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
151	0.01442	0.3104	b1395	paaH	-15.43	0.013105	189 -- 216	8 -- 31	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________188__________________________217\n_____________\|____________________________\|\n5'-GGC...GUUCA______AAUA_C________________AAACU...UGU-3'\n______________CGGGGA____G_AUGAUGAUAAAUGUGC\n______________\|:\|\|\|\|____\|_\|\|\|\|\|:\|:\|\|\|\|\|:\|\|\n______________GUCCCU____C_UACUAUUGUUUACGCG\n3'-UUU...CUUAA______A_____________________CAGAAAG-5'\n_____________\|____________________________\|\n_____________32___________________________7\n	210 -- 216	8 -- 14	-28.6523 kcal/mol	5.47369 kcal/mol	7.74551 kcal/mol	188 217@LB@ \| \|@LB@5'-GGC...GUUCA AAUA C AAACU...UGU-3'@LB@ CGGGGA G AUGAUGAUAAAUGUGC@LB@ \|:\|\|\|\| \| \|\|\|\|\|:\|:\|\|\|\|\|:\|\|@LB@ GUCCCU C UACUAUUGUUUACGCG@LB@3'-UUU...CUUAA A CAGAAAG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -28.6523 kcal/mol@LB@Unfolding Energy - mRNA 5.47369 kcal/mol@LB@Unfolding Energy - sRNA 7.74551 kcal/mol@LB@@LB@Position - mRNA 189 -- 216@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 8 -- 14@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@
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@
154	0.01456	0.3104	b2048	cpsG	-9.02	0.175967	42 -- 71	4 -- 44	phosphomannomutase	_____________41________________________________________72\n_____________\|_________________________________________\|\n5'-GGG...GGCUC___________GA___________UG_______________CGCGG...GCG-3'\n______________UUAUCUC_GAA_____GGAUGAUG_________GUGCGUUU\n______________\|:\|\|\|\|\|_\|\|\|_____\|\|\|\|\|\|\|\|_________\|:\|\|\|\|:\|\n______________AGUAGAG_CUU_____CCUACUAC_________CGCGCAGA\n3'-UUU...UUUAA_______A___AAGUC________UAUUGUUUA________AAG-5'\n_____________\|_________________________________________\|\n_____________45________________________________________3\n	65 -- 71	4 -- 10	-28.9111 kcal/mol	10.4373 kcal/mol	9.45546 kcal/mol	41 72@LB@ \| \|@LB@5'-GGG...GGCUC GA UG CGCGG...GCG-3'@LB@ UUAUCUC GAA GGAUGAUG GUGCGUUU@LB@ \|:\|\|\|\|\| \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|:\|@LB@ AGUAGAG CUU CCUACUAC CGCGCAGA@LB@3'-UUU...UUUAA A AAGUC UAUUGUUUA AAG-5'@LB@ \| \|@LB@ 45 3@LB@@LB@@LB@Energy -9.02 kcal/mol@LB@Hybridization Energy -28.9111 kcal/mol@LB@Unfolding Energy - mRNA 10.4373 kcal/mol@LB@Unfolding Energy - sRNA 9.45546 kcal/mol@LB@@LB@Position - mRNA 42 -- 71@LB@Position - sRNA 4 -- 44@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 4 -- 10@LB@
155	0.0146	0.3104	b2614	grpE	-10.46	0.101070	105 -- 125	1 -- 22	heat shock protein	_____________104____________________126\n_____________\|______________________\|\n5'-GAG...AAGAU______________A__GC___CCUUG...CUG-3'\n______________UGAUGACAA_UGUG_GU__UUC\n______________\|\|\|\|:\|\|\|\|_\|\|:\|_\|\|__\|\|\|\n______________ACUAUUGUU_ACGC_CA__AAG\n3'-UUU...CUACU_________U____G__GA___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	107 -- 113	14 -- 20	-17.1017 kcal/mol	5.37697 kcal/mol	1.25963 kcal/mol	104 126@LB@ \| \|@LB@5'-GAG...AAGAU A GC CCUUG...CUG-3'@LB@ UGAUGACAA UGUG GU UUC@LB@ \|\|\|\|:\|\|\|\| \|\|:\| \|\| \|\|\|@LB@ ACUAUUGUU ACGC CA AAG@LB@3'-UUU...CUACU U G GA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.46 kcal/mol@LB@Hybridization Energy -17.1017 kcal/mol@LB@Unfolding Energy - mRNA 5.37697 kcal/mol@LB@Unfolding Energy - sRNA 1.25963 kcal/mol@LB@@LB@Position - mRNA 105 -- 125@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 107 -- 113@LB@Position Seed - sRNA 14 -- 20@LB@
156	0.01464	0.3104	b4105	phnD	-8.45	0.216438	196 -- 209	4 -- 18	phosphonate ABC transporter periplasmic binding protein	_____________195_____________210\n_____________\|_______________\|\n5'-CCG...AGGAA________AA_____AAGAU...UGA-3'\n______________AACGAAUG__CG_CU\n______________\|\|\|:\|\|\|\|__\|\|_\|\|\n______________UUGUUUAC__GC_GA\n3'-UUU...UACUA________GC__A__AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	197 -- 203	11 -- 17	-10.9184 kcal/mol	1.23392 kcal/mol	1.22995 kcal/mol	195 210@LB@ \| \|@LB@5'-CCG...AGGAA AA AAGAU...UGA-3'@LB@ AACGAAUG CG CU@LB@ \|\|\|:\|\|\|\| \|\| \|\|@LB@ UUGUUUAC GC GA@LB@3'-UUU...UACUA GC A AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -8.45 kcal/mol@LB@Hybridization Energy -10.9184 kcal/mol@LB@Unfolding Energy - mRNA 1.23392 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 196 -- 209@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 197 -- 203@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@
158	0.01496	0.3104	b4278	insG	-10.00	0.121023	32 -- 48	3 -- 20	IS4 transposase	_____________31_________________49\n_____________\|__________________\|\n5'-GUU...UCCAC________A_________GUUAC...CUC-3'\n______________AUAACAAA__CGCGUUUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAUUGUUU__GCGCAGAA\n3'-UUU...ACUAC________AC________AG-5'\n_____________\|__________________\|\n_____________21_________________2\n	42 -- 48	3 -- 9	-15.3953 kcal/mol	4.13684 kcal/mol	1.25547 kcal/mol	31 49@LB@ \| \|@LB@5'-GUU...UCCAC A GUUAC...CUC-3'@LB@ AUAACAAA CGCGUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAUUGUUU GCGCAGAA@LB@3'-UUU...ACUAC AC AG-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -15.3953 kcal/mol@LB@Unfolding Energy - mRNA 4.13684 kcal/mol@LB@Unfolding Energy - sRNA 1.25547 kcal/mol@LB@@LB@Position - mRNA 32 -- 48@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 3 -- 9@LB@
159	0.01499	0.3104	b2476	purC	-11.66	0.062723	28 -- 49	4 -- 22	phosphoribosylaminoimidazole-succinocarboxamide synthetase	_____________27_____________________50\n_____________\|______________________\|\n5'-GGA...UGAUA_____C____AC__________GCAGG...CAG-3'\n______________UGAUA_GCAA__GUGUGCGUCU\n______________\|\|\|\|\|_:\|\|\|__:\|\|:\|\|\|\|\|\|\n______________ACUAU_UGUU__UACGCGCAGA\n3'-UUU...CUACU______________________AAG-5'\n_____________\|______________________\|\n_____________23_____________________3\n	43 -- 49	4 -- 10	-20.6907 kcal/mol	7.77162 kcal/mol	1.2572 kcal/mol	27 50@LB@ \| \|@LB@5'-GGA...UGAUA C AC GCAGG...CAG-3'@LB@ UGAUA GCAA GUGUGCGUCU@LB@ \|\|\|\|\| :\|\|\| :\|\|:\|\|\|\|\|\|@LB@ ACUAU UGUU UACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -20.6907 kcal/mol@LB@Unfolding Energy - mRNA 7.77162 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 28 -- 49@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 4 -- 10@LB@
160	0.015	0.3104	b2022	hisB	-11.12	0.077869	165 -- 171	5 -- 11	histidinol-phosphatase and imidazoleglycerol-phosphate dehydratase	_____________164_____172\n_____________\|_______\|\n5'-CAG...AGCCA_______AUUGA...AAC-3'\n______________GCGCGUC\n______________\|\|\|\|\|\|\|\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	165 -- 171	5 -- 11	-14.7431 kcal/mol	2.50821 kcal/mol	1.11145 kcal/mol	164 172@LB@ \| \|@LB@5'-CAG...AGCCA AUUGA...AAC-3'@LB@ GCGCGUC@LB@ \|\|\|\|\|\|\|@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.12 kcal/mol@LB@Hybridization Energy -14.7431 kcal/mol@LB@Unfolding Energy - mRNA 2.50821 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 165 -- 171@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 5 -- 11@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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