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
51	0.002326	0.1469	b2780	pyrG	-6.37	0.158020	19 -- 28	33 -- 42	CTP synthetase	_____________18_________29\n_____________\|__________\|\n5'-UGU...AUGAC__________UUUGC...GCC-3'\n______________AAGCGCUUGA\n______________\|\|\|\|:\|\|\|:\|\n______________UUCGUGAAUU\n3'-UUU...CGUUC__________UUUUA...CAA-5'\n_____________\|__________\|\n_____________43_________32\n	22 -- 28	33 -- 39	-10.9983 kcal/mol	3.00927 kcal/mol	1.61944 kcal/mol	18 29@LB@ \| \|@LB@5'-UGU...AUGAC UUUGC...GCC-3'@LB@ AAGCGCUUGA@LB@ \|\|\|\|:\|\|\|:\|@LB@ UUCGUGAAUU@LB@3'-UUU...CGUUC UUUUA...CAA-5'@LB@ \| \|@LB@ 43 32@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -10.9983 kcal/mol@LB@Unfolding Energy - mRNA 3.00927 kcal/mol@LB@Unfolding Energy - sRNA 1.61944 kcal/mol@LB@@LB@Position - mRNA 19 -- 28@LB@Position - sRNA 33 -- 42@LB@Position Seed - mRNA 22 -- 28@LB@Position Seed - sRNA 33 -- 39@LB@
52	0.002466	0.1527	b3527	yhjJ	-8.40	0.046956	207 -- 220	25 -- 41	putative periplasmic M16 family chaperone	_____________206_______________221\n_____________\|_________________\|\n5'-CUC...UGCAG_________________ACUUU...GGC-3'\n______________GGCAC___AAAAAUUCG\n______________:\|\|\|\|___\|\|\|\|\|\|\|\|\|\n______________UCGUG___UUUUUAAGC\n3'-UUU...GUUCU_____AAU_________AAUGU...CAA-5'\n_____________\|_________________\|\n_____________42________________24\n	214 -- 220	25 -- 31	-13.4116 kcal/mol	3.36563 kcal/mol	1.64839 kcal/mol	206 221@LB@ \| \|@LB@5'-CUC...UGCAG ACUUU...GGC-3'@LB@ GGCAC AAAAAUUCG@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ UCGUG UUUUUAAGC@LB@3'-UUU...GUUCU AAU AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -13.4116 kcal/mol@LB@Unfolding Energy - mRNA 3.36563 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 207 -- 220@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 25 -- 31@LB@
53	0.002646	0.1597	b1704	aroH	-6.03	0.190589	111 -- 120	31 -- 40	3-deoxy-D-arabino-heptulosonate-7-phosphate synthase tryptophan repressible	_____________110________121\n_____________\|__________\|\n5'-CCA...ACCUC__________UCAGC...CCC-3'\n______________GCACUUGAAA\n______________\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUU\n3'-UUU...UUCUU__________UUAAG...CAA-5'\n_____________\|__________\|\n_____________41_________30\n	114 -- 120	31 -- 37	-11.574 kcal/mol	3.92769 kcal/mol	1.61955 kcal/mol	110 121@LB@ \| \|@LB@5'-CCA...ACCUC UCAGC...CCC-3'@LB@ GCACUUGAAA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUU@LB@3'-UUU...UUCUU UUAAG...CAA-5'@LB@ \| \|@LB@ 41 30@LB@@LB@@LB@Energy -6.03 kcal/mol@LB@Hybridization Energy -11.574 kcal/mol@LB@Unfolding Energy - mRNA 3.92769 kcal/mol@LB@Unfolding Energy - sRNA 1.61955 kcal/mol@LB@@LB@Position - mRNA 111 -- 120@LB@Position - sRNA 31 -- 40@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 31 -- 37@LB@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@LB@
56	0.002803	0.1597	b2514	hisS	-5.93	0.201249	279 -- 295	24 -- 41	histidyl tRNA synthetase	_____________278_________________296\n_____________\|___________________\|\n5'-AUG...UUGAA_____AC____________GCUCG-3'\n______________GGCAC__UGAAAAA__CGU\n______________:\|\|\|\|__\|:\|\|\|\|\|__\|\|\|\n______________UCGUG__AUUUUUU__GCA\n3'-UUU...GUUCU_____A________AA___AUGUG...CAA-5'\n_____________\|___________________\|\n_____________42__________________23\n	286 -- 292	29 -- 35	-10.1195 kcal/mol	2.54562 kcal/mol	1.64881 kcal/mol	278 296@LB@ \| \|@LB@5'-AUG...UUGAA AC GCUCG-3'@LB@ GGCAC UGAAAAA CGU@LB@ :\|\|\|\| \|:\|\|\|\|\| \|\|\|@LB@ UCGUG AUUUUUU GCA@LB@3'-UUU...GUUCU A AA AUGUG...CAA-5'@LB@ \| \|@LB@ 42 23@LB@@LB@@LB@Energy -5.93 kcal/mol@LB@Hybridization Energy -10.1195 kcal/mol@LB@Unfolding Energy - mRNA 2.54562 kcal/mol@LB@Unfolding Energy - sRNA 1.64881 kcal/mol@LB@@LB@Position - mRNA 279 -- 295@LB@Position - sRNA 24 -- 41@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 29 -- 35@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@
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@LB@
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin	_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@LB@
60	0.00317	0.1645	b0466	ybaM	-6.37	0.157728	143 -- 158	25 -- 40	DUF2496 family protein	_____________142_______________159\n_____________\|_________________\|\n5'-GCA...GCCAU_____GG__________AAAAC...CGC-3'\n______________GCGCU__AAAAAAU_CG\n______________\|\|:\|\|__\|\|\|\|\|\|\|_\|\|\n______________CGUGA__UUUUUUA_GC\n3'-UUU...UUCUU_____A________A__AAUGU...CAA-5'\n_____________\|_________________\|\n_____________41________________24\n	150 -- 156	28 -- 34	-11.3444 kcal/mol	3.32327 kcal/mol	1.64821 kcal/mol	142 159@LB@ \| \|@LB@5'-GCA...GCCAU GG AAAAC...CGC-3'@LB@ GCGCU AAAAAAU CG@LB@ \|\|:\|\| \|\|\|\|\|\|\| \|\|@LB@ CGUGA UUUUUUA GC@LB@3'-UUU...UUCUU A A AAUGU...CAA-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -6.37 kcal/mol@LB@Hybridization Energy -11.3444 kcal/mol@LB@Unfolding Energy - mRNA 3.32327 kcal/mol@LB@Unfolding Energy - sRNA 1.64821 kcal/mol@LB@@LB@Position - mRNA 143 -- 158@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 28 -- 34@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)

Job resubmission

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service.

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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