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
189	0.005044	0.1227	pa4284	recB	-12.92	0.038081	40 -- 56	70 -- 89	exodeoxyribonuclease V subunit beta	_____________39___________________57\n_____________\|____________________\|\n5'-CCC...ACGAG____________A_______GGGCG...UCA-3'\n______________GGAGGGUUCGGC____UGGG\n______________\|:\|\|:\|\|:\|\|:\|____\|\|\|\|\n______________CUUCUCAGGCUG____ACCC\n3'-UUU...UUAGA____________ACGC____AGAGA...GUU-5'\n_____________\|____________________\|\n_____________90___________________69\n	45 -- 51	78 -- 84	-22.2148 kcal/mol	3.43278 kcal/mol	5.86471 kcal/mol	39 57@LB@ \| \|@LB@5'-CCC...ACGAG A GGGCG...UCA-3'@LB@ GGAGGGUUCGGC UGGG@LB@ \|:\|\|:\|\|:\|\|:\| \|\|\|\|@LB@ CUUCUCAGGCUG ACCC@LB@3'-UUU...UUAGA ACGC AGAGA...GUU-5'@LB@ \| \|@LB@ 90 69@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -22.2148 kcal/mol@LB@Unfolding Energy - mRNA 3.43278 kcal/mol@LB@Unfolding Energy - sRNA 5.86471 kcal/mol@LB@@LB@Position - mRNA 40 -- 56@LB@Position - sRNA 70 -- 89@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 78 -- 84@LB@
131	0.002644	0.0912	pa4772	N/A	-11.20	0.098904	193 -- 209	105 -- 123	ferredoxin	_____________192__________________210\n_____________\|____________________\|\n5'-CCG...CCGAG________A___________CCGAU...ACG-3'\n______________GAAAGCCG_UGA___GCCUG\n______________:\|\|\|:\|\|\|_\|\|\|___\|\|\|\|\|\n______________UUUUUGGC_ACU___CGGAC\n3'-UUU...CCCAG____________AAU_____UACUC...GUU-5'\n_____________\|____________________\|\n_____________124__________________104\n	194 -- 200	116 -- 122	-17.7993 kcal/mol	4.35882 kcal/mol	2.24275 kcal/mol	192 210@LB@ \| \|@LB@5'-CCG...CCGAG A CCGAU...ACG-3'@LB@ GAAAGCCG UGA GCCUG@LB@ :\|\|\|:\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUUGGC ACU CGGAC@LB@3'-UUU...CCCAG AAU UACUC...GUU-5'@LB@ \| \|@LB@ 124 104@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -17.7993 kcal/mol@LB@Unfolding Energy - mRNA 4.35882 kcal/mol@LB@Unfolding Energy - sRNA 2.24275 kcal/mol@LB@@LB@Position - mRNA 193 -- 209@LB@Position - sRNA 105 -- 123@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 116 -- 122@LB@
155	0.003654	0.1083	pa1551	N/A	-14.46	0.014645	185 -- 205	100 -- 119	ferredoxin	_____________184___________________206\n_____________\|_____________________\|\n5'-ACC...CCACU________AC__A________CAAAC...GGG-3'\n______________GCCGUGGU__GC_CUGAUGAG\n______________:\|\|\|\|\|:\|__\|\|_\|\|\|\|\|\|\|\|\n______________UGGCACUA__CG_GACUACUC\n3'-UUU...GUUUU________AU___________CUCUA...GUU-5'\n_____________\|_____________________\|\n_____________120___________________99\n	199 -- 205	100 -- 106	-27.0785 kcal/mol	10.3705 kcal/mol	2.24903 kcal/mol	184 206@LB@ \| \|@LB@5'-ACC...CCACU AC A CAAAC...GGG-3'@LB@ GCCGUGGU GC CUGAUGAG@LB@ :\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|\|@LB@ UGGCACUA CG GACUACUC@LB@3'-UUU...GUUUU AU CUCUA...GUU-5'@LB@ \| \|@LB@ 120 99@LB@@LB@@LB@Energy -14.46 kcal/mol@LB@Hybridization Energy -27.0785 kcal/mol@LB@Unfolding Energy - mRNA 10.3705 kcal/mol@LB@Unfolding Energy - sRNA 2.24903 kcal/mol@LB@@LB@Position - mRNA 185 -- 205@LB@Position - sRNA 100 -- 119@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 100 -- 106@LB@
8	1.007e-05	0.004211	pa3621	fdxA	-18.47	0.000724	244 -- 255	71 -- 82	ferredoxin I	_____________243__________256\n_____________\|____________\|\n5'-CCU...AUACA____________AAGUC...UGG-3'\n______________CCGACUGCGUGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUGACGCACC\n3'-UUU...UCUCA____________CAGAG...GUU-5'\n_____________\|____________\|\n_____________83___________70\n	249 -- 255	71 -- 77	-26.3412 kcal/mol	3.76302 kcal/mol	4.10469 kcal/mol	243 256@LB@ \| \|@LB@5'-CCU...AUACA AAGUC...UGG-3'@LB@ CCGACUGCGUGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUGACGCACC@LB@3'-UUU...UCUCA CAGAG...GUU-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -18.47 kcal/mol@LB@Hybridization Energy -26.3412 kcal/mol@LB@Unfolding Energy - mRNA 3.76302 kcal/mol@LB@Unfolding Energy - sRNA 4.10469 kcal/mol@LB@@LB@Position - mRNA 244 -- 255@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 71 -- 77@LB@
30	8.033e-05	0.01177	pa3717	N/A	-10.05	0.175331	209 -- 216	75 -- 82	FkbP-type peptidyl-prolyl cis-trans isomerase	_____________208______217\n_____________\|________\|\n5'-UCU...AACGA________AGAUC...AAG-3'\n______________CCGACUGC\n______________\|\|\|\|\|\|\|\|\n______________GGCUGACG\n3'-UUU...UCUCA________CACCC...GUU-5'\n_____________\|________\|\n_____________83_______74\n	210 -- 216	75 -- 81	-16.1929 kcal/mol	2.05248 kcal/mol	4.09516 kcal/mol	208 217@LB@ \| \|@LB@5'-UCU...AACGA AGAUC...AAG-3'@LB@ CCGACUGC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUGACG@LB@3'-UUU...UCUCA CACCC...GUU-5'@LB@ \| \|@LB@ 83 74@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -16.1929 kcal/mol@LB@Unfolding Energy - mRNA 2.05248 kcal/mol@LB@Unfolding Energy - sRNA 4.09516 kcal/mol@LB@@LB@Position - mRNA 209 -- 216@LB@Position - sRNA 75 -- 82@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 75 -- 81@LB@
35	0.0001057	0.01388	pa1103	N/A	-18.12	0.000977	185 -- 207	81 -- 102	flagellar assembly protein FliH	_____________184_____________________208\n_____________\|_______________________\|\n5'-CGA...GUGGC_________________U_____CCCAC...AGC-3'\n______________GAGGAGAUGAUCUGAGG_GGUCC\n______________\|\|\|\|\|\|\|\|:\|\|\|\|\|\|:\|_:\|\|\|\|\n______________CUCCUCUAUUAGACUUC_UCAGG\n3'-UUU...GACUA_______________________CUGAC...GUU-5'\n_____________\|_______________________\|\n_____________103_____________________80\n	195 -- 201	86 -- 92	-35.642 kcal/mol	10.0244 kcal/mol	7.49511 kcal/mol	184 208@LB@ \| \|@LB@5'-CGA...GUGGC U CCCAC...AGC-3'@LB@ GAGGAGAUGAUCUGAGG GGUCC@LB@ \|\|\|\|\|\|\|\|:\|\|\|\|\|\|:\| :\|\|\|\|@LB@ CUCCUCUAUUAGACUUC UCAGG@LB@3'-UUU...GACUA CUGAC...GUU-5'@LB@ \| \|@LB@ 103 80@LB@@LB@@LB@Energy -18.12 kcal/mol@LB@Hybridization Energy -35.642 kcal/mol@LB@Unfolding Energy - mRNA 10.0244 kcal/mol@LB@Unfolding Energy - sRNA 7.49511 kcal/mol@LB@@LB@Position - mRNA 185 -- 207@LB@Position - sRNA 81 -- 102@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 86 -- 92@LB@
179	0.004617	0.1185	pa4812	fdnG	-14.50	0.014314	180 -- 196	94 -- 109	formate dehydrogenase-O major subunit	_____________179_______________197\n_____________\|_________________\|\n5'-CCC...CCUUU________C________CACGA...CCG-3'\n______________GCCUGAUG_AGGAGAUG\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|:\n______________CGGACUAC_UCCUCUAU\n3'-UUU...CUAAU_________________UAGAC...GUU-5'\n_____________\|_________________\|\n_____________110_______________93\n	190 -- 196	94 -- 100	-26.4921 kcal/mol	6.69504 kcal/mol	5.30224 kcal/mol	179 197@LB@ \| \|@LB@5'-CCC...CCUUU C CACGA...CCG-3'@LB@ GCCUGAUG AGGAGAUG@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|:@LB@ CGGACUAC UCCUCUAU@LB@3'-UUU...CUAAU UAGAC...GUU-5'@LB@ \| \|@LB@ 110 93@LB@@LB@@LB@Energy -14.50 kcal/mol@LB@Hybridization Energy -26.4921 kcal/mol@LB@Unfolding Energy - mRNA 6.69504 kcal/mol@LB@Unfolding Energy - sRNA 5.30224 kcal/mol@LB@@LB@Position - mRNA 180 -- 196@LB@Position - sRNA 94 -- 109@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 94 -- 100@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@
82	0.000993	0.05566	pa5549	glmS	-14.85	0.011343	179 -- 208	71 -- 110	glucosamine--fructose-6-phosphate aminotransferase	_____________178______________________________________209\n_____________\|________________________________________\|\n5'-CCG...GUCGA_______A__________________CC__A_________AAUCG...GCG-3'\n______________GGCCUGA__AGGAGA_______AAGA__CC___UGUGUGG\n______________:\|\|\|\|\|\|__\|\|\|\|\|\|_______\|\|\|\|__\|\|___\|\|:\|\|\|\|\n______________UCGGACU__UCCUCU_______UUCU__GG___ACGCACC\n3'-UUU...ACUAA_______AC______AUUAGAC____CA__CUG_______CAGAG...GUU-5'\n_____________\|________________________________________\|\n_____________111______________________________________70\n	202 -- 208	71 -- 77	-33.9361 kcal/mol	6.17828 kcal/mol	12.9138 kcal/mol	178 209@LB@ \| \|@LB@5'-CCG...GUCGA A CC A AAUCG...GCG-3'@LB@ GGCCUGA AGGAGA AAGA CC UGUGUGG@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|\| \|\| \|\|:\|\|\|\|@LB@ UCGGACU UCCUCU UUCU GG ACGCACC@LB@3'-UUU...ACUAA AC AUUAGAC CA CUG CAGAG...GUU-5'@LB@ \| \|@LB@ 111 70@LB@@LB@@LB@Energy -14.85 kcal/mol@LB@Hybridization Energy -33.9361 kcal/mol@LB@Unfolding Energy - mRNA 6.17828 kcal/mol@LB@Unfolding Energy - sRNA 12.9138 kcal/mol@LB@@LB@Position - mRNA 179 -- 208@LB@Position - sRNA 71 -- 110@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 71 -- 77@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@

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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usability assessment

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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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