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
176	0.02022	0.37	b0495	ybbA	-5.55	0.244939	212 -- 247	24 -- 59	putative ABC transporter ATPase	_____________211___________________________________248\n_____________\|_____________________________________\|\n5'-GCC...GCGGA____A_____G____UCAUCAU___________C___CGGUC...UCA-3'\n______________AAAC_UUGUU_AAGU________CUUAAGAAGU_CGU\n______________\|\|\|\|_\|\|\|:\|_\|\|\|:________\|\|\|\|\|:\|\|:\|_\|\|\|\n______________UUUG_AACGA_UUCG________GAAUUUUUUA_GCA\n3'-UUU...CCUAC__________A____UUCUUCGU__________A___AUGUG...CAA-5'\n_____________\|_____________________________________\|\n_____________60____________________________________23\n	235 -- 241	30 -- 36	-18.4731 kcal/mol	6.64875 kcal/mol	6.27609 kcal/mol	211 248@LB@ \| \|@LB@5'-GCC...GCGGA A G UCAUCAU C CGGUC...UCA-3'@LB@ AAAC UUGUU AAGU CUUAAGAAGU CGU@LB@ \|\|\|\| \|\|\|:\| \|\|\|: \|\|\|\|\|:\|\|:\| \|\|\|@LB@ UUUG AACGA UUCG GAAUUUUUUA GCA@LB@3'-UUU...CCUAC A UUCUUCGU A AUGUG...CAA-5'@LB@ \| \|@LB@ 60 23@LB@@LB@@LB@Energy -5.55 kcal/mol@LB@Hybridization Energy -18.4731 kcal/mol@LB@Unfolding Energy - mRNA 6.64875 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 212 -- 247@LB@Position - sRNA 24 -- 59@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 30 -- 36@LB@
44	0.001875	0.1369	b4485	ytfR	-11.10	0.007490	215 -- 227	10 -- 22	putative sugar ABC transporter ATPase	_____________214___________228\n_____________\|_____________\|\n5'-CCU...GACCA_____________CUCCG...GCC-3'\n______________ACACCAGGAGAUC\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________UGUGGUCCUUUAG\n3'-UUU...AGCAA_____________ACUAC...CAA-5'\n_____________\|_____________\|\n_____________23____________9\n	221 -- 227	10 -- 16	-21.5971 kcal/mol	2.94097 kcal/mol	7.55838 kcal/mol	214 228@LB@ \| \|@LB@5'-CCU...GACCA CUCCG...GCC-3'@LB@ ACACCAGGAGAUC@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ UGUGGUCCUUUAG@LB@3'-UUU...AGCAA ACUAC...CAA-5'@LB@ \| \|@LB@ 23 9@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -21.5971 kcal/mol@LB@Unfolding Energy - mRNA 2.94097 kcal/mol@LB@Unfolding Energy - sRNA 7.55838 kcal/mol@LB@@LB@Position - mRNA 215 -- 227@LB@Position - sRNA 10 -- 22@LB@Position Seed - mRNA 221 -- 227@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@
159	0.01739	0.3504	b2426	ucpA	-8.50	0.043854	215 -- 229	36 -- 49	furfural resistance protein putative short-chain oxidoreductase	_____________214_____________230\n_____________\|_______________\|\n5'-GUG...CUCAC________C______GAUUA...UAA-3'\n______________GGGCAAGA_AGCACU\n______________::\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UUCGUUCU_UCGUGA\n3'-UUU...ACGAA_______________AUUUU...CAA-5'\n_____________\|_______________\|\n_____________50______________35\n	216 -- 222	42 -- 48	-19.0239 kcal/mol	4.4828 kcal/mol	6.03645 kcal/mol	214 230@LB@ \| \|@LB@5'-GUG...CUCAC C GAUUA...UAA-3'@LB@ GGGCAAGA AGCACU@LB@ ::\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UUCGUUCU UCGUGA@LB@3'-UUU...ACGAA AUUUU...CAA-5'@LB@ \| \|@LB@ 50 35@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -19.0239 kcal/mol@LB@Unfolding Energy - mRNA 4.4828 kcal/mol@LB@Unfolding Energy - sRNA 6.03645 kcal/mol@LB@@LB@Position - mRNA 215 -- 229@LB@Position - sRNA 36 -- 49@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 42 -- 48@LB@
95	0.007016	0.2379	b0464	acrR	-8.52	0.043413	219 -- 228	37 -- 46	transcriptional repressor	_____________218________229\n_____________\|__________\|\n5'-AAG...CCAAA__________AAGAA...CGC-3'\n______________CAAGAAGCGC\n______________\|\|\|\|\|\|\|\|:\|\n______________GUUCUUCGUG\n3'-UUU...AAUUC__________AAUUU...CAA-5'\n_____________\|__________\|\n_____________47_________36\n	222 -- 228	37 -- 43	-15.2794 kcal/mol	1.54243 kcal/mol	5.21654 kcal/mol	218 229@LB@ \| \|@LB@5'-AAG...CCAAA AAGAA...CGC-3'@LB@ CAAGAAGCGC@LB@ \|\|\|\|\|\|\|\|:\|@LB@ GUUCUUCGUG@LB@3'-UUU...AAUUC AAUUU...CAA-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -8.52 kcal/mol@LB@Hybridization Energy -15.2794 kcal/mol@LB@Unfolding Energy - mRNA 1.54243 kcal/mol@LB@Unfolding Energy - sRNA 5.21654 kcal/mol@LB@@LB@Position - mRNA 219 -- 228@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 37 -- 43@LB@
57	0.002825	0.1597	b2233	yfaL	-10.30	0.013161	220 -- 233	34 -- 47	adhesin	_____________219____________234\n_____________\|______________\|\n5'-UAU...UCUAC______________UCUUU...CAU-3'\n______________GCAAGGAGUAUUUA\n______________\|\|\|\|\|:\|\|:\|:\|\|\|\n______________CGUUCUUCGUGAAU\n3'-UUU...GAAUU______________UUUUU...CAA-5'\n_____________\|______________\|\n_____________48_____________33\n	227 -- 233	34 -- 40	-18.4969 kcal/mol	2.11117 kcal/mol	6.08192 kcal/mol	219 234@LB@ \| \|@LB@5'-UAU...UCUAC UCUUU...CAU-3'@LB@ GCAAGGAGUAUUUA@LB@ \|\|\|\|\|:\|\|:\|:\|\|\|@LB@ CGUUCUUCGUGAAU@LB@3'-UUU...GAAUU UUUUU...CAA-5'@LB@ \| \|@LB@ 48 33@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -18.4969 kcal/mol@LB@Unfolding Energy - mRNA 2.11117 kcal/mol@LB@Unfolding Energy - sRNA 6.08192 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 34 -- 47@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 34 -- 40@LB@
87	0.005861	0.217	b3083	higB	-4.01	0.492619	220 -- 233	28 -- 42	mRNA interferase toxin of the HigB-HigA toxin-antitoxin system	_____________219_____________234\n_____________\|_______________\|\n5'-GCA...UCAAA_______________GCUGC...GAU-3'\n______________AAGCAUU_GAAAGAU\n______________\|\|\|\|\|:\|_:\|\|\|:\|\|\n______________UUCGUGA_UUUUUUA\n3'-UUU...CGUUC_______A_______AGCAA...CAA-5'\n_____________\|_______________\|\n_____________43______________27\n	220 -- 226	36 -- 42	-9.16043 kcal/mol	3.51035 kcal/mol	1.63711 kcal/mol	219 234@LB@ \| \|@LB@5'-GCA...UCAAA GCUGC...GAU-3'@LB@ AAGCAUU GAAAGAU@LB@ \|\|\|\|\|:\| :\|\|\|:\|\|@LB@ UUCGUGA UUUUUUA@LB@3'-UUU...CGUUC A AGCAA...CAA-5'@LB@ \| \|@LB@ 43 27@LB@@LB@@LB@Energy -4.01 kcal/mol@LB@Hybridization Energy -9.16043 kcal/mol@LB@Unfolding Energy - mRNA 3.51035 kcal/mol@LB@Unfolding Energy - sRNA 1.63711 kcal/mol@LB@@LB@Position - mRNA 220 -- 233@LB@Position - sRNA 28 -- 42@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 36 -- 42@LB@
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@
123	0.0108	0.2828	b2606	rplS	-6.81	0.122900	220 -- 252	37 -- 58	50S ribosomal subunit protein L19	_____________219_______________________________253\n_____________\|_________________________________\|\n5'-AUA...UAAGC______AACAAGAGCAGAUG________C____CUUCC...UUG-3'\n______________AACUUG______________AAGCAGGA_GUAC\n______________\|\|\|\|\|\|______________\|\|\|\|\|:\|\|_\|:\|\|\n______________UUGAAC______________UUCGUUCU_CGUG\n3'-UUU...CUACU______GAA___________________U____AAUUU...CAA-5'\n_____________\|_________________________________\|\n_____________59________________________________36\n	241 -- 247	42 -- 48	-17.5998 kcal/mol	4.54246 kcal/mol	6.24354 kcal/mol	219 253@LB@ \| \|@LB@5'-AUA...UAAGC AACAAGAGCAGAUG C CUUCC...UUG-3'@LB@ AACUUG AAGCAGGA GUAC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\| \|:\|\|@LB@ UUGAAC UUCGUUCU CGUG@LB@3'-UUU...CUACU GAA U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -17.5998 kcal/mol@LB@Unfolding Energy - mRNA 4.54246 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 220 -- 252@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 42 -- 48@LB@
79	0.005218	0.2128	b1264	trpE	-7.84	0.066605	225 -- 250	34 -- 59	component I of anthranilate synthase	_____________224__________________________251\n_____________\|____________________________\|\n5'-UGU...CUCUC_________AACCU______________UCGCG...CGG-3'\n______________GAAC_UGCU_____GCGA_AGGCGCUUA\n______________:\|\|\|_\|\|\|\|_____\|\|:\|_\|:\|\|:\|\|\|\|\n______________UUUG_ACGA_____CGUU_UUCGUGAAU\n3'-UUU...CCUAC____A____AUU______C_________UUUUU...CAA-5'\n_____________\|____________________________\|\n_____________60___________________________33\n	244 -- 250	34 -- 40	-20.2106 kcal/mol	6.10702 kcal/mol	6.26371 kcal/mol	224 251@LB@ \| \|@LB@5'-UGU...CUCUC AACCU UCGCG...CGG-3'@LB@ GAAC UGCU GCGA AGGCGCUUA@LB@ :\|\|\| \|\|\|\| \|\|:\| \|:\|\|:\|\|\|\|@LB@ UUUG ACGA CGUU UUCGUGAAU@LB@3'-UUU...CCUAC A AUU C UUUUU...CAA-5'@LB@ \| \|@LB@ 60 33@LB@@LB@@LB@Energy -7.84 kcal/mol@LB@Hybridization Energy -20.2106 kcal/mol@LB@Unfolding Energy - mRNA 6.10702 kcal/mol@LB@Unfolding Energy - sRNA 6.26371 kcal/mol@LB@@LB@Position - mRNA 225 -- 250@LB@Position - sRNA 34 -- 59@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 34 -- 40@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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