Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
118	0.01863	0.5155	b0738	tolR	-11.80	0.040697	190 -- 199	50 -- 59	membrane spanning protein in TolA-TolQ-TolR complex	_____________189________200\n_____________\|__________\|\n5'-UGG...CAACA__________CAUGG...UGG-3'\n______________AGGGGUAAGC\n______________\|\|\|\|\|\|\|\|:\|\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	193 -- 199	50 -- 56	-16.6396 kcal/mol	4.1136 kcal/mol	0.728772 kcal/mol	189 200@LB@ \| \|@LB@5'-UGG...CAACA CAUGG...UGG-3'@LB@ AGGGGUAAGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -16.6396 kcal/mol@LB@Unfolding Energy - mRNA 4.1136 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 190 -- 199@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 50 -- 56@LB@
90	0.01478	0.5059	b0740	tolB	-11.20	0.054749	186 -- 207	1 -- 21	periplasmic protein	_____________185_____________________208\n_____________\|_______________________\|\n5'-UCC...GUCCA_______GAGAU___________AGGCA...CCG-3'\n______________GAUAAGG_____AUGAUGA_AGC\n______________:\|\|\|\|:\|_____\|\|\|\|\|\|\|_\|\|\|\n______________UUAUUUC_____UACUACU_UCG\n3'-UUU...AUUAU_______AAU_________A___-5'\n_____________\|______________________\|\n_____________22_____________________1\n	198 -- 204	5 -- 11	-16.1118 kcal/mol	4.84175 kcal/mol	0.0669945 kcal/mol	185 208@LB@ \| \|@LB@5'-UCC...GUCCA GAGAU AGGCA...CCG-3'@LB@ GAUAAGG AUGAUGA AGC@LB@ :\|\|\|\|:\| \|\|\|\|\|\|\| \|\|\|@LB@ UUAUUUC UACUACU UCG@LB@3'-UUU...AUUAU AAU A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -16.1118 kcal/mol@LB@Unfolding Energy - mRNA 4.84175 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 186 -- 207@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 5 -- 11@LB@
107	0.01649	0.5059	b0830	gsiB	-12.67	0.025954	282 -- 298	1 -- 18	glutathione ABC transporter periplasmic binding protein	_____________281________________299\n_____________\|__________________\|\n5'-GGC...CUGCC____AU____________GG-3'\n______________AAAG___GUGGUGGUGGC\n______________\|\|\|\|___:\|\|:\|\|:\|:\|\|\n______________UUUC___UACUACUAUCG\n3'-UUU...AUUUA____AAU___________-5'\n_____________\|_________________\|\n_____________19________________1\n	292 -- 298	1 -- 7	-15.5562 kcal/mol	2.82856 kcal/mol	0.0611543 kcal/mol	281 299@LB@ \| \|@LB@5'-GGC...CUGCC AU GG-3'@LB@ AAAG GUGGUGGUGGC@LB@ \|\|\|\| :\|\|:\|\|:\|:\|\|@LB@ UUUC UACUACUAUCG@LB@3'-UUU...AUUUA AAU -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.67 kcal/mol@LB@Hybridization Energy -15.5562 kcal/mol@LB@Unfolding Energy - mRNA 2.82856 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 282 -- 298@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
65	0.009342	0.4523	b0871	poxB	-9.00	0.151653	248 -- 256	51 -- 59	pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding	_____________247_______257\n_____________\|_________\|\n5'-CCG...UCGGC_________ACGCA...GUG-3'\n______________AGGGGUGAA\n______________\|\|\|\|\|\|:\|\|\n______________UCCCCAUUU\n3'-UUU...CUUUA_________GUCUG...UCG-5'\n_____________\|_________\|\n_____________60________50\n	250 -- 256	51 -- 57	-12.9194 kcal/mol	3.39064 kcal/mol	0.532875 kcal/mol	247 257@LB@ \| \|@LB@5'-CCG...UCGGC ACGCA...GUG-3'@LB@ AGGGGUGAA@LB@ \|\|\|\|\|\|:\|\|@LB@ UCCCCAUUU@LB@3'-UUU...CUUUA GUCUG...UCG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -9.00 kcal/mol@LB@Hybridization Energy -12.9194 kcal/mol@LB@Unfolding Energy - mRNA 3.39064 kcal/mol@LB@Unfolding Energy - sRNA 0.532875 kcal/mol@LB@@LB@Position - mRNA 248 -- 256@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 51 -- 57@LB@
69	0.009861	0.4523	b0879	macB	-12.35	0.030572	144 -- 182	1 -- 59	macrolide ABC transporter peremase/ATPase	_____________143___________________________________________________________183\n_____________\|_____________________________________________________________\|\n5'-AAU...GUCAA____CUUG_____________________________________________________CAAAC...CGG-3'\n______________AGGG____AAGCGGGC_______GAUGAA_G_UGGUGAU____________UGGUGA_GGC\n______________\|\|\|\|____\|\|:\|:\|:\|_______:\|\|\|\|\|_\|_:\|\|\|:\|\|____________\|\|:\|\|\|_:\|\|\n______________UCCC____UUUGUCUG_______UUACUU_C_GCCAUUA____________ACUACU_UCG\n3'-UUU...CUUUA____CA__________UAAGUCU______A_U_______UUUAUUUCAAUU______A___-5'\n_____________\|____________________________________________________________\|\n_____________60___________________________________________________________1\n	167 -- 173	23 -- 29	-29.0987 kcal/mol	10.4067 kcal/mol	6.33764 kcal/mol	143 183@LB@ \| \|@LB@5'-AAU...GUCAA CUUG CAAAC...CGG-3'@LB@ AGGG AAGCGGGC GAUGAA G UGGUGAU UGGUGA GGC@LB@ \|\|\|\| \|\|:\|:\|:\| :\|\|\|\|\| \| :\|\|\|:\|\| \|\|:\|\|\| :\|\|@LB@ UCCC UUUGUCUG UUACUU C GCCAUUA ACUACU UCG@LB@3'-UUU...CUUUA CA UAAGUCU A U UUUAUUUCAAUU A -5'@LB@ \| \|@LB@ 60 1@LB@@LB@@LB@Energy -12.35 kcal/mol@LB@Hybridization Energy -29.0987 kcal/mol@LB@Unfolding Energy - mRNA 10.4067 kcal/mol@LB@Unfolding Energy - sRNA 6.33764 kcal/mol@LB@@LB@Position - mRNA 144 -- 182@LB@Position - sRNA 1 -- 59@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 23 -- 29@LB@
1	2.411e-07	0.0007914	b0889	lrp	-21.69	0.000065	168 -- 212	1 -- 64	leucine-responsive global transcriptional regulator	_____________167_______________________________________________________________213\n_____________\|_________________________________________________________________\|\n5'-GUG...AGACA_________AA_______AUA_____________________________________A______AAGAA...AGC-3'\n______________GGAGUAGGG______GGA____CAGAGA_____GAC_______AAUAA___UAAUGGU_GAUAGC\n______________\|:\|:\|\|\|\|\|______:\|\|____\|\|\|\|:\|_____\|\|\|_______\|\|\|\|\|___\|\|\|\|\|:\|_\|\|\|\|\|\|\n______________CUUUAUCCC______UCU____GUCUUU_____CUG_______UUAUU___AUUACUA_CUAUCG\n3'-UUU...GCCAA_________CAUUUG___GUAA______ACUUA___CCAUUAU_____UCA______________-5'\n_____________\|________________________________________________________________\|\n_____________65_______________________________________________________________1\n	199 -- 205	7 -- 13	-30.6118 kcal/mol	2.57614 kcal/mol	6.344 kcal/mol	167 213@LB@ \| \|@LB@5'-GUG...AGACA AA AUA A AAGAA...AGC-3'@LB@ GGAGUAGGG GGA CAGAGA GAC AAUAA UAAUGGU GAUAGC@LB@ \|:\|:\|\|\|\|\| :\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\| \|\|\|\|\|:\| \|\|\|\|\|\|@LB@ CUUUAUCCC UCU GUCUUU CUG UUAUU AUUACUA CUAUCG@LB@3'-UUU...GCCAA CAUUUG GUAA ACUUA CCAUUAU UCA -5'@LB@ \| \|@LB@ 65 1@LB@@LB@@LB@Energy -21.69 kcal/mol@LB@Hybridization Energy -30.6118 kcal/mol@LB@Unfolding Energy - mRNA 2.57614 kcal/mol@LB@Unfolding Energy - sRNA 6.344 kcal/mol@LB@@LB@Position - mRNA 168 -- 212@LB@Position - sRNA 1 -- 64@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@LB@
34	0.003196	0.3086	b0896	dmsC	-10.70	0.070045	189 -- 235	4 -- 59	dimethyl sulfoxide reductase anaerobic subunit C	_____________188_______________________________________________________236\n_____________\|_________________________________________________________\|\n5'-CUG...CCCGA___A____UG__________________________________CCGC_________CUUCA...AAG-3'\n______________AGG_GGUG___AGAUG___GGAAGUGGAUGGC____AUGAAUGG______UGAUGAU\n______________\|\|\|_\|\|\|:___\|\|\|::___:\|\|\|:\|\|:\|\|\|:\|____\|\|:\|\|\|::______\|\|\|\|\|\|\|\n______________UCC_CCAU___UCUGU___UCUUUACUUACUG____UAUUUAUU______ACUACUA\n3'-UUU...CUUUA________UUG_____AAG_____________CCAU________UCAAUU_______UCG-5'\n_____________\|_________________________________________________________\|\n_____________60________________________________________________________3\n	229 -- 235	4 -- 10	-34.4804 kcal/mol	17.4476 kcal/mol	6.33761 kcal/mol	188 236@LB@ \| \|@LB@5'-CUG...CCCGA A UG CCGC CUUCA...AAG-3'@LB@ AGG GGUG AGAUG GGAAGUGGAUGGC AUGAAUGG UGAUGAU@LB@ \|\|\| \|\|\|: \|\|\|:: :\|\|\|:\|\|:\|\|\|:\| \|\|:\|\|\|:: \|\|\|\|\|\|\|@LB@ UCC CCAU UCUGU UCUUUACUUACUG UAUUUAUU ACUACUA@LB@3'-UUU...CUUUA UUG AAG CCAU UCAAUU UCG-5'@LB@ \| \|@LB@ 60 3@LB@@LB@@LB@Energy -10.70 kcal/mol@LB@Hybridization Energy -34.4804 kcal/mol@LB@Unfolding Energy - mRNA 17.4476 kcal/mol@LB@Unfolding Energy - sRNA 6.33761 kcal/mol@LB@@LB@Position - mRNA 189 -- 235@LB@Position - sRNA 4 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 4 -- 10@LB@
119	0.019	0.5155	b0904	focA	-10.20	0.088413	192 -- 208	1 -- 18	formate channel	_____________191________________209\n_____________\|__________________\|\n5'-GAG...AAGAG______________A___UGACA...AGA-3'\n______________AGAGUUAGUG_UGA_AGC\n______________\|:\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\n______________UUUCAAUUAC_ACU_UCG\n3'-UUU...AUUUA__________U___A___-5'\n_____________\|_________________\|\n_____________19________________1\n	195 -- 201	9 -- 15	-16.1977 kcal/mol	5.93514 kcal/mol	0.0611543 kcal/mol	191 209@LB@ \| \|@LB@5'-GAG...AAGAG A UGACA...AGA-3'@LB@ AGAGUUAGUG UGA AGC@LB@ \|:\|\|\|\|\|:\|\| \|\|\| \|\|\|@LB@ UUUCAAUUAC ACU UCG@LB@3'-UUU...AUUUA U A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -16.1977 kcal/mol@LB@Unfolding Energy - mRNA 5.93514 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 9 -- 15@LB@
186	0.03152	0.5492	b0922	mukF	-11.29	0.052395	27 -- 43	42 -- 57	chromosome condensin MukBEF kleisin-like subunit binds calcium	_____________26________________44\n_____________\|_________________\|\n5'-CUG...AUUAU____A____________GCGUG...UGG-3'\n______________GGGU_AGACAGGCGUUC\n______________\|\|\|\|_\|:\|\|\|\|:\|:\|\|\|\n______________CCCA_UUUGUCUGUAAG\n3'-UUU...UUAUC_________________UCUUU...UCG-5'\n_____________\|_________________\|\n_____________58________________41\n	33 -- 39	46 -- 52	-21.5353 kcal/mol	3.99758 kcal/mol	6.24533 kcal/mol	26 44@LB@ \| \|@LB@5'-CUG...AUUAU A GCGUG...UGG-3'@LB@ GGGU AGACAGGCGUUC@LB@ \|\|\|\| \|:\|\|\|\|:\|:\|\|\|@LB@ CCCA UUUGUCUGUAAG@LB@3'-UUU...UUAUC UCUUU...UCG-5'@LB@ \| \|@LB@ 58 41@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -21.5353 kcal/mol@LB@Unfolding Energy - mRNA 3.99758 kcal/mol@LB@Unfolding Energy - sRNA 6.24533 kcal/mol@LB@@LB@Position - mRNA 27 -- 43@LB@Position - sRNA 42 -- 57@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 46 -- 52@LB@
4	6.512e-06	0.005344	b0929	ompF	-18.50	0.000749	185 -- 210	1 -- 33	outer membrane porin 1a (Ia;b;F)	_____________184_______________________________211\n_____________\|_________________________________\|\n5'-GUU...AAACC____G____________________________GCAAU...UAG-3'\n______________AUGA_GGUAAUAAAUA______AUGAUGA_AGC\n______________\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\|______\|\|\|\|\|\|\|_\|\|\|\n______________UACU_CCAUUAUUUAU______UACUACU_UCG\n3'-UUU...UUACU____G___________UUCAAU_______A___-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	201 -- 207	5 -- 11	-27.1062 kcal/mol	3.13427 kcal/mol	5.47105 kcal/mol	184 211@LB@ \| \|@LB@5'-GUU...AAACC G GCAAU...UAG-3'@LB@ AUGA GGUAAUAAAUA AUGAUGA AGC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ UACU CCAUUAUUUAU UACUACU UCG@LB@3'-UUU...UUACU G UUCAAU A -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -18.50 kcal/mol@LB@Hybridization Energy -27.1062 kcal/mol@LB@Unfolding Energy - mRNA 3.13427 kcal/mol@LB@Unfolding Energy - sRNA 5.47105 kcal/mol@LB@@LB@Position - mRNA 185 -- 210@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 5 -- 11@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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