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
53	0.005067	0.3217	b3666	uhpT	-10.07	0.266829	134 -- 177	167 -- 215	hexose phosphate transporter		_____________133_______________________________________________________178\n_____________\|_________________________________________________________\|\n5'-GCC...UGGAC____UCU____CC______________________UA________AUGCC_______GGUAU...UGG-3'\n______________GCUA___CAGG__UGAUUUGCU_GC___UGAUUUU____CAAUGC_____UCACGCA\n______________:\|:\|___\|\|\|\|__\|:\|\|:\|\|\|\|_\|\|___\|\|\|\|\|\|\|____\|\|\|\|:\|_____\|\|\|\|:\|\|\n______________UGGU___GUCC__AUUAGACGA_CG___ACUAAAA____GUUAUG_____AGUGUGU\n____3'-UUUUUUU____C______AU_________C__CCC_______UGUG______AGUC________ACUAC...UAG-5'\n_____________\|_________________________________________________________\|\n_____________216_______________________________________________________166\n	171 -- 177	167 -- 173	-37.7334 kcal/mol	11.6521 kcal/mol	18.4949 kcal/mol	133 178@LB@ \| \|@LB@5'-GCC...UGGAC UCU CC UA AUGCC GGUAU...UGG-3'@LB@ GCUA CAGG UGAUUUGCU GC UGAUUUU CAAUGC UCACGCA@LB@ :\|:\| \|\|\|\| \|:\|\|:\|\|\|\| \|\| \|\|\|\|\|\|\| \|\|\|\|:\| \|\|\|\|:\|\|@LB@ UGGU GUCC AUUAGACGA CG ACUAAAA GUUAUG AGUGUGU@LB@ 3'-UUUUUUU C AU C CCC UGUG AGUC ACUAC...UAG-5'@LB@ \| \|@LB@ 216 166@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -37.7334 kcal/mol@LB@Unfolding Energy - mRNA 11.6521 kcal/mol@LB@Unfolding Energy - sRNA 18.4949 kcal/mol@LB@@LB@Position - mRNA 134 -- 177@LB@Position - sRNA 167 -- 215@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 167 -- 173@LB@
80	0.008443	0.3551	b3791	wecE	-14.19	0.039608	22 -- 66	14 -- 64	TDP-4-oxo-6-deoxy-D-glucose transaminase		_____________21______________67\n_____________\|_______________\|\n5'-GAC...ACCGC_______________GGUGA...CCC-3'\n______________GUACU_GGUUAUACA\n______________:\|\|\|\|_:\|\|:\|:\|\|\|\n______________UAUGA_UCAGUGUGU\n3'-UUU...GUGGU_____G_________ACUAC...UAG-5'\n_____________\|_______________\|\n_____________65______________13\n	185 -- 191	167 -- 173	-12.5686 kcal/mol	2.73267 kcal/mol	0.435744 kcal/mol	21 67@LB@ \| \|@LB@5'-GAC...ACCGC GGUGA...CCC-3'@LB@ GUACU GGUUAUACA@LB@ :\|\|\|\| :\|\|:\|:\|\|\|@LB@ UAUGA UCAGUGUGU@LB@3'-UUU...GUGGU G ACUAC...UAG-5'@LB@ \| \|@LB@ 65 13@LB@@LB@@LB@Energy -14.19 kcal/mol@LB@Hybridization Energy -12.5686 kcal/mol@LB@Unfolding Energy - mRNA 2.73267 kcal/mol@LB@Unfolding Energy - sRNA 0.435744 kcal/mol@LB@@LB@Position - mRNA 22 -- 66@LB@Position - sRNA 14 -- 64@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 167 -- 173@LB@
5	0.0001254	0.08442	b4481	wecF	-11.27	0.155862	165 -- 206	62 -- 99	TDP-Fuc4NAc:lipidIIFuc4NAc transferase		_____________164_____________________________________207\n_____________\|_______________________________________\|\n5'-UUU...GCGUC___G_____U_____UC__GC___________CAG____CUUUA...ACG-3'\n______________ACU_CGGUU_UAUAU__UG__GG_AAGUCAGC___UUCA\n______________\|\|\|_\|:\|\|:_:\|:\|\|__\|\|__\|\|_\|\|\|\|\|\|:\|___\|\|\|\|\n______________UGA_GUCAG_GUGUA__AC__CC_UUCAGUUG___AAGU\n3'-UUU...GGUUA_________U_____CU__GU__G________A______CUUAA...UAG-5'\n_____________\|_______________________________________\|\n_____________100_____________________________________61\n	54 -- 60	149 -- 155	-25.8626 kcal/mol	10.7241 kcal/mol	8.38318 kcal/mol	164 207@LB@ \| \|@LB@5'-UUU...GCGUC G U UC GC CAG CUUUA...ACG-3'@LB@ ACU CGGUU UAUAU UG GG AAGUCAGC UUCA@LB@ \|\|\| \|:\|\|: :\|:\|\| \|\| \|\| \|\|\|\|\|\|:\| \|\|\|\|@LB@ UGA GUCAG GUGUA AC CC UUCAGUUG AAGU@LB@3'-UUU...GGUUA U CU GU G A CUUAA...UAG-5'@LB@ \| \|@LB@ 100 61@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -25.8626 kcal/mol@LB@Unfolding Energy - mRNA 10.7241 kcal/mol@LB@Unfolding Energy - sRNA 8.38318 kcal/mol@LB@@LB@Position - mRNA 165 -- 206@LB@Position - sRNA 62 -- 99@LB@Position Seed - mRNA 54 -- 60@LB@Position Seed - sRNA 149 -- 155@LB@
172	0.01969	0.3812	b0213	yafS	-9.47	0.344290	95 -- 113	1 -- 19	putative S-adenosyl-L-methionine-dependent methyltransferase		_____________94________114\n_____________\|_________\|\n5'-UGG...UCAAA_________CUCCU...UCA-3'\n______________CUGUCGUGG\n______________\|\|\|\|\|\|:\|\|\n______________GACAGCGCC\n3'-UUU...GAAGC_________AUUUU...UAG-5'\n_____________\|_________\|\n_____________20________0\n	228 -- 234	50 -- 56	-16.2917 kcal/mol	2.78861 kcal/mol	4.02 kcal/mol	94 114@LB@ \| \|@LB@5'-UGG...UCAAA CUCCU...UCA-3'@LB@ CUGUCGUGG@LB@ \|\|\|\|\|\|:\|\|@LB@ GACAGCGCC@LB@3'-UUU...GAAGC AUUUU...UAG-5'@LB@ \| \|@LB@ 20 0@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -16.2917 kcal/mol@LB@Unfolding Energy - mRNA 2.78861 kcal/mol@LB@Unfolding Energy - sRNA 4.02 kcal/mol@LB@@LB@Position - mRNA 95 -- 113@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 50 -- 56@LB@
182	0.02094	0.3833	b0248	yafX	-12.67	0.081205	189 -- 235	52 -- 92	CP4-6 prophage; uncharacterized protein	b2643	_____________188______________________236\n_____________\|________________________\|\n5'-CCG...ACACA___G_________C____ACC___UAACC...GGC-3'\n______________GAC_CAGCACGAC_UCGC___CGC\n______________:\|\|_\|\|\|\|\|\|:\|\|_\|\|\|\|___\|\|\|\n______________UUG_GUCGUGUUG_AGCG___GCG\n3'-UUU...UUGCG_____________A____ACA___CCAUU...UAG-5'\n_____________\|________________________\|\n_____________93_______________________51\n	218 -- 224	63 -- 69	-27.2596 kcal/mol	3.0161 kcal/mol	15.5954 kcal/mol	188 236@LB@ \| \|@LB@5'-CCG...ACACA G C ACC UAACC...GGC-3'@LB@ GAC CAGCACGAC UCGC CGC@LB@ :\|\| \|\|\|\|\|\|:\|\| \|\|\|\| \|\|\|@LB@ UUG GUCGUGUUG AGCG GCG@LB@3'-UUU...UUGCG A ACA CCAUU...UAG-5'@LB@ \| \|@LB@ 93 51@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -27.2596 kcal/mol@LB@Unfolding Energy - mRNA 3.0161 kcal/mol@LB@Unfolding Energy - sRNA 15.5954 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 52 -- 92@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 63 -- 69@LB@
98	0.01073	0.3575	b0424	yajL	-11.45	0.143367	14 -- 29	155 -- 170	oxidative-stress-resistance chaperone		_____________13_______________30\n_____________\|________________\|\n5'-AGA...GUGAU________________UUGAU...CCA-3'\n______________UACGUGAUGCAGGUGA\n______________:\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GUGUACUACGUCCGUU\n3'-UUU...UCAGU________________CAGUU...UAG-5'\n_____________\|________________\|\n_____________171______________154\n	22 -- 28	156 -- 162	-24.1359 kcal/mol	6.48358 kcal/mol	7.06607 kcal/mol	13 30@LB@ \| \|@LB@5'-AGA...GUGAU UUGAU...CCA-3'@LB@ UACGUGAUGCAGGUGA@LB@ :\|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GUGUACUACGUCCGUU@LB@3'-UUU...UCAGU CAGUU...UAG-5'@LB@ \| \|@LB@ 171 154@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -24.1359 kcal/mol@LB@Unfolding Energy - mRNA 6.48358 kcal/mol@LB@Unfolding Energy - sRNA 7.06607 kcal/mol@LB@@LB@Position - mRNA 14 -- 29@LB@Position - sRNA 155 -- 170@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 156 -- 162@LB@
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter		_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@LB@
102	0.01106	0.3575	b0647	ybeT	-15.01	0.026876	192 -- 264	115 -- 176	Sel1 family TPR-like repeat protein		_____________191___________265\n_____________\|_____________\|\n5'-AUA...CGAAG__U__________AUAAA...UGG-3'\n______________CA_UCACACAUGA\n______________\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GU_AGUGUGUACU\n3'-UUU...UAUGA__C__________ACGUC...UAG-5'\n_____________\|_____________\|\n_____________177___________114\n	198 -- 204	164 -- 170	-15.9732 kcal/mol	2.87622 kcal/mol	4.17773 kcal/mol	191 265@LB@ \| \|@LB@5'-AUA...CGAAG U AUAAA...UGG-3'@LB@ CA UCACACAUGA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|@LB@ GU AGUGUGUACU@LB@3'-UUU...UAUGA C ACGUC...UAG-5'@LB@ \| \|@LB@ 177 114@LB@@LB@@LB@Energy -15.01 kcal/mol@LB@Hybridization Energy -15.9732 kcal/mol@LB@Unfolding Energy - mRNA 2.87622 kcal/mol@LB@Unfolding Energy - sRNA 4.17773 kcal/mol@LB@@LB@Position - mRNA 192 -- 264@LB@Position - sRNA 115 -- 176@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 164 -- 170@LB@
45	0.003942	0.2948	b0686	ybfF	-11.97	0.113030	234 -- 245	63 -- 74	acyl-CoA esterase		_____________233__________246\n_____________\|____________\|\n5'-CUU...CACAA____________AAUUC...GCG-3'\n______________AACCAGCACAAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUGGUCGUGUUG\n3'-UUU...UUGCG____________AAGCG...UAG-5'\n_____________\|____________\|\n_____________75___________62\n	239 -- 245	63 -- 69	-18.9732 kcal/mol	1.15073 kcal/mol	9.24135 kcal/mol	233 246@LB@ \| \|@LB@5'-CUU...CACAA AAUUC...GCG-3'@LB@ AACCAGCACAAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUGGUCGUGUUG@LB@3'-UUU...UUGCG AAGCG...UAG-5'@LB@ \| \|@LB@ 75 62@LB@@LB@@LB@Energy -11.97 kcal/mol@LB@Hybridization Energy -18.9732 kcal/mol@LB@Unfolding Energy - mRNA 1.15073 kcal/mol@LB@Unfolding Energy - sRNA 9.24135 kcal/mol@LB@@LB@Position - mRNA 234 -- 245@LB@Position - sRNA 63 -- 74@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 63 -- 69@LB@
66	0.006473	0.3261	b0712	ybgK	-17.58	0.008094	217 -- 255	130 -- 164	putative allophanate hydrolase subunit 2		_____________216________________________________________________________256\n_____________\|__________________________________________________________\|\n5'-CGC...GGAGU_____GA__A____U_____________U__AUACC___GUG______G_________ACGGU...AUA-3'\n______________AUGCU__AG_UUAU_C___GUGCGGGCA_GU_____ACU___CAGGAU_GCGGUCGUC\n______________\|\|:\|\|__\|\|_\|:\|:_\|___:\|\|\|:\|\|\|\|_\|\|_____\|\|\|___\|\|\|:\|\|_\|\|\|\|\|\|:\|\|\n______________UAUGA__UC_AGUG_G___UACGUCCGU_CA_____UGA___GUCUUA_CGCCAGUAG\n3'-UUU...GUGGU_____G________U_UAC_________U__GU______AA_______A_________GGUGA...UAG-5'\n_____________\|__________________________________________________________\|\n_____________165________________________________________________________129\n	249 -- 255	130 -- 136	-44.2735 kcal/mol	15.0195 kcal/mol	15.1988 kcal/mol	216 256@LB@ \| \|@LB@5'-CGC...GGAGU GA A U U AUACC GUG G ACGGU...AUA-3'@LB@ AUGCU AG UUAU C GUGCGGGCA GU ACU CAGGAU GCGGUCGUC@LB@ \|\|:\|\| \|\| \|:\|: \| :\|\|\|:\|\|\|\| \|\| \|\|\| \|\|\|:\|\| \|\|\|\|\|\|:\|\|@LB@ UAUGA UC AGUG G UACGUCCGU CA UGA GUCUUA CGCCAGUAG@LB@3'-UUU...GUGGU G U UAC U GU AA A GGUGA...UAG-5'@LB@ \| \|@LB@ 165 129@LB@@LB@@LB@Energy -17.58 kcal/mol@LB@Hybridization Energy -44.2735 kcal/mol@LB@Unfolding Energy - mRNA 15.0195 kcal/mol@LB@Unfolding Energy - sRNA 15.1988 kcal/mol@LB@@LB@Position - mRNA 217 -- 255@LB@Position - sRNA 130 -- 164@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 130 -- 136@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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