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
189	0.03168	0.5492	b1533	eamA	-9.19	0.139150	178 -- 226	1 -- 49	cysteine and O-acetyl-L-serine efflux system	_____________177_______________________________________________________227\n_____________\|_________________________________________________________\|\n5'-GUU...ACAAA____GAA______________________AAU__CGCGA____A________U____GCUAC...UGA-3'\n______________AGAU___AUUCAGA_______GGCGGUAG___GU_____AAAG_UGG_GGUG_UGGC\n______________\|\|\|:___\|\|\|\|\|\|\|_______\|:\|\|\|\|\|:___:\|_____\|\|\|\|_\|::_\|:\|\|_\|:\|\|\n______________UCUG___UAAGUCU_______CUGCCAUU___UA_____UUUC_AUU_CUAC_AUCG\n3'-UUU...AUUUG______________UUACUUA________AUU___________A___A____U____-5'\n_____________\|________________________________________________________\|\n_____________50_______________________________________________________1\n	193 -- 199	24 -- 30	-25.3484 kcal/mol	9.82981 kcal/mol	6.32371 kcal/mol	177 227@LB@ \| \|@LB@5'-GUU...ACAAA GAA AAU CGCGA A U GCUAC...UGA-3'@LB@ AGAU AUUCAGA GGCGGUAG GU AAAG UGG GGUG UGGC@LB@ \|\|\|: \|\|\|\|\|\|\| \|:\|\|\|\|\|: :\| \|\|\|\| \|:: \|:\|\| \|:\|\|@LB@ UCUG UAAGUCU CUGCCAUU UA UUUC AUU CUAC AUCG@LB@3'-UUU...AUUUG UUACUUA AUU A A U -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -25.3484 kcal/mol@LB@Unfolding Energy - mRNA 9.82981 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 178 -- 226@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 24 -- 30@LB@
49	0.00563	0.3739	b2239	glpQ	-9.17	0.140723	61 -- 103	1 -- 49	periplasmic glycerophosphodiester phosphodiesterase	_____________60__________________________________________________104\n_____________\|___________________________________________________\|\n5'-CGG...ACCGU____UUC_____CUG__________CUU______U________________GGCAG...UCA-3'\n______________GGAC___UUCGG____GGAUGGCGG_______UA_GG_UAAUGAU__UGGC\n______________:\|\|\|___\|\|\|:\|____\|:\|\|\|:\|\|\|_______\|\|_:\|_\|\|\|\|\|\|\|__\|:\|\|\n______________UCUG___AAGUC____CUUACUGCC_______AU_UC_AUUACUA__AUCG\n3'-UUU...AUUUG____U_______UUUA_________AUUAUUU__U__A_______CU____-5'\n_____________\|__________________________________________________\|\n_____________50_________________________________________________1\n	93 -- 99	7 -- 13	-28.1898 kcal/mol	12.697 kcal/mol	6.32371 kcal/mol	60 104@LB@ \| \|@LB@5'-CGG...ACCGU UUC CUG CUU U GGCAG...UCA-3'@LB@ GGAC UUCGG GGAUGGCGG UA GG UAAUGAU UGGC@LB@ :\|\|\| \|\|\|:\| \|:\|\|\|:\|\|\| \|\| :\| \|\|\|\|\|\|\| \|:\|\|@LB@ UCUG AAGUC CUUACUGCC AU UC AUUACUA AUCG@LB@3'-UUU...AUUUG U UUUA AUUAUUU U A CU -5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -28.1898 kcal/mol@LB@Unfolding Energy - mRNA 12.697 kcal/mol@LB@Unfolding Energy - sRNA 6.32371 kcal/mol@LB@@LB@Position - mRNA 61 -- 103@LB@Position - sRNA 1 -- 49@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 7 -- 13@LB@
132	0.0212	0.526	b2455	eutE	-9.17	0.140915	224 -- 235	1 -- 12	aldehyde oxidoreductase ethanolamine utilization protein	_____________223__________236\n_____________\|____________\|\n5'-GGU...GAACA________A___GGUAC...UCG-3'\n______________GGUGGUGA_AGC\n______________::\|\|:\|\|\|_\|\|\|\n______________UUACUACU_UCG\n3'-UUU...UUCAA________A___-5'\n_____________\|___________\|\n_____________13__________1\n	225 -- 231	5 -- 11	-12.5804 kcal/mol	3.3751 kcal/mol	0.0394463 kcal/mol	223 236@LB@ \| \|@LB@5'-GGU...GAACA A GGUAC...UCG-3'@LB@ GGUGGUGA AGC@LB@ ::\|\|:\|\|\| \|\|\|@LB@ UUACUACU UCG@LB@3'-UUU...UUCAA A -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -9.17 kcal/mol@LB@Hybridization Energy -12.5804 kcal/mol@LB@Unfolding Energy - mRNA 3.3751 kcal/mol@LB@Unfolding Energy - sRNA 0.0394463 kcal/mol@LB@@LB@Position - mRNA 224 -- 235@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
126	0.01995	0.5155	b2452	eutH	-9.16	0.141344	190 -- 206	5 -- 22	ethanolamine transporter	_____________189________________207\n_____________\|__________________\|\n5'-UUG...ACAGG________GC________AUUAA...UCC-3'\n______________GAGUAAAG__GAUGG_GA\n______________:\|:\|\|\|\|\|__:\|\|\|:_\|\|\n______________UUUAUUUC__UUACU_CU\n3'-UUU...CAUUA________AA_____A__AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	191 -- 197	15 -- 21	-11.7395 kcal/mol	2.48279 kcal/mol	0.0977783 kcal/mol	189 207@LB@ \| \|@LB@5'-UUG...ACAGG GC AUUAA...UCC-3'@LB@ GAGUAAAG GAUGG GA@LB@ :\|:\|\|\|\|\| :\|\|\|: \|\|@LB@ UUUAUUUC UUACU CU@LB@3'-UUU...CAUUA AA A AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.16 kcal/mol@LB@Hybridization Energy -11.7395 kcal/mol@LB@Unfolding Energy - mRNA 2.48279 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 190 -- 206@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 15 -- 21@LB@
199	0.03375	0.5555	b3860	dsbA	-9.14	0.142422	273 -- 281	48 -- 56	periplasmic protein disulfide isomerase I	_____________272_______282\n_____________\|_________\|\n5'-UUU...AAGAU_________UACAC...AAC-3'\n______________GGUAAACAG\n______________\|\|\|\|\|\|\|\|\|\n______________CCAUUUGUC\n3'-UUU...UAUCC_________UGUAA...UCG-5'\n_____________\|_________\|\n_____________57________47\n	275 -- 281	48 -- 54	-12.2563 kcal/mol	1.07557 kcal/mol	2.03935 kcal/mol	272 282@LB@ \| \|@LB@5'-UUU...AAGAU UACAC...AAC-3'@LB@ GGUAAACAG@LB@ \|\|\|\|\|\|\|\|\|@LB@ CCAUUUGUC@LB@3'-UUU...UAUCC UGUAA...UCG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.14 kcal/mol@LB@Hybridization Energy -12.2563 kcal/mol@LB@Unfolding Energy - mRNA 1.07557 kcal/mol@LB@Unfolding Energy - sRNA 2.03935 kcal/mol@LB@@LB@Position - mRNA 273 -- 281@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 48 -- 54@LB@
156	0.02543	0.526	b2805	fucR	-9.08	0.146396	128 -- 135	52 -- 59	l-fucose operon activator	_____________127______136\n_____________\|________\|\n5'-CAC...AAAAA________CACCG...AAA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	129 -- 135	52 -- 58	-12.2757 kcal/mol	3.13783 kcal/mol	0.0599826 kcal/mol	127 136@LB@ \| \|@LB@5'-CAC...AAAAA CACCG...AAA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.08 kcal/mol@LB@Hybridization Energy -12.2757 kcal/mol@LB@Unfolding Energy - mRNA 3.13783 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 128 -- 135@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 52 -- 58@LB@
82	0.0113	0.4523	b3747	kup	-9.05	0.148352	64 -- 70	53 -- 59	potassium transporter	_____________63______71\n_____________\|_______\|\n5'-AAA...AAAGG_______UUUUU...GUG-3'\n______________GGGGGUA\n______________:\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	64 -- 70	53 -- 59	-11.6233 kcal/mol	2.51972 kcal/mol	0.0564539 kcal/mol	63 71@LB@ \| \|@LB@5'-AAA...AAAGG UUUUU...GUG-3'@LB@ GGGGGUA@LB@ :\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -11.6233 kcal/mol@LB@Unfolding Energy - mRNA 2.51972 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 53 -- 59@LB@
154	0.02518	0.526	b1602	pntB	-9.01	0.150855	190 -- 197	52 -- 59	pyridine nucleotide transhydrogenase beta subunit	_____________189______198\n_____________\|________\|\n5'-GCU...AAUUA________CAUAU...GUA-3'\n______________AGGGGUAA\n______________\|\|\|\|\|\|\|\|\n______________UCCCCAUU\n3'-UUU...CUUUA________UGUCU...UCG-5'\n_____________\|________\|\n_____________60_______51\n	191 -- 197	52 -- 58	-12.5664 kcal/mol	3.49825 kcal/mol	0.0599826 kcal/mol	189 198@LB@ \| \|@LB@5'-GCU...AAUUA CAUAU...GUA-3'@LB@ AGGGGUAA@LB@ \|\|\|\|\|\|\|\|@LB@ UCCCCAUU@LB@3'-UUU...CUUUA UGUCU...UCG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -12.5664 kcal/mol@LB@Unfolding Energy - mRNA 3.49825 kcal/mol@LB@Unfolding Energy - sRNA 0.0599826 kcal/mol@LB@@LB@Position - mRNA 190 -- 197@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 52 -- 58@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@
98	0.01586	0.5059	b1860	ruvB	-8.95	0.154425	184 -- 211	1 -- 30	ATP-dependent DNA helicase component of RuvABC resolvasome	_____________183_____________________________212\n_____________\|_______________________________\|\n5'-ACG...GCGCC___U__UG_______________U_______AGACC...GUC-3'\n______________GCG_UA__AGGUAAAG__GAUGA_UGA_AGC\n______________:\|\|_\|\|__\|::\|\|\|\|\|__:\|\|\|\|_\|\|\|_\|\|\|\n______________UGC_AU__UUUAUUUC__UUACU_ACU_UCG\n3'-UUU...CUUAC___C__UA________AA_________A___-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	193 -- 199	15 -- 21	-17.0174 kcal/mol	5.93551 kcal/mol	2.12822 kcal/mol	183 212@LB@ \| \|@LB@5'-ACG...GCGCC U UG U AGACC...GUC-3'@LB@ GCG UA AGGUAAAG GAUGA UGA AGC@LB@ :\|\| \|\| \|::\|\|\|\|\| :\|\|\|\| \|\|\| \|\|\|@LB@ UGC AU UUUAUUUC UUACU ACU UCG@LB@3'-UUU...CUUAC C UA AA A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -8.95 kcal/mol@LB@Hybridization Energy -17.0174 kcal/mol@LB@Unfolding Energy - mRNA 5.93551 kcal/mol@LB@Unfolding Energy - sRNA 2.12822 kcal/mol@LB@@LB@Position - mRNA 184 -- 211@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 15 -- 21@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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