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
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@
175	0.004467	0.1171	pa2047	N/A	-7.63	0.467709	171 -- 177	103 -- 109	transcriptional regulator	_____________170_____178\n_____________\|_______\|\n5'-CCC...UGCUU_______CCUGC...CCG-3'\n______________GCCUGAU\n______________\|\|\|\|\|\|\|\n______________CGGACUA\n3'-UUU...CUAAU_______CUCCU...GUU-5'\n_____________\|_______\|\n_____________110_____102\n	171 -- 177	103 -- 109	-11.5321 kcal/mol	1.79595 kcal/mol	2.10421 kcal/mol	170 178@LB@ \| \|@LB@5'-CCC...UGCUU CCUGC...CCG-3'@LB@ GCCUGAU@LB@ \|\|\|\|\|\|\|@LB@ CGGACUA@LB@3'-UUU...CUAAU CUCCU...GUU-5'@LB@ \| \|@LB@ 110 102@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -11.5321 kcal/mol@LB@Unfolding Energy - mRNA 1.79595 kcal/mol@LB@Unfolding Energy - sRNA 2.10421 kcal/mol@LB@@LB@Position - mRNA 171 -- 177@LB@Position - sRNA 103 -- 109@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 103 -- 109@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@
69	0.0007462	0.0493	pa0882	N/A	-13.09	0.034380	240 -- 255	104 -- 119	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________239______________256\n_____________\|________________\|\n5'-CAA...GCAUC________C_______AGCAC...AUC-3'\n______________ACCGUGGU_AGCCUGG\n______________\|\|\|\|\|\|:\|_\|\|\|\|\|\|:\n______________UGGCACUA_UCGGACU\n3'-UUU...GUUUU________A_______ACUCC...GUU-5'\n_____________\|________________\|\n_____________120______________103\n	249 -- 255	104 -- 110	-23.473 kcal/mol	8.14152 kcal/mol	2.24159 kcal/mol	239 256@LB@ \| \|@LB@5'-CAA...GCAUC C AGCAC...AUC-3'@LB@ ACCGUGGU AGCCUGG@LB@ \|\|\|\|\|\|:\| \|\|\|\|\|\|:@LB@ UGGCACUA UCGGACU@LB@3'-UUU...GUUUU A ACUCC...GUU-5'@LB@ \| \|@LB@ 120 103@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -23.473 kcal/mol@LB@Unfolding Energy - mRNA 8.14152 kcal/mol@LB@Unfolding Energy - sRNA 2.24159 kcal/mol@LB@@LB@Position - mRNA 240 -- 255@LB@Position - sRNA 104 -- 119@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 104 -- 110@LB@
128	0.00255	0.0912	pa3463	N/A	-7.51	0.486845	225 -- 240	104 -- 122	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________224_________________241\n_____________\|___________________\|\n5'-UCG...UGCUC_______ACAC________ACAAC...CGC-3'\n______________GAAGCCG_______CCUGA\n______________:\|\|:\|\|\|_______\|\|\|\|\|\n______________UUUUGGC_______GGACU\n3'-UUU...CCAGU_______ACUAAUC_____ACUCC...GUU-5'\n_____________\|___________________\|\n_____________123_________________103\n	225 -- 231	116 -- 122	-12.6194 kcal/mol	2.87159 kcal/mol	2.24249 kcal/mol	224 241@LB@ \| \|@LB@5'-UCG...UGCUC ACAC ACAAC...CGC-3'@LB@ GAAGCCG CCUGA@LB@ :\|\|:\|\|\| \|\|\|\|\|@LB@ UUUUGGC GGACU@LB@3'-UUU...CCAGU ACUAAUC ACUCC...GUU-5'@LB@ \| \|@LB@ 123 103@LB@@LB@@LB@Energy -7.51 kcal/mol@LB@Hybridization Energy -12.6194 kcal/mol@LB@Unfolding Energy - mRNA 2.87159 kcal/mol@LB@Unfolding Energy - sRNA 2.24249 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 104 -- 122@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 116 -- 122@LB@
162	0.00407	0.1155	pa4993	N/A	-9.83	0.193366	13 -- 32	104 -- 121	'Product name confidence: class 4 (Homologs of previously reported genes of unknown function or no similarity to any previously reported sequences)'	_____________12___________________33\n_____________\|____________________\|\n5'-CGA...CGCGC_____C___AAAA_______ACCAU...GCC-3'\n______________AAGCC_UGA____GGCCUGA\n______________\|\|:\|\|_\|\|\|____:\|\|\|\|\|\|\n______________UUUGG_ACU____UCGGACU\n3'-UUU...CAGUU_____C___AA_________ACUCC...GUU-5'\n_____________\|____________________\|\n_____________122__________________103\n	26 -- 32	104 -- 110	-17.5213 kcal/mol	5.44748 kcal/mol	2.24203 kcal/mol	12 33@LB@ \| \|@LB@5'-CGA...CGCGC C AAAA ACCAU...GCC-3'@LB@ AAGCC UGA GGCCUGA@LB@ \|\|:\|\| \|\|\| :\|\|\|\|\|\|@LB@ UUUGG ACU UCGGACU@LB@3'-UUU...CAGUU C AA ACUCC...GUU-5'@LB@ \| \|@LB@ 122 103@LB@@LB@@LB@Energy -9.83 kcal/mol@LB@Hybridization Energy -17.5213 kcal/mol@LB@Unfolding Energy - mRNA 5.44748 kcal/mol@LB@Unfolding Energy - sRNA 2.24203 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 104 -- 121@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 104 -- 110@LB@
138	0.002776	0.09245	pa0440	N/A	-11.93	0.067049	197 -- 216	104 -- 120	oxidoreductase	_____________196__________________217\n_____________\|____________________\|\n5'-CGA...GCUAC_________CGAUUC_____ACCAC...AGG-3'\n______________AACCGUGAU______CCUGA\n______________\|\|\|\|\|\|\|\|\|______\|\|\|\|\|\n______________UUGGCACUA______GGACU\n3'-UUU...AGUUU_________AUC________ACUCC...GUU-5'\n_____________\|____________________\|\n_____________121__________________103\n	199 -- 205	112 -- 118	-17.8806 kcal/mol	3.71535 kcal/mol	2.24182 kcal/mol	196 217@LB@ \| \|@LB@5'-CGA...GCUAC CGAUUC ACCAC...AGG-3'@LB@ AACCGUGAU CCUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUGGCACUA GGACU@LB@3'-UUU...AGUUU AUC ACUCC...GUU-5'@LB@ \| \|@LB@ 121 103@LB@@LB@@LB@Energy -11.93 kcal/mol@LB@Hybridization Energy -17.8806 kcal/mol@LB@Unfolding Energy - mRNA 3.71535 kcal/mol@LB@Unfolding Energy - sRNA 2.24182 kcal/mol@LB@@LB@Position - mRNA 197 -- 216@LB@Position - sRNA 104 -- 120@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 112 -- 118@LB@
163	0.004151	0.1159	pa3263	N/A	-13.17	0.032863	133 -- 150	104 -- 121	recombination associated protein RdgC	_____________132________________151\n_____________\|__________________\|\n5'-GUA...GCGAC______G___________GCCGC...CCU-3'\n______________GGACCG_GGUUGGCCUGA\n______________::\|\|\|\|_\|:\|\|:\|\|\|\|\|\|\n______________UUUGGC_CUAAUCGGACU\n3'-UUU...CAGUU______A___________ACUCC...GUU-5'\n_____________\|__________________\|\n_____________122________________103\n	144 -- 150	104 -- 110	-25.1519 kcal/mol	9.74439 kcal/mol	2.24203 kcal/mol	132 151@LB@ \| \|@LB@5'-GUA...GCGAC G GCCGC...CCU-3'@LB@ GGACCG GGUUGGCCUGA@LB@ ::\|\|\|\| \|:\|\|:\|\|\|\|\|\|@LB@ UUUGGC CUAAUCGGACU@LB@3'-UUU...CAGUU A ACUCC...GUU-5'@LB@ \| \|@LB@ 122 103@LB@@LB@@LB@Energy -13.17 kcal/mol@LB@Hybridization Energy -25.1519 kcal/mol@LB@Unfolding Energy - mRNA 9.74439 kcal/mol@LB@Unfolding Energy - sRNA 2.24203 kcal/mol@LB@@LB@Position - mRNA 133 -- 150@LB@Position - sRNA 104 -- 121@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 104 -- 110@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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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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