Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
56	0.0008344	0.05242	b3651	trmH	-7.19	0.238334	68 -- 84	17 -- 32	tRNA mG18-2'-O-methyltransferase SAM-dependent	_____________67________________85\n_____________\|_________________\|\n5'-CGC...GAAGA_________UC______ACAGC...UUU-3'\n______________GAAAGAUGG__GCGUCU\n______________\|\|\|\|\|\|\|:\|__:\|:\|\|\|\n______________CUUUCUAUC__UGUAGA\n3'-AUU...CCAGA_________U_______AUGGA...AUG-5'\n_____________\|_________________\|\n_____________33________________16\n	70 -- 76	24 -- 30	-18.3937 kcal/mol	6.9506 kcal/mol	4.26839 kcal/mol	67 85@LB@ \| \|@LB@5'-CGC...GAAGA UC ACAGC...UUU-3'@LB@ GAAAGAUGG GCGUCU@LB@ \|\|\|\|\|\|\|:\| :\|:\|\|\|@LB@ CUUUCUAUC UGUAGA@LB@3'-AUU...CCAGA U AUGGA...AUG-5'@LB@ \| \|@LB@ 33 16@LB@@LB@@LB@Energy -7.19 kcal/mol@LB@Hybridization Energy -18.3937 kcal/mol@LB@Unfolding Energy - mRNA 6.9506 kcal/mol@LB@Unfolding Energy - sRNA 4.26839 kcal/mol@LB@@LB@Position - mRNA 68 -- 84@LB@Position - sRNA 17 -- 32@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 24 -- 30@LB@
135	0.004796	0.125	b3634	coaD	-9.06	0.083023	69 -- 85	49 -- 66	pantetheine-phosphate adenylyltransferase	_____________68_________________86\n_____________\|__________________\|\n5'-GGA...UUUAC________CG________CGUAG...UUC-3'\n______________UCA_CCGA__CCGAUUAC\n______________\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|\n______________AGU_GGUU__GGCUAAUG\n3'-AUU...UUAUA___C____UA________CACUU...AUG-5'\n_____________\|__________________\|\n_____________67_________________48\n	79 -- 85	49 -- 55	-17.7938 kcal/mol	2.54845 kcal/mol	6.20469 kcal/mol	68 86@LB@ \| \|@LB@5'-GGA...UUUAC CG CGUAG...UUC-3'@LB@ UCA CCGA CCGAUUAC@LB@ \|\|\| \|\|:\| \|\|\|\|\|\|\|\|@LB@ AGU GGUU GGCUAAUG@LB@3'-AUU...UUAUA C UA CACUU...AUG-5'@LB@ \| \|@LB@ 67 48@LB@@LB@@LB@Energy -9.06 kcal/mol@LB@Hybridization Energy -17.7938 kcal/mol@LB@Unfolding Energy - mRNA 2.54845 kcal/mol@LB@Unfolding Energy - sRNA 6.20469 kcal/mol@LB@@LB@Position - mRNA 69 -- 85@LB@Position - sRNA 49 -- 66@LB@Position Seed - mRNA 79 -- 85@LB@Position Seed - sRNA 49 -- 55@LB@
7	1.5e-05	0.00754	b0720	gltA	-8.97	0.087950	70 -- 79	4 -- 13	citrate synthase	_____________69_________80\n_____________\|__________\|\n5'-CGG...CAGAG__________AGGUU...GUA-3'\n______________CUCUGUACCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________GAGACAUGGG\n3'-AUU...GAAUG__________AUG-5'\n_____________\|__________\|\n_____________14_________3\n	73 -- 79	4 -- 10	-18.8657 kcal/mol	4.79377 kcal/mol	5.12835 kcal/mol	69 80@LB@ \| \|@LB@5'-CGG...CAGAG AGGUU...GUA-3'@LB@ CUCUGUACCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ GAGACAUGGG@LB@3'-AUU...GAAUG AUG-5'@LB@ \| \|@LB@ 14 3@LB@@LB@@LB@Energy -8.97 kcal/mol@LB@Hybridization Energy -18.8657 kcal/mol@LB@Unfolding Energy - mRNA 4.79377 kcal/mol@LB@Unfolding Energy - sRNA 5.12835 kcal/mol@LB@@LB@Position - mRNA 70 -- 79@LB@Position - sRNA 4 -- 13@LB@Position Seed - mRNA 73 -- 79@LB@Position Seed - sRNA 4 -- 10@LB@
48	0.0005438	0.03933	b0811	glnH	-6.95	0.268265	70 -- 77	1 -- 8	glutamine transporter subunit	_____________69_______78\n_____________\|________\|\n5'-AUC...GGUAU________AAAUC...CCG-3'\n______________UGCCCUAU\n______________\|:\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	71 -- 77	1 -- 7	-10.5963 kcal/mol	1.549 kcal/mol	2.11603 kcal/mol	69 78@LB@ \| \|@LB@5'-AUC...GGUAU AAAUC...CCG-3'@LB@ UGCCCUAU@LB@ \|:\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.95 kcal/mol@LB@Hybridization Energy -10.5963 kcal/mol@LB@Unfolding Energy - mRNA 1.549 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 70 -- 77@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 71 -- 77@LB@Position Seed - sRNA 1 -- 7@LB@
39	0.0004396	0.03766	b3669	uhpA	-8.50	0.116685	77 -- 96	47 -- 66	response regulator in two-component regulatory system wtih UhpB	_____________76___________________97\n_____________\|____________________\|\n5'-UCA...CGUAA______C_______CG____UUAAC...UUG-3'\n______________UCAGUC_GAUCCGA__AUGU\n______________\|\|\|\|:\|_:\|\|\|\|\|\|__\|:\|\|\n______________AGUCGG_UUAGGCU__UGCA\n3'-AUU...UUAUA______U_______AA____CUUCA...AUG-5'\n_____________\|____________________\|\n_____________67___________________46\n	84 -- 90	53 -- 59	-21.6061 kcal/mol	5.63687 kcal/mol	7.4916 kcal/mol	76 97@LB@ \| \|@LB@5'-UCA...CGUAA C CG UUAAC...UUG-3'@LB@ UCAGUC GAUCCGA AUGU@LB@ \|\|\|\|:\| :\|\|\|\|\|\| \|:\|\|@LB@ AGUCGG UUAGGCU UGCA@LB@3'-AUU...UUAUA U AA CUUCA...AUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -21.6061 kcal/mol@LB@Unfolding Energy - mRNA 5.63687 kcal/mol@LB@Unfolding Energy - sRNA 7.4916 kcal/mol@LB@@LB@Position - mRNA 77 -- 96@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 53 -- 59@LB@
125	0.004186	0.1178	b0781	moaA	-8.90	0.091954	79 -- 99	4 -- 23	molybdopterin biosynthesis protein A	_____________78____________________100\n_____________\|_____________________\|\n5'-ACG...CACUA____C___A_______C____GGGUC...CGG-3'\n______________AACA_UCU_GCCUCUG_ACCU\n______________\|\|\|\|_\|\|\|_:\|\|\|\|\|\|_\|\|\|:\n______________UUGU_AGA_UGGAGAC_UGGG\n3'-AUU...CUAUC________A_______A____AUG-5'\n_____________\|_____________________\|\n_____________24____________________3\n	88 -- 94	9 -- 15	-21.7522 kcal/mol	4.86496 kcal/mol	8.01134 kcal/mol	78 100@LB@ \| \|@LB@5'-ACG...CACUA C A C GGGUC...CGG-3'@LB@ AACA UCU GCCUCUG ACCU@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\| \|\|\|:@LB@ UUGU AGA UGGAGAC UGGG@LB@3'-AUU...CUAUC A A AUG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -21.7522 kcal/mol@LB@Unfolding Energy - mRNA 4.86496 kcal/mol@LB@Unfolding Energy - sRNA 8.01134 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 9 -- 15@LB@
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter	_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@LB@
17	5.719e-05	0.01183	b3675	yidG	-12.05	0.010096	82 -- 130	1 -- 56	inner membrane protein	_____________81_____________________________________________________________131\n_____________\|______________________________________________________________\|\n5'-CGC...UUGCG_________CAAU_A_____CGAUGC__________GG________________________ACCAA...CGU-3'\n______________CUGGUUACG____G_AAAAG______GUCUGAAAGA___________ACCU____GCCCUAC\n______________\|:\|:\|\|\|\|\|____\|_\|\|\|\|\|______\|\|\|\|\|\|\|\|\|\|___________\|\|\|\|____:\|\|\|\|\|\|\n______________GGCUAAUGC____C_UUUUC______CAGACUUUCU___________UGGA____UGGGAUG\n3'-AUU...GUUUA_________ACUU_A_____________________AUCUUGUAGAA____GACA_______-5'\n_____________\|_____________________________________________________________\|\n_____________57____________________________________________________________1\n	124 -- 130	1 -- 7	-38.348 kcal/mol	13.6157 kcal/mol	12.7022 kcal/mol	81 131@LB@ \| \|@LB@5'-CGC...UUGCG CAAU A CGAUGC GG ACCAA...CGU-3'@LB@ CUGGUUACG G AAAAG GUCUGAAAGA ACCU GCCCUAC@LB@ \|:\|:\|\|\|\|\| \| \|\|\|\|\| \|\|\|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|@LB@ GGCUAAUGC C UUUUC CAGACUUUCU UGGA UGGGAUG@LB@3'-AUU...GUUUA ACUU A AUCUUGUAGAA GACA -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -12.05 kcal/mol@LB@Hybridization Energy -38.348 kcal/mol@LB@Unfolding Energy - mRNA 13.6157 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 82 -- 130@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 1 -- 7@LB@
187	0.008276	0.1556	b0827	moeA	-6.51	0.330510	82 -- 91	23 -- 32	molybdopterin molybdenumtransferase; molybdopterin biosynthesis protein	_____________81_________92\n_____________\|__________\|\n5'-AUU...AUAUA__________UAUGG...UAC-3'\n______________GAAAGAUGGA\n______________\|\|\|\|\|\|\|:\|\|\n______________CUUUCUAUCU\n3'-AUU...CCAGA__________UGUAG...AUG-5'\n_____________\|__________\|\n_____________33_________22\n	85 -- 91	23 -- 29	-12.1772 kcal/mol	2.37895 kcal/mol	3.23951 kcal/mol	81 92@LB@ \| \|@LB@5'-AUU...AUAUA UAUGG...UAC-3'@LB@ GAAAGAUGGA@LB@ \|\|\|\|\|\|\|:\|\|@LB@ CUUUCUAUCU@LB@3'-AUU...CCAGA UGUAG...AUG-5'@LB@ \| \|@LB@ 33 22@LB@@LB@@LB@Energy -6.51 kcal/mol@LB@Hybridization Energy -12.1772 kcal/mol@LB@Unfolding Energy - mRNA 2.37895 kcal/mol@LB@Unfolding Energy - sRNA 3.23951 kcal/mol@LB@@LB@Position - mRNA 82 -- 91@LB@Position - sRNA 23 -- 32@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 23 -- 29@LB@
31	0.0003178	0.03519	b3588	aldB	-11.98	0.010708	83 -- 100	1 -- 16	aldehyde dehydrogenase B	_____________82_________________101\n_____________\|__________________\|\n5'-GAA...UCAAC__________A___U___CCGUA...GGG-3'\n______________UAUCUCUGUA_CCC_UGC\n______________\|\|:\|\|\|\|\|\|\|_\|\|\|_\|:\|\n______________AUGGAGACAU_GGG_AUG\n3'-AUU...GUAGA__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	86 -- 92	7 -- 13	-19.6311 kcal/mol	1.07825 kcal/mol	6.59719 kcal/mol	82 101@LB@ \| \|@LB@5'-GAA...UCAAC A U CCGUA...GGG-3'@LB@ UAUCUCUGUA CCC UGC@LB@ \|\|:\|\|\|\|\|\|\| \|\|\| \|:\|@LB@ AUGGAGACAU GGG AUG@LB@3'-AUU...GUAGA -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -11.98 kcal/mol@LB@Hybridization Energy -19.6311 kcal/mol@LB@Unfolding Energy - mRNA 1.07825 kcal/mol@LB@Unfolding Energy - sRNA 6.59719 kcal/mol@LB@@LB@Position - mRNA 83 -- 100@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 7 -- 13@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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