Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
83	0.002775	0.1082	b2049	cpsB	-6.85	0.497101	286 -- 298	17 -- 31	mannose-1-phosphate guanyltransferase	_____________285_____________299\n_____________\|_______________\|\n5'-ACA...UCCCA_______________CC-3'\n______________AGC_AGU_UUUUAUG\n______________\|\|\|_\|\|:_\|\|\|\|\|\|\|\n______________UCG_UCG_AAAAUAC\n3'-UUU...CCAUG___A___U_______CCAAU...UCG-5'\n_____________\|_______________\|\n_____________32______________16\n	292 -- 298	17 -- 23	-8.99018 kcal/mol	0.716641 kcal/mol	1.4259 kcal/mol	285 299@LB@ \| \|@LB@5'-ACA...UCCCA CC-3'@LB@ AGC AGU UUUUAUG@LB@ \|\|\| \|\|: \|\|\|\|\|\|\|@LB@ UCG UCG AAAAUAC@LB@3'-UUU...CCAUG A U CCAAU...UCG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -8.99018 kcal/mol@LB@Unfolding Energy - mRNA 0.716641 kcal/mol@LB@Unfolding Energy - sRNA 1.4259 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 17 -- 23@LB@
92	0.00311	0.1126	b1042	csgA	-13.02	0.037954	257 -- 281	29 -- 49	curlin subunit amyloid curli fibers cryptic	_____________256_______________________282\n_____________\|_________________________\|\n5'-CAA...GCUCU__C_____UU______CA_______GGCGG...GUG-3'\n______________GG_AGGUG__GUUCCU__GUACGGC\n______________\|\|_\|\|\|\|\|__\|\|\|\|\|\|__\|\|\|\|:\|\|\n______________CC_UCCAC__CAAGGA__CAUGUCG\n3'-UUU...CGAUU________________C________AUCGU...UCG-5'\n_____________\|_________________________\|\n_____________50________________________28\n	275 -- 281	29 -- 35	-27.0821 kcal/mol	9.75964 kcal/mol	4.30143 kcal/mol	256 282@LB@ \| \|@LB@5'-CAA...GCUCU C UU CA GGCGG...GUG-3'@LB@ GG AGGUG GUUCCU GUACGGC@LB@ \|\| \|\|\|\|\| \|\|\|\|\|\| \|\|\|\|:\|\|@LB@ CC UCCAC CAAGGA CAUGUCG@LB@3'-UUU...CGAUU C AUCGU...UCG-5'@LB@ \| \|@LB@ 50 28@LB@@LB@@LB@Energy -13.02 kcal/mol@LB@Hybridization Energy -27.0821 kcal/mol@LB@Unfolding Energy - mRNA 9.75964 kcal/mol@LB@Unfolding Energy - sRNA 4.30143 kcal/mol@LB@@LB@Position - mRNA 257 -- 281@LB@Position - sRNA 29 -- 49@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 29 -- 35@LB@
70	0.00193	0.09081	b1823	cspC	-11.95	0.067388	30 -- 62	1 -- 36	stress protein member of the CspA-family	_____________29___________________________________63\n_____________\|____________________________________\|\n5'-UAU...AACGA____________UG______U__GGCA_________AAAGA...UCU-3'\n______________GGUACAGUU__C__UUUAUG_GU_____UUUUCAGU\n______________\|\|\|\|\|\|\|:\|__\|__\|\|\|\|\|\|_\|\|_____\|\|\|\|\|\|\|:\n______________CCAUGUCGA__G__AAAUAC_CA_____AAAAGUCG\n3'-UUU...AAGGA_________UC_UA______C__AUACA________-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	56 -- 62	1 -- 7	-24.9618 kcal/mol	11.5162 kcal/mol	1.49509 kcal/mol	29 63@LB@ \| \|@LB@5'-UAU...AACGA UG U GGCA AAAGA...UCU-3'@LB@ GGUACAGUU C UUUAUG GU UUUUCAGU@LB@ \|\|\|\|\|\|\|:\| \| \|\|\|\|\|\| \|\| \|\|\|\|\|\|\|:@LB@ CCAUGUCGA G AAAUAC CA AAAAGUCG@LB@3'-UUU...AAGGA UC UA C AUACA -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -11.95 kcal/mol@LB@Hybridization Energy -24.9618 kcal/mol@LB@Unfolding Energy - mRNA 11.5162 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 30 -- 62@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 1 -- 7@LB@
54	0.001244	0.07744	b1874	cutC	-11.77	0.073856	3 -- 15	22 -- 35	copper homeostasis protein	_____________2______________16\n_____________\|______________\|\n_________5'-CC______________GCUUU...AGG-3'\n______________GUGC_GCUGGCAUU\n______________\|\|:\|_\|\|\|:\|\|\|\|\|\n______________CAUG_CGAUCGUAA\n3'-UUU...AGGAC____U_________AAUAC...UCG-5'\n_____________\|______________\|\n_____________36_____________21\n	9 -- 15	22 -- 28	-17.4456 kcal/mol	4.24515 kcal/mol	1.43095 kcal/mol	2 16@LB@ \| \|@LB@ 5'-CC GCUUU...AGG-3'@LB@ GUGC GCUGGCAUU@LB@ \|\|:\| \|\|\|:\|\|\|\|\|@LB@ CAUG CGAUCGUAA@LB@3'-UUU...AGGAC U AAUAC...UCG-5'@LB@ \| \|@LB@ 36 21@LB@@LB@@LB@Energy -11.77 kcal/mol@LB@Hybridization Energy -17.4456 kcal/mol@LB@Unfolding Energy - mRNA 4.24515 kcal/mol@LB@Unfolding Energy - sRNA 1.43095 kcal/mol@LB@@LB@Position - mRNA 3 -- 15@LB@Position - sRNA 22 -- 35@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 22 -- 28@LB@
84	0.00278	0.1082	b1418	cybB	-11.15	0.099871	281 -- 297	37 -- 49	cytochrome b561	_____________280_______________298\n_____________\|_________________\|\n5'-AAC...GCAAU____UUUC_________UCC-3'\n______________GGAG____GUGGUUUCU\n______________\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CCUC____CACCAAGGA\n3'-UUU...CGAUU_________________CCAUG...UCG-5'\n_____________\|_________________\|\n_____________50________________36\n	291 -- 297	37 -- 43	-16.7846 kcal/mol	2.49998 kcal/mol	3.13428 kcal/mol	280 298@LB@ \| \|@LB@5'-AAC...GCAAU UUUC UCC-3'@LB@ GGAG GUGGUUUCU@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CCUC CACCAAGGA@LB@3'-UUU...CGAUU CCAUG...UCG-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -16.7846 kcal/mol@LB@Unfolding Energy - mRNA 2.49998 kcal/mol@LB@Unfolding Energy - sRNA 3.13428 kcal/mol@LB@@LB@Position - mRNA 281 -- 297@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 37 -- 43@LB@
123	0.005173	0.1413	b0839	dacC	-12.36	0.054489	29 -- 38	24 -- 33	D-alanyl-D-alanine carboxypeptidase; penicillin-binding protein 6a	_____________28_________39\n_____________\|__________\|\n5'-AUG...AAGCA__________AAAAA...AAG-3'\n______________ACAGCUGGCA\n______________\|\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	32 -- 38	24 -- 30	-17.0494 kcal/mol	3.2632 kcal/mol	1.42716 kcal/mol	28 39@LB@ \| \|@LB@5'-AUG...AAGCA AAAAA...AAG-3'@LB@ ACAGCUGGCA@LB@ \|\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -17.0494 kcal/mol@LB@Unfolding Energy - mRNA 3.2632 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 29 -- 38@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 24 -- 30@LB@
192	0.01101	0.1919	b2478	dapA	-6.78	0.505920	248 -- 269	25 -- 47	dihydrodipicolinate synthase	_____________247_____________________270\n_____________\|_______________________\|\n5'-GGC...GAAAA____AAUG____UCG________UUGAA...CCA-3'\n______________AGGU____UCUG____GGCUAGC\n______________\|\|\|\|____:\|\|\|____:\|\|\|\|\|\|\n______________UCCA____GGAC____UCGAUCG\n3'-UUU...AUUCC____CCAA____CAUG_______UAAAA...UCG-5'\n_____________\|_______________________\|\n_____________48______________________24\n	263 -- 269	25 -- 31	-19.6963 kcal/mol	8.35751 kcal/mol	4.55753 kcal/mol	247 270@LB@ \| \|@LB@5'-GGC...GAAAA AAUG UCG UUGAA...CCA-3'@LB@ AGGU UCUG GGCUAGC@LB@ \|\|\|\| :\|\|\| :\|\|\|\|\|\|@LB@ UCCA GGAC UCGAUCG@LB@3'-UUU...AUUCC CCAA CAUG UAAAA...UCG-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -19.6963 kcal/mol@LB@Unfolding Energy - mRNA 8.35751 kcal/mol@LB@Unfolding Energy - sRNA 4.55753 kcal/mol@LB@@LB@Position - mRNA 248 -- 269@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 25 -- 31@LB@
46	0.00106	0.07744	b3234	degQ	-13.26	0.033170	226 -- 262	1 -- 35	serine endoprotease periplasmic	_____________225____________________________________263\n_____________\|______________________________________\|\n5'-CUG...GUUGA______________AAG___C______ACUCUC_____GUCAU...UUG-3'\n______________GUGCA_UUAGCGUU___UGU_GGGUUA______UCGGC\n______________\|\|:\|\|_:\|\|\|\|:\|\|___\|:\|_\|\|\|\|\|\|______\|\|:\|\|\n______________CAUGU_GAUCGUAA___AUA_CCCAAU______AGUCG\n3'-UUU...AGGAC_____C________A____________ACAAAA_____-5'\n_____________\|_____________________________________\|\n_____________36____________________________________1\n	232 -- 238	22 -- 28	-28.0432 kcal/mol	13.2904 kcal/mol	1.49508 kcal/mol	225 263@LB@ \| \|@LB@5'-CUG...GUUGA AAG C ACUCUC GUCAU...UUG-3'@LB@ GUGCA UUAGCGUU UGU GGGUUA UCGGC@LB@ \|\|:\|\| :\|\|\|\|:\|\| \|:\| \|\|\|\|\|\| \|\|:\|\|@LB@ CAUGU GAUCGUAA AUA CCCAAU AGUCG@LB@3'-UUU...AGGAC C A ACAAAA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -13.26 kcal/mol@LB@Hybridization Energy -28.0432 kcal/mol@LB@Unfolding Energy - mRNA 13.2904 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 226 -- 262@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 22 -- 28@LB@
50	0.001175	0.07744	b3543	dppB	-14.13	0.019609	196 -- 210	1 -- 17	dipeptide/heme ABC transporter permease	_____________195_______________211\n_____________\|_________________\|\n5'-CGG...AAUCC__________G______UUAUU...AUC-3'\n______________GGGUUAUGUU___CAGU\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|:\n______________CCCAAUACAA___GUCG\n3'-UUU...AAAUA__________AAA____-5'\n_____________\|________________\|\n_____________18_______________1\n	199 -- 205	8 -- 14	-17.9134 kcal/mol	2.84721 kcal/mol	0.931609 kcal/mol	195 211@LB@ \| \|@LB@5'-CGG...AAUCC G UUAUU...AUC-3'@LB@ GGGUUAUGUU CAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ CCCAAUACAA GUCG@LB@3'-UUU...AAAUA AAA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -17.9134 kcal/mol@LB@Unfolding Energy - mRNA 2.84721 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 8 -- 14@LB@
65	0.001744	0.09016	b3541	dppD	-12.71	0.044996	114 -- 148	14 -- 40	dipeptide/heme ABC transporter ATPas	_____________113_________________________________149\n_____________\|___________________________________\|\n5'-UUU...GGCGA_____CUG___GU__________AACCUG______GACGG...GCG-3'\n______________UCCUG___ACG__GCUGGCAUUU______AUGGGU\n______________\|\|\|\|\|___\|\|:__\|\|\|:\|\|\|\|\|\|______\|\|\|\|\|\|\n______________AGGAC___UGU__CGAUCGUAAA______UACCCA\n3'-UUU...CACCA_____CA________________A___________AUACA...UCG-5'\n_____________\|___________________________________\|\n_____________41__________________________________13\n	130 -- 136	21 -- 27	-26.5011 kcal/mol	9.21659 kcal/mol	4.57003 kcal/mol	113 149@LB@ \| \|@LB@5'-UUU...GGCGA CUG GU AACCUG GACGG...GCG-3'@LB@ UCCUG ACG GCUGGCAUUU AUGGGU@LB@ \|\|\|\|\| \|\|: \|\|\|:\|\|\|\|\|\| \|\|\|\|\|\|@LB@ AGGAC UGU CGAUCGUAAA UACCCA@LB@3'-UUU...CACCA CA A AUACA...UCG-5'@LB@ \| \|@LB@ 41 13@LB@@LB@@LB@Energy -12.71 kcal/mol@LB@Hybridization Energy -26.5011 kcal/mol@LB@Unfolding Energy - mRNA 9.21659 kcal/mol@LB@Unfolding Energy - sRNA 4.57003 kcal/mol@LB@@LB@Position - mRNA 114 -- 148@LB@Position - sRNA 14 -- 40@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 21 -- 27@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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