Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase	_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
116	0.01184	0.3104	b1218	chaC	-12.45	0.045440	10 -- 29	8 -- 30	cation transport regulator	_____________9_______________________30\n_____________\|_______________________\|\n5'-AUA...GCCAA_______________________AUAAA...CGC-3'\n______________AGGG__GAUGAUGAUAAAUG_GC\n______________\|\|\|\|__\|\|\|\|\|\|:\|:\|\|\|\|\|_\|\|\n______________UCCC__CUACUAUUGUUUAC_CG\n3'-UUU...UUAAG____UA______________G__CAGAAAG-5'\n_____________\|_______________________\|\n_____________31______________________7\n	21 -- 27	11 -- 17	-25.0616 kcal/mol	5.19055 kcal/mol	7.41684 kcal/mol	9 30@LB@ \| \|@LB@5'-AUA...GCCAA AUAAA...CGC-3'@LB@ AGGG GAUGAUGAUAAAUG GC@LB@ \|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|\| \|\|@LB@ UCCC CUACUAUUGUUUAC CG@LB@3'-UUU...UUAAG UA G CAGAAAG-5'@LB@ \| \|@LB@ 31 7@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -25.0616 kcal/mol@LB@Unfolding Energy - mRNA 5.19055 kcal/mol@LB@Unfolding Energy - sRNA 7.41684 kcal/mol@LB@@LB@Position - mRNA 10 -- 29@LB@Position - sRNA 8 -- 30@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 11 -- 17@LB@
157	0.01467	0.3104	b0906	ycaP	-12.44	0.045773	54 -- 69	5 -- 18	UPF0702 family putative inner membrane protein	_____________53_______________70\n_____________\|________________\|\n5'-AGU...CCGGG_________UU_____AUGAA...UCU-3'\n______________GAUAAAUGU__GCGUC\n______________:\|:\|\|\|\|\|:__\|\|\|\|\|\n______________UUGUUUACG__CGCAG\n3'-UUU...UACUA________________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	56 -- 62	10 -- 16	-16.0437 kcal/mol	2.38303 kcal/mol	1.2243 kcal/mol	53 70@LB@ \| \|@LB@5'-AGU...CCGGG UU AUGAA...UCU-3'@LB@ GAUAAAUGU GCGUC@LB@ :\|:\|\|\|\|\|: \|\|\|\|\|@LB@ UUGUUUACG CGCAG@LB@3'-UUU...UACUA AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -16.0437 kcal/mol@LB@Unfolding Energy - mRNA 2.38303 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 54 -- 69@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 10 -- 16@LB@
153	0.0145	0.3104	b3866	yihI	-12.31	0.048207	234 -- 252	5 -- 21	activator of Der GTPase	_____________233_________________253\n_____________\|___________________\|\n5'-GAA...GCAAA___CAU_____A_______GAAAA...GUC-3'\n______________GGU___GCAAA_GCGCGUC\n______________\|:\|___:\|\|\|\|_\|\|\|\|\|\|\|\n______________CUA___UGUUU_CGCGCAG\n3'-UUU...UACUA___U_______A_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	246 -- 252	5 -- 11	-18.8767 kcal/mol	5.31745 kcal/mol	1.24955 kcal/mol	233 253@LB@ \| \|@LB@5'-GAA...GCAAA CAU A GAAAA...GUC-3'@LB@ GGU GCAAA GCGCGUC@LB@ \|:\| :\|\|\|\| \|\|\|\|\|\|\|@LB@ CUA UGUUU CGCGCAG@LB@3'-UUU...UACUA U A AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.31 kcal/mol@LB@Hybridization Energy -18.8767 kcal/mol@LB@Unfolding Energy - mRNA 5.31745 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 234 -- 252@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 5 -- 11@LB@
12	0.0003263	0.08948	b4036	lamB	-12.21	0.050157	189 -- 218	8 -- 32	maltose outer membrane porin (maltoporin)	_____________188____________________________219\n_____________\|______________________________\|\n5'-CGC...AUGAC_____A___A_A________UACUC_____AAACU...GUU-3'\n______________UCAGG_GAU_G_AUGAUGAU_____UGCGC\n______________\|\|\|\|\|_\|\|\|_\|_\|\|\|\|\|:\|:_____\|\|\|\|\|\n______________AGUCC_CUA_C_UACUAUUG_____ACGCG\n3'-UUU...ACUUA____________________UUU_______CAGAAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________7\n	202 -- 208	16 -- 22	-24.7132 kcal/mol	4.6775 kcal/mol	7.82314 kcal/mol	188 219@LB@ \| \|@LB@5'-CGC...AUGAC A A A UACUC AAACU...GUU-3'@LB@ UCAGG GAU G AUGAUGAU UGCGC@LB@ \|\|\|\|\| \|\|\| \| \|\|\|\|\|:\|: \|\|\|\|\|@LB@ AGUCC CUA C UACUAUUG ACGCG@LB@3'-UUU...ACUUA UUU CAGAAAG-5'@LB@ \| \|@LB@ 33 7@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.7132 kcal/mol@LB@Unfolding Energy - mRNA 4.6775 kcal/mol@LB@Unfolding Energy - sRNA 7.82314 kcal/mol@LB@@LB@Position - mRNA 189 -- 218@LB@Position - sRNA 8 -- 32@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 16 -- 22@LB@
152	0.01445	0.3104	b0385	yaiC	-12.21	0.050169	39 -- 67	12 -- 42	diguanylate cyclase cellulose regualtor	_____________38_______________________________68\n_____________\|________________________________\|\n5'-CAA...CAACA_______________U______C_________UUAUG...CCG-3'\n______________AUCUCUGAA___AGG_GAUGAU_GUAAUAAGU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|_\|\|\|\|\|\|_:\|\|\|:\|\|:\|\n______________UAGAGACUU___UCC_CUACUA_UAUUGUUUA\n3'-UUU...UAAAG_________AAG__________C_________CGCGC...AAG-5'\n_____________\|________________________________\|\n_____________43_______________________________11\n	40 -- 46	35 -- 41	-28.8147 kcal/mol	7.19368 kcal/mol	9.40905 kcal/mol	38 68@LB@ \| \|@LB@5'-CAA...CAACA U C UUAUG...CCG-3'@LB@ AUCUCUGAA AGG GAUGAU GUAAUAAGU@LB@ \|\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|\|\| :\|\|\|:\|\|:\|@LB@ UAGAGACUU UCC CUACUA UAUUGUUUA@LB@3'-UUU...UAAAG AAG C CGCGC...AAG-5'@LB@ \| \|@LB@ 43 11@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -28.8147 kcal/mol@LB@Unfolding Energy - mRNA 7.19368 kcal/mol@LB@Unfolding Energy - sRNA 9.40905 kcal/mol@LB@@LB@Position - mRNA 39 -- 67@LB@Position - sRNA 12 -- 42@LB@Position Seed - mRNA 40 -- 46@LB@Position Seed - sRNA 35 -- 41@LB@
58	0.00518	0.3024	b4068	yjcH	-12.19	0.050580	228 -- 240	8 -- 21	DUF485 family inner membrane protein	_____________227____________241\n_____________\|______________\|\n5'-ACC...GGAUA__A___________AUUUC...UGC-3'\n______________GA_GAC_AAUGCGC\n______________\|\|_:\|\|_\|\|\|\|\|\|\|\n______________CU_UUG_UUACGCG\n3'-UUU...UACUA__A___U_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	234 -- 240	8 -- 14	-14.481 kcal/mol	1.05266 kcal/mol	1.23638 kcal/mol	227 241@LB@ \| \|@LB@5'-ACC...GGAUA A AUUUC...UGC-3'@LB@ GA GAC AAUGCGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|@LB@ CU UUG UUACGCG@LB@3'-UUU...UACUA A U CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -12.19 kcal/mol@LB@Hybridization Energy -14.481 kcal/mol@LB@Unfolding Energy - mRNA 1.05266 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 228 -- 240@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 8 -- 14@LB@
165	0.01591	0.3104	b4393	trpR	-12.13	0.051953	230 -- 246	5 -- 21	transcriptional repressor tryptophan-binding	_____________229_______________247\n_____________\|_________________\|\n5'-GAG...GCAGC_________ACA_____ACCAG...AUC-3'\n______________GAUGGCAGA___GCGUC\n______________\|\|\|::\|\|:\|___\|\|\|\|\|\n______________CUAUUGUUU___CGCAG\n3'-UUU...UACUA_________ACG_____AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	232 -- 238	13 -- 19	-18.7652 kcal/mol	5.38929 kcal/mol	1.24955 kcal/mol	229 247@LB@ \| \|@LB@5'-GAG...GCAGC ACA ACCAG...AUC-3'@LB@ GAUGGCAGA GCGUC@LB@ \|\|\|::\|\|:\| \|\|\|\|\|@LB@ CUAUUGUUU CGCAG@LB@3'-UUU...UACUA ACG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.7652 kcal/mol@LB@Unfolding Energy - mRNA 5.38929 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 230 -- 246@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 13 -- 19@LB@
85	0.008151	0.3104	b0914	msbA	-12.09	0.052799	181 -- 198	1 -- 18	lipid ABC transporter permease/ATPase	_____________180________________199\n_____________\|__________________\|\n5'-AGC...AUUUC_________UG_______GAAUG...CGU-3'\n______________AACAAAUGC__GUUUUUU\n______________\|\|\|\|\|\|\|\|\|__\|\|:\|\|\|:\n______________UUGUUUACG__CAGAAAG\n3'-UUU...UACUA_________CG_______-5'\n_____________\|_________________\|\n_____________19________________1\n	192 -- 198	1 -- 7	-16.7201 kcal/mol	3.39277 kcal/mol	1.24077 kcal/mol	180 199@LB@ \| \|@LB@5'-AGC...AUUUC UG GAAUG...CGU-3'@LB@ AACAAAUGC GUUUUUU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ UUGUUUACG CAGAAAG@LB@3'-UUU...UACUA CG -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -16.7201 kcal/mol@LB@Unfolding Energy - mRNA 3.39277 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 1 -- 7@LB@
15	0.000461	0.102	b2140	dusC	-12.07	0.053129	194 -- 211	3 -- 22	tRNA-dihydrouridine synthase C	_____________193__________________212\n_____________\|____________________\|\n5'-AAU...GCGGG_________________G__ACUGG...UUG-3'\n______________UGAUGAU__AUGCGUGU_UU\n______________\|\|\|\|:\|:__\|\|\|\|\|:\|\|_\|\|\n______________ACUAUUG__UACGCGCA_AA\n3'-UUU...CUACU_______UU________G__AG-5'\n_____________\|____________________\|\n_____________23___________________2\n	202 -- 208	6 -- 12	-18.0697 kcal/mol	4.73944 kcal/mol	1.259 kcal/mol	193 212@LB@ \| \|@LB@5'-AAU...GCGGG G ACUGG...UUG-3'@LB@ UGAUGAU AUGCGUGU UU@LB@ \|\|\|\|:\|: \|\|\|\|\|:\|\| \|\|@LB@ ACUAUUG UACGCGCA AA@LB@3'-UUU...CUACU UU G AG-5'@LB@ \| \|@LB@ 23 2@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -18.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.73944 kcal/mol@LB@Unfolding Energy - sRNA 1.259 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 3 -- 22@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@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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