Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
34	0.007003	0.6129	b4199	yjfY	-12.43	0.013073	184 -- 195	46 -- 57	YhcN family protein periplasmic	_____________183__________196\n_____________\|____________\|\n5'-AGG...GUCAG____________UAUCU...ACG-3'\n______________CCGUCGAGGAGG\n______________\|\|\|\|\|:\|:\|\|\|\|\n______________GGCAGUUUCUCC\n3'-UUU...AACCG____________UUAAA...ACA-5'\n_____________\|____________\|\n_____________58___________45\n	189 -- 195	46 -- 52	-19.9606 kcal/mol	4.79886 kcal/mol	2.7365 kcal/mol	183 196@LB@ \| \|@LB@5'-AGG...GUCAG UAUCU...ACG-3'@LB@ CCGUCGAGGAGG@LB@ \|\|\|\|\|:\|:\|\|\|\|@LB@ GGCAGUUUCUCC@LB@3'-UUU...AACCG UUAAA...ACA-5'@LB@ \| \|@LB@ 58 45@LB@@LB@@LB@Energy -12.43 kcal/mol@LB@Hybridization Energy -19.9606 kcal/mol@LB@Unfolding Energy - mRNA 4.79886 kcal/mol@LB@Unfolding Energy - sRNA 2.7365 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 46 -- 57@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 46 -- 52@LB@
169	0.03425	0.6177	b0336	codB	-12.15	0.014930	188 -- 202	38 -- 52	cytosine transporter	_____________187_____________203\n_____________\|_______________\|\n5'-CCA...GCAAA_______________GUCGC...UUU-3'\n______________AAGGGGGAAUUUCGU\n______________\|\|:\|:\|\|\|\|\|\|\|\|:\|\n______________UUUCUCCUUAAAGUA\n3'-UUU...GGCAG_______________AAAAA...ACA-5'\n_____________\|_______________\|\n_____________53______________37\n	196 -- 202	38 -- 44	-18.3448 kcal/mol	5.13025 kcal/mol	1.0693 kcal/mol	187 203@LB@ \| \|@LB@5'-CCA...GCAAA GUCGC...UUU-3'@LB@ AAGGGGGAAUUUCGU@LB@ \|\|:\|:\|\|\|\|\|\|\|\|:\|@LB@ UUUCUCCUUAAAGUA@LB@3'-UUU...GGCAG AAAAA...ACA-5'@LB@ \| \|@LB@ 53 37@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.3448 kcal/mol@LB@Unfolding Energy - mRNA 5.13025 kcal/mol@LB@Unfolding Energy - sRNA 1.0693 kcal/mol@LB@@LB@Position - mRNA 188 -- 202@LB@Position - sRNA 38 -- 52@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 38 -- 44@LB@
16	0.003381	0.593	b0956	matP	-12.11	0.015217	269 -- 280	42 -- 53	Ter macrodomain organizer matS-binding protein	_____________268__________281\n_____________\|____________\|\n5'-UUU...CAUCG____________AAUCA...AAG-3'\n______________CGAAGGGGAGUU\n______________\|:\|\|\|:\|\|\|:\|\|\n______________GUUUCUCCUUAA\n3'-UUU...GGGCA____________AGUAA...ACA-5'\n_____________\|____________\|\n_____________54___________41\n	274 -- 280	42 -- 48	-15.3716 kcal/mol	2.33274 kcal/mol	0.933904 kcal/mol	268 281@LB@ \| \|@LB@5'-UUU...CAUCG AAUCA...AAG-3'@LB@ CGAAGGGGAGUU@LB@ \|:\|\|\|:\|\|\|:\|\|@LB@ GUUUCUCCUUAA@LB@3'-UUU...GGGCA AGUAA...ACA-5'@LB@ \| \|@LB@ 54 41@LB@@LB@@LB@Energy -12.11 kcal/mol@LB@Hybridization Energy -15.3716 kcal/mol@LB@Unfolding Energy - mRNA 2.33274 kcal/mol@LB@Unfolding Energy - sRNA 0.933904 kcal/mol@LB@@LB@Position - mRNA 269 -- 280@LB@Position - sRNA 42 -- 53@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 42 -- 48@LB@
99	0.01953	0.6177	b2473	ypfH	-12.09	0.015349	8 -- 40	44 -- 76	palmitoyl-CoA esterase activity uncertain physiological substrate	_____________7__________________________________41\n_____________\|__________________________________\|\n____5'-ACUUUCA_____CAAGA_____C___________C______GAGGC...GGG-3'\n______________GGCCG_____UGUUA_UGGUCCGUCAG_G_GGAA\n______________\|\|\|\|:_____:\|:\|\|_\|\|\|:\|\|\|\|\|\|:_\|_\|\|\|\|\n______________CCGGU_____GCGAU_ACCGGGCAGUU_C_CCUU\n___3'-UUUUUUUA_____UAUA______A___________U_U____AAAGU...ACA-5'\n_____________\|__________________________________\|\n_____________77_________________________________43\n	28 -- 34	51 -- 57	-34.8713 kcal/mol	9.35151 kcal/mol	13.433 kcal/mol	7 41@LB@ \| \|@LB@ 5'-ACUUUCA CAAGA C C GAGGC...GGG-3'@LB@ GGCCG UGUUA UGGUCCGUCAG G GGAA@LB@ \|\|\|\|: :\|:\|\| \|\|\|:\|\|\|\|\|\|: \| \|\|\|\|@LB@ CCGGU GCGAU ACCGGGCAGUU C CCUU@LB@ 3'-UUUUUUUA UAUA A U U AAAGU...ACA-5'@LB@ \| \|@LB@ 77 43@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -34.8713 kcal/mol@LB@Unfolding Energy - mRNA 9.35151 kcal/mol@LB@Unfolding Energy - sRNA 13.433 kcal/mol@LB@@LB@Position - mRNA 8 -- 40@LB@Position - sRNA 44 -- 76@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
7	0.001184	0.5444	b0817	mntR	-11.99	0.016054	285 -- 294	46 -- 55	Mn(2+)-responsive manganese regulon transcriptional regulator	_____________284________295\n_____________\|__________\|\n5'-CUU...GCCAG__________CGCAUC-3'\n______________GUCAGAGAGG\n______________\|\|\|\|:\|\|\|\|\|\n______________CAGUUUCUCC\n3'-UUU...CCGGG__________UUAAA...ACA-5'\n_____________\|__________\|\n_____________56_________45\n	288 -- 294	46 -- 52	-16.1275 kcal/mol	3.21103 kcal/mol	0.924411 kcal/mol	284 295@LB@ \| \|@LB@5'-CUU...GCCAG CGCAUC-3'@LB@ GUCAGAGAGG@LB@ \|\|\|\|:\|\|\|\|\|@LB@ CAGUUUCUCC@LB@3'-UUU...CCGGG UUAAA...ACA-5'@LB@ \| \|@LB@ 56 45@LB@@LB@@LB@Energy -11.99 kcal/mol@LB@Hybridization Energy -16.1275 kcal/mol@LB@Unfolding Energy - mRNA 3.21103 kcal/mol@LB@Unfolding Energy - sRNA 0.924411 kcal/mol@LB@@LB@Position - mRNA 285 -- 294@LB@Position - sRNA 46 -- 55@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 46 -- 52@LB@
43	0.008509	0.6129	b4322	uxuA	-11.91	0.016653	184 -- 195	44 -- 55	mannonate hydrolase	_____________183__________196\n_____________\|____________\|\n5'-CAU...ACUAU__G_________AAAUC...AUA-3'\n______________GU_AAAGAGGAA\n______________\|\|_\|\|\|\|\|\|\|\|\|\n______________CA_UUUCUCCUU\n3'-UUU...CCGGG__G_________AAAGU...ACA-5'\n_____________\|____________\|\n_____________56___________43\n	189 -- 195	44 -- 50	-15.5118 kcal/mol	2.65561 kcal/mol	0.941432 kcal/mol	183 196@LB@ \| \|@LB@5'-CAU...ACUAU G AAAUC...AUA-3'@LB@ GU AAAGAGGAA@LB@ \|\| \|\|\|\|\|\|\|\|\|@LB@ CA UUUCUCCUU@LB@3'-UUU...CCGGG G AAAGU...ACA-5'@LB@ \| \|@LB@ 56 43@LB@@LB@@LB@Energy -11.91 kcal/mol@LB@Hybridization Energy -15.5118 kcal/mol@LB@Unfolding Energy - mRNA 2.65561 kcal/mol@LB@Unfolding Energy - sRNA 0.941432 kcal/mol@LB@@LB@Position - mRNA 184 -- 195@LB@Position - sRNA 44 -- 55@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 44 -- 50@LB@
6	0.0006545	0.351	b1857	znuA	-11.78	0.017745	58 -- 67	45 -- 54	zinc ABC transporter periplasmic binding protein	_____________57_________68\n_____________\|__________\|\n5'-GCG...ACACA__________CGCGG...AAC-3'\n______________UCAGAGAGGA\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	61 -- 67	45 -- 51	-14.7441 kcal/mol	2.03423 kcal/mol	0.929144 kcal/mol	57 68@LB@ \| \|@LB@5'-GCG...ACACA CGCGG...AAC-3'@LB@ UCAGAGAGGA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -14.7441 kcal/mol@LB@Unfolding Energy - mRNA 2.03423 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 58 -- 67@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 45 -- 51@LB@
21	0.004054	0.5992	b2076	mdtC	-11.67	0.018717	158 -- 193	45 -- 78	multidrug efflux system subunit C	_____________157____________________________________194\n_____________\|______________________________________\|\n5'-CUC...GCAUU____A____AAGC____UU__________UG_______GGCGU...CGG-3'\n______________GUGG_CCAA____CGCU____GCCCGUCA__AAGAGGA\n______________:\|\|\|_\|\|\|\|____\|\|\|\|____\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|\n______________UACC_GGUU____GCGA____CGGGCAGU__UUCUCCU\n_____3'-UUUUUU_________AUA_____UAAC_________________UAAAG...ACA-5'\n_____________\|______________________________________\|\n_____________79_____________________________________44\n	187 -- 193	45 -- 51	-37.8051 kcal/mol	12.6053 kcal/mol	13.5316 kcal/mol	157 194@LB@ \| \|@LB@5'-CUC...GCAUU A AAGC UU UG GGCGU...CGG-3'@LB@ GUGG CCAA CGCU GCCCGUCA AAGAGGA@LB@ :\|\|\| \|\|\|\| \|\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UACC GGUU GCGA CGGGCAGU UUCUCCU@LB@ 3'-UUUUUU AUA UAAC UAAAG...ACA-5'@LB@ \| \|@LB@ 79 44@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -37.8051 kcal/mol@LB@Unfolding Energy - mRNA 12.6053 kcal/mol@LB@Unfolding Energy - sRNA 13.5316 kcal/mol@LB@@LB@Position - mRNA 158 -- 193@LB@Position - sRNA 45 -- 78@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 45 -- 51@LB@
8	0.001474	0.5928	b1048	opgG	-11.67	0.018726	159 -- 168	44 -- 53	OPG biosynthetic periplasmic beta-1 6 branching glycosyltransferase	_____________158________169\n_____________\|__________\|\n5'-ACA...GCACA__________AGUGC...AAU-3'\n______________CAAAGGGGGA\n______________\|\|\|\|\|:\|\|:\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-12.9473 kcal/mol	0.352192 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-ACA...GCACA AGUGC...AAU-3'@LB@ CAAAGGGGGA@LB@ \|\|\|\|\|:\|\|:\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -12.9473 kcal/mol@LB@Unfolding Energy - mRNA 0.352192 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
30	0.005789	0.6127	b2688	gshA	-11.51	0.020183	254 -- 264	45 -- 55	glutamate-cysteine ligase	_____________253_________265\n_____________\|___________\|\n5'-UGU...CAGGC___________UACAG...UUA-3'\n______________GUUAAAGGGGA\n______________\|\|:\|\|\|\|:\|\|\|\n______________CAGUUUCUCCU\n3'-UUU...CCGGG___________UAAAG...ACA-5'\n_____________\|___________\|\n_____________56__________44\n	258 -- 264	45 -- 51	-13.8935 kcal/mol	1.45381 kcal/mol	0.930875 kcal/mol	253 265@LB@ \| \|@LB@5'-UGU...CAGGC UACAG...UUA-3'@LB@ GUUAAAGGGGA@LB@ \|\|:\|\|\|\|:\|\|\|@LB@ CAGUUUCUCCU@LB@3'-UUU...CCGGG UAAAG...ACA-5'@LB@ \| \|@LB@ 56 44@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -13.8935 kcal/mol@LB@Unfolding Energy - mRNA 1.45381 kcal/mol@LB@Unfolding Energy - sRNA 0.930875 kcal/mol@LB@@LB@Position - mRNA 254 -- 264@LB@Position - sRNA 45 -- 55@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 45 -- 51@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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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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