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
72	0.0007723	0.0493	pa2659	N/A	-15.67	0.006436	157 -- 217	75 -- 121	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________156____________________________________________________________218\n_____________\|______________________________________________________________\|\n5'-UUG...UCUGC_______C__A____AACAC__U___UUCCCAC_____GAU__CCA______AA________CCUGU...UGC-3'\n______________AAACCGU_GA__AGC_____GA_UGA_______GGAGA___UC___UGAAGA__CUGACUGC\n______________\|\|\|\|\|\|\|_\|\|__\|\|\|_____\|\|_\|\|\|_______\|\|\|\|\|___\|\|___\|\|\|\|\|\|__\|:\|\|\|\|\|\|\n______________UUUGGCA_CU__UCG_____CU_ACU_______CCUCU___AG___ACUUCU__GGCUGACG\n3'-UUU...CAGUU__________AA___GA_____________________AUU___________CA________CACCC...GUU-5'\n_____________\|______________________________________________________________\|\n_____________122____________________________________________________________74\n	211 -- 217	75 -- 81	-37.728 kcal/mol	9.87154 kcal/mol	12.1884 kcal/mol	156 218@LB@ \| \|@LB@5'-UUG...UCUGC C A AACAC U UUCCCAC GAU CCA AA CCUGU...UGC-3'@LB@ AAACCGU GA AGC GA UGA GGAGA UC UGAAGA CUGACUGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\| \|\| \|\|\| \|\|\|\|\| \|\| \|\|\|\|\|\| \|:\|\|\|\|\|\|@LB@ UUUGGCA CU UCG CU ACU CCUCU AG ACUUCU GGCUGACG@LB@3'-UUU...CAGUU AA GA AUU CA CACCC...GUU-5'@LB@ \| \|@LB@ 122 74@LB@@LB@@LB@Energy -15.67 kcal/mol@LB@Hybridization Energy -37.728 kcal/mol@LB@Unfolding Energy - mRNA 9.87154 kcal/mol@LB@Unfolding Energy - sRNA 12.1884 kcal/mol@LB@@LB@Position - mRNA 157 -- 217@LB@Position - sRNA 75 -- 121@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 75 -- 81@LB@
83	0.001018	0.05635	pa1553	ccoO1	-12.95	0.037511	176 -- 198	75 -- 98	cbb3-type cytochrome C oxidase subunit II	pa1556	_____________175______________________199\n_____________\|________________________\|\n5'-AAC...CGCGC____CGC________C________AAAUG...UGU-3'\n______________AGAU___CUGAGGAG_CCGAC_GU\n______________\|\|\|\|___\|\|\|\|:\|\|\|_\|\|\|\|\|_\|:\n______________UCUA___GACUUCUC_GGCUG_CG\n3'-UUU...ACUCC____UUA________A_____A__CACCC...GUU-5'\n_____________\|________________________\|\n_____________99_______________________74\n	184 -- 190	84 -- 90	-23.7581 kcal/mol	4.66617 kcal/mol	6.14905 kcal/mol	175 199@LB@ \| \|@LB@5'-AAC...CGCGC CGC C AAAUG...UGU-3'@LB@ AGAU CUGAGGAG CCGAC GU@LB@ \|\|\|\| \|\|\|\|:\|\|\| \|\|\|\|\| \|:@LB@ UCUA GACUUCUC GGCUG CG@LB@3'-UUU...ACUCC UUA A A CACCC...GUU-5'@LB@ \| \|@LB@ 99 74@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 4.66617 kcal/mol@LB@Unfolding Energy - sRNA 6.14905 kcal/mol@LB@@LB@Position - mRNA 176 -- 198@LB@Position - sRNA 75 -- 98@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 84 -- 90@LB@
93	0.001289	0.06355	pa4454	N/A	-9.11	0.266760	170 -- 178	75 -- 83	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________169_______179\n_____________\|_________\|\n5'-CCG...UUCAU_________UUUGA...UGG-3'\n______________UCUGACUGC\n______________\|\|:\|\|\|\|\|\|\n______________AGGCUGACG\n3'-UUU...UUCUC_________CACCC...GUU-5'\n_____________\|_________\|\n_____________84________74\n	172 -- 178	75 -- 81	-14.8179 kcal/mol	1.6159 kcal/mol	4.09544 kcal/mol	169 179@LB@ \| \|@LB@5'-CCG...UUCAU UUUGA...UGG-3'@LB@ UCUGACUGC@LB@ \|\|:\|\|\|\|\|\|@LB@ AGGCUGACG@LB@3'-UUU...UUCUC CACCC...GUU-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -9.11 kcal/mol@LB@Hybridization Energy -14.8179 kcal/mol@LB@Unfolding Energy - mRNA 1.6159 kcal/mol@LB@Unfolding Energy - sRNA 4.09544 kcal/mol@LB@@LB@Position - mRNA 170 -- 178@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 172 -- 178@LB@Position Seed - sRNA 75 -- 81@LB@
94	0.001308	0.06355	pa1587	lpdG	-9.92	0.185926	282 -- 296	75 -- 91	2-oxoglutarate dehydrogenase complex dihydrolipoyl dehydrogenase		_____________281_______________297\n_____________\|_________________\|\n5'-GUG...UGGGC____________C____AUCG-3'\n______________CUGAAGA__CCG_CUGC\n______________\|\|\|\|\|\|\|__\|\|\|_\|\|\|\|\n______________GACUUCU__GGC_GACG\n3'-UUU...UAUUA_______CA___U____CACCC...GUU-5'\n_____________\|_________________\|\n_____________92________________74\n	282 -- 288	85 -- 91	-18.2743 kcal/mol	2.47066 kcal/mol	5.88668 kcal/mol	281 297@LB@ \| \|@LB@5'-GUG...UGGGC C AUCG-3'@LB@ CUGAAGA CCG CUGC@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|@LB@ GACUUCU GGC GACG@LB@3'-UUU...UAUUA CA U CACCC...GUU-5'@LB@ \| \|@LB@ 92 74@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -18.2743 kcal/mol@LB@Unfolding Energy - mRNA 2.47066 kcal/mol@LB@Unfolding Energy - sRNA 5.88668 kcal/mol@LB@@LB@Position - mRNA 282 -- 296@LB@Position - sRNA 75 -- 91@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 85 -- 91@LB@
98	0.001381	0.06477	pa5040	pilQ	-10.76	0.123916	69 -- 120	75 -- 117	type 4 fimbrial biogenesis outer membrane protein PilQ		_____________68_____________________________________________________121\n_____________\|______________________________________________________\|\n5'-GUG...AUAGA______CGAAAUCGUU_____CGGA_______ACUGG______C__________AGCCU...CAC-3'\n______________CGUGAU__________CCUGA____GAGGGGA_____CUGGAG_GUCCG_C_GC\n______________\|\|\|\|\|\|__________\|\|\|\|\|____\|\|\|\|:\|\|_____\|\|\|:\|\|_\|\|\|\|\|_\|_\|\|\n______________GCACUA__________GGACU____CUCCUCU_____GACUUC_CAGGC_G_CG\n3'-UUU...UUUUG______AUC____________A__________AUUA_______U_____U_A__CACCC...GUU-5'\n_____________\|______________________________________________________\|\n_____________118____________________________________________________74\n	94 -- 100	96 -- 102	-39.923 kcal/mol	16.9987 kcal/mol	12.1721 kcal/mol	68 121@LB@ \| \|@LB@5'-GUG...AUAGA CGAAAUCGUU CGGA ACUGG C AGCCU...CAC-3'@LB@ CGUGAU CCUGA GAGGGGA CUGGAG GUCCG C GC@LB@ \|\|\|\|\|\| \|\|\|\|\| \|\|\|\|:\|\| \|\|\|:\|\| \|\|\|\|\| \| \|\|@LB@ GCACUA GGACU CUCCUCU GACUUC CAGGC G CG@LB@3'-UUU...UUUUG AUC A AUUA U U A CACCC...GUU-5'@LB@ \| \|@LB@ 118 74@LB@@LB@@LB@Energy -10.76 kcal/mol@LB@Hybridization Energy -39.923 kcal/mol@LB@Unfolding Energy - mRNA 16.9987 kcal/mol@LB@Unfolding Energy - sRNA 12.1721 kcal/mol@LB@@LB@Position - mRNA 69 -- 120@LB@Position - sRNA 75 -- 117@LB@Position Seed - mRNA 94 -- 100@LB@Position Seed - sRNA 96 -- 102@LB@
109	0.001808	0.07562	pa0202	N/A	-7.70	0.456423	178 -- 185	75 -- 82	amidase	pa4342	_____________177______186\n_____________\|________\|\n5'-CCC...CCUUC________CAAGG...UGC-3'\n______________UCGACUGC\n______________:\|\|\|\|\|\|\|\n______________GGCUGACG\n3'-UUU...UCUCA________CACCC...GUU-5'\n_____________\|________\|\n_____________83_______74\n	179 -- 185	75 -- 81	-13.4138 kcal/mol	1.61599 kcal/mol	4.09516 kcal/mol	177 186@LB@ \| \|@LB@5'-CCC...CCUUC CAAGG...UGC-3'@LB@ UCGACUGC@LB@ :\|\|\|\|\|\|\|@LB@ GGCUGACG@LB@3'-UUU...UCUCA CACCC...GUU-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -7.70 kcal/mol@LB@Hybridization Energy -13.4138 kcal/mol@LB@Unfolding Energy - mRNA 1.61599 kcal/mol@LB@Unfolding Energy - sRNA 4.09516 kcal/mol@LB@@LB@Position - mRNA 178 -- 185@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 75 -- 81@LB@
178	0.004573	0.1181	pa0900	N/A	-12.48	0.049102	209 -- 242	75 -- 111	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________208___________________________________243\n_____________\|_____________________________________\|\n5'-UCC...UCCGA_______CAACU_____CC________UA_____G__ACCCA...UGU-3'\n______________UAGCCUG_______GAU__UC_GAAGA__CCGAC_GC\n______________\|\|\|\|\|\|\|_______\|\|\|__\|\|_\|\|\|\|\|__\|\|\|\|\|_\|\|\n______________AUCGGAC_______CUA__AG_CUUCU__GGCUG_CG\n3'-UUU...CACUA_______UACUCCU___UU__A_____CA_____A__CACCC...GUU-5'\n_____________\|_____________________________________\|\n_____________112___________________________________74\n	209 -- 215	105 -- 111	-29.9732 kcal/mol	5.9478 kcal/mol	11.5432 kcal/mol	208 243@LB@ \| \|@LB@5'-UCC...UCCGA CAACU CC UA G ACCCA...UGU-3'@LB@ UAGCCUG GAU UC GAAGA CCGAC GC@LB@ \|\|\|\|\|\|\| \|\|\| \|\| \|\|\|\|\| \|\|\|\|\| \|\|@LB@ AUCGGAC CUA AG CUUCU GGCUG CG@LB@3'-UUU...CACUA UACUCCU UU A CA A CACCC...GUU-5'@LB@ \| \|@LB@ 112 74@LB@@LB@@LB@Energy -12.48 kcal/mol@LB@Hybridization Energy -29.9732 kcal/mol@LB@Unfolding Energy - mRNA 5.9478 kcal/mol@LB@Unfolding Energy - sRNA 11.5432 kcal/mol@LB@@LB@Position - mRNA 209 -- 242@LB@Position - sRNA 75 -- 111@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 105 -- 111@LB@
91	0.001223	0.06177	pa3618	N/A	-14.35	0.015718	191 -- 224	76 -- 123	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________190_______________________________________________225\n_____________\|_________________________________________________\|\n5'-GAG...CCCUG______A_____GAC_______________________________C__ACCGC...CCG-3'\n______________GAGAAC_GUGAU___CCUGAUG_______________GAGUCCGAC_UG\n______________:\|:\|\|\|_\|\|\|\|\|___\|\|\|\|\|\|\|_______________\|\|\|\|\|\|\|\|\|_\|\|\n______________UUUUUG_CACUA___GGACUAC_______________CUCAGGCUG_AC\n3'-UUU...CCCAG______G_____AUC_______UCCUCUAUUAGACUU____________GCACC...GUU-5'\n_____________\|_________________________________________________\|\n_____________124_______________________________________________75\n	215 -- 221	78 -- 84	-35.9898 kcal/mol	9.49172 kcal/mol	12.1513 kcal/mol	190 225@LB@ \| \|@LB@5'-GAG...CCCUG A GAC C ACCGC...CCG-3'@LB@ GAGAAC GUGAU CCUGAUG GAGUCCGAC UG@LB@ :\|:\|\|\| \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|@LB@ UUUUUG CACUA GGACUAC CUCAGGCUG AC@LB@3'-UUU...CCCAG G AUC UCCUCUAUUAGACUU GCACC...GUU-5'@LB@ \| \|@LB@ 124 75@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -35.9898 kcal/mol@LB@Unfolding Energy - mRNA 9.49172 kcal/mol@LB@Unfolding Energy - sRNA 12.1513 kcal/mol@LB@@LB@Position - mRNA 191 -- 224@LB@Position - sRNA 76 -- 123@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 78 -- 84@LB@
9	1.098e-05	0.004211	pa0119	N/A	-18.72	0.000584	256 -- 296	78 -- 118	C4-dicarboxylate transporter DctA	pa5479 pa1183	_____________255________________________________________297\n_____________\|__________________________________________\|\n5'-GCC...GCAAG__________________UA__C________C__________AUUC-3'\n______________UCGUGAUUGGCCUGGUGA__GG_GUGAUCUG_GGGGU_CGGC\n______________:\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|__:\|_:\|:\|\|\|\|\|_:\|:\|\|_\|\|:\|\n______________GGCACUAAUCGGACUACU__UC_UAUUAGAC_UCUCA_GCUG\n3'-UUU...UUUUU__________________CC___________U_____G____ACGCA...GUU-5'\n_____________\|__________________________________________\|\n_____________119________________________________________77\n	267 -- 273	101 -- 107	-51.6638 kcal/mol	20.8263 kcal/mol	12.1236 kcal/mol	255 297@LB@ \| \|@LB@5'-GCC...GCAAG UA C C AUUC-3'@LB@ UCGUGAUUGGCCUGGUGA GG GUGAUCUG GGGGU CGGC@LB@ :\|\|\|\|\|\|\|:\|\|\|\|\|:\|\|\| :\| :\|:\|\|\|\|\| :\|:\|\| \|\|:\|@LB@ GGCACUAAUCGGACUACU UC UAUUAGAC UCUCA GCUG@LB@3'-UUU...UUUUU CC U G ACGCA...GUU-5'@LB@ \| \|@LB@ 119 77@LB@@LB@@LB@Energy -18.72 kcal/mol@LB@Hybridization Energy -51.6638 kcal/mol@LB@Unfolding Energy - mRNA 20.8263 kcal/mol@LB@Unfolding Energy - sRNA 12.1236 kcal/mol@LB@@LB@Position - mRNA 256 -- 296@LB@Position - sRNA 78 -- 118@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 101 -- 107@LB@
95	0.001333	0.06355	pa5380	gbdR	-10.99	0.110367	154 -- 228	78 -- 123	protein GbdR		_____________153_________________________________________________________________________229\n_____________\|___________________________________________________________________________\|\n5'-UGC...AUAAA_______UC____GA______CUUGCUCAGC___________CACCCA___CCACGUACGCGCCC_______C__CACAG...CGG-3'\n______________AAAAGCC__GUGA__GGCCUG__________GUGAGGAGAUA______UGA______________GGAGUCC_AC\n______________\|\|\|\|:\|\|__\|\|\|\|__:\|\|\|\|\|__________:\|\|\|\|\|\|\|\|\|\|______\|\|\|______________:\|\|\|\|\|\|_\|\|\n______________UUUUUGG__CACU__UCGGAC__________UACUCCUCUAU______ACU______________UCUCAGG_UG\n3'-UUU...CCCAG_____________AA___________________________UAG___________________________C__ACGCA...GUU-5'\n_____________\|___________________________________________________________________________\|\n_____________124_________________________________________________________________________77\n	219 -- 225	81 -- 87	-45.4439 kcal/mol	22.3385 kcal/mol	12.1238 kcal/mol	153 229@LB@ \| \|@LB@5'-UGC...AUAAA UC GA CUUGCUCAGC CACCCA CCACGUACGCGCCC C CACAG...CGG-3'@LB@ AAAAGCC GUGA GGCCUG GUGAGGAGAUA UGA GGAGUCC AC@LB@ \|\|\|\|:\|\| \|\|\|\| :\|\|\|\|\| :\|\|\|\|\|\|\|\|\|\| \|\|\| :\|\|\|\|\|\| \|\|@LB@ UUUUUGG CACU UCGGAC UACUCCUCUAU ACU UCUCAGG UG@LB@3'-UUU...CCCAG AA UAG C ACGCA...GUU-5'@LB@ \| \|@LB@ 124 77@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -45.4439 kcal/mol@LB@Unfolding Energy - mRNA 22.3385 kcal/mol@LB@Unfolding Energy - sRNA 12.1238 kcal/mol@LB@@LB@Position - mRNA 154 -- 228@LB@Position - sRNA 78 -- 123@LB@Position Seed - mRNA 219 -- 225@LB@Position Seed - sRNA 81 -- 87@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

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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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