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
70	0.001371	0.06901	b2989	yghU	-9.78	0.124117	251 -- 269	4 -- 23	putative S-transferase	_____________250__________________270\n_____________\|____________________\|\n5'-UUA...AAAUC_________GC_________AAUAU...CGC-3'\n______________CGC_UGGCG__GCGUUCGCC\n______________\|\|\|_\|\|:\|\|__\|\|:\|\|\|:\|\|\n______________GCG_ACUGC__CGUAAGUGG\n3'-UUU...GGGUA___A_____AA_________ACG-5'\n_____________\|____________________\|\n_____________24___________________3\n	263 -- 269	4 -- 10	-26.6155 kcal/mol	8.73321 kcal/mol	8.10973 kcal/mol	250 270@LB@ \| \|@LB@5'-UUA...AAAUC GC AAUAU...CGC-3'@LB@ CGC UGGCG GCGUUCGCC@LB@ \|\|\| \|\|:\|\| \|\|:\|\|\|:\|\|@LB@ GCG ACUGC CGUAAGUGG@LB@3'-UUU...GGGUA A AA ACG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -26.6155 kcal/mol@LB@Unfolding Energy - mRNA 8.73321 kcal/mol@LB@Unfolding Energy - sRNA 8.10973 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 4 -- 10@LB@
58	0.0009751	0.05816	b3809	dapF	-9.70	0.129467	46 -- 52	1 -- 7	diaminopimelate epimerase	_____________45______53\n_____________\|_______\|\n5'-UCU...UUUCC_______AGAUA...UGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	46 -- 52	1 -- 7	-13.4276 kcal/mol	1.39772 kcal/mol	2.34039 kcal/mol	45 53@LB@ \| \|@LB@5'-UCU...UUUCC AGAUA...UGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -13.4276 kcal/mol@LB@Unfolding Energy - mRNA 1.39772 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 46 -- 52@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
183	0.007971	0.1528	b1874	cutC	-9.62	0.134922	271 -- 300	54 -- 87	copper homeostasis protein	_____________270________________________________300\n_____________\|__________________________________\|\n5'-CCG...AGACA_____G____A__________CCC___________-3'\n______________GAGUU_AAUU_UGC___GCAG_____CAAAAGAGG\n______________\|\|:\|:_\|\|\|\|_\|\|\|___\|\|\|\|_____\|\|\|\|\|:\|\|\|\n______________CUUAG_UUAA_ACG___CGUC_____GUUUUUUCC\n3'-UUU...GCAUG__________C___AUA____AUUAA_________UUCAU...ACG-5'\n_____________\|___________________________________\|\n_____________88__________________________________53\n	294 -- 300	54 -- 60	-18.7273 kcal/mol	5.34866 kcal/mol	3.76003 kcal/mol	270 300@LB@ \| \|@LB@5'-CCG...AGACA G A CCC -3'@LB@ GAGUU AAUU UGC GCAG CAAAAGAGG@LB@ \|\|:\|: \|\|\|\| \|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CUUAG UUAA ACG CGUC GUUUUUUCC@LB@3'-UUU...GCAUG C AUA AUUAA UUCAU...ACG-5'@LB@ \| \|@LB@ 88 53@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -18.7273 kcal/mol@LB@Unfolding Energy - mRNA 5.34866 kcal/mol@LB@Unfolding Energy - sRNA 3.76003 kcal/mol@LB@@LB@Position - mRNA 271 -- 300@LB@Position - sRNA 54 -- 87@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 54 -- 60@LB@
76	0.001842	0.08273	b1717	rpmI	-9.61	0.135308	218 -- 256	48 -- 92	50S ribosomal subunit protein L35	_____________217___________________________________________257\n_____________\|_____________________________________________\|\n5'-GCG...AAGAC_____________GC_____A___C____________ACC_____AGGUG...UGA-3'\n______________CGUACG___CGGU__UGCUA_GCG____UUCAAAAAA___GGUAA\n______________\|\|\|\|\|\|___\|::\|__\|\|\|\|\|_\|\|:____\|\|\|\|\|\|\|\|\|___:\|\|\|\|\n______________GCAUGC___GUUA__ACGAU_CGU____AAGUUUUUU___UCAUU\n3'-UUU...CCGCA______UUA____AC_____A___CAUU_________CCU_____CUGUU...ACG-5'\n_____________\|_____________________________________________\|\n_____________93____________________________________________47\n	242 -- 248	56 -- 62	-26.2826 kcal/mol	11.8203 kcal/mol	4.85131 kcal/mol	217 257@LB@ \| \|@LB@5'-GCG...AAGAC GC A C ACC AGGUG...UGA-3'@LB@ CGUACG CGGU UGCUA GCG UUCAAAAAA GGUAA@LB@ \|\|\|\|\|\| \|::\| \|\|\|\|\| \|\|: \|\|\|\|\|\|\|\|\| :\|\|\|\|@LB@ GCAUGC GUUA ACGAU CGU AAGUUUUUU UCAUU@LB@3'-UUU...CCGCA UUA AC A CAUU CCU CUGUU...ACG-5'@LB@ \| \|@LB@ 93 47@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -26.2826 kcal/mol@LB@Unfolding Energy - mRNA 11.8203 kcal/mol@LB@Unfolding Energy - sRNA 4.85131 kcal/mol@LB@@LB@Position - mRNA 218 -- 256@LB@Position - sRNA 48 -- 92@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 56 -- 62@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@
131	0.004841	0.1302	b3242	aaeX	-9.57	0.138370	170 -- 176	1 -- 7	DUF1656 family putative inner membrane efflux pump associated protein	_____________169_____177\n_____________\|_______\|\n5'-GCG...AAUAA_______UCUCU...GGG-3'\n______________CGCCUGC\n______________\|:\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	170 -- 176	1 -- 7	-12.9142 kcal/mol	1.00865 kcal/mol	2.34039 kcal/mol	169 177@LB@ \| \|@LB@5'-GCG...AAUAA UCUCU...GGG-3'@LB@ CGCCUGC@LB@ \|:\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -12.9142 kcal/mol@LB@Unfolding Energy - mRNA 1.00865 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 170 -- 176@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 1 -- 7@LB@
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@
38	0.0003163	0.02889	b4315	fimI	-9.52	0.141947	182 -- 216	45 -- 80	fimbrial protein involved in type 1 pilus biosynthesis	_____________181___________________________________217\n_____________\|_____________________________________\|\n5'-UGC...CACCC______GAUAAAAAUAACGAU________________UAUUU...AAU-3'\n______________UUGUGC_______________GAAAAGGAAG__AGAU\n______________\|\|\|\|\|\|_______________:\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________AACACG_______________UUUUUCCUUC__UCUG\n3'-UUU...UAGUU______AUACGUCAUUAAGU___________AU____UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________81____________________________________44\n	206 -- 212	51 -- 57	-20.4045 kcal/mol	5.26447 kcal/mol	5.61905 kcal/mol	181 217@LB@ \| \|@LB@5'-UGC...CACCC GAUAAAAAUAACGAU UAUUU...AAU-3'@LB@ UUGUGC GAAAAGGAAG AGAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ AACACG UUUUUCCUUC UCUG@LB@3'-UUU...UAGUU AUACGUCAUUAAGU AU UUAUA...ACG-5'@LB@ \| \|@LB@ 81 44@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -20.4045 kcal/mol@LB@Unfolding Energy - mRNA 5.26447 kcal/mol@LB@Unfolding Energy - sRNA 5.61905 kcal/mol@LB@@LB@Position - mRNA 182 -- 216@LB@Position - sRNA 45 -- 80@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 51 -- 57@LB@
102	0.003332	0.1114	b1279	yciS	-9.50	0.143375	3 -- 9	1 -- 7	DUF1049 family inner membrane protein function unknown	_____________2_______10\n_____________\|_______\|\n_________5'-AC_______GGAAG...UGU-3'\n______________CACCUGC\n______________\|\|\|\|\|\|\|\n______________GUGGACG\n3'-UUU...CGUAA_______-5'\n_____________\|______\|\n_____________8______1\n	3 -- 9	1 -- 7	-13.2462 kcal/mol	1.40693 kcal/mol	2.34039 kcal/mol	2 10@LB@ \| \|@LB@ 5'-AC GGAAG...UGU-3'@LB@ CACCUGC@LB@ \|\|\|\|\|\|\|@LB@ GUGGACG@LB@3'-UUU...CGUAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.50 kcal/mol@LB@Hybridization Energy -13.2462 kcal/mol@LB@Unfolding Energy - mRNA 1.40693 kcal/mol@LB@Unfolding Energy - sRNA 2.34039 kcal/mol@LB@@LB@Position - mRNA 3 -- 9@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 1 -- 7@LB@
145	0.00562	0.1365	b2532	trmJ	-9.44	0.148020	215 -- 233	68 -- 84	tRNA mC32 mU32 2'-O-methyltransferase SAM-dependent	_____________214_________________234\n_____________\|___________________\|\n5'-CGU...AAUAU__G__________G__G__ACGUC...UGU-3'\n______________UC_AAUUGUGCUG_UG_AG\n______________\|\|_\|\|\|\|\|\|\|\|\|:_\|\|_\|\|\n______________AG_UUAACACGAU_AC_UC\n3'-UUU...UGCUU________________G__AUUAA...ACG-5'\n_____________\|___________________\|\n_____________85__________________67\n	221 -- 227	73 -- 79	-16.7979 kcal/mol	3.71432 kcal/mol	3.64047 kcal/mol	214 234@LB@ \| \|@LB@5'-CGU...AAUAU G G G ACGUC...UGU-3'@LB@ UC AAUUGUGCUG UG AG@LB@ \|\| \|\|\|\|\|\|\|\|\|: \|\| \|\|@LB@ AG UUAACACGAU AC UC@LB@3'-UUU...UGCUU G AUUAA...ACG-5'@LB@ \| \|@LB@ 85 67@LB@@LB@@LB@Energy -9.44 kcal/mol@LB@Hybridization Energy -16.7979 kcal/mol@LB@Unfolding Energy - mRNA 3.71432 kcal/mol@LB@Unfolding Energy - sRNA 3.64047 kcal/mol@LB@@LB@Position - mRNA 215 -- 233@LB@Position - sRNA 68 -- 84@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 73 -- 79@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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