Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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	Additional homologs
85	0.009065	0.3575	b3155	yhbQ	-10.34	0.236900	54 -- 88	123 -- 160	GIY-YIG nuclease superfamily protein		_____________53______________________89\n_____________\|_______________________\|\n5'-UUU...GAUCC_____G__GACAAUAA_______ACCGG...GCG-3'\n______________GUACC_CC________GCUUUAU\n______________\|:\|\|\|_\|\|________\|\|\|\|:\|\|\n______________CGUGG_GG________CGAAGUA\n3'-UUU...UACCC_____G__AA_____________G-5'\n_____________\|_______________________\|\n_____________161_____________________122\n	245 -- 251	2 -- 8	-16.2438 kcal/mol	1.2562 kcal/mol	7.2187 kcal/mol	53 89@LB@ \| \|@LB@5'-UUU...GAUCC G GACAAUAA ACCGG...GCG-3'@LB@ GUACC CC GCUUUAU@LB@ \|:\|\|\| \|\| \|\|\|\|:\|\|@LB@ CGUGG GG CGAAGUA@LB@3'-UUU...UACCC G AA G-5'@LB@ \| \|@LB@ 161 122@LB@@LB@@LB@Energy -10.34 kcal/mol@LB@Hybridization Energy -16.2438 kcal/mol@LB@Unfolding Energy - mRNA 1.2562 kcal/mol@LB@Unfolding Energy - sRNA 7.2187 kcal/mol@LB@@LB@Position - mRNA 54 -- 88@LB@Position - sRNA 123 -- 160@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 2 -- 8@LB@
35	0.002845	0.2736	b3887	dtd	-14.98	0.027287	55 -- 74	191 -- 211	D-tyr-tRNA(Tyr) deacylase		_____________54____________________75\n_____________\|_____________________\|\n5'-GGA...UCAUU______G______________CCCCA...UCG-3'\n______________UAUGGU_UGCUGGCGG_UGAU\n______________\|\|\|::\|_\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________AUAUUA_ACGACCGCC_ACUA\n3'-UUU...CGUCC______G_________C____AAAUG...UAG-5'\n_____________\|_____________________\|\n_____________212___________________190\n	64 -- 70	196 -- 202	-27.702 kcal/mol	6.2401 kcal/mol	11.5765 kcal/mol	54 75@LB@ \| \|@LB@5'-GGA...UCAUU G CCCCA...UCG-3'@LB@ UAUGGU UGCUGGCGG UGAU@LB@ \|\|\|::\| \|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ AUAUUA ACGACCGCC ACUA@LB@3'-UUU...CGUCC G C AAAUG...UAG-5'@LB@ \| \|@LB@ 212 190@LB@@LB@@LB@Energy -14.98 kcal/mol@LB@Hybridization Energy -27.702 kcal/mol@LB@Unfolding Energy - mRNA 6.2401 kcal/mol@LB@Unfolding Energy - sRNA 11.5765 kcal/mol@LB@@LB@Position - mRNA 55 -- 74@LB@Position - sRNA 191 -- 211@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 196 -- 202@LB@
25	0.002009	0.2633	b0134	panB	-9.88	0.290153	57 -- 67	176 -- 186	3-methyl-2-oxobutanoate hydroxymethyltransferase		_____________56__________68\n_____________\|___________\|\n5'-CAG...AAAGC___________UCCAG...UUG-3'\n______________CACCAGUACUU\n______________\|\|\|\|\|:\|\|\|\|:\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________187_________175\n	61 -- 67	176 -- 182	-15.2136 kcal/mol	0.973349 kcal/mol	3.38772 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAGC UCCAG...UUG-3'@LB@ CACCAGUACUU@LB@ \|\|\|\|\|:\|\|\|\|:@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 187 175@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -15.2136 kcal/mol@LB@Unfolding Energy - mRNA 0.973349 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 176 -- 186@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 176 -- 182@LB@
199	0.02363	0.3833	b4141	yjeH	-8.04	0.585705	57 -- 67	64 -- 74	putative transporter		_____________56_____________68\n_____________\|______________\|\n5'-CAG...AAAUC___G_______C__AAAUU...CUG-3'\n______________UAC_CAGUUGC_CA\n______________\|\|\|_\|\|\|\|::\|_\|\|\n______________AUG_GUCAGUG_GU\n3'-UUU...UGGUU___A_______U__ACUAC...UAG-5'\n_____________\|______________\|\n_____________75_____________63\n	163 -- 169	170 -- 176	-11.2481 kcal/mol	2.09942 kcal/mol	0.433965 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAUC G C AAAUU...CUG-3'@LB@ UAC CAGUUGC CA@LB@ \|\|\| \|\|\|\|::\| \|\|@LB@ AUG GUCAGUG GU@LB@3'-UUU...UGGUU A U ACUAC...UAG-5'@LB@ \| \|@LB@ 75 63@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -11.2481 kcal/mol@LB@Unfolding Energy - mRNA 2.09942 kcal/mol@LB@Unfolding Energy - sRNA 0.433965 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 64 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 170 -- 176@LB@
10	0.0006004	0.1842	b3656	yicI	-12.42	0.091283	58 -- 101	169 -- 207	putative alpha-glucosidase		_____________57_________102\n_____________\|__________\|\n5'-ACA...GAUAA__________G-3'\n______________UGAAAUGGUG\n______________\|:\|\|\|\|:\|\|\|\n______________AUUUUAUCAC\n3'-UUU...GCGCC__________GACUA...UAG-5'\n_____________\|__________\|\n_____________208________168\n	293 -- 299	40 -- 46	-9.13222 kcal/mol	0.486237 kcal/mol	4.51378 kcal/mol	57 102@LB@ \| \|@LB@5'-ACA...GAUAA G-3'@LB@ UGAAAUGGUG@LB@ \|:\|\|\|\|:\|\|\|@LB@ AUUUUAUCAC@LB@3'-UUU...GCGCC GACUA...UAG-5'@LB@ \| \|@LB@ 208 168@LB@@LB@@LB@Energy -12.42 kcal/mol@LB@Hybridization Energy -9.13222 kcal/mol@LB@Unfolding Energy - mRNA 0.486237 kcal/mol@LB@Unfolding Energy - sRNA 4.51378 kcal/mol@LB@@LB@Position - mRNA 58 -- 101@LB@Position - sRNA 169 -- 207@LB@Position Seed - mRNA 293 -- 299@LB@Position Seed - sRNA 40 -- 46@LB@
77	0.007981	0.3458	b1738	chbB	-9.80	0.299184	58 -- 71	174 -- 187	N N'-diacetylchitobiose-specific enzyme IIB component of PTS		_____________57_______________________________72\n_____________\|________________________________\|\n5'-AAU...UAUAA___CAAAGAA______U_______G__U____CGUAU...CGG-3'\n______________GGU_______AUACUA_UGCUCAG_UC_AUAC\n______________\|\|\|_______\|:\|\|:\|_\|:\|\|\|\|\|_\|\|_\|:\|\|\n______________CCA_______UGUGGU_AUGAGUC_AG_UGUG\n3'-UUU...ACCGC___CUAAAA_______U_______________UACUA...UAG-5'\n_____________\|________________________________\|\n_____________188______________________________173\n	65 -- 71	174 -- 180	-20.4225 kcal/mol	4.13376 kcal/mol	5.03959 kcal/mol	57 72@LB@ \| \|@LB@5'-AAU...UAUAA CAAAGAA U G U CGUAU...CGG-3'@LB@ GGU AUACUA UGCUCAG UC AUAC@LB@ \|\|\| \|:\|\|:\| \|:\|\|\|\|\| \|\| \|:\|\|@LB@ CCA UGUGGU AUGAGUC AG UGUG@LB@3'-UUU...ACCGC CUAAAA U UACUA...UAG-5'@LB@ \| \|@LB@ 188 173@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -20.4225 kcal/mol@LB@Unfolding Energy - mRNA 4.13376 kcal/mol@LB@Unfolding Energy - sRNA 5.03959 kcal/mol@LB@@LB@Position - mRNA 58 -- 71@LB@Position - sRNA 174 -- 187@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 174 -- 180@LB@
95	0.01047	0.3575	b4232	fbp	-15.00	0.027086	59 -- 98	140 -- 173	fructose-1 6-bisphosphatase I		_____________58_______________________________________________99\n_____________\|________________________________________________\|\n5'-AAA...CUGCC_____UU____________U_________G_GAAAC__A_________AAUCC...CCA-3'\n______________GCUCA__UUACGCAU_AUG_CGGGCAAGU_A_____GC_UUUCAGGAU\n______________:\|\|\|\|__\|:\|\|:\|\|\|_\|\|\|_\|:\|\|\|\|\|\|\|_\|_____:\|_\|\|\|\|\|\|:\|\|\n______________UGAGU__AGUGUGUA_UAC_GUCCGUUCA_U_____UG_AAAGUCUUA\n3'-UUU...GGUUA_____C_________C_____________G__________________ACGCC...UAG-5'\n_____________\|________________________________________________\|\n_____________174______________________________________________139\n	92 -- 98	140 -- 146	-39.7088 kcal/mol	14.0477 kcal/mol	8.83532 kcal/mol	58 99@LB@ \| \|@LB@5'-AAA...CUGCC UU U G GAAAC A AAUCC...CCA-3'@LB@ GCUCA UUACGCAU AUG CGGGCAAGU A GC UUUCAGGAU@LB@ :\|\|\|\| \|:\|\|:\|\|\| \|\|\| \|:\|\|\|\|\|\|\| \| :\| \|\|\|\|\|\|:\|\|@LB@ UGAGU AGUGUGUA UAC GUCCGUUCA U UG AAAGUCUUA@LB@3'-UUU...GGUUA C C G ACGCC...UAG-5'@LB@ \| \|@LB@ 174 139@LB@@LB@@LB@Energy -15.00 kcal/mol@LB@Hybridization Energy -39.7088 kcal/mol@LB@Unfolding Energy - mRNA 14.0477 kcal/mol@LB@Unfolding Energy - sRNA 8.83532 kcal/mol@LB@@LB@Position - mRNA 59 -- 98@LB@Position - sRNA 140 -- 173@LB@Position Seed - mRNA 92 -- 98@LB@Position Seed - sRNA 140 -- 146@LB@
145	0.01541	0.3575	b1191	cvrA	-14.91	0.028165	61 -- 91	128 -- 160	putative cation/proton antiporter		_____________60___________________________________92\n_____________\|____________________________________\|\n5'-UGA...CGGGA_____CUC_______GA___________________GUUCU...CUA-3'\n______________AGGCA___AGUUGAC__UUA_____GCGGUCAUCCU\n______________\|\|\|\|\|___\|\|\|::\|\|__\|:\|_____\|\|\|\|\|\|\|\|\|\|:\n______________UCCGU___UCAGUUG__AGU_____CGCCAGUAGGG\n3'-UUU...CUACG_______________AA___CUUAA___________UGACG...UAG-5'\n_____________\|____________________________________\|\n_____________161__________________________________127\n	85 -- 91	128 -- 134	-32.547 kcal/mol	9.03914 kcal/mol	12.2557 kcal/mol	60 92@LB@ \| \|@LB@5'-UGA...CGGGA CUC GA GUUCU...CUA-3'@LB@ AGGCA AGUUGAC UUA GCGGUCAUCCU@LB@ \|\|\|\|\| \|\|\|::\|\| \|:\| \|\|\|\|\|\|\|\|\|\|:@LB@ UCCGU UCAGUUG AGU CGCCAGUAGGG@LB@3'-UUU...CUACG AA CUUAA UGACG...UAG-5'@LB@ \| \|@LB@ 161 127@LB@@LB@@LB@Energy -14.91 kcal/mol@LB@Hybridization Energy -32.547 kcal/mol@LB@Unfolding Energy - mRNA 9.03914 kcal/mol@LB@Unfolding Energy - sRNA 12.2557 kcal/mol@LB@@LB@Position - mRNA 61 -- 91@LB@Position - sRNA 128 -- 160@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 128 -- 134@LB@
195	0.02319	0.3833	b1233	ychJ	-7.86	0.620262	61 -- 80	1 -- 18	UPF0225 family protein		_____________60____________________________________81\n_____________\|_____________________________________\|\n5'-CUU...GCUAC_______________A___CUACU_____________ACGCC...UCA-3'\n______________UGCUCGGUUA_ACAU_GUG_____CAGGC_GGUUAAU\n______________\|:\|\|\|:\|\|:\|_\|\|\|\|_:\|\|_____\|\|\|\|\|_:\|\|:\|\|:\n______________AUGAGUCAGU_UGUA_UAC_____GUCCG_UCAGUUG\n3'-UUU...UGGUU__________G____C_____________U_______AAAGU...UAG-5'\n_____________\|_____________________________________\|\n_____________19____________________________________0\n	139 -- 145	171 -- 177	-29.0991 kcal/mol	9.80481 kcal/mol	8.18679 kcal/mol	60 81@LB@ \| \|@LB@5'-CUU...GCUAC A CUACU ACGCC...UCA-3'@LB@ UGCUCGGUUA ACAU GUG CAGGC GGUUAAU@LB@ \|:\|\|\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\| :\|\|:\|\|:@LB@ AUGAGUCAGU UGUA UAC GUCCG UCAGUUG@LB@3'-UUU...UGGUU G C U AAAGU...UAG-5'@LB@ \| \|@LB@ 19 0@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -29.0991 kcal/mol@LB@Unfolding Energy - mRNA 9.80481 kcal/mol@LB@Unfolding Energy - sRNA 8.18679 kcal/mol@LB@@LB@Position - mRNA 61 -- 80@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 171 -- 177@LB@
15	0.0008498	0.1886	b4254	argI	-15.11	0.025648	62 -- 84	167 -- 185	ornithine carbamoyltransferase 1	b0273	_____________61______________________85\n_____________\|_______________________\|\n5'-UUC...GUCCU__________UUAUU________CCACU...AUA-3'\n______________GCCGAUACUC_____GUCACACA\n______________:\|\|:\|\|\|\|\|\|_____\|\|\|\|\|\|\|\|\n______________UGGUUAUGAG_____CAGUGUGU\n3'-UUU...AAAUG__________U____________ACUAC...UAG-5'\n_____________\|_______________________\|\n_____________186_____________________166\n	78 -- 84	167 -- 173	-24.735 kcal/mol	3.62809 kcal/mol	5.02083 kcal/mol	61 85@LB@ \| \|@LB@5'-UUC...GUCCU UUAUU CCACU...AUA-3'@LB@ GCCGAUACUC GUCACACA@LB@ :\|\|:\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UGGUUAUGAG CAGUGUGU@LB@3'-UUU...AAAUG U ACUAC...UAG-5'@LB@ \| \|@LB@ 186 166@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -24.735 kcal/mol@LB@Unfolding Energy - mRNA 3.62809 kcal/mol@LB@Unfolding Energy - sRNA 5.02083 kcal/mol@LB@@LB@Position - mRNA 62 -- 84@LB@Position - sRNA 167 -- 185@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 167 -- 173@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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