5'\n_____________\|___________\|\n_____________111_________99\n	126 -- 132	100 -- 106	-17.6316 kcal/mol	5.13362 kcal/mol	2.15723 kcal/mol	121 133@LB@ \| \|@LB@5'-CAU...CGAUG CGUUG...GCU-3'@LB@ AGCCUGAUGGG@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ UCGGACUACUC@LB@3'-UUU...ACUAA CUCUA...GUU-5'@LB@ \| \|@LB@ 111 99@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -17.6316 kcal/mol@LB@Unfolding Energy - mRNA 5.13362 kcal/mol@LB@Unfolding Energy - sRNA 2.15723 kcal/mol@LB@@LB@Position - mRNA 122 -- 132@LB@Position - sRNA 100 -- 110@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 100 -- 106@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@
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@
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@
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@
137	0.002719	0.09122	pa5476	citA	-9.77	0.199491	137 -- 148	71 -- 82	citrate transporter	pa0703 pa4343	_____________136__________149\n_____________\|____________\|\n5'-UCG...CGUAC___C________CCAUC...CCG-3'\n______________CCG_CUGCGUGG\n______________\|\|\|_\|\|\|\|\|\|\|\|\n______________GGC_GACGCACC\n3'-UUU...UCUCA___U________CAGAG...GUU-5'\n_____________\|____________\|\n_____________83___________70\n	142 -- 148	71 -- 77	-20.5392 kcal/mol	6.66778 kcal/mol	4.10469 kcal/mol	136 149@LB@ \| \|@LB@5'-UCG...CGUAC C CCAUC...CCG-3'@LB@ CCG CUGCGUGG@LB@ \|\|\| \|\|\|\|\|\|\|\|@LB@ GGC GACGCACC@LB@3'-UUU...UCUCA U CAGAG...GUU-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -20.5392 kcal/mol@LB@Unfolding Energy - mRNA 6.66778 kcal/mol@LB@Unfolding Energy - sRNA 4.10469 kcal/mol@LB@@LB@Position - mRNA 137 -- 148@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 71 -- 77@LB@
59	0.0005101	0.0395	pa2173a	N/A	-13.53	0.026409	139 -- 150	107 -- 119			_____________138___________151\n_____________\|_____________\|\n5'-CAA...AACCU_____________AUGGG...CCC-3'\n______________GCCGUGAU_AGCC\n______________:\|\|\|\|\|\|\|_\|\|\|\|\n______________UGGCACUA_UCGG\n3'-UUU...GUUUU________A____ACUAC...GUU-5'\n_____________\|_____________\|\n_____________120___________106\n	140 -- 146	112 -- 118	-18.4805 kcal/mol	2.71645 kcal/mol	2.23484 kcal/mol	138 151@LB@ \| \|@LB@5'-CAA...AACCU AUGGG...CCC-3'@LB@ GCCGUGAU AGCC@LB@ :\|\|\|\|\|\|\| \|\|\|\|@LB@ UGGCACUA UCGG@LB@3'-UUU...GUUUU A ACUAC...GUU-5'@LB@ \| \|@LB@ 120 106@LB@@LB@@LB@Energy -13.53 kcal/mol@LB@Hybridization Energy -18.4805 kcal/mol@LB@Unfolding Energy - mRNA 2.71645 kcal/mol@LB@Unfolding Energy - sRNA 2.23484 kcal/mol@LB@@LB@Position - mRNA 139 -- 150@LB@Position - sRNA 107 -- 119@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 112 -- 118@LB@
97	0.001341	0.06355	pa3929	cioB	-12.35	0.052798	141 -- 190	33 -- 89	cyanide insensitive terminal oxidase		_____________140____________________________________________________________191\n_____________\|______________________________________________________________\|\n5'-UCG...UCGAC______CA____G______________C__GCA_G____C______________GACAA___GAACU...UCU-3'\n______________GAAGAG__CGAC_GC__________CA_GC___A_CGGC_GA_C_CGCGACCAG_____GAG\n______________\|\|\|\|\|\|__\|\|\|\|_\|\|__________\|\|_\|\|___\|_\|\|\|\|_\|\|_\|_\|\|\|\|\|\|\|\|\|_____\|\|\|\n______________CUUCUC__GCUG_CG__________GU_CG___U_GCCG_CU_G_GCGCUGGUC_____CUC\n3'-UUU...UUAGA______AG____A__CACCCAGAGA_____AA__G____A__A_A_________AA______ACUGU...GUU-5'\n_____________\|______________________________________________________________\|\n_____________90_____________________________________________________________32\n	176 -- 182	38 -- 44	-47.0211 kcal/mol	15.6367 kcal/mol	19.0341 kcal/mol	140 191@LB@ \| \|@LB@5'-UCG...UCGAC CA G C GCA G C GACAA GAACU...UCU-3'@LB@ GAAGAG CGAC GC CA GC A CGGC GA C CGCGACCAG GAG@LB@ \|\|\|\|\|\| \|\|\|\| \|\| \|\| \|\| \| \|\|\|\| \|\| \| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ CUUCUC GCUG CG GU CG U GCCG CU G GCGCUGGUC CUC@LB@3'-UUU...UUAGA AG A CACCCAGAGA AA G A A A AA ACUGU...GUU-5'@LB@ \| \|@LB@ 90 32@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -47.0211 kcal/mol@LB@Unfolding Energy - mRNA 15.6367 kcal/mol@LB@Unfolding Energy - sRNA 19.0341 kcal/mol@LB@@LB@Position - mRNA 141 -- 190@LB@Position - sRNA 33 -- 89@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 38 -- 44@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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