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
112	0.001904	0.07812	pa5310	N/A	-10.92	0.114175	276 -- 285	74 -- 83	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________275________286\n_____________\|__________\|\n5'-CGA...CCCUC__________CCAGC...CGC-3'\n______________UCCGGCUGCG\n______________\|\|\|\|:\|\|\|\|\|\n______________AGGCUGACGC\n3'-UUU...UUCUC__________ACCCA...GUU-5'\n_____________\|__________\|\n_____________84_________73\n	279 -- 285	74 -- 80	-18.1359 kcal/mol	3.11348 kcal/mol	4.10139 kcal/mol	275 286@LB@ \| \|@LB@5'-CGA...CCCUC CCAGC...CGC-3'@LB@ UCCGGCUGCG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ AGGCUGACGC@LB@3'-UUU...UUCUC ACCCA...GUU-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -18.1359 kcal/mol@LB@Unfolding Energy - mRNA 3.11348 kcal/mol@LB@Unfolding Energy - sRNA 4.10139 kcal/mol@LB@@LB@Position - mRNA 276 -- 285@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 74 -- 80@LB@
36	0.0001485	0.01896	pa2147	katE	-15.32	0.008256	177 -- 207	74 -- 109	catalase HPII		_____________176_____________________________________208\n_____________\|_______________________________________\|\n5'-CGU...UUCAU___CAG_____________________AA_____GA___AGCAG...AUC-3'\n______________GCC___GAUGAGGAGA________GGA__CCGAU__GCG\n______________\|\|\|___\|\|\|\|\|\|\|\|\|\|________:\|\|__\|\|\|\|:__\|\|\|\n______________CGG___CUACUCCUCU________UCU__GGCUG__CGC\n3'-UUU...CUAAU___A____________AUUAGACU___CA_____A____ACCCA...GUU-5'\n_____________\|_______________________________________\|\n_____________110_____________________________________73\n	186 -- 192	96 -- 102	-32.3599 kcal/mol	5.50185 kcal/mol	11.5406 kcal/mol	176 208@LB@ \| \|@LB@5'-CGU...UUCAU CAG AA GA AGCAG...AUC-3'@LB@ GCC GAUGAGGAGA GGA CCGAU GCG@LB@ \|\|\| \|\|\|\|\|\|\|\|\|\| :\|\| \|\|\|\|: \|\|\|@LB@ CGG CUACUCCUCU UCU GGCUG CGC@LB@3'-UUU...CUAAU A AUUAGACU CA A ACCCA...GUU-5'@LB@ \| \|@LB@ 110 73@LB@@LB@@LB@Energy -15.32 kcal/mol@LB@Hybridization Energy -32.3599 kcal/mol@LB@Unfolding Energy - mRNA 5.50185 kcal/mol@LB@Unfolding Energy - sRNA 11.5406 kcal/mol@LB@@LB@Position - mRNA 177 -- 207@LB@Position - sRNA 74 -- 109@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 96 -- 102@LB@
38	0.0001678	0.02029	pa4131	N/A	-10.32	0.153559	164 -- 172	74 -- 82	iron-sulfur protein		_____________163_______173\n_____________\|_________\|\n5'-CUC...GGGAA_________CCCCU...GCG-3'\n______________CCGGCUGCG\n______________\|\|\|:\|\|\|\|\|\n______________GGCUGACGC\n3'-UUU...UCUCA_________ACCCA...GUU-5'\n_____________\|_________\|\n_____________83________73\n	166 -- 172	74 -- 80	-17.7171 kcal/mol	3.29242 kcal/mol	4.10111 kcal/mol	163 173@LB@ \| \|@LB@5'-CUC...GGGAA CCCCU...GCG-3'@LB@ CCGGCUGCG@LB@ \|\|\|:\|\|\|\|\|@LB@ GGCUGACGC@LB@3'-UUU...UCUCA ACCCA...GUU-5'@LB@ \| \|@LB@ 83 73@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -17.7171 kcal/mol@LB@Unfolding Energy - mRNA 3.29242 kcal/mol@LB@Unfolding Energy - sRNA 4.10111 kcal/mol@LB@@LB@Position - mRNA 164 -- 172@LB@Position - sRNA 74 -- 82@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 74 -- 80@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@
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@
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@
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@
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@
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@
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@

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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