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
186	0.004909	0.1213	pa3889	N/A	-13.61	0.025105	195 -- 204	101 -- 110	ABC transporter		_____________194________205\n_____________\|__________\|\n5'-GUC...AAGGA__________ACCGA...UCA-3'\n______________GGCCUGAUGA\n______________:\|\|\|\|\|\|\|\|\|\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	198 -- 204	101 -- 107	-17.7978 kcal/mol	2.07405 kcal/mol	2.11196 kcal/mol	194 205@LB@ \| \|@LB@5'-GUC...AAGGA ACCGA...UCA-3'@LB@ GGCCUGAUGA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -17.7978 kcal/mol@LB@Unfolding Energy - mRNA 2.07405 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 195 -- 204@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 101 -- 107@LB@
187	0.004933	0.1213	pa0613	N/A	-16.40	0.003821	197 -- 220	101 -- 120	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________196______________________221\n_____________\|________________________\|\n5'-GAC...GACAC_________CAA____AUC_____AAUGC...CCA-3'\n______________GACCGUGAU___AGCC___GAUGA\n______________:\|\|\|\|\|\|\|\|___\|\|\|\|___\|\|\|\|\|\n______________UUGGCACUA___UCGG___CUACU\n3'-UUU...AGUUU_________A______A_______CCUCU...GUU-5'\n_____________\|________________________\|\n_____________121______________________100\n	199 -- 205	112 -- 118	-24.1405 kcal/mol	5.50451 kcal/mol	2.2437 kcal/mol	196 221@LB@ \| \|@LB@5'-GAC...GACAC CAA AUC AAUGC...CCA-3'@LB@ GACCGUGAU AGCC GAUGA@LB@ :\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|@LB@ UUGGCACUA UCGG CUACU@LB@3'-UUU...AGUUU A A CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -24.1405 kcal/mol@LB@Unfolding Energy - mRNA 5.50451 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 197 -- 220@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 112 -- 118@LB@
199	0.005488	0.1268	pa1158	N/A	-11.27	0.095596	213 -- 231	101 -- 120	two-component sensor		_____________212__________________232\n_____________\|____________________\|\n5'-GCG...GACGC_____C_CGC__________ACGGC...CCG-3'\n______________AGCCG_G____GCCUGAUGA\n______________\|:\|\|\|_\|____\|\|\|\|\|\|\|\|\|\n______________UUGGC_C____CGGACUACU\n3'-UUU...AGUUU_____A_UAAU_________CCUCU...GUU-5'\n_____________\|____________________\|\n_____________121__________________100\n	225 -- 231	101 -- 107	-21.6813 kcal/mol	8.17512 kcal/mol	2.2437 kcal/mol	212 232@LB@ \| \|@LB@5'-GCG...GACGC C CGC ACGGC...CCG-3'@LB@ AGCCG G GCCUGAUGA@LB@ \|:\|\|\| \| \|\|\|\|\|\|\|\|\|@LB@ UUGGC C CGGACUACU@LB@3'-UUU...AGUUU A UAAU CCUCU...GUU-5'@LB@ \| \|@LB@ 121 100@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -21.6813 kcal/mol@LB@Unfolding Energy - mRNA 8.17512 kcal/mol@LB@Unfolding Energy - sRNA 2.2437 kcal/mol@LB@@LB@Position - mRNA 213 -- 231@LB@Position - sRNA 101 -- 120@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 101 -- 107@LB@
63	0.0005567	0.04061	pa4538	ndh	-15.78	0.005953	57 -- 71	102 -- 118	NADH dehydrogenase		_____________56________________72\n_____________\|_________________\|\n5'-AGG...UCCGC_________________UUCGU...UCA-3'\n______________CCGUGGUU__CCUGAUG\n______________\|\|\|\|\|:\|\|__\|\|\|\|\|\|\|\n______________GGCACUAA__GGACUAC\n3'-UUU...UUUUU________UC_______UCCUC...GUU-5'\n_____________\|_________________\|\n_____________119_______________101\n	65 -- 71	102 -- 108	-20.7877 kcal/mol	2.76363 kcal/mol	2.2426 kcal/mol	56 72@LB@ \| \|@LB@5'-AGG...UCCGC UUCGU...UCA-3'@LB@ CCGUGGUU CCUGAUG@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|\|\|@LB@ GGCACUAA GGACUAC@LB@3'-UUU...UUUUU UC UCCUC...GUU-5'@LB@ \| \|@LB@ 119 101@LB@@LB@@LB@Energy -15.78 kcal/mol@LB@Hybridization Energy -20.7877 kcal/mol@LB@Unfolding Energy - mRNA 2.76363 kcal/mol@LB@Unfolding Energy - sRNA 2.2426 kcal/mol@LB@@LB@Position - mRNA 57 -- 71@LB@Position - sRNA 102 -- 118@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 102 -- 108@LB@
157	0.003825	0.112	pa0687	N/A	-10.29	0.156397	189 -- 203	102 -- 118	type II secretion system protein	pa3102	_____________188_______________204\n_____________\|_________________\|\n5'-AGC...GUGAC___G__C__________CAGAC...GCG-3'\n______________CCG_GA___GCCUGAUG\n______________\|\|\|_\|\|___\|\|\|\|\|\|\|\|\n______________GGC_CU___CGGACUAC\n3'-UUU...UUUUU___A__AAU________UCCUC...GUU-5'\n_____________\|_________________\|\n_____________119_______________101\n	197 -- 203	102 -- 108	-18.3707 kcal/mol	5.84542 kcal/mol	2.2426 kcal/mol	188 204@LB@ \| \|@LB@5'-AGC...GUGAC G C CAGAC...GCG-3'@LB@ CCG GA GCCUGAUG@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ GGC CU CGGACUAC@LB@3'-UUU...UUUUU A AAU UCCUC...GUU-5'@LB@ \| \|@LB@ 119 101@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -18.3707 kcal/mol@LB@Unfolding Energy - mRNA 5.84542 kcal/mol@LB@Unfolding Energy - sRNA 2.2426 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 102 -- 118@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 102 -- 108@LB@
193	0.005243	0.1243	pa3725	recJ	-10.65	0.130688	184 -- 203	102 -- 119	single-stranded-DNA-specific exonuclease RecJ		_____________183__________________204\n_____________\|____________________\|\n5'-CGU...GUCGA____AAC__GUGA_______CGUAU...GCG-3'\n______________GCCG___GA____CCUGAUG\n______________:\|\|\|___\|\|____\|\|\|\|\|\|\|\n______________UGGC___CU____GGACUAC\n3'-UUU...GUUUU____A____AAUC_______UCCUC...GUU-5'\n_____________\|____________________\|\n_____________120__________________101\n	197 -- 203	102 -- 108	-15.7224 kcal/mol	2.82992 kcal/mol	2.24274 kcal/mol	183 204@LB@ \| \|@LB@5'-CGU...GUCGA AAC GUGA CGUAU...GCG-3'@LB@ GCCG GA CCUGAUG@LB@ :\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UGGC CU GGACUAC@LB@3'-UUU...GUUUU A AAUC UCCUC...GUU-5'@LB@ \| \|@LB@ 120 101@LB@@LB@@LB@Energy -10.65 kcal/mol@LB@Hybridization Energy -15.7224 kcal/mol@LB@Unfolding Energy - mRNA 2.82992 kcal/mol@LB@Unfolding Energy - sRNA 2.24274 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 102 -- 119@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 102 -- 108@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@
47	0.0003012	0.02946	pa1776	sigX	-11.73	0.074706	90 -- 102	103 -- 115	RNA polymerase sigma factor SigX		_____________89____________103\n_____________\|_____________\|\n5'-CGU...CGAUA___C_________CUCAC...UGU-3'\n______________UGA_UGGCCUGAU\n______________\|\|\|_\|:\|\|\|\|\|\|\|\n______________ACU_AUCGGACUA\n3'-UUU...UUGGC___A_________CUCCU...GUU-5'\n_____________\|_____________\|\n_____________116___________102\n	96 -- 102	103 -- 109	-16.1519 kcal/mol	2.30076 kcal/mol	2.12156 kcal/mol	89 103@LB@ \| \|@LB@5'-CGU...CGAUA C CUCAC...UGU-3'@LB@ UGA UGGCCUGAU@LB@ \|\|\| \|:\|\|\|\|\|\|\|@LB@ ACU AUCGGACUA@LB@3'-UUU...UUGGC A CUCCU...GUU-5'@LB@ \| \|@LB@ 116 102@LB@@LB@@LB@Energy -11.73 kcal/mol@LB@Hybridization Energy -16.1519 kcal/mol@LB@Unfolding Energy - mRNA 2.30076 kcal/mol@LB@Unfolding Energy - sRNA 2.12156 kcal/mol@LB@@LB@Position - mRNA 90 -- 102@LB@Position - sRNA 103 -- 115@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 103 -- 109@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@
113	0.001932	0.07857	pa1964	N/A	-9.53	0.221537	258 -- 274	103 -- 120	ABC-F family ATPase		_____________257________________275\n_____________\|__________________\|\n5'-GCA...ACGGC_____CUAC_________CGGCG...CGA-3'\n______________AACCG_____GGCCUGAU\n______________\|\|\|\|\|_____:\|\|\|\|\|\|\|\n______________UUGGC_____UCGGACUA\n3'-UUU...AGUUU_____ACUAA________CUCCU...GUU-5'\n_____________\|__________________\|\n_____________121________________102\n	268 -- 274	103 -- 109	-16.8873 kcal/mol	5.11311 kcal/mol	2.24268 kcal/mol	257 275@LB@ \| \|@LB@5'-GCA...ACGGC CUAC CGGCG...CGA-3'@LB@ AACCG GGCCUGAU@LB@ \|\|\|\|\| :\|\|\|\|\|\|\|@LB@ UUGGC UCGGACUA@LB@3'-UUU...AGUUU ACUAA CUCCU...GUU-5'@LB@ \| \|@LB@ 121 102@LB@@LB@@LB@Energy -9.53 kcal/mol@LB@Hybridization Energy -16.8873 kcal/mol@LB@Unfolding Energy - mRNA 5.11311 kcal/mol@LB@Unfolding Energy - sRNA 2.24268 kcal/mol@LB@@LB@Position - mRNA 258 -- 274@LB@Position - sRNA 103 -- 120@LB@Position Seed - mRNA 268 -- 274@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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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

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