Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
180	0.007638	0.1495	b2007	yeeX	-12.65	0.022752	43 -- 93	41 -- 87	UPF0265 family protein	_____________42____________________________________________________94\n_____________\|_____________________________________________________\|\n5'-AUC...CUUCA______UCU______C___UUC_______C______UAAAG____U_______AAAAG...AAA-3'\n______________GAAUCA____UGCUG_UGC___GAUUCAG__AAGGA_____GGUA_GAUAGUG\n______________\|\|\|\|\|\|____\|\|\|\|:_\|\|\|___:\|\|\|\|\|:__\|\|\|\|\|_____:\|\|\|_\|\|:\|:\|:\n______________CUUAGU____ACGAU_ACG___UUAAGUU__UUCCU_____UCAU_CUGUUAU\n3'-UUU...GCAUG______UAAC_________UCA_______UU______________U_______ACCUC...ACG-5'\n_____________\|_____________________________________________________\|\n_____________88____________________________________________________40\n	87 -- 93	41 -- 47	-32.6236 kcal/mol	14.1148 kcal/mol	5.85929 kcal/mol	42 94@LB@ \| \|@LB@5'-AUC...CUUCA UCU C UUC C UAAAG U AAAAG...AAA-3'@LB@ GAAUCA UGCUG UGC GAUUCAG AAGGA GGUA GAUAGUG@LB@ \|\|\|\|\|\| \|\|\|\|: \|\|\| :\|\|\|\|\|: \|\|\|\|\| :\|\|\| \|\|:\|:\|:@LB@ CUUAGU ACGAU ACG UUAAGUU UUCCU UCAU CUGUUAU@LB@3'-UUU...GCAUG UAAC UCA UU U ACCUC...ACG-5'@LB@ \| \|@LB@ 88 40@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -32.6236 kcal/mol@LB@Unfolding Energy - mRNA 14.1148 kcal/mol@LB@Unfolding Energy - sRNA 5.85929 kcal/mol@LB@@LB@Position - mRNA 43 -- 93@LB@Position - sRNA 41 -- 87@LB@Position Seed - mRNA 87 -- 93@LB@Position Seed - sRNA 41 -- 47@LB@
192	0.008587	0.1548	b2366	dsdA	-12.64	0.022913	191 -- 232	21 -- 49	D-serine dehydratase	_____________190________________________________________233\n_____________\|__________________________________________\|\n5'-AUU...GCAAA______UAC______AAA___UAAAAUGAACU__________CCAGU...CCU-3'\n______________GAGACG___UAUGGA___CGC___________CGCUCAUCGC\n______________:\|\|\|\|:___\|\|\|\|\|\|___\|\|\|___________\|\|\|:\|\|\|\|\|\|\n______________UUCUGU___AUACCU___GCG___________GCGGGUAGCG\n3'-UUU...CUUCA______U________C_____UU___________________AACUG...ACG-5'\n_____________\|__________________________________________\|\n_____________50_________________________________________20\n	226 -- 232	21 -- 27	-32.1247 kcal/mol	5.89431 kcal/mol	13.5917 kcal/mol	190 233@LB@ \| \|@LB@5'-AUU...GCAAA UAC AAA UAAAAUGAACU CCAGU...CCU-3'@LB@ GAGACG UAUGGA CGC CGCUCAUCGC@LB@ :\|\|\|\|: \|\|\|\|\|\| \|\|\| \|\|\|:\|\|\|\|\|\|@LB@ UUCUGU AUACCU GCG GCGGGUAGCG@LB@3'-UUU...CUUCA U C UU AACUG...ACG-5'@LB@ \| \|@LB@ 50 20@LB@@LB@@LB@Energy -12.64 kcal/mol@LB@Hybridization Energy -32.1247 kcal/mol@LB@Unfolding Energy - mRNA 5.89431 kcal/mol@LB@Unfolding Energy - sRNA 13.5917 kcal/mol@LB@@LB@Position - mRNA 191 -- 232@LB@Position - sRNA 21 -- 49@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 21 -- 27@LB@
33	0.0002072	0.02212	b2101	yegW	-12.62	0.023301	188 -- 205	37 -- 56	putative DNA-binding transcriptional regulator	_____________187__________________206\n_____________\|____________________\|\n5'-CGG...CCGGC_____A______________ACAAG...AAA-3'\n______________AGGAA__AAGACAA_AUGGA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UCCUU__UUCUGUU_UACCU\n3'-UUU...UUUUU_____CA_______A_____CGCGU...ACG-5'\n_____________\|____________________\|\n_____________57___________________36\n	194 -- 200	43 -- 49	-17.4469 kcal/mol	1.13054 kcal/mol	3.6645 kcal/mol	187 206@LB@ \| \|@LB@5'-CGG...CCGGC A ACAAG...AAA-3'@LB@ AGGAA AAGACAA AUGGA@LB@ \|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UCCUU UUCUGUU UACCU@LB@3'-UUU...UUUUU CA A CGCGU...ACG-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -12.62 kcal/mol@LB@Hybridization Energy -17.4469 kcal/mol@LB@Unfolding Energy - mRNA 1.13054 kcal/mol@LB@Unfolding Energy - sRNA 3.6645 kcal/mol@LB@@LB@Position - mRNA 188 -- 205@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 43 -- 49@LB@
29	0.0001601	0.01945	b3472	dcrB	-12.60	0.023536	186 -- 203	41 -- 59	putative lipoprotein	_____________185_________________204\n_____________\|___________________\|\n5'-UGG...UUAUC_____________U_____CGCAA...UCG-3'\n______________GAAAGGAAG_AAG_CAAUG\n______________:\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|\|:\n______________UUUUCCUUC_UUC_GUUAU\n3'-UUU...AAGUU_________A___U_____ACCUC...ACG-5'\n_____________\|___________________\|\n_____________60__________________40\n	188 -- 194	51 -- 57	-16.362 kcal/mol	1.80431 kcal/mol	1.95655 kcal/mol	185 204@LB@ \| \|@LB@5'-UGG...UUAUC U CGCAA...UCG-3'@LB@ GAAAGGAAG AAG CAAUG@LB@ :\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:@LB@ UUUUCCUUC UUC GUUAU@LB@3'-UUU...AAGUU A U ACCUC...ACG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.362 kcal/mol@LB@Unfolding Energy - mRNA 1.80431 kcal/mol@LB@Unfolding Energy - sRNA 1.95655 kcal/mol@LB@@LB@Position - mRNA 186 -- 203@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 51 -- 57@LB@
48	0.0005049	0.03706	b2331	smrB	-12.55	0.024312	152 -- 200	43 -- 92	putative DNA endonuclease	_____________151__________________________________________________201\n_____________\|____________________________________________________\|\n5'-UCA...GAUUG__C__________GUAAAC_______GAAAA_______UA___AC_______AUGAA...GAC-3'\n______________CG_UACGAGUCGG________UGUAG_____UUAGAAA__GAG___AGAUAA\n______________\|\|_\|\|\|\|\|:\|\|::________\|\|:\|\|_____\|:\|:\|\|\|__\|\|:___\|\|\|:\|\|\n______________GC_AUGCUUAGUU________ACGUC_____AGUUUUU__CUU___UCUGUU\n3'-UUU...CCGCA_____________AACACGAU_____AUUA________UC___CAU______AUACC...ACG-5'\n_____________\|____________________________________________________\|\n_____________93___________________________________________________42\n	158 -- 164	81 -- 87	-25.319 kcal/mol	6.91043 kcal/mol	5.86211 kcal/mol	151 201@LB@ \| \|@LB@5'-UCA...GAUUG C GUAAAC GAAAA UA AC AUGAA...GAC-3'@LB@ CG UACGAGUCGG UGUAG UUAGAAA GAG AGAUAA@LB@ \|\| \|\|\|\|\|:\|\|:: \|\|:\|\| \|:\|:\|\|\| \|\|: \|\|\|:\|\|@LB@ GC AUGCUUAGUU ACGUC AGUUUUU CUU UCUGUU@LB@3'-UUU...CCGCA AACACGAU AUUA UC CAU AUACC...ACG-5'@LB@ \| \|@LB@ 93 42@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -25.319 kcal/mol@LB@Unfolding Energy - mRNA 6.91043 kcal/mol@LB@Unfolding Energy - sRNA 5.86211 kcal/mol@LB@@LB@Position - mRNA 152 -- 200@LB@Position - sRNA 43 -- 92@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 81 -- 87@LB@
67	0.00114	0.05992	b4141	yjeH	-12.53	0.024616	129 -- 146	73 -- 89	putative transporter	_____________128________________147\n_____________\|__________________\|\n5'-CAG...CAUAA_______U__________CCAUC...CUG-3'\n______________GCGAAUC_GAUUGUGCUA\n______________:\|\|\|\|\|\|_:\|\|\|\|\|\|\|\|\|\n______________UGCUUAG_UUAACACGAU\n3'-UUU...CAGCA__________________ACGUC...ACG-5'\n_____________\|__________________\|\n_____________90_________________72\n	140 -- 146	73 -- 79	-22.1843 kcal/mol	7.4128 kcal/mol	2.24587 kcal/mol	128 147@LB@ \| \|@LB@5'-CAG...CAUAA U CCAUC...CUG-3'@LB@ GCGAAUC GAUUGUGCUA@LB@ :\|\|\|\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UGCUUAG UUAACACGAU@LB@3'-UUU...CAGCA ACGUC...ACG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -22.1843 kcal/mol@LB@Unfolding Energy - mRNA 7.4128 kcal/mol@LB@Unfolding Energy - sRNA 2.24587 kcal/mol@LB@@LB@Position - mRNA 129 -- 146@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 140 -- 146@LB@Position Seed - sRNA 73 -- 79@LB@
30	0.0001707	0.01997	b1847	yebF	-12.53	0.024655	175 -- 194	68 -- 88	extracellular Colicin M immunity family protein	_____________174___________________195\n_____________\|_____________________\|\n5'-AAC...UCUCC__________________G__AAAAA...CAA-3'\n______________UGAAUC_AUUGUGCUAUG_AG\n______________:\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\|_\|\|\n______________GCUUAG_UAACACGAUAC_UC\n3'-UUU...AGCAU______U___________G__AUUAA...ACG-5'\n_____________\|_____________________\|\n_____________89____________________67\n	185 -- 191	71 -- 77	-25.1828 kcal/mol	8.15856 kcal/mol	4.50023 kcal/mol	174 195@LB@ \| \|@LB@5'-AAC...UCUCC G AAAAA...CAA-3'@LB@ UGAAUC AUUGUGCUAUG AG@LB@ :\|\|\|\|\| \|\|\|\|\|\|\|\|\|\|\| \|\|@LB@ GCUUAG UAACACGAUAC UC@LB@3'-UUU...AGCAU U G AUUAA...ACG-5'@LB@ \| \|@LB@ 89 67@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -25.1828 kcal/mol@LB@Unfolding Energy - mRNA 8.15856 kcal/mol@LB@Unfolding Energy - sRNA 4.50023 kcal/mol@LB@@LB@Position - mRNA 175 -- 194@LB@Position - sRNA 68 -- 88@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 71 -- 77@LB@
42	0.0003514	0.02948	b3847	pepQ	-12.53	0.024661	145 -- 205	37 -- 89	proline dipeptidase	_____________144______________________________________________________________206\n_____________\|________________________________________________________________\|\n5'-UUG...UCUGG_________________AGA_____AGACU___GG________ACA____GGUAA___A_____AUCAC...UUC-3'\n______________AUGAA_CGA_UGUGCUA___UGCGG_____UAA__UCAAAAAA___GAAG______AA_AUGGA\n______________\|:\|\|\|_\|:\|_\|\|\|\|\|\|\|___\|\|\|:\|_____\|\|\|__\|\|\|\|\|\|\|\|___\|\|\|\|______\|\|_\|\|\|\|\|\n______________UGCUU_GUU_ACACGAU___ACGUC_____AUU__AGUUUUUU___CUUC______UU_UACCU\n3'-UUU...CAGCA_____A___A_______________________A_________C______AUUCUG__A_____CGCGU...ACG-5'\n_____________\|________________________________________________________________\|\n_____________90_______________________________________________________________36\n	153 -- 159	73 -- 79	-31.666 kcal/mol	11.3417 kcal/mol	7.78939 kcal/mol	144 206@LB@ \| \|@LB@5'-UUG...UCUGG AGA AGACU GG ACA GGUAA A AUCAC...UUC-3'@LB@ AUGAA CGA UGUGCUA UGCGG UAA UCAAAAAA GAAG AA AUGGA@LB@ \|:\|\|\| \|:\| \|\|\|\|\|\|\| \|\|\|:\| \|\|\| \|\|\|\|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|@LB@ UGCUU GUU ACACGAU ACGUC AUU AGUUUUUU CUUC UU UACCU@LB@3'-UUU...CAGCA A A A C AUUCUG A CGCGU...ACG-5'@LB@ \| \|@LB@ 90 36@LB@@LB@@LB@Energy -12.53 kcal/mol@LB@Hybridization Energy -31.666 kcal/mol@LB@Unfolding Energy - mRNA 11.3417 kcal/mol@LB@Unfolding Energy - sRNA 7.78939 kcal/mol@LB@@LB@Position - mRNA 145 -- 205@LB@Position - sRNA 37 -- 89@LB@Position Seed - mRNA 153 -- 159@LB@Position Seed - sRNA 73 -- 79@LB@
21	6.29e-05	0.01049	b4040	ubiA	-12.44	0.026053	187 -- 207	35 -- 59	p-hydroxybenzoate octaprenyltransferase	_____________186_______________________208\n_____________\|_________________________\|\n5'-AGC...GUACU________AAA______________GGAGU...UAU-3'\n______________AAGAGGAA_______AAUAUGGAGU\n______________\|\|:\|\|\|\|\|_______\|\|\|\|\|\|\|\|\|:\n______________UUUUCCUU_______UUAUACCUCG\n3'-UUU...AAGUU________CAUUCUG__________CGUUG...ACG-5'\n_____________\|_________________________\|\n_____________60________________________34\n	201 -- 207	35 -- 41	-18.3412 kcal/mol	1.63668 kcal/mol	4.22714 kcal/mol	186 208@LB@ \| \|@LB@5'-AGC...GUACU AAA GGAGU...UAU-3'@LB@ AAGAGGAA AAUAUGGAGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|\|\|\|\|:@LB@ UUUUCCUU UUAUACCUCG@LB@3'-UUU...AAGUU CAUUCUG CGUUG...ACG-5'@LB@ \| \|@LB@ 60 34@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -18.3412 kcal/mol@LB@Unfolding Energy - mRNA 1.63668 kcal/mol@LB@Unfolding Energy - sRNA 4.22714 kcal/mol@LB@@LB@Position - mRNA 187 -- 207@LB@Position - sRNA 35 -- 59@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 35 -- 41@LB@
81	0.001932	0.08273	b2763	cysI	-12.36	0.027367	234 -- 285	1 -- 58	sulfite reductase beta subunit NAD(P)-binding heme-binding	_____________233_________________________________________________________286\n_____________\|___________________________________________________________\|\n5'-GAA...UGGUC_______AACU_____ACGCC__________AA______A___AA_____AC_______GCGGC...CGG-3'\n______________GAAGGAA____GACAG_____GAGCGC_AUG______GC_UGA____GCA__UACCUGC\n______________:\|\|\|\|\|\|____\|\|\|\|:_____\|\|\|\|\|\|_\|:\|______\|\|_\|\|\|____\|\|\|__:\|\|\|\|\|\|\n______________UUUCCUU____CUGUU_____CUCGCG_UGC______CG_ACU____CGU__GUGGACG\n3'-UUU...AGUUU_______CAUU_____AUAC_______U___GGGUAG__A___GCAA___AA_______-5'\n_____________\|__________________________________________________________\|\n_____________59_________________________________________________________1\n	279 -- 285	1 -- 7	-40.3147 kcal/mol	11.0832 kcal/mol	16.8724 kcal/mol	233 286@LB@ \| \|@LB@5'-GAA...UGGUC AACU ACGCC AA A AA AC GCGGC...CGG-3'@LB@ GAAGGAA GACAG GAGCGC AUG GC UGA GCA UACCUGC@LB@ :\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|\| \|:\| \|\| \|\|\| \|\|\| :\|\|\|\|\|\|@LB@ UUUCCUU CUGUU CUCGCG UGC CG ACU CGU GUGGACG@LB@3'-UUU...AGUUU CAUU AUAC U GGGUAG A GCAA AA -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -12.36 kcal/mol@LB@Hybridization Energy -40.3147 kcal/mol@LB@Unfolding Energy - mRNA 11.0832 kcal/mol@LB@Unfolding Energy - sRNA 16.8724 kcal/mol@LB@@LB@Position - mRNA 234 -- 285@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 1 -- 7@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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