Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
121	0.01302	0.3615	b0966	hspQ	-14.11	0.039362	113 -- 134	1 -- 23	heat shock protein involved in degradation of mutant DnaA; hemimethylated oriC DNA-binding protein	_____________112_____________________135\n_____________\|_______________________\|\n5'-AGA...CUAUA____AA_______G_________GUCAU...CUG-3'\n______________UCUG__AGGGUUU_CCUG_UCGC\n______________\|\|:\|__\|\|\|\|\|:\|_\|\|\|\|_\|\|\|\|\n______________AGGC__UCCCAGA_GGAC_AGCG\n3'-UUU...CCAAG____GC_______A____U____-5'\n_____________\|______________________\|\n_____________24_____________________1\n	119 -- 125	11 -- 17	-28.2829 kcal/mol	6.57487 kcal/mol	7.59819 kcal/mol	112 135@LB@ \| \|@LB@5'-AGA...CUAUA AA G GUCAU...CUG-3'@LB@ UCUG AGGGUUU CCUG UCGC@LB@ \|\|:\| \|\|\|\|\|:\| \|\|\|\| \|\|\|\|@LB@ AGGC UCCCAGA GGAC AGCG@LB@3'-UUU...CCAAG GC A U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -14.11 kcal/mol@LB@Hybridization Energy -28.2829 kcal/mol@LB@Unfolding Energy - mRNA 6.57487 kcal/mol@LB@Unfolding Energy - sRNA 7.59819 kcal/mol@LB@@LB@Position - mRNA 113 -- 134@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 11 -- 17@LB@
122	0.01331	0.3627	b0078	ilvH	-10.99	0.130728	66 -- 84	41 -- 61	acetolactate synthase 3 small subunit valine-sensitive	_____________65____________________85\n_____________\|_____________________\|\n5'-GCC...GAGGC_______________C_____AAUCG...UGA-3'\n______________GCUGGAA_CAG_GUG_GCAAU\n______________:\|\|\|\|\|\|_\|\|:_\|\|\|_\|\|\|\|\|\n______________UGACCUU_GUU_CAC_CGUUA\n3'-UUU...CAUUA_______C___A___U_____CAGCA...GCG-5'\n_____________\|_____________________\|\n_____________62____________________40\n	66 -- 72	55 -- 61	-20.2432 kcal/mol	5.95009 kcal/mol	3.30062 kcal/mol	65 85@LB@ \| \|@LB@5'-GCC...GAGGC C AAUCG...UGA-3'@LB@ GCUGGAA CAG GUG GCAAU@LB@ :\|\|\|\|\|\| \|\|: \|\|\| \|\|\|\|\|@LB@ UGACCUU GUU CAC CGUUA@LB@3'-UUU...CAUUA C A U CAGCA...GCG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -20.2432 kcal/mol@LB@Unfolding Energy - mRNA 5.95009 kcal/mol@LB@Unfolding Energy - sRNA 3.30062 kcal/mol@LB@@LB@Position - mRNA 66 -- 84@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 66 -- 72@LB@Position Seed - sRNA 55 -- 61@LB@
123	0.0134	0.3627	b3774	ilvC	-11.90	0.092739	9 -- 41	1 -- 25	ketol-acid reductoisomerase NAD(P)-binding	_____________8__________________________________42\n_____________\|__________________________________\|\n___5'-AUGGCGGC_______CAGAUGCAG__A_______A_______GUAAA...GCU-3'\n______________UUUCCGC_________GA_GGUUUUC__GAUCGC\n______________\|:\|\|\|\|\|_________\|\|_\|\|\|:\|\|\|__\|\|\|\|\|\|\n______________AGAGGCG_________CU_CCAGAAG__CUAGCG\n3'-UUU...GUCCA__________________C_______GA______-5'\n_____________\|_________________________________\|\n_____________26________________________________1\n	28 -- 34	9 -- 15	-28.1375 kcal/mol	8.51703 kcal/mol	7.71912 kcal/mol	8 42@LB@ \| \|@LB@ 5'-AUGGCGGC CAGAUGCAG A A GUAAA...GCU-3'@LB@ UUUCCGC GA GGUUUUC GAUCGC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\| \|\|\|\|\|\|@LB@ AGAGGCG CU CCAGAAG CUAGCG@LB@3'-UUU...GUCCA C GA -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.90 kcal/mol@LB@Hybridization Energy -28.1375 kcal/mol@LB@Unfolding Energy - mRNA 8.51703 kcal/mol@LB@Unfolding Energy - sRNA 7.71912 kcal/mol@LB@@LB@Position - mRNA 9 -- 41@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 9 -- 15@LB@
124	0.01356	0.3627	b2232	ubiG	-16.56	0.014945	261 -- 300	44 -- 89	bifunctional 3-demethylubiquinone-9 3-methyltransferase/ 2-octaprenyl-6-hydroxy phenol methylase	_____________260_____________________________________________300\n_____________\|_______________________________________________\|\n5'-CUU...AAUUU_______U_____CCC______GG________________________-3'\n______________GAAGCCG_CGCCU___GCUGGU_____GAU_CUGGAAG____GUGAGU\n______________:\|\|\|\|\|:_\|:\|\|:___\|\|\|\|\|:_____:\|\|_\|\|\|\|\|\|\|____\|\|\|\|\|:\n______________UUUCGGU_GUGGG___CGACCG_____UUA_GACCUUC____CACUCG\n__________3'-U_______C_____C________AUUCA___U_______GUUA______UUACA...GCG-5'\n_____________\|________________________________________________\|\n_____________90_______________________________________________43\n	288 -- 294	54 -- 60	-44.5757 kcal/mol	13.1093 kcal/mol	14.9095 kcal/mol	260 300@LB@ \| \|@LB@5'-CUU...AAUUU U CCC GG -3'@LB@ GAAGCCG CGCCU GCUGGU GAU CUGGAAG GUGAGU@LB@ :\|\|\|\|\|: \|:\|\|: \|\|\|\|\|: :\|\| \|\|\|\|\|\|\| \|\|\|\|\|:@LB@ UUUCGGU GUGGG CGACCG UUA GACCUUC CACUCG@LB@ 3'-U C C AUUCA U GUUA UUACA...GCG-5'@LB@ \| \|@LB@ 90 43@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -44.5757 kcal/mol@LB@Unfolding Energy - mRNA 13.1093 kcal/mol@LB@Unfolding Energy - sRNA 14.9095 kcal/mol@LB@@LB@Position - mRNA 261 -- 300@LB@Position - sRNA 44 -- 89@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 54 -- 60@LB@
125	0.0136	0.3627	b3647	ligB	-15.20	0.025592	210 -- 279	1 -- 59	DNA ligase NAD(+)-dependent	_____________209_____________________________________________________________________280\n_____________\|_______________________________________________________________________\|\n5'-GGC...AAGUA____U______AUUAAUA____UC________GG__AUCA___G______C_____GUCCGG_________CAGCC...AAA-3'\n______________UGGA_GGCGAU_______GGUA___UUGUGCU__CA____UCU_UGUGGG_GGUCU______CCUGGUCGC\n______________\|\|\|\|_:\|\|:\|\|_______:\|:\|___\|:\|\|\|\|\|__\|\|____\|\|\|_:\|:\|:\|_\|\|\|\|\|______\|\|\|\|:\|\|\|\|\n______________ACCU_UCGUUA_______UCGU___AGCACGA__GU____AGA_GCGCUC_CCAGA______GGACUAGCG\n3'-UUU...UUAUG___________CAC________UAC_______AA__CCA____G____________A______________-5'\n_____________\|______________________________________________________________________\|\n_____________60_____________________________________________________________________1\n	273 -- 279	1 -- 7	-52.2567 kcal/mol	22.9457 kcal/mol	14.1095 kcal/mol	209 280@LB@ \| \|@LB@5'-GGC...AAGUA U AUUAAUA UC GG AUCA G C GUCCGG CAGCC...AAA-3'@LB@ UGGA GGCGAU GGUA UUGUGCU CA UCU UGUGGG GGUCU CCUGGUCGC@LB@ \|\|\|\| :\|\|:\|\| :\|:\| \|:\|\|\|\|\| \|\| \|\|\| :\|:\|:\| \|\|\|\|\| \|\|\|\|:\|\|\|\|@LB@ ACCU UCGUUA UCGU AGCACGA GU AGA GCGCUC CCAGA GGACUAGCG@LB@3'-UUU...UUAUG CAC UAC AA CCA G A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -15.20 kcal/mol@LB@Hybridization Energy -52.2567 kcal/mol@LB@Unfolding Energy - mRNA 22.9457 kcal/mol@LB@Unfolding Energy - sRNA 14.1095 kcal/mol@LB@@LB@Position - mRNA 210 -- 279@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 1 -- 7@LB@
126	0.01361	0.3627	b2135	yohC	-14.18	0.038247	192 -- 212	38 -- 58	Yip1 family inner membrane protein	_____________191___________________213\n_____________\|_____________________\|\n5'-CAU...AACAA_________A_____C_____UGGGG...UUU-3'\n______________GGGGGCGGU_UGAGC_AUGUC\n______________\|\|::\|\|::\|_\|\|\|\|\|_\|\|\|\|\|\n______________CCUUCGUUA_ACUCG_UACAG\n3'-UUU...UAUGA_________C_____U_____CACGA...GCG-5'\n_____________\|_____________________\|\n_____________59____________________37\n	192 -- 198	52 -- 58	-26.6444 kcal/mol	9.24504 kcal/mol	3.21639 kcal/mol	191 213@LB@ \| \|@LB@5'-CAU...AACAA A C UGGGG...UUU-3'@LB@ GGGGGCGGU UGAGC AUGUC@LB@ \|\|::\|\|::\| \|\|\|\|\| \|\|\|\|\|@LB@ CCUUCGUUA ACUCG UACAG@LB@3'-UUU...UAUGA C U CACGA...GCG-5'@LB@ \| \|@LB@ 59 37@LB@@LB@@LB@Energy -14.18 kcal/mol@LB@Hybridization Energy -26.6444 kcal/mol@LB@Unfolding Energy - mRNA 9.24504 kcal/mol@LB@Unfolding Energy - sRNA 3.21639 kcal/mol@LB@@LB@Position - mRNA 192 -- 212@LB@Position - sRNA 38 -- 58@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 52 -- 58@LB@
127	0.01387	0.3627	b1224	narG	-12.01	0.089072	151 -- 160	37 -- 46	nitrate reductase 1 alpha subunit	_____________150________161\n_____________\|__________\|\n5'-UAA...ACAUU__________AUUUA...AGG-3'\n______________AGCAAUGUCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________UCGUUACAGC\n3'-UUU...UACAC__________ACGAA...GCG-5'\n_____________\|__________\|\n_____________47_________36\n	154 -- 160	37 -- 43	-14.8133 kcal/mol	1.65076 kcal/mol	1.15554 kcal/mol	150 161@LB@ \| \|@LB@5'-UAA...ACAUU AUUUA...AGG-3'@LB@ AGCAAUGUCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ UCGUUACAGC@LB@3'-UUU...UACAC ACGAA...GCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -14.8133 kcal/mol@LB@Unfolding Energy - mRNA 1.65076 kcal/mol@LB@Unfolding Energy - sRNA 1.15554 kcal/mol@LB@@LB@Position - mRNA 151 -- 160@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 37 -- 43@LB@
128	0.01397	0.3627	b1656	sodB	-9.64	0.214388	197 -- 205	38 -- 46	superoxide dismutase Fe	_____________196_______206\n_____________\|_________\|\n5'-UCU...AGAGU_________AUUCG...AGA-3'\n______________AGCAAUGUC\n______________\|\|\|\|\|\|\|\|\|\n______________UCGUUACAG\n3'-UUU...UACAC_________CACGA...GCG-5'\n_____________\|_________\|\n_____________47________37\n	199 -- 205	38 -- 44	-13.5738 kcal/mol	2.78264 kcal/mol	1.15511 kcal/mol	196 206@LB@ \| \|@LB@5'-UCU...AGAGU AUUCG...AGA-3'@LB@ AGCAAUGUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ UCGUUACAG@LB@3'-UUU...UACAC CACGA...GCG-5'@LB@ \| \|@LB@ 47 37@LB@@LB@@LB@Energy -9.64 kcal/mol@LB@Hybridization Energy -13.5738 kcal/mol@LB@Unfolding Energy - mRNA 2.78264 kcal/mol@LB@Unfolding Energy - sRNA 1.15511 kcal/mol@LB@@LB@Position - mRNA 197 -- 205@LB@Position - sRNA 38 -- 46@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
129	0.01401	0.3627	b0696	kdpC	-11.63	0.102829	282 -- 295	49 -- 63	potassium translocating ATPase subunit C	_____________281_____________296\n_____________\|_______________\|\n5'-GCG...CCACC_______________GUGGU-3'\n______________GUACUGG_GGCAAUG\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\n______________UAUGACC_UCGUUAC\n3'-UUU...UUCAU_______U_______ACUCG...GCG-5'\n_____________\|_______________\|\n_____________64______________48\n	289 -- 295	49 -- 55	-18.0603 kcal/mol	3.42021 kcal/mol	3.01015 kcal/mol	281 296@LB@ \| \|@LB@5'-GCG...CCACC GUGGU-3'@LB@ GUACUGG GGCAAUG@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|@LB@ UAUGACC UCGUUAC@LB@3'-UUU...UUCAU U ACUCG...GCG-5'@LB@ \| \|@LB@ 64 48@LB@@LB@@LB@Energy -11.63 kcal/mol@LB@Hybridization Energy -18.0603 kcal/mol@LB@Unfolding Energy - mRNA 3.42021 kcal/mol@LB@Unfolding Energy - sRNA 3.01015 kcal/mol@LB@@LB@Position - mRNA 282 -- 295@LB@Position - sRNA 49 -- 63@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 49 -- 55@LB@
130	0.01403	0.3627	b3531	bcsZ	-10.44	0.160598	268 -- 291	50 -- 82	endo-1 4-D-glucanase	_____________267_______________________________292\n_____________\|_________________________________\|\n5'-UCA...AGCCU_________CU______________________UUAAA...AGG-3'\n______________GUACCUGGC__GC_________CUGGGAGCAGU\n______________\|:\|\|\|:\|\|\|__\|\|_________\|\|\|\|:\|\|\|\|:\|\n______________CGUGGGCCG__CG_________GACCUUCGUUA\n___3'-UUUUCGGU_________AC__AUUCAUUAU___________CACUC...GCG-5'\n_____________\|_________________________________\|\n_____________83________________________________49\n	283 -- 289	52 -- 58	-33.5305 kcal/mol	8.70748 kcal/mol	14.3864 kcal/mol	267 292@LB@ \| \|@LB@5'-UCA...AGCCU CU UUAAA...AGG-3'@LB@ GUACCUGGC GC CUGGGAGCAGU@LB@ \|:\|\|\|:\|\|\| \|\| \|\|\|\|:\|\|\|\|:\|@LB@ CGUGGGCCG CG GACCUUCGUUA@LB@ 3'-UUUUCGGU AC AUUCAUUAU CACUC...GCG-5'@LB@ \| \|@LB@ 83 49@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -33.5305 kcal/mol@LB@Unfolding Energy - mRNA 8.70748 kcal/mol@LB@Unfolding Energy - sRNA 14.3864 kcal/mol@LB@@LB@Position - mRNA 268 -- 291@LB@Position - sRNA 50 -- 82@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 52 -- 58@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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