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
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@
53	0.0004056	0.03518	pa1750	N/A	-9.05	0.272805	157 -- 194	32 -- 72	phospho-2-dehydro-3-deoxyheptonate aldolase		_____________156________________________________________195\n_____________\|__________________________________________\|\n5'-ACU...GCAGG___C___C____G_______GC___________U_A______ACCAC...CCC-3'\n______________GGG_CUC_CGGC__GCCGGC____C_CGUGACC_G_UUGAGU\n______________\|\|\|_\|\|\|_\|:\|\|__:\|\|\|\|\|____\|_\|\|:\|\|\|\|_\|_\|\|\|\|\|\|\n______________CCC_GAG_GUCG__UGGCCG____G_GCGCUGG_C_AACUCA\n3'-UUU...ACGCA___A___A____AA______ACUA_A_______U________CUGUA...GUU-5'\n_____________\|__________________________________________\|\n_____________73_________________________________________31\n	179 -- 185	40 -- 46	-44.8167 kcal/mol	16.8729 kcal/mol	18.8965 kcal/mol	156 195@LB@ \| \|@LB@5'-ACU...GCAGG C C G GC U A ACCAC...CCC-3'@LB@ GGG CUC CGGC GCCGGC C CGUGACC G UUGAGU@LB@ \|\|\| \|\|\| \|:\|\| :\|\|\|\|\| \| \|\|:\|\|\|\| \| \|\|\|\|\|\|@LB@ CCC GAG GUCG UGGCCG G GCGCUGG C AACUCA@LB@3'-UUU...ACGCA A A AA ACUA A U CUGUA...GUU-5'@LB@ \| \|@LB@ 73 31@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -44.8167 kcal/mol@LB@Unfolding Energy - mRNA 16.8729 kcal/mol@LB@Unfolding Energy - sRNA 18.8965 kcal/mol@LB@@LB@Position - mRNA 157 -- 194@LB@Position - sRNA 32 -- 72@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 40 -- 46@LB@
126	0.002419	0.08825	pa0452	N/A	-8.57	0.332234	172 -- 209	83 -- 122	'Product name confidence: class 3 (Function proposed based on presence of conserved amino acid motif structural feature or limited sequence similarity to an experimentally studied gene)'		_____________171_______________________________________210\n_____________\|_________________________________________\|\n5'-AGU...UCCUG_______C_C___________A_________A____U____AUUUC...UGG-3'\n______________GAAGUCG_G__UGGCC_GAUG_AGGAGGUGG__UGA_GGGU\n______________:\|\|::\|\|_\|__\|:\|\|\|_\|\|\|\|_\|\|\|\|\|:\|::__\|\|\|_\|:\|\|\n______________UUUUGGC_C__AUCGG_CUAC_UCCUCUAUU__ACU_CUCA\n3'-UUU...CCAGU_______A_UA_____A______________AG___U____GGCUG...GUU-5'\n_____________\|_________________________________________\|\n_____________123_______________________________________82\n	193 -- 199	94 -- 100	-32.4047 kcal/mol	13.786 kcal/mol	10.0547 kcal/mol	171 210@LB@ \| \|@LB@5'-AGU...UCCUG C C A A U AUUUC...UGG-3'@LB@ GAAGUCG G UGGCC GAUG AGGAGGUGG UGA GGGU@LB@ :\|\|::\|\| \| \|:\|\|\| \|\|\|\| \|\|\|\|\|:\|:: \|\|\| \|:\|\|@LB@ UUUUGGC C AUCGG CUAC UCCUCUAUU ACU CUCA@LB@3'-UUU...CCAGU A UA A AG U GGCUG...GUU-5'@LB@ \| \|@LB@ 123 82@LB@@LB@@LB@Energy -8.57 kcal/mol@LB@Hybridization Energy -32.4047 kcal/mol@LB@Unfolding Energy - mRNA 13.786 kcal/mol@LB@Unfolding Energy - sRNA 10.0547 kcal/mol@LB@@LB@Position - mRNA 172 -- 209@LB@Position - sRNA 83 -- 122@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 94 -- 100@LB@
117	0.002052	0.07999	pa0290	N/A	-8.56	0.333144	143 -- 150	40 -- 47	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________142______151\n_____________\|________\|\n5'-CCU...UAUCG________CCUGC...AAC-3'\n______________UCGCGACC\n______________\|\|\|\|\|\|\|\|\n______________AGCGCUGG\n3'-UUU...ACUAG________UCAAC...GUU-5'\n_____________\|________\|\n_____________48_______39\n	144 -- 150	40 -- 46	-14.5279 kcal/mol	2.30284 kcal/mol	3.66533 kcal/mol	142 151@LB@ \| \|@LB@5'-CCU...UAUCG CCUGC...AAC-3'@LB@ UCGCGACC@LB@ \|\|\|\|\|\|\|\|@LB@ AGCGCUGG@LB@3'-UUU...ACUAG UCAAC...GUU-5'@LB@ \| \|@LB@ 48 39@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -14.5279 kcal/mol@LB@Unfolding Energy - mRNA 2.30284 kcal/mol@LB@Unfolding Energy - sRNA 3.66533 kcal/mol@LB@@LB@Position - mRNA 143 -- 150@LB@Position - sRNA 40 -- 47@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 40 -- 46@LB@
104	0.00171	0.07531	pa4333	N/A	-8.52	0.338548	151 -- 157	40 -- 46	fumarase		_____________150_____158\n_____________\|_______\|\n5'-UAG...GGCUC_______CUGCC...AUG-3'\n______________CGUGACC\n______________\|\|:\|\|\|\|\n______________GCGCUGG\n3'-UUU...CUAGA_______UCAAC...GUU-5'\n_____________\|_______\|\n_____________47______39\n	151 -- 157	40 -- 46	-12.3245 kcal/mol	0.149051 kcal/mol	3.65718 kcal/mol	150 158@LB@ \| \|@LB@5'-UAG...GGCUC CUGCC...AUG-3'@LB@ CGUGACC@LB@ \|\|:\|\|\|\|@LB@ GCGCUGG@LB@3'-UUU...CUAGA UCAAC...GUU-5'@LB@ \| \|@LB@ 47 39@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -12.3245 kcal/mol@LB@Unfolding Energy - mRNA 0.149051 kcal/mol@LB@Unfolding Energy - sRNA 3.65718 kcal/mol@LB@@LB@Position - mRNA 151 -- 157@LB@Position - sRNA 40 -- 46@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 40 -- 46@LB@
159	0.003984	0.115	pa2627	N/A	-8.37	0.359084	22 -- 39	38 -- 59	high frequency lysogenization protein HflD		_____________21_____________________40\n_____________\|______________________\|\n5'-CGC...UGCGC_______A______________GACUG...CCC-3'\n______________UACCGGC_GA____GCGACCAG\n______________\|\|\|\|\|\|\|_\|\|____\|\|\|\|\|\|\|\|\n______________AUGGCCG_CU____CGCUGGUC\n3'-UUU...GUCGA_______A__AGAG________AACUC...GUU-5'\n_____________\|______________________\|\n_____________60_____________________37\n	33 -- 39	38 -- 44	-28.3931 kcal/mol	8.63241 kcal/mol	11.3994 kcal/mol	21 40@LB@ \| \|@LB@5'-CGC...UGCGC A GACUG...CCC-3'@LB@ UACCGGC GA GCGACCAG@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\|\|\|\|\|@LB@ AUGGCCG CU CGCUGGUC@LB@3'-UUU...GUCGA A AGAG AACUC...GUU-5'@LB@ \| \|@LB@ 60 37@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -28.3931 kcal/mol@LB@Unfolding Energy - mRNA 8.63241 kcal/mol@LB@Unfolding Energy - sRNA 11.3994 kcal/mol@LB@@LB@Position - mRNA 22 -- 39@LB@Position - sRNA 38 -- 59@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 38 -- 44@LB@
17	3.089e-05	0.008352	pa5396	N/A	-7.92	0.424136	180 -- 186	104 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________179_____187\n_____________\|_______\|\n5'-CGC...CGCCC_______AAGGG...GCC-3'\n______________AGCCUGA\n______________\|\|\|\|\|\|\|\n______________UCGGACU\n3'-UUU...ACUAA_______ACUCC...GUU-5'\n_____________\|_______\|\n_____________111_____103\n	180 -- 186	104 -- 110	-11.2317 kcal/mol	1.21017 kcal/mol	2.10482 kcal/mol	179 187@LB@ \| \|@LB@5'-CGC...CGCCC AAGGG...GCC-3'@LB@ AGCCUGA@LB@ \|\|\|\|\|\|\|@LB@ UCGGACU@LB@3'-UUU...ACUAA ACUCC...GUU-5'@LB@ \| \|@LB@ 111 103@LB@@LB@@LB@Energy -7.92 kcal/mol@LB@Hybridization Energy -11.2317 kcal/mol@LB@Unfolding Energy - mRNA 1.21017 kcal/mol@LB@Unfolding Energy - sRNA 2.10482 kcal/mol@LB@@LB@Position - mRNA 180 -- 186@LB@Position - sRNA 104 -- 110@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 104 -- 110@LB@
114	0.001956	0.07883	pa1616	N/A	-7.83	0.436748	16 -- 25	101 -- 110	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'		_____________15_________26\n_____________\|__________\|\n5'-GGC...ACGGC__________CUUUC...AGA-3'\n______________AGCCUGAUGG\n______________\|\|\|\|\|\|\|\|\|:\n______________UCGGACUACU\n3'-UUU...ACUAA__________CCUCU...GUU-5'\n_____________\|__________\|\n_____________111________100\n	19 -- 25	101 -- 107	-16.0192 kcal/mol	6.07491 kcal/mol	2.11196 kcal/mol	15 26@LB@ \| \|@LB@5'-GGC...ACGGC CUUUC...AGA-3'@LB@ AGCCUGAUGG@LB@ \|\|\|\|\|\|\|\|\|:@LB@ UCGGACUACU@LB@3'-UUU...ACUAA CCUCU...GUU-5'@LB@ \| \|@LB@ 111 100@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -16.0192 kcal/mol@LB@Unfolding Energy - mRNA 6.07491 kcal/mol@LB@Unfolding Energy - sRNA 2.11196 kcal/mol@LB@@LB@Position - mRNA 16 -- 25@LB@Position - sRNA 101 -- 110@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 101 -- 107@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@

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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