Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
152	0.005935	0.1368	b2701	mltB	-9.57	0.138424	83 -- 107	69 -- 92	membrane-bound lytic murein transglycosylase B	_____________82________________________108\n_____________\|_________________________\|\n5'-AGA...GAUAG__AG_G____G_____A________AAGUC...GAA-3'\n______________CG__G_GAAU_AGUUG_GUUAUGUA\n______________\|\|__:_\|\|\|\|_\|:\|\|\|_\|:\|\|\|\|:\|\n______________GC__U_CUUA_UUAAC_CGAUACGU\n3'-UUU...CCGCA__A__G____G_____A________CAUUA...ACG-5'\n_____________\|_________________________\|\n_____________93________________________68\n	101 -- 107	69 -- 75	-19.8359 kcal/mol	5.60429 kcal/mol	4.66371 kcal/mol	82 108@LB@ \| \|@LB@5'-AGA...GAUAG AG G G A AAGUC...GAA-3'@LB@ CG G GAAU AGUUG GUUAUGUA@LB@ \|\| : \|\|\|\| \|:\|\|\| \|:\|\|\|\|:\|@LB@ GC U CUUA UUAAC CGAUACGU@LB@3'-UUU...CCGCA A G G A CAUUA...ACG-5'@LB@ \| \|@LB@ 93 68@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -19.8359 kcal/mol@LB@Unfolding Energy - mRNA 5.60429 kcal/mol@LB@Unfolding Energy - sRNA 4.66371 kcal/mol@LB@@LB@Position - mRNA 83 -- 107@LB@Position - sRNA 69 -- 92@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 69 -- 75@LB@
175	0.007208	0.145	b1444	patD	-10.32	0.092173	197 -- 205	69 -- 77	gamma-aminobutyraldehyde dehydrogenase	_____________196_______206\n_____________\|_________\|\n5'-UCG...GAAUA_________ACAUA...UUG-3'\n______________UGCUAUGCA\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAUACGU\n3'-UUU...UUAAC_________CAUUA...ACG-5'\n_____________\|_________\|\n_____________78________68\n	199 -- 205	69 -- 75	-13.9965 kcal/mol	1.91367 kcal/mol	1.75858 kcal/mol	196 206@LB@ \| \|@LB@5'-UCG...GAAUA ACAUA...UUG-3'@LB@ UGCUAUGCA@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAUACGU@LB@3'-UUU...UUAAC CAUUA...ACG-5'@LB@ \| \|@LB@ 78 68@LB@@LB@@LB@Energy -10.32 kcal/mol@LB@Hybridization Energy -13.9965 kcal/mol@LB@Unfolding Energy - mRNA 1.91367 kcal/mol@LB@Unfolding Energy - sRNA 1.75858 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 69 -- 77@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 69 -- 75@LB@
129	0.00462	0.126	b1795	yeaQ	-13.29	0.014930	139 -- 150	70 -- 81	UPF0410 family protein	_____________138__________151\n_____________\|____________\|\n5'-AUA...CCGAU____________UUUUU...UCC-3'\n______________GUUGUGCUAUGC\n______________:\|\|\|\|\|\|\|\|\|\|\|\n______________UAACACGAUACG\n3'-UUU...UUAGU____________UCAUU...ACG-5'\n_____________\|____________\|\n_____________82___________69\n	144 -- 150	70 -- 76	-18.6071 kcal/mol	3.49189 kcal/mol	1.8201 kcal/mol	138 151@LB@ \| \|@LB@5'-AUA...CCGAU UUUUU...UCC-3'@LB@ GUUGUGCUAUGC@LB@ :\|\|\|\|\|\|\|\|\|\|\|@LB@ UAACACGAUACG@LB@3'-UUU...UUAGU UCAUU...ACG-5'@LB@ \| \|@LB@ 82 69@LB@@LB@@LB@Energy -13.29 kcal/mol@LB@Hybridization Energy -18.6071 kcal/mol@LB@Unfolding Energy - mRNA 3.49189 kcal/mol@LB@Unfolding Energy - sRNA 1.8201 kcal/mol@LB@@LB@Position - mRNA 139 -- 150@LB@Position - sRNA 70 -- 81@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 70 -- 76@LB@
164	0.006461	0.1377	b0864	artP	-11.21	0.055481	74 -- 84	70 -- 80	arginine ABC transporter ATPase	_____________73__________85\n_____________\|___________\|\n5'-AAA...UUAUU___________UUAUU...UAC-3'\n______________UUGUGCUAUGU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________AACACGAUACG\n3'-UUU...UAGUU___________UCAUU...ACG-5'\n_____________\|___________\|\n_____________81__________69\n	78 -- 84	70 -- 76	-15.8897 kcal/mol	2.86206 kcal/mol	1.81863 kcal/mol	73 85@LB@ \| \|@LB@5'-AAA...UUAUU UUAUU...UAC-3'@LB@ UUGUGCUAUGU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ AACACGAUACG@LB@3'-UUU...UAGUU UCAUU...ACG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.21 kcal/mol@LB@Hybridization Energy -15.8897 kcal/mol@LB@Unfolding Energy - mRNA 2.86206 kcal/mol@LB@Unfolding Energy - sRNA 1.81863 kcal/mol@LB@@LB@Position - mRNA 74 -- 84@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 70 -- 76@LB@
67	0.00114	0.05992	b4141	yjeH	-12.53	0.024616	129 -- 146	73 -- 89	putative transporter	_____________128________________147\n_____________\|__________________\|\n5'-CAG...CAUAA_______U__________CCAUC...CUG-3'\n______________GCGAAUC_GAUUGUGCUA\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UGCUUAG_UUAACACGAU\n3'-UUU...CAGCA__________________ACGUC...ACG-5'\n_____________\|__________________\|\n_____________90_________________72\n	140 -- 146	73 -- 79	-22.1843 kcal/mol	7.4128 kcal/mol	2.24587 kcal/mol	128 147@LB@ \| \|@LB@5'-CAG...CAUAA U CCAUC...CUG-3'@LB@ GCGAAUC GAUUGUGCUA@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UGCUUAG UUAACACGAU@LB@3'-UUU...CAGCA ACGUC...ACG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -22.1843 kcal/mol@LB@Unfolding Energy - mRNA 7.4128 kcal/mol@LB@Unfolding Energy - sRNA 2.24587 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 73 -- 79@LB@
95	0.002866	0.1063	b1338	abgA	-10.09	0.104797	206 -- 225	73 -- 94	p-aminobenzoyl-glutamate hydrolase A subunit	_____________205____________________226\n_____________\|______________________\|\n5'-GAU...AUGGA___UU_________________AUUCG...UCC-3'\n______________GUC___UGAAUCAAUU_UGUUA\n______________\|\|\|___:\|\|\|\|\|\|\|\|\|_\|\|:\|\|\n______________CAG___GCUUAGUUAA_ACGAU\n3'-UUU...AGCCG___CAU__________C_____ACGUC...ACG-5'\n_____________\|______________________\|\n_____________95_____________________72\n	214 -- 220	79 -- 85	-14.4971 kcal/mol	2.01447 kcal/mol	2.39569 kcal/mol	205 226@LB@ \| \|@LB@5'-GAU...AUGGA UU AUUCG...UCC-3'@LB@ GUC UGAAUCAAUU UGUUA@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|:\|\|@LB@ CAG GCUUAGUUAA ACGAU@LB@3'-UUU...AGCCG CAU C ACGUC...ACG-5'@LB@ \| \|@LB@ 95 72@LB@@LB@@LB@Energy -10.09 kcal/mol@LB@Hybridization Energy -14.4971 kcal/mol@LB@Unfolding Energy - mRNA 2.01447 kcal/mol@LB@Unfolding Energy - sRNA 2.39569 kcal/mol@LB@@LB@Position - mRNA 206 -- 225@LB@Position - sRNA 73 -- 94@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 79 -- 85@LB@
120	0.004053	0.119	b2441	eutB	-6.09	0.606518	293 -- 299	73 -- 79	ethanolamine ammonia-lyase large subunit heavy chain	_____________292_____300\n_____________\|_______\|\n5'-CUG...GGGGA_______G-3'\n______________UGUGCUG\n______________\|\|\|\|\|\|:\n______________ACACGAU\n3'-UUU...AGUUA_______ACGUC...ACG-5'\n_____________\|_______\|\n_____________80______72\n	293 -- 299	73 -- 79	-8.7652 kcal/mol	1.34517 kcal/mol	1.33434 kcal/mol	292 300@LB@ \| \|@LB@5'-CUG...GGGGA G-3'@LB@ UGUGCUG@LB@ \|\|\|\|\|\|:@LB@ ACACGAU@LB@3'-UUU...AGUUA ACGUC...ACG-5'@LB@ \| \|@LB@ 80 72@LB@@LB@@LB@Energy -6.09 kcal/mol@LB@Hybridization Energy -8.7652 kcal/mol@LB@Unfolding Energy - mRNA 1.34517 kcal/mol@LB@Unfolding Energy - sRNA 1.33434 kcal/mol@LB@@LB@Position - mRNA 293 -- 299@LB@Position - sRNA 73 -- 79@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 73 -- 79@LB@
60	0.001013	0.05816	b2207	napD	-8.99	0.186283	27 -- 46	75 -- 92	assembly protein for periplasmic nitrate reductase	_____________26___________________47\n_____________\|____________________\|\n5'-GUU...CCUGG_____C_________AA___CGCCG...AAG-3'\n______________CGUAU_AGUCAGUUG__UGC\n______________\|\|\|\|:_\|:\|\|\|:\|\|\|__\|\|\|\n______________GCAUG_UUAGUUAAC__ACG\n3'-UUU...CCGCA_____C______________AUACG...ACG-5'\n_____________\|____________________\|\n_____________93___________________74\n	35 -- 41	78 -- 84	-16.0375 kcal/mol	4.6767 kcal/mol	2.37539 kcal/mol	26 47@LB@ \| \|@LB@5'-GUU...CCUGG C AA CGCCG...AAG-3'@LB@ CGUAU AGUCAGUUG UGC@LB@ \|\|\|\|: \|:\|\|\|:\|\|\| \|\|\|@LB@ GCAUG UUAGUUAAC ACG@LB@3'-UUU...CCGCA C AUACG...ACG-5'@LB@ \| \|@LB@ 93 74@LB@@LB@@LB@Energy -8.99 kcal/mol@LB@Hybridization Energy -16.0375 kcal/mol@LB@Unfolding Energy - mRNA 4.6767 kcal/mol@LB@Unfolding Energy - sRNA 2.37539 kcal/mol@LB@@LB@Position - mRNA 27 -- 46@LB@Position - sRNA 75 -- 92@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 78 -- 84@LB@
104	0.00334	0.1114	b1923	fliC	-7.97	0.300066	194 -- 205	75 -- 89	flagellar filament structural protein (flagellin)	_____________193_____________206\n_____________\|_______________\|\n5'-GUU...GGAUA_______________ACAAG...CUU-3'\n______________ACGAAUCA__UG_GC\n______________\|\|\|\|\|\|\|\|__\|\|_\|\|\n______________UGCUUAGU__AC_CG\n3'-UUU...CAGCA________UA__A__AUACG...ACG-5'\n_____________\|_______________\|\n_____________90______________74\n	195 -- 201	82 -- 88	-12.363 kcal/mol	2.14901 kcal/mol	2.24483 kcal/mol	193 206@LB@ \| \|@LB@5'-GUU...GGAUA ACAAG...CUU-3'@LB@ ACGAAUCA UG GC@LB@ \|\|\|\|\|\|\|\| \|\| \|\|@LB@ UGCUUAGU AC CG@LB@3'-UUU...CAGCA UA A AUACG...ACG-5'@LB@ \| \|@LB@ 90 74@LB@@LB@@LB@Energy -7.97 kcal/mol@LB@Hybridization Energy -12.363 kcal/mol@LB@Unfolding Energy - mRNA 2.14901 kcal/mol@LB@Unfolding Energy - sRNA 2.24483 kcal/mol@LB@@LB@Position - mRNA 194 -- 205@LB@Position - sRNA 75 -- 89@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 82 -- 88@LB@
178	0.007484	0.1481	b1243	oppA	-9.58	0.138030	24 -- 34	81 -- 91	oligopeptide ABC transporter periplasmic binding protein	_____________23__________35\n_____________\|___________\|\n5'-UGU...ACACA___________CAUAA...UCA-3'\n______________GUACGAAUCGA\n______________\|\|\|\|\|\|\|\|\|:\|\n______________CAUGCUUAGUU\n3'-UUU...CGCAG___________AACAC...ACG-5'\n_____________\|___________\|\n_____________92__________80\n	28 -- 34	81 -- 87	-14.5847 kcal/mol	2.82098 kcal/mol	2.19089 kcal/mol	23 35@LB@ \| \|@LB@5'-UGU...ACACA CAUAA...UCA-3'@LB@ GUACGAAUCGA@LB@ \|\|\|\|\|\|\|\|\|:\|@LB@ CAUGCUUAGUU@LB@3'-UUU...CGCAG AACAC...ACG-5'@LB@ \| \|@LB@ 92 80@LB@@LB@@LB@Energy -9.58 kcal/mol@LB@Hybridization Energy -14.5847 kcal/mol@LB@Unfolding Energy - mRNA 2.82098 kcal/mol@LB@Unfolding Energy - sRNA 2.19089 kcal/mol@LB@@LB@Position - mRNA 24 -- 34@LB@Position - sRNA 81 -- 91@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 81 -- 87@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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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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