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
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@
193	0.01107	0.1919	b3532	bcsB	-10.24	0.150531	226 -- 241	15 -- 35	regulator of cellulose synthase cyclic di-GMP binding	_____________225___________________242\n_____________\|_____________________\|\n5'-AAG...GAUUU_______G_____________GAUGA...UCA-3'\n______________GUGCAGU__GC____UAUGGG\n______________\|\|:\|\|\|:__\|\|____\|\|\|\|\|\|\n______________CAUGUCG__CG____AUACCC\n3'-UUU...AGGAC_______AU__UAAA______AAUAC...UCG-5'\n_____________\|_____________________\|\n_____________36____________________14\n	226 -- 232	29 -- 35	-18.7324 kcal/mol	7.03896 kcal/mol	1.4496 kcal/mol	225 242@LB@ \| \|@LB@5'-AAG...GAUUU G GAUGA...UCA-3'@LB@ GUGCAGU GC UAUGGG@LB@ \|\|:\|\|\|: \|\| \|\|\|\|\|\|@LB@ CAUGUCG CG AUACCC@LB@3'-UUU...AGGAC AU UAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 36 14@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -18.7324 kcal/mol@LB@Unfolding Energy - mRNA 7.03896 kcal/mol@LB@Unfolding Energy - sRNA 1.4496 kcal/mol@LB@@LB@Position - mRNA 226 -- 241@LB@Position - sRNA 15 -- 35@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 29 -- 35@LB@
67	0.00183	0.09081	b1607	ydgC	-12.69	0.045650	228 -- 262	1 -- 36	GlpM family inner membrane protein	_____________227__________________________________263\n_____________\|____________________________________\|\n5'-AUG...CGCUC_____________GUGCUGUUGAUUG__G_______AAAAA...CAC-3'\n______________GGUGC_GCUGGUA_____________GU_UUUUAGC\n______________\|\|\|:\|_\|\|\|:\|:\|_____________\|\|_\|\|\|:\|\|\|\n______________CCAUG_CGAUCGU_____________CA_AAAGUCG\n3'-UUU...AAGGA_____U_______AAAAUACCCAAUA__A_______-5'\n_____________\|___________________________________\|\n_____________37__________________________________1\n	256 -- 262	1 -- 7	-24.769 kcal/mol	10.5859 kcal/mol	1.49509 kcal/mol	227 263@LB@ \| \|@LB@5'-AUG...CGCUC GUGCUGUUGAUUG G AAAAA...CAC-3'@LB@ GGUGC GCUGGUA GU UUUUAGC@LB@ \|\|\|:\| \|\|\|:\|:\| \|\| \|\|\|:\|\|\|@LB@ CCAUG CGAUCGU CA AAAGUCG@LB@3'-UUU...AAGGA U AAAAUACCCAAUA A -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -12.69 kcal/mol@LB@Hybridization Energy -24.769 kcal/mol@LB@Unfolding Energy - mRNA 10.5859 kcal/mol@LB@Unfolding Energy - sRNA 1.49509 kcal/mol@LB@@LB@Position - mRNA 228 -- 262@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 1 -- 7@LB@
183	0.01048	0.1919	b1250	kch	-17.60	0.001460	228 -- 258	1 -- 33	voltage-gated potassium channel	_____________227_______________________________259\n_____________\|_________________________________\|\n5'-AAC...AACAA_____AACAAA_________GACCC________ACGAC...UUA-3'\n______________ACAGC______UUUAUGGGU_______UUCGGC\n______________\|\|\|\|\|______\|\|\|\|\|\|\|\|\|_______\|\|\|:\|\|\n______________UGUCG______AAAUACCCA_______AAGUCG\n3'-UUU...GACCA_____AUCGUA_________AUACAAA______-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	241 -- 247	14 -- 20	-24.8286 kcal/mol	5.73827 kcal/mol	1.49313 kcal/mol	227 259@LB@ \| \|@LB@5'-AAC...AACAA AACAAA GACCC ACGAC...UUA-3'@LB@ ACAGC UUUAUGGGU UUCGGC@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|:\|\|@LB@ UGUCG AAAUACCCA AAGUCG@LB@3'-UUU...GACCA AUCGUA AUACAAA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -17.60 kcal/mol@LB@Hybridization Energy -24.8286 kcal/mol@LB@Unfolding Energy - mRNA 5.73827 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 228 -- 258@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 14 -- 20@LB@
177	0.009845	0.1869	b3241	aaeA	-6.34	0.565531	229 -- 235	29 -- 35	p-hydroxybenzoic acid efflux system component	_____________228_____236\n_____________\|_______\|\n5'-UCC...CUCCC_______CAUCA...CCG-3'\n______________GUACGGC\n______________\|\|\|\|:\|\|\n______________CAUGUCG\n3'-UUU...AGGAC_______AUCGU...UCG-5'\n_____________\|_______\|\n_____________36______28\n	229 -- 235	29 -- 35	-10.2139 kcal/mol	2.71034 kcal/mol	1.16584 kcal/mol	228 236@LB@ \| \|@LB@5'-UCC...CUCCC CAUCA...CCG-3'@LB@ GUACGGC@LB@ \|\|\|\|:\|\|@LB@ CAUGUCG@LB@3'-UUU...AGGAC AUCGU...UCG-5'@LB@ \| \|@LB@ 36 28@LB@@LB@@LB@Energy -6.34 kcal/mol@LB@Hybridization Energy -10.2139 kcal/mol@LB@Unfolding Energy - mRNA 2.71034 kcal/mol@LB@Unfolding Energy - sRNA 1.16584 kcal/mol@LB@@LB@Position - mRNA 229 -- 235@LB@Position - sRNA 29 -- 35@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 29 -- 35@LB@
43	0.0008959	0.07003	b3068	mug	-12.52	0.050096	232 -- 248	1 -- 17	G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase	_____________231_______________249\n_____________\|_________________\|\n5'-UGG...GUUAC____C_______G____AUCAA...CGG-3'\n______________GGGU_GUGUUUU_CGGU\n______________\|\|\|\|_:\|\|\|\|\|\|_\|:\|:\n______________CCCA_UACAAAA_GUCG\n3'-UUU...AAAUA____A_______A____-5'\n_____________\|________________\|\n_____________18_______________1\n	237 -- 243	6 -- 12	-17.5569 kcal/mol	4.10869 kcal/mol	0.931609 kcal/mol	231 249@LB@ \| \|@LB@5'-UGG...GUUAC C G AUCAA...CGG-3'@LB@ GGGU GUGUUUU CGGU@LB@ \|\|\|\| :\|\|\|\|\|\| \|:\|:@LB@ CCCA UACAAAA GUCG@LB@3'-UUU...AAAUA A A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -12.52 kcal/mol@LB@Hybridization Energy -17.5569 kcal/mol@LB@Unfolding Energy - mRNA 4.10869 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 232 -- 248@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 6 -- 12@LB@
108	0.004185	0.1296	b2158	yeiH	-13.47	0.029300	232 -- 260	12 -- 35	UPF0324 family inner membrane protein	_____________231___________________________261\n_____________\|_____________________________\|\n5'-CAC...ACAUC_____CUG___________UCCG______GCCCU...GUG-3'\n______________GUACA___UGGCAUUUUAU____GGGUUA\n______________\|\|\|\|\|___\|:\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\|\n______________CAUGU___AUCGUAAAAUA____CCCAAU\n3'-UUU...AGGAC_____CG______________________ACAAA...UCG-5'\n_____________\|_____________________________\|\n_____________36____________________________11\n	244 -- 250	18 -- 24	-22.9966 kcal/mol	8.07046 kcal/mol	1.45491 kcal/mol	231 261@LB@ \| \|@LB@5'-CAC...ACAUC CUG UCCG GCCCU...GUG-3'@LB@ GUACA UGGCAUUUUAU GGGUUA@LB@ \|\|\|\|\| \|:\|\|\|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ CAUGU AUCGUAAAAUA CCCAAU@LB@3'-UUU...AGGAC CG ACAAA...UCG-5'@LB@ \| \|@LB@ 36 11@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -22.9966 kcal/mol@LB@Unfolding Energy - mRNA 8.07046 kcal/mol@LB@Unfolding Energy - sRNA 1.45491 kcal/mol@LB@@LB@Position - mRNA 232 -- 260@LB@Position - sRNA 12 -- 35@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 18 -- 24@LB@
39	0.0008004	0.06626	b1533	eamA	-12.23	0.058236	233 -- 264	16 -- 49	cysteine and O-acetyl-L-serine efflux system	_____________232_________________________________265\n_____________\|___________________________________\|\n5'-GUU...CUACU__UA_____CGUA___G_______A__________UCAUC...UGA-3'\n______________GG__GUGGU____UGG___GGCUA__AUUUUGUGG\n______________\|\|__\|\|\|\|\|____\|\|\|___:\|\|\|\|__\|\|\|\|\|:\|\|\|\n______________CC__CACCA____ACC___UCGAU__UAAAAUACC\n3'-UUU...CGAUU__UC_____AGG____AUG_____CG_________CAAUA...UCG-5'\n_____________\|___________________________________\|\n_____________50__________________________________15\n	258 -- 264	16 -- 22	-27.5137 kcal/mol	10.7081 kcal/mol	4.57266 kcal/mol	232 265@LB@ \| \|@LB@5'-GUU...CUACU UA CGUA G A UCAUC...UGA-3'@LB@ GG GUGGU UGG GGCUA AUUUUGUGG@LB@ \|\| \|\|\|\|\| \|\|\| :\|\|\|\| \|\|\|\|\|:\|\|\|@LB@ CC CACCA ACC UCGAU UAAAAUACC@LB@3'-UUU...CGAUU UC AGG AUG CG CAAUA...UCG-5'@LB@ \| \|@LB@ 50 15@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -27.5137 kcal/mol@LB@Unfolding Energy - mRNA 10.7081 kcal/mol@LB@Unfolding Energy - sRNA 4.57266 kcal/mol@LB@@LB@Position - mRNA 233 -- 264@LB@Position - sRNA 16 -- 49@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
168	0.00897	0.1795	b3139	agaC	-13.68	0.025868	233 -- 273	1 -- 39	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________232________________________________________274\n_____________\|__________________________________________\|\n5'-AAC...UUAUC_____CG_________U___GUUC____GAU__A________UGGAA...CGA-3'\n______________CCUGG__GC_GUUAGU_UUU____UGGG___UG_UUUUUGGC\n______________\|\|\|\|\|__:\|_\|:\|\|\|:_\|\|\|____\|\|\|\|___\|\|_\|\|\|\|::\|\|\n______________GGACC__UG_CGAUCG_AAA____ACCC___AC_AAAAGUCG\n3'-UUU...ACCAA_____A___U______U___AU______AAU__A________-5'\n_____________\|_________________________________________\|\n_____________40________________________________________1\n	267 -- 273	1 -- 7	-31.3276 kcal/mol	13.0397 kcal/mol	4.60651 kcal/mol	232 274@LB@ \| \|@LB@5'-AAC...UUAUC CG U GUUC GAU A UGGAA...CGA-3'@LB@ CCUGG GC GUUAGU UUU UGGG UG UUUUUGGC@LB@ \|\|\|\|\| :\| \|:\|\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|::\|\|@LB@ GGACC UG CGAUCG AAA ACCC AC AAAAGUCG@LB@3'-UUU...ACCAA A U U AU AAU A -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -13.68 kcal/mol@LB@Hybridization Energy -31.3276 kcal/mol@LB@Unfolding Energy - mRNA 13.0397 kcal/mol@LB@Unfolding Energy - sRNA 4.60651 kcal/mol@LB@@LB@Position - mRNA 233 -- 273@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
133	0.005817	0.146	b3461	rpoH	-7.67	0.391921	235 -- 243	24 -- 32	RNA polymerase sigma 32 (sigma H) factor	_____________234_______244\n_____________\|_________\|\n5'-GGA...AGCCC_________ACCUG...AGG-3'\n______________CAGUUGGCA\n______________\|\|\|:\|:\|\|\|\n______________GUCGAUCGU\n3'-UUU...ACCAU_________AAAAU...UCG-5'\n_____________\|_________\|\n_____________33________23\n	237 -- 243	24 -- 30	-13.04 kcal/mol	3.94405 kcal/mol	1.424 kcal/mol	234 244@LB@ \| \|@LB@5'-GGA...AGCCC ACCUG...AGG-3'@LB@ CAGUUGGCA@LB@ \|\|\|:\|:\|\|\|@LB@ GUCGAUCGU@LB@3'-UUU...ACCAU AAAAU...UCG-5'@LB@ \| \|@LB@ 33 23@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 3.94405 kcal/mol@LB@Unfolding Energy - sRNA 1.424 kcal/mol@LB@@LB@Position - mRNA 235 -- 243@LB@Position - sRNA 24 -- 32@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 24 -- 30@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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