Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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_000913 Escherichia coli str. K-12 substr. MG1655

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
28	0.0008326	0.09021	b2563	acpS	-7.40	0.086911	170 -- 193	37 -- 61	holo-[acyl-carrier-protein] synthase 1	_____________169_______________________194\n_____________\|_________________________\|\n5'-GCC...AGAAA______GU___GAU__U________GUGGC...GCG-3'\n______________UGAAGC___CU___GC_GGAAGCGC\n______________\|\|\|\|:\|___\|\|___\|\|_:\|\|\|\|\|:\|\n______________ACUUUG___GA___CG_UCUUCGUG\n3'-UUU...GCCCU______AAC__AUU__U________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________62________________________36\n	187 -- 193	37 -- 43	-21.5547 kcal/mol	6.80255 kcal/mol	7.3495 kcal/mol	169 194@LB@ \| \|@LB@5'-GCC...AGAAA GU GAU U GUGGC...GCG-3'@LB@ UGAAGC CU GC GGAAGCGC@LB@ \|\|\|\|:\| \|\| \|\| :\|\|\|\|\|:\|@LB@ ACUUUG GA CG UCUUCGUG@LB@3'-UUU...GCCCU AAC AUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -7.40 kcal/mol@LB@Hybridization Energy -21.5547 kcal/mol@LB@Unfolding Energy - mRNA 6.80255 kcal/mol@LB@Unfolding Energy - sRNA 7.3495 kcal/mol@LB@@LB@Position - mRNA 170 -- 193@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 37 -- 43@LB@
77	0.004637	0.1935	b0407	yajC	-7.39	0.087827	147 -- 158	37 -- 48	SecYEG protein translocase auxillary subunit	_____________146__________159\n_____________\|____________\|\n5'-UCU...UCAGG____________CACCU...UUU-3'\n______________GGCGAGAAGUAC\n______________:\|\|:\|\|\|\|\|:\|\|\n______________UCGUUCUUCGUG\n3'-UUU...CGAAU____________AAUUU...CAA-5'\n_____________\|____________\|\n_____________49___________36\n	152 -- 158	37 -- 43	-17.5904 kcal/mol	4.37033 kcal/mol	5.83483 kcal/mol	146 159@LB@ \| \|@LB@5'-UCU...UCAGG CACCU...UUU-3'@LB@ GGCGAGAAGUAC@LB@ :\|\|:\|\|\|\|\|:\|\|@LB@ UCGUUCUUCGUG@LB@3'-UUU...CGAAU AAUUU...CAA-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -7.39 kcal/mol@LB@Hybridization Energy -17.5904 kcal/mol@LB@Unfolding Energy - mRNA 4.37033 kcal/mol@LB@Unfolding Energy - sRNA 5.83483 kcal/mol@LB@@LB@Position - mRNA 147 -- 158@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 37 -- 43@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@LB@
41	0.001644	0.1292	b1918	yecS	-7.37	0.088723	192 -- 214	37 -- 60	ABC family putative inner membrane permease	_____________191_______________________215\n_____________\|_________________________\|\n5'-GGC...CUCCG__________CAU_______A____ACAAC...GCU-3'\n______________GAAAC__GCU___GCAAGAA_GUAU\n______________\|\|\|\|\|__\|\|\|___\|\|\|\|\|\|\|_\|:\|:\n______________CUUUG__CGA___CGUUCUU_CGUG\n3'-UUU...CCCUA_____AA___AUU____________AAUUU...CAA-5'\n_____________\|_________________________\|\n_____________61________________________36\n	203 -- 209	41 -- 47	-18.5053 kcal/mol	4.89056 kcal/mol	6.24651 kcal/mol	191 215@LB@ \| \|@LB@5'-GGC...CUCCG CAU A ACAAC...GCU-3'@LB@ GAAAC GCU GCAAGAA GUAU@LB@ \|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|:\|:@LB@ CUUUG CGA CGUUCUU CGUG@LB@3'-UUU...CCCUA AA AUU AAUUU...CAA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -7.37 kcal/mol@LB@Hybridization Energy -18.5053 kcal/mol@LB@Unfolding Energy - mRNA 4.89056 kcal/mol@LB@Unfolding Energy - sRNA 6.24651 kcal/mol@LB@@LB@Position - mRNA 192 -- 214@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 41 -- 47@LB@
164	0.01824	0.3566	b1854	pykA	-7.33	0.090768	1 -- 31	25 -- 60	pyruvate kinase II	______________1___________________________________32\n______________\|___________________________________\|\n___________5'-_____GG__CA_____________________A___CGUUU...ACG-3'\n______________GAAGC__GU______AAGAAGCGCU_GAAGGA_UCG\n______________\|\|\|:\|__\|:______\|\|\|\|\|\|\|:\|\|_:\|\|::\|_\|\|\|\n______________CUUUG__CG______UUCUUCGUGA_UUUUUU_AGC\n3'-UUU...CCCUA_____AA__AAUUCG__________A______A___AAUGU...CAA-5'\n_____________\|____________________________________\|\n_____________61___________________________________24\n	15 -- 21	36 -- 42	-23.5606 kcal/mol	9.95433 kcal/mol	6.27609 kcal/mol	1 32@LB@ \| \|@LB@ 5'- GG CA A CGUUU...ACG-3'@LB@ GAAGC GU AAGAAGCGCU GAAGGA UCG@LB@ \|\|\|:\| \|: \|\|\|\|\|\|\|:\|\| :\|\|::\| \|\|\|@LB@ CUUUG CG UUCUUCGUGA UUUUUU AGC@LB@3'-UUU...CCCUA AA AAUUCG A A AAUGU...CAA-5'@LB@ \| \|@LB@ 61 24@LB@@LB@@LB@Energy -7.33 kcal/mol@LB@Hybridization Energy -23.5606 kcal/mol@LB@Unfolding Energy - mRNA 9.95433 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 1 -- 31@LB@Position - sRNA 25 -- 60@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 36 -- 42@LB@
165	0.01827	0.3566	b2937	speB	-7.30	0.092452	5 -- 22	25 -- 41	agmatinase	_____________4__________________23\n_____________\|__________________\|\n_______5'-CAAC___UC_____________AGGCA...CAG-3'\n______________AGU__CUUGAAGAGUUCG\n______________\|\|:__\|\|\|:\|\|:\|:\|\|\|\|\n______________UCG__GAAUUUUUUAAGC\n3'-UUU...GUUCU___U______________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	16 -- 22	25 -- 31	-14.9284 kcal/mol	5.98061 kcal/mol	1.64839 kcal/mol	4 23@LB@ \| \|@LB@ 5'-CAAC UC AGGCA...CAG-3'@LB@ AGU CUUGAAGAGUUCG@LB@ \|\|: \|\|\|:\|\|:\|:\|\|\|\|@LB@ UCG GAAUUUUUUAAGC@LB@3'-UUU...GUUCU U AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -7.30 kcal/mol@LB@Hybridization Energy -14.9284 kcal/mol@LB@Unfolding Energy - mRNA 5.98061 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 5 -- 22@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 25 -- 31@LB@
119	0.01022	0.2766	b0123	cueO	-7.29	0.093095	47 -- 59	29 -- 41	multicopper oxidase (laccase)	_____________46____________60\n_____________\|_____________\|\n5'-CUG...UACCA__G__________GAUAA...CGU-3'\n______________GG_GCUUAAAGAA\n______________:\|_:\|\|\|\|\|\|:\|\|\n______________UC_UGAAUUUUUU\n3'-UUU...GUUCU__G__________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	53 -- 59	29 -- 35	-11.0144 kcal/mol	2.10364 kcal/mol	1.62306 kcal/mol	46 60@LB@ \| \|@LB@5'-CUG...UACCA G GAUAA...CGU-3'@LB@ GG GCUUAAAGAA@LB@ :\| :\|\|\|\|\|\|:\|\|@LB@ UC UGAAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -11.0144 kcal/mol@LB@Unfolding Energy - mRNA 2.10364 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 47 -- 59@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 29 -- 35@LB@
64	0.003339	0.1645	b3166	truB	-7.27	0.093914	187 -- 199	36 -- 48	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________186___________200\n_____________\|_____________\|\n5'-GGC...ACGAC_________G___AAUGA...AAC-3'\n______________AGCAAGGAG_ACU\n______________\|\|\|\|\|\|:\|\|_\|\|\|\n______________UCGUUCUUC_UGA\n3'-UUU...CGAAU_________G___AUUUU...CAA-5'\n_____________\|_____________\|\n_____________49____________35\n	189 -- 195	40 -- 46	-16.8762 kcal/mol	3.76451 kcal/mol	5.83861 kcal/mol	186 200@LB@ \| \|@LB@5'-GGC...ACGAC G AAUGA...AAC-3'@LB@ AGCAAGGAG ACU@LB@ \|\|\|\|\|\|:\|\| \|\|\|@LB@ UCGUUCUUC UGA@LB@3'-UUU...CGAAU G AUUUU...CAA-5'@LB@ \| \|@LB@ 49 35@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -16.8762 kcal/mol@LB@Unfolding Energy - mRNA 3.76451 kcal/mol@LB@Unfolding Energy - sRNA 5.83861 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 36 -- 48@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
24	0.000694	0.09021	b2531	iscR	-7.21	0.097486	53 -- 65	27 -- 41	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________52______________66\n_____________\|_______________\|\n5'-AUG...AAAAU_______________AAAUA...AAC-3'\n______________GGCACU__GAAGGUU\n______________:\|\|\|\|\|__:\|\|::\|\|\n______________UCGUGA__UUUUUAA\n3'-UUU...GUUCU______AU_______GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	59 -- 65	27 -- 33	-10.1429 kcal/mol	1.29 kcal/mol	1.6427 kcal/mol	52 66@LB@ \| \|@LB@5'-AUG...AAAAU AAAUA...AAC-3'@LB@ GGCACU GAAGGUU@LB@ :\|\|\|\|\| :\|\|::\|\|@LB@ UCGUGA UUUUUAA@LB@3'-UUU...GUUCU AU GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -10.1429 kcal/mol@LB@Unfolding Energy - mRNA 1.29 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 53 -- 65@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 27 -- 33@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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