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	Additional homologs
26	0.001545	0.1943	b1678	ldtE	-10.42	0.102915	208 -- 217	2 -- 11	murein L D-transpeptidase		_____________207________218\n_____________\|__________\|\n5'-UCU...GAAAC__________GCUUA...GCC-3'\n______________GCGCGUCUUU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CGCGCAGAAA\n3'-UUU...GUUUA__________G-5'\n_____________\|__________\|\n_____________12_________1\n	211 -- 217	2 -- 8	-16.5846 kcal/mol	4.99595 kcal/mol	1.16977 kcal/mol	207 218@LB@ \| \|@LB@5'-UCU...GAAAC GCUUA...GCC-3'@LB@ GCGCGUCUUU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CGCGCAGAAA@LB@3'-UUU...GUUUA G-5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.42 kcal/mol@LB@Hybridization Energy -16.5846 kcal/mol@LB@Unfolding Energy - mRNA 4.99595 kcal/mol@LB@Unfolding Energy - sRNA 1.16977 kcal/mol@LB@@LB@Position - mRNA 208 -- 217@LB@Position - sRNA 2 -- 11@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 2 -- 8@LB@
54	0.004897	0.3024	b1949	fliQ	-8.93	0.181731	208 -- 239	7 -- 38	flagellar biosynthesis protein		_____________207_______________________________240\n_____________\|_________________________________\|\n5'-UUC...GACAC__________UC__________G__C__AA___AUGAA...UUA-3'\n______________CUGAA_UCGG__AUGAUGAUGG_GA_UG__GCG\n______________\|\|\|\|\|_\|\|:\|__\|\|\|\|\|\|\|\|::_:\|_\|\|__\|\|\|\n______________GACUU_AGUC__UACUACUAUU_UU_AC__CGC\n3'-UUU...GUAGA_____A____CC__________G__U__G____AGAAAG-5'\n_____________\|_________________________________\|\n_____________39________________________________6\n	222 -- 228	17 -- 23	-27.1148 kcal/mol	8.82457 kcal/mol	9.35859 kcal/mol	207 240@LB@ \| \|@LB@5'-UUC...GACAC UC G C AA AUGAA...UUA-3'@LB@ CUGAA UCGG AUGAUGAUGG GA UG GCG@LB@ \|\|\|\|\| \|\|:\| \|\|\|\|\|\|\|\|:: :\| \|\| \|\|\|@LB@ GACUU AGUC UACUACUAUU UU AC CGC@LB@3'-UUU...GUAGA A CC G U G AGAAAG-5'@LB@ \| \|@LB@ 39 6@LB@@LB@@LB@Energy -8.93 kcal/mol@LB@Hybridization Energy -27.1148 kcal/mol@LB@Unfolding Energy - mRNA 8.82457 kcal/mol@LB@Unfolding Energy - sRNA 9.35859 kcal/mol@LB@@LB@Position - mRNA 208 -- 239@LB@Position - sRNA 7 -- 38@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 17 -- 23@LB@
83	0.007683	0.3104	b4244	pyrI	-7.62	0.290375	210 -- 222	10 -- 21	aspartate carbamoyltransferase regulatory subunit		_____________209___________223\n_____________\|_____________\|\n5'-UUC...CACAC__________U__AGGUU...UCA-3'\n______________GAUAAUAAAU_GC\n______________\|\|\|\|\|:\|\|\|\|_\|\|\n______________CUAUUGUUUA_CG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	213 -- 219	12 -- 18	-11.1174 kcal/mol	2.26673 kcal/mol	1.23076 kcal/mol	209 223@LB@ \| \|@LB@5'-UUC...CACAC U AGGUU...UCA-3'@LB@ GAUAAUAAAU GC@LB@ \|\|\|\|\|:\|\|\|\| \|\|@LB@ CUAUUGUUUA CG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -11.1174 kcal/mol@LB@Unfolding Energy - mRNA 2.26673 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 210 -- 222@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 12 -- 18@LB@
67	0.006163	0.3087	b0773	ybhB	-10.36	0.105479	214 -- 228	7 -- 20	kinase inhibitor homolog UPF0098 family	b0545	_____________213_____________229\n_____________\|_______________\|\n5'-UGU...CAUCA_______UC______AUGGC...AUC-3'\n______________GUAACGA__UGCGCG\n______________:\|\|\|\|:\|__\|\|\|\|\|\|\n______________UAUUGUU__ACGCGC\n3'-UUU...ACUAC_______U_______AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	214 -- 220	14 -- 20	-16.0436 kcal/mol	4.44842 kcal/mol	1.23906 kcal/mol	213 229@LB@ \| \|@LB@5'-UGU...CAUCA UC AUGGC...AUC-3'@LB@ GUAACGA UGCGCG@LB@ :\|\|\|\|:\| \|\|\|\|\|\|@LB@ UAUUGUU ACGCGC@LB@3'-UUU...ACUAC U AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -10.36 kcal/mol@LB@Hybridization Energy -16.0436 kcal/mol@LB@Unfolding Energy - mRNA 4.44842 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 214 -- 228@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 14 -- 20@LB@
134	0.01294	0.3104	b2234	nrdA	-13.57	0.028625	217 -- 231	7 -- 22	ribonucleoside-diphosphate reductase 1 alpha subunit		_____________216______________232\n_____________\|________________\|\n5'-GAC...UCUGC________________ACGGU...UGC-3'\n______________UGGUGACAAA_GCGCG\n______________\|\|:\|:\|\|\|\|\|_\|\|\|\|\|\n______________ACUAUUGUUU_CGCGC\n3'-UUU...CUACU__________A_____AGAAAG-5'\n_____________\|________________\|\n_____________23_______________6\n	220 -- 226	13 -- 19	-19.6051 kcal/mol	4.78775 kcal/mol	1.24379 kcal/mol	216 232@LB@ \| \|@LB@5'-GAC...UCUGC ACGGU...UGC-3'@LB@ UGGUGACAAA GCGCG@LB@ \|\|:\|:\|\|\|\|\| \|\|\|\|\|@LB@ ACUAUUGUUU CGCGC@LB@3'-UUU...CUACU A AGAAAG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -19.6051 kcal/mol@LB@Unfolding Energy - mRNA 4.78775 kcal/mol@LB@Unfolding Energy - sRNA 1.24379 kcal/mol@LB@@LB@Position - mRNA 217 -- 231@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 13 -- 19@LB@
115	0.01182	0.3104	b3367	nirC	-10.39	0.104055	218 -- 233	4 -- 19	nitrite transporter		_____________217______________234\n_____________\|________________\|\n5'-AUG...ACUAU_____________G__AACGC...UGG-3'\n______________UAAUAAGUGUGCG_CU\n______________\|\|\|:\|\|:\|\|:\|\|\|_\|\|\n______________AUUGUUUACGCGC_GA\n3'-UUU...CUACU_____________A__AAG-5'\n_____________\|________________\|\n_____________20_______________3\n	224 -- 230	7 -- 13	-17.3607 kcal/mol	5.72929 kcal/mol	1.2406 kcal/mol	217 234@LB@ \| \|@LB@5'-AUG...ACUAU G AACGC...UGG-3'@LB@ UAAUAAGUGUGCG CU@LB@ \|\|\|:\|\|:\|\|:\|\|\| \|\|@LB@ AUUGUUUACGCGC GA@LB@3'-UUU...CUACU A AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -10.39 kcal/mol@LB@Hybridization Energy -17.3607 kcal/mol@LB@Unfolding Energy - mRNA 5.72929 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 218 -- 233@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 7 -- 13@LB@
178	0.01756	0.3104	b2017	yefM	-12.99	0.036476	219 -- 231	5 -- 18	antitoxin of the YoeB-YefM toxin-antitoxin system		_____________218____________232\n_____________\|______________\|\n5'-AUU...GCUAC______________AGAAU...AUG-3'\n______________AGCGAA_GCGCGUC\n______________\|:\|:\|\|_\|\|\|\|\|\|\|\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	225 -- 231	5 -- 11	-18.6086 kcal/mol	4.39571 kcal/mol	1.2243 kcal/mol	218 232@LB@ \| \|@LB@5'-AUU...GCUAC AGAAU...AUG-3'@LB@ AGCGAA GCGCGUC@LB@ \|:\|:\|\| \|\|\|\|\|\|\|@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -12.99 kcal/mol@LB@Hybridization Energy -18.6086 kcal/mol@LB@Unfolding Energy - mRNA 4.39571 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 219 -- 231@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 5 -- 11@LB@
20	0.0008552	0.1448	b4137	cutA	-9.23	0.162618	220 -- 236	1 -- 16	divalent-cation tolerance protein copper sensitivity		_____________219_______________237\n_____________\|_________________\|\n5'-CAA...AAGUU_____AC_______G__GUGGU...CGG-3'\n______________CGAAU__CGCGUCU_UC\n______________\|:\|\|\|__\|\|\|\|\|\|\|_\|\|\n______________GUUUA__GCGCAGA_AG\n3'-UUU...CUAUU_____C________A__-5'\n_____________\|________________\|\n_____________17_______________1\n	227 -- 233	4 -- 10	-14.9299 kcal/mol	4.46216 kcal/mol	1.23857 kcal/mol	219 237@LB@ \| \|@LB@5'-CAA...AAGUU AC G GUGGU...CGG-3'@LB@ CGAAU CGCGUCU UC@LB@ \|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUUUA GCGCAGA AG@LB@3'-UUU...CUAUU C A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -14.9299 kcal/mol@LB@Unfolding Energy - mRNA 4.46216 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 220 -- 236@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@LB@
81	0.007385	0.3087	b0736	ybgC	-11.71	0.061637	220 -- 237	4 -- 21	acyl-CoA thioester hydrolase		_____________219________________238\n_____________\|__________________\|\n5'-UUG...GUUUC______C___U_______ACUAU...AAA-3'\n______________GAUGGC_GGU_CGCGUCU\n______________\|\|\|::\|_::\|_\|\|\|\|\|\|\|\n______________CUAUUG_UUA_GCGCAGA\n3'-UUU...UACUA______U___C_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	231 -- 237	4 -- 10	-19.027 kcal/mol	6.06673 kcal/mol	1.2552 kcal/mol	219 238@LB@ \| \|@LB@5'-UUG...GUUUC C U ACUAU...AAA-3'@LB@ GAUGGC GGU CGCGUCU@LB@ \|\|\|::\| ::\| \|\|\|\|\|\|\|@LB@ CUAUUG UUA GCGCAGA@LB@3'-UUU...UACUA U C AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -19.027 kcal/mol@LB@Unfolding Energy - mRNA 6.06673 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@LB@
87	0.008927	0.3104	b0195	tsaA	-8.24	0.234029	220 -- 237	1 -- 18	tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase SAM-dependent		_____________219________________238\n_____________\|__________________\|\n5'-GAA...GUUCG_______AG_____A___GCUCG...ACG-3'\n______________AGCAAAU__GCGUU_UUC\n______________\|:\|\|\|\|\|__\|\|\|\|:_\|\|\|\n______________UUGUUUA__CGCAG_AAG\n3'-UUU...UACUA_______CG_____A___-5'\n_____________\|_________________\|\n_____________19________________1\n	220 -- 226	12 -- 18	-15.6275 kcal/mol	6.14962 kcal/mol	1.24077 kcal/mol	219 238@LB@ \| \|@LB@5'-GAA...GUUCG AG A GCUCG...ACG-3'@LB@ AGCAAAU GCGUU UUC@LB@ \|:\|\|\|\|\| \|\|\|\|: \|\|\|@LB@ UUGUUUA CGCAG AAG@LB@3'-UUU...UACUA CG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -8.24 kcal/mol@LB@Hybridization Energy -15.6275 kcal/mol@LB@Unfolding Energy - mRNA 6.14962 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 220 -- 237@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 12 -- 18@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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

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service.

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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