Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
101	0.007657	0.2442	b3928	zapB	-6.83	0.122013	220 -- 239	38 -- 54	FtsZ stabilizer septal ring assembly factor cell division stimulator	_____________219__________________240\n_____________\|____________________\|\n5'-UUU...AGAAG________AAACU_______AAAGU...AAG-3'\n______________UGUUUGAG_____GGAAGCA\n______________\|\|:\|\|:\|\|_____:\|\|\|\|\|\|\n______________ACGAAUUC_____UCUUCGU\n3'-UUU...UUUGA________GU__________GAAUU...CAA-5'\n_____________\|____________________\|\n_____________55___________________37\n	233 -- 239	38 -- 44	-16.6983 kcal/mol	3.7204 kcal/mol	6.15149 kcal/mol	219 240@LB@ \| \|@LB@5'-UUU...AGAAG AAACU AAAGU...AAG-3'@LB@ UGUUUGAG GGAAGCA@LB@ \|\|:\|\|:\|\| :\|\|\|\|\|\|@LB@ ACGAAUUC UCUUCGU@LB@3'-UUU...UUUGA GU GAAUU...CAA-5'@LB@ \| \|@LB@ 55 37@LB@@LB@@LB@Energy -6.83 kcal/mol@LB@Hybridization Energy -16.6983 kcal/mol@LB@Unfolding Energy - mRNA 3.7204 kcal/mol@LB@Unfolding Energy - sRNA 6.15149 kcal/mol@LB@@LB@Position - mRNA 220 -- 239@LB@Position - sRNA 38 -- 54@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 38 -- 44@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@LB@
103	0.00845	0.2642	b0936	ssuA	-4.91	0.333979	11 -- 31	10 -- 40	aliphatic sulfonate ABC transporter periplasmic binding protein	_____________10______________________________32\n_____________\|_______________________________\|\n5'-AGU...UAAGC_______________________________CUGCA...AUC-3'\n______________GCAC_UGAAA________GC_UCAGGAGAUC\n______________\|\|\|\|_\|:\|\|\|________:\|_:\|\|\|\|\|:\|\|\|\n______________CGUG_AUUUU________UG_GGUCCUUUAG\n3'-UUU...UUCUU____A_____UUAAGCAA__U__________ACUAC...CAA-5'\n_____________\|_______________________________\|\n_____________41______________________________9\n	25 -- 31	10 -- 16	-20.0893 kcal/mol	5.95403 kcal/mol	9.22048 kcal/mol	10 32@LB@ \| \|@LB@5'-AGU...UAAGC CUGCA...AUC-3'@LB@ GCAC UGAAA GC UCAGGAGAUC@LB@ \|\|\|\| \|:\|\|\| :\| :\|\|\|\|\|:\|\|\|@LB@ CGUG AUUUU UG GGUCCUUUAG@LB@3'-UUU...UUCUU A UUAAGCAA U ACUAC...CAA-5'@LB@ \| \|@LB@ 41 9@LB@@LB@@LB@Energy -4.91 kcal/mol@LB@Hybridization Energy -20.0893 kcal/mol@LB@Unfolding Energy - mRNA 5.95403 kcal/mol@LB@Unfolding Energy - sRNA 9.22048 kcal/mol@LB@@LB@Position - mRNA 11 -- 31@LB@Position - sRNA 10 -- 40@LB@Position Seed - mRNA 25 -- 31@LB@Position Seed - sRNA 10 -- 16@LB@
104	0.008606	0.2665	b0956	matP	-4.56	0.392859	215 -- 228	25 -- 38	Ter macrodomain organizer matS-binding protein	_____________214____________229\n_____________\|______________\|\n5'-UUU...CAACA_________UC___AAAGC...AAG-3'\n______________ACUUGAAAA__UUG\n______________\|\|\|\|:\|\|\|\|__\|:\|\n______________UGAAUUUUU__AGC\n3'-UUU...CUUCG_________UA___AAUGU...CAA-5'\n_____________\|______________\|\n_____________39_____________24\n	216 -- 222	31 -- 37	-8.38693 kcal/mol	2.39574 kcal/mol	1.4343 kcal/mol	214 229@LB@ \| \|@LB@5'-UUU...CAACA UC AAAGC...AAG-3'@LB@ ACUUGAAAA UUG@LB@ \|\|\|\|:\|\|\|\| \|:\|@LB@ UGAAUUUUU AGC@LB@3'-UUU...CUUCG UA AAUGU...CAA-5'@LB@ \| \|@LB@ 39 24@LB@@LB@@LB@Energy -4.56 kcal/mol@LB@Hybridization Energy -8.38693 kcal/mol@LB@Unfolding Energy - mRNA 2.39574 kcal/mol@LB@Unfolding Energy - sRNA 1.4343 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 25 -- 38@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 31 -- 37@LB@
105	0.008762	0.2688	b2735	ygbI	-7.10	0.103888	185 -- 196	38 -- 49	DeoR family putative transcriptional regulator	_____________184__________197\n_____________\|____________\|\n5'-UUC...GGACA___G________AAAGU...AUA-3'\n______________AAG_AAGGAGCA\n______________\|\|\|_\|\|\|:\|\|\|\|\n______________UUC_UUCUUCGU\n3'-UUU...ACGAA___G________GAAUU...CAA-5'\n_____________\|____________\|\n_____________50___________37\n	190 -- 196	38 -- 44	-14.2659 kcal/mol	1.1364 kcal/mol	6.02696 kcal/mol	184 197@LB@ \| \|@LB@5'-UUC...GGACA G AAAGU...AUA-3'@LB@ AAG AAGGAGCA@LB@ \|\|\| \|\|\|:\|\|\|\|@LB@ UUC UUCUUCGU@LB@3'-UUU...ACGAA G GAAUU...CAA-5'@LB@ \| \|@LB@ 50 37@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -14.2659 kcal/mol@LB@Unfolding Energy - mRNA 1.1364 kcal/mol@LB@Unfolding Energy - sRNA 6.02696 kcal/mol@LB@@LB@Position - mRNA 185 -- 196@LB@Position - sRNA 38 -- 49@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 38 -- 44@LB@
106	0.009044	0.2693	b3360	pabA	-9.65	0.020637	134 -- 165	7 -- 41	aminodeoxychorismate synthase subunit II	_____________133_________________________________166\n_____________\|___________________________________\|\n5'-GCG...UAUUU____AAGUGGUAAG___AA________________GUAAA...CGU-3'\n______________AGCA___________CG____GCCGGGGAAUCUGA\n______________\|\|\|\|___________\|\|____:\|\|:\|\|:\|\|\|\|\|\|\|\n______________UCGU___________GC____UGGUCCUUUAGACU\n3'-UUU...GUUCU____GAAUUUUUUAA__AAUG______________ACACAA-5'\n_____________\|___________________________________\|\n_____________42__________________________________6\n	156 -- 162	10 -- 16	-26.3396 kcal/mol	7.46958 kcal/mol	9.22092 kcal/mol	133 166@LB@ \| \|@LB@5'-GCG...UAUUU AAGUGGUAAG AA GUAAA...CGU-3'@LB@ AGCA CG GCCGGGGAAUCUGA@LB@ \|\|\|\| \|\| :\|\|:\|\|:\|\|\|\|\|\|\|@LB@ UCGU GC UGGUCCUUUAGACU@LB@3'-UUU...GUUCU GAAUUUUUUAA AAUG ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -26.3396 kcal/mol@LB@Unfolding Energy - mRNA 7.46958 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 134 -- 165@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 10 -- 16@LB@
107	0.009263	0.2693	b3034	nudF	-7.86	0.065629	202 -- 214	42 -- 54	ADP-ribose pyrophosphatase	_____________201___________215\n_____________\|_____________\|\n5'-AUU...AACAA_________C___CAACC...UUU-3'\n______________UGCUUAAGC_AGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\n______________ACGAAUUCG_UCU\n3'-UUU...UUUGA_________U___UCGUG...CAA-5'\n_____________\|_____________\|\n_____________55____________41\n	204 -- 210	46 -- 52	-15.7149 kcal/mol	1.83586 kcal/mol	6.01534 kcal/mol	201 215@LB@ \| \|@LB@5'-AUU...AACAA C CAACC...UUU-3'@LB@ UGCUUAAGC AGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|@LB@ ACGAAUUCG UCU@LB@3'-UUU...UUUGA U UCGUG...CAA-5'@LB@ \| \|@LB@ 55 41@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -15.7149 kcal/mol@LB@Unfolding Energy - mRNA 1.83586 kcal/mol@LB@Unfolding Energy - sRNA 6.01534 kcal/mol@LB@@LB@Position - mRNA 202 -- 214@LB@Position - sRNA 42 -- 54@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 46 -- 52@LB@
108	0.009338	0.2693	b0639	nadD	-9.48	0.023112	42 -- 61	34 -- 53	nicotinic acid mononucleotide adenylyltransferase NAD(P)-dependent	_____________41___________________62\n_____________\|____________________\|\n5'-AUG...AAAUC________C___C___G___CGUCA...CGC-3'\n______________GCUUAAGU_AGA_GCA_UUA\n______________\|\|\|\|\|\|\|:_\|\|\|_\|\|\|_\|\|\|\n______________CGAAUUCG_UCU_CGU_AAU\n3'-UUU...UUGAA________U___U___G___UUUUU...CAA-5'\n_____________\|____________________\|\n_____________54___________________33\n	42 -- 48	47 -- 53	-20.1483 kcal/mol	4.55179 kcal/mol	6.11529 kcal/mol	41 62@LB@ \| \|@LB@5'-AUG...AAAUC C C G CGUCA...CGC-3'@LB@ GCUUAAGU AGA GCA UUA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\| \|\|\|@LB@ CGAAUUCG UCU CGU AAU@LB@3'-UUU...UUGAA U U G UUUUU...CAA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -20.1483 kcal/mol@LB@Unfolding Energy - mRNA 4.55179 kcal/mol@LB@Unfolding Energy - sRNA 6.11529 kcal/mol@LB@@LB@Position - mRNA 42 -- 61@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 47 -- 53@LB@
109	0.009396	0.2693	b1958	yedI	-10.22	0.013950	83 -- 110	33 -- 54	DUF808 family inner membrane protein	_____________82_____________________________111\n_____________\|______________________________\|\n5'-AAA...CAUUC______________AUAUAAUU________UUGUU...CCG-3'\n______________UGCU__GGCGAGAG________GCACUUGA\n______________\|\|\|\|__:\|\|:\|\|\|:________\|\|\|\|\|\|:\|\n______________ACGA__UCGUUCUU________CGUGAAUU\n3'-UUU...UUUGA____AU________________________UUUUA...CAA-5'\n_____________\|______________________________\|\n_____________55_____________________________32\n	104 -- 110	33 -- 39	-21.3805 kcal/mol	4.98239 kcal/mol	6.17798 kcal/mol	82 111@LB@ \| \|@LB@5'-AAA...CAUUC AUAUAAUU UUGUU...CCG-3'@LB@ UGCU GGCGAGAG GCACUUGA@LB@ \|\|\|\| :\|\|:\|\|\|: \|\|\|\|\|\|:\|@LB@ ACGA UCGUUCUU CGUGAAUU@LB@3'-UUU...UUUGA AU UUUUA...CAA-5'@LB@ \| \|@LB@ 55 32@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -21.3805 kcal/mol@LB@Unfolding Energy - mRNA 4.98239 kcal/mol@LB@Unfolding Energy - sRNA 6.17798 kcal/mol@LB@@LB@Position - mRNA 83 -- 110@LB@Position - sRNA 33 -- 54@LB@Position Seed - mRNA 104 -- 110@LB@Position Seed - sRNA 33 -- 39@LB@
110	0.009505	0.2693	b0632	dacA	-12.82	0.002052	146 -- 175	26 -- 57	D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5)	_____________145______________________________176\n_____________\|________________________________\|\n5'-CCU...AGUGC_______AU______________UUUU_____CAUCA...AUA-3'\n______________AUUUGCU__AGUAGG__GCACUU____AAUUC\n______________\|:\|\|\|\|\|__\|\|:\|:\|__\|\|\|\|\|\|____\|\|\|\|\|\n______________UGAACGA__UCGUUC__CGUGAA____UUAAG\n3'-UUU...UACUU_______AU______UU______UUUU_____CAAUG...CAA-5'\n_____________\|________________________________\|\n_____________58_______________________________25\n	146 -- 152	51 -- 57	-23.8315 kcal/mol	4.73353 kcal/mol	6.27605 kcal/mol	145 176@LB@ \| \|@LB@5'-CCU...AGUGC AU UUUU CAUCA...AUA-3'@LB@ AUUUGCU AGUAGG GCACUU AAUUC@LB@ \|:\|\|\|\|\| \|\|:\|:\| \|\|\|\|\|\| \|\|\|\|\|@LB@ UGAACGA UCGUUC CGUGAA UUAAG@LB@3'-UUU...UACUU AU UU UUUU CAAUG...CAA-5'@LB@ \| \|@LB@ 58 25@LB@@LB@@LB@Energy -12.82 kcal/mol@LB@Hybridization Energy -23.8315 kcal/mol@LB@Unfolding Energy - mRNA 4.73353 kcal/mol@LB@Unfolding Energy - sRNA 6.27605 kcal/mol@LB@@LB@Position - mRNA 146 -- 175@LB@Position - sRNA 26 -- 57@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 51 -- 57@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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