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	Additional homologs
129	0.005449	0.142	b2502	ppx	-11.35	0.090652	145 -- 164	17 -- 36	exopolyphosphatase		_____________144__________________165\n_____________\|____________________\|\n5'-GGC...GUACG__C__________A______ACUAC...GUG-3'\n______________GG_GCAGUUGGCG_UUUAUG\n______________\|\|_:\|\|\|:\|:\|\|:_\|\|\|\|\|\|\n______________CC_UGUCGAUCGU_AAAUAC\n3'-UUU...AAGGA__A__________A______CCAAU...UCG-5'\n_____________\|____________________\|\n_____________37___________________16\n	151 -- 157	24 -- 30	-21.6291 kcal/mol	8.82633 kcal/mol	1.44969 kcal/mol	144 165@LB@ \| \|@LB@5'-GGC...GUACG C A ACUAC...GUG-3'@LB@ GG GCAGUUGGCG UUUAUG@LB@ \|\| :\|\|\|:\|:\|\|: \|\|\|\|\|\|@LB@ CC UGUCGAUCGU AAAUAC@LB@3'-UUU...AAGGA A A CCAAU...UCG-5'@LB@ \| \|@LB@ 37 16@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -21.6291 kcal/mol@LB@Unfolding Energy - mRNA 8.82633 kcal/mol@LB@Unfolding Energy - sRNA 1.44969 kcal/mol@LB@@LB@Position - mRNA 145 -- 164@LB@Position - sRNA 17 -- 36@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 24 -- 30@LB@
82	0.002694	0.1082	b2474	tmcA	-11.34	0.091143	115 -- 147	1 -- 34	elongator methionine tRNA (ac4C34) acetyltransferase		_____________114________________________________148\n_____________\|__________________________________\|\n5'-GAU...AACGC__________UUAAACGU____UCGACAG_____GAUCC...UUG-3'\n______________UACAGCUGGU________GGUU________CGGC\n______________\|\|\|\|\|\|\|:\|:________\|\|\|\|________\|:\|\|\n______________AUGUCGAUCG________CCAA________GUCG\n3'-UUU...GGACC__________UAAAAUAC____UACAAAAA____-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	118 -- 124	25 -- 31	-23.7384 kcal/mol	10.9014 kcal/mol	1.49507 kcal/mol	114 148@LB@ \| \|@LB@5'-GAU...AACGC UUAAACGU UCGACAG GAUCC...UUG-3'@LB@ UACAGCUGGU GGUU CGGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\| \|:\|\|@LB@ AUGUCGAUCG CCAA GUCG@LB@3'-UUU...GGACC UAAAAUAC UACAAAAA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -23.7384 kcal/mol@LB@Unfolding Energy - mRNA 10.9014 kcal/mol@LB@Unfolding Energy - sRNA 1.49507 kcal/mol@LB@@LB@Position - mRNA 115 -- 147@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 25 -- 31@LB@
136	0.005909	0.146	b1291	sapD	-11.34	0.091029	118 -- 151	12 -- 36	antimicrobial peptide ABC transporter ATPase		_____________117________________________________152\n_____________\|__________________________________\|\n5'-AUC...UGCCA________AAUUAUGAU______G____U_____ACCUC...GUG-3'\n______________GGUGCGGC_________UAGCGU_UUGU_GGUUA\n______________\|\|\|:\|:\|\|_________\|\|\|\|:\|_\|\|:\|_\|\|\|\|\|\n______________CCAUGUCG_________AUCGUA_AAUA_CCAAU\n3'-UUU...AAGGA_______________________A____C_____ACAAA...UCG-5'\n_____________\|__________________________________\|\n_____________37_________________________________11\n	119 -- 125	29 -- 35	-24.3443 kcal/mol	11.5428 kcal/mol	1.45699 kcal/mol	117 152@LB@ \| \|@LB@5'-AUC...UGCCA AAUUAUGAU G U ACCUC...GUG-3'@LB@ GGUGCGGC UAGCGU UUGU GGUUA@LB@ \|\|\|:\|:\|\| \|\|\|\|:\| \|\|:\| \|\|\|\|\|@LB@ CCAUGUCG AUCGUA AAUA CCAAU@LB@3'-UUU...AAGGA A C ACAAA...UCG-5'@LB@ \| \|@LB@ 37 11@LB@@LB@@LB@Energy -11.34 kcal/mol@LB@Hybridization Energy -24.3443 kcal/mol@LB@Unfolding Energy - mRNA 11.5428 kcal/mol@LB@Unfolding Energy - sRNA 1.45699 kcal/mol@LB@@LB@Position - mRNA 118 -- 151@LB@Position - sRNA 12 -- 36@LB@Position Seed - mRNA 119 -- 125@LB@Position Seed - sRNA 29 -- 35@LB@
150	0.00729	0.1634	b3184	yhbE	-11.29	0.093352	190 -- 235	1 -- 50	EamA family inner membrane putative transporter		_____________189_________________________________________________236\n_____________\|___________________________________________________\|\n5'-AAG...UUGCA____AUAC___A____AA_____A____GGCAU___CAUUC__________GCUCA...UGG-3'\n______________GGGA____GGU___UG__GCAGC_GGCA_____UGG________UUUUGGC\n______________:\|\|\|____\|\|\|___\|\|__:\|\|\|\|_:\|\|\|_____\|\|\|________\|\|\|::\|\|\n______________UCCU____CCA___AC__UGUCG_UCGU_____ACC________AAAGUCG\n3'-UUU...CCGAU____CCA____AGG__CA_____A____AAAAU___CAAUACAA_______-5'\n_____________\|__________________________________________________\|\n_____________51_________________________________________________1\n	229 -- 235	1 -- 7	-25.8939 kcal/mol	9.93833 kcal/mol	4.6634 kcal/mol	189 236@LB@ \| \|@LB@5'-AAG...UUGCA AUAC A AA A GGCAU CAUUC GCUCA...UGG-3'@LB@ GGGA GGU UG GCAGC GGCA UGG UUUUGGC@LB@ :\|\|\| \|\|\| \|\| :\|\|\|\| :\|\|\| \|\|\| \|\|\|::\|\|@LB@ UCCU CCA AC UGUCG UCGU ACC AAAGUCG@LB@3'-UUU...CCGAU CCA AGG CA A AAAAU CAAUACAA -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -11.29 kcal/mol@LB@Hybridization Energy -25.8939 kcal/mol@LB@Unfolding Energy - mRNA 9.93833 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 190 -- 235@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
174	0.009477	0.1831	b3186	rplU	-11.27	0.094314	2 -- 27	9 -- 34	50S ribosomal subunit protein L21		_____________1____________________________28\n_____________\|____________________________\|\n__________5'-U_________G_A_____A____GAU___ACUGA...UUG-3'\n______________UAUGGUUAG_A___UAU_GGGU___UGU\n______________\|\|::\|:\|\|\|_\|___\|\|\|_\|\|\|\|___\|\|\|\n______________AUGUCGAUC_U___AUA_CCCA___ACA\n3'-UUU...GGACC_________G_AAA________AU____AAAAGUCG-5'\n_____________\|____________________________\|\n_____________35___________________________8\n	4 -- 10	26 -- 32	-16.432 kcal/mol	3.67439 kcal/mol	1.48697 kcal/mol	1 28@LB@ \| \|@LB@ 5'-U G A A GAU ACUGA...UUG-3'@LB@ UAUGGUUAG A UAU GGGU UGU@LB@ \|\|::\|:\|\|\| \| \|\|\| \|\|\|\| \|\|\|@LB@ AUGUCGAUC U AUA CCCA ACA@LB@3'-UUU...GGACC G AAA AU AAAAGUCG-5'@LB@ \| \|@LB@ 35 8@LB@@LB@@LB@Energy -11.27 kcal/mol@LB@Hybridization Energy -16.432 kcal/mol@LB@Unfolding Energy - mRNA 3.67439 kcal/mol@LB@Unfolding Energy - sRNA 1.48697 kcal/mol@LB@@LB@Position - mRNA 2 -- 27@LB@Position - sRNA 9 -- 34@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 26 -- 32@LB@
147	0.006963	0.1592	b0723	sdhA	-11.23	0.096056	156 -- 186	10 -- 46	succinate dehydrogenase flavoprotein subunit		_____________155_______________________________________187\n_____________\|_________________________________________\|\n5'-GGU...GCACU________AC_____________A_______AUUC______GUGUG...GUG-3'\n______________GGUGGUUU____________GUG_UUUAUGG____GUUGUG\n______________\|\|\|\|\|\|\|:____________\|::_\|\|\|\|\|\|\|____\|\|\|:\|\|\n______________CCACCAAG____________CGU_AAAUACC____CAAUAC\n3'-UUU...UUCCU________GACCAUGUCGAU___A_________________AAAAA...UCG-5'\n_____________\|_________________________________________\|\n_____________47________________________________________9\n	170 -- 176	16 -- 22	-22.0315 kcal/mol	6.19365 kcal/mol	4.60552 kcal/mol	155 187@LB@ \| \|@LB@5'-GGU...GCACU AC A AUUC GUGUG...GUG-3'@LB@ GGUGGUUU GUG UUUAUGG GUUGUG@LB@ \|\|\|\|\|\|\|: \|:: \|\|\|\|\|\|\| \|\|\|:\|\|@LB@ CCACCAAG CGU AAAUACC CAAUAC@LB@3'-UUU...UUCCU GACCAUGUCGAU A AAAAA...UCG-5'@LB@ \| \|@LB@ 47 9@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -22.0315 kcal/mol@LB@Unfolding Energy - mRNA 6.19365 kcal/mol@LB@Unfolding Energy - sRNA 4.60552 kcal/mol@LB@@LB@Position - mRNA 156 -- 186@LB@Position - sRNA 10 -- 46@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 16 -- 22@LB@
188	0.01085	0.1919	b1878	flhE	-11.23	0.096033	252 -- 283	16 -- 51	proton seal during flagellar secretion		_____________251__________________________________284\n_____________\|____________________________________\|\n5'-CGU...CCGCC__________A__G___CA____A____GUG_____AAUUA...AUC-3'\n______________GGGGAGG_GG__U_UGG___GGC_AGUA___UA_GG\n______________::\|\|\|\|\|_\|\|__:_\|\|\|___:\|\|_\|\|:\|___\|\|_\|\|\n______________UUCCUCC_CC__G_ACC___UCG_UCGU___AU_CC\n3'-UUU...UCCGA_______A__AA_G___AUG___A____AAA__A__CAAUA...UCG-5'\n_____________\|____________________________________\|\n_____________52___________________________________15\n	252 -- 258	45 -- 51	-25.2373 kcal/mol	9.34808 kcal/mol	4.65624 kcal/mol	251 284@LB@ \| \|@LB@5'-CGU...CCGCC A G CA A GUG AAUUA...AUC-3'@LB@ GGGGAGG GG U UGG GGC AGUA UA GG@LB@ ::\|\|\|\|\| \|\| : \|\|\| :\|\| \|\|:\| \|\| \|\|@LB@ UUCCUCC CC G ACC UCG UCGU AU CC@LB@3'-UUU...UCCGA A AA G AUG A AAA A CAAUA...UCG-5'@LB@ \| \|@LB@ 52 15@LB@@LB@@LB@Energy -11.23 kcal/mol@LB@Hybridization Energy -25.2373 kcal/mol@LB@Unfolding Energy - mRNA 9.34808 kcal/mol@LB@Unfolding Energy - sRNA 4.65624 kcal/mol@LB@@LB@Position - mRNA 252 -- 283@LB@Position - sRNA 16 -- 51@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 45 -- 51@LB@
6	7.051e-06	0.00395	b1213	ychQ	-11.22	0.096653	74 -- 98	15 -- 40	SIRB family inner membrane protein		_____________73___________________________99\n_____________\|____________________________\|\n5'-GAC...UCUGC______AAC__________GCA______CGAAG...AUC-3'\n______________UUCUGG___AUGGCUGGCA______GGG\n______________\|:\|\|\|\|___\|::\|\|\|:\|\|\|______\|\|\|\n______________AGGACC___UGUCGAUCGU______CCC\n3'-UUU...CACCA______A____________AAAAUA___AAUAC...UCG-5'\n_____________\|____________________________\|\n_____________41___________________________14\n	86 -- 92	24 -- 30	-24.2509 kcal/mol	8.46179 kcal/mol	4.56973 kcal/mol	73 99@LB@ \| \|@LB@5'-GAC...UCUGC AAC GCA CGAAG...AUC-3'@LB@ UUCUGG AUGGCUGGCA GGG@LB@ \|:\|\|\|\| \|::\|\|\|:\|\|\| \|\|\|@LB@ AGGACC UGUCGAUCGU CCC@LB@3'-UUU...CACCA A AAAAUA AAUAC...UCG-5'@LB@ \| \|@LB@ 41 14@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -24.2509 kcal/mol@LB@Unfolding Energy - mRNA 8.46179 kcal/mol@LB@Unfolding Energy - sRNA 4.56973 kcal/mol@LB@@LB@Position - mRNA 74 -- 98@LB@Position - sRNA 15 -- 40@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 24 -- 30@LB@
80	0.002475	0.104	b2468	aegA	-11.19	0.098238	223 -- 245	11 -- 33	putative oxidoreductase FeS binding subunit/NAD/FAD-binding subunit		_____________222_____________________246\n_____________\|_______________________\|\n5'-UCU...GGCCA_____C____AUGUC________CAUGC...UGA-3'\n______________ACAGU_AGCA_____UGGGUUGU\n______________\|\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|:\|\n______________UGUCG_UCGU_____ACCCAAUA\n3'-UUU...GACCA_____A____AAAAU________CAAAA...UCG-5'\n_____________\|_______________________\|\n_____________34______________________10\n	239 -- 245	11 -- 17	-21.0997 kcal/mol	8.44489 kcal/mol	1.46958 kcal/mol	222 246@LB@ \| \|@LB@5'-UCU...GGCCA C AUGUC CAUGC...UGA-3'@LB@ ACAGU AGCA UGGGUUGU@LB@ \|\|\|\|: \|\|\|\| \|\|\|\|\|\|:\|@LB@ UGUCG UCGU ACCCAAUA@LB@3'-UUU...GACCA A AAAAU CAAAA...UCG-5'@LB@ \| \|@LB@ 34 10@LB@@LB@@LB@Energy -11.19 kcal/mol@LB@Hybridization Energy -21.0997 kcal/mol@LB@Unfolding Energy - mRNA 8.44489 kcal/mol@LB@Unfolding Energy - sRNA 1.46958 kcal/mol@LB@@LB@Position - mRNA 223 -- 245@LB@Position - sRNA 11 -- 33@LB@Position Seed - mRNA 239 -- 245@LB@Position Seed - sRNA 11 -- 17@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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