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
175	0.01743	0.3104	b0921	smtA	-12.81	0.039244	146 -- 164	2 -- 20	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________145_________________165\n_____________\|___________________\|\n5'-AUC...UGGCU________AUA________AUCAG...AUC-3'\n______________GUGACAAA___GCGUCUUU\n______________:\|:\|\|\|\|\|___\|\|\|\|\|\|\|\|\n______________UAUUGUUU___CGCAGAAA\n3'-UUU...ACUAC________ACG________G-5'\n_____________\|___________________\|\n_____________21__________________1\n	158 -- 164	2 -- 8	-18.7664 kcal/mol	4.69909 kcal/mol	1.25604 kcal/mol	145 165@LB@ \| \|@LB@5'-AUC...UGGCU AUA AUCAG...AUC-3'@LB@ GUGACAAA GCGUCUUU@LB@ :\|:\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UAUUGUUU CGCAGAAA@LB@3'-UUU...ACUAC ACG G-5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -12.81 kcal/mol@LB@Hybridization Energy -18.7664 kcal/mol@LB@Unfolding Energy - mRNA 4.69909 kcal/mol@LB@Unfolding Energy - sRNA 1.25604 kcal/mol@LB@@LB@Position - mRNA 146 -- 164@LB@Position - sRNA 2 -- 20@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 2 -- 8@LB@
33	0.002096	0.2094	b0937	ssuE	-11.36	0.070700	201 -- 209	5 -- 13	NAD(P)H-dependent FMN reductase	_____________200_______210\n_____________\|_________\|\n5'-CUG...AGAGU_________AUCAC...AGG-3'\n______________AUGCGUGUC\n______________\|\|\|\|\|:\|\|\|\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	203 -- 209	5 -- 11	-14.6108 kcal/mol	2.09491 kcal/mol	1.15134 kcal/mol	200 210@LB@ \| \|@LB@5'-CUG...AGAGU AUCAC...AGG-3'@LB@ AUGCGUGUC@LB@ \|\|\|\|\|:\|\|\|@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.6108 kcal/mol@LB@Unfolding Energy - mRNA 2.09491 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 201 -- 209@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 5 -- 11@LB@
142	0.01346	0.3104	b0729	sucD	-11.71	0.061414	39 -- 57	3 -- 21	succinyl-CoA synthetase NAD(P)-binding alpha subunit	_____________38__________________58\n_____________\|___________________\|\n5'-GUU...GGCGC_________A___G__G__AACGU...CUA-3'\n______________GGUAGCAGA_GUG_GU_UU\n______________\|:\|\|:\|\|:\|_\|:\|_\|\|_\|\|\n______________CUAUUGUUU_CGC_CA_AA\n3'-UUU...UACUA_________A___G__G__AG-5'\n_____________\|___________________\|\n_____________22__________________2\n	41 -- 47	13 -- 19	-17.4316 kcal/mol	4.46052 kcal/mol	1.257 kcal/mol	38 58@LB@ \| \|@LB@5'-GUU...GGCGC A G G AACGU...CUA-3'@LB@ GGUAGCAGA GUG GU UU@LB@ \|:\|\|:\|\|:\| \|:\| \|\| \|\|@LB@ CUAUUGUUU CGC CA AA@LB@3'-UUU...UACUA A G G AG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -11.71 kcal/mol@LB@Hybridization Energy -17.4316 kcal/mol@LB@Unfolding Energy - mRNA 4.46052 kcal/mol@LB@Unfolding Energy - sRNA 1.257 kcal/mol@LB@@LB@Position - mRNA 39 -- 57@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 13 -- 19@LB@
167	0.01599	0.3104	b4220	tamA	-9.57	0.142740	193 -- 207	4 -- 21	translocation and assembly module for autotransporter export outer membrane subunit	_____________192________________208\n_____________\|__________________\|\n5'-CGC...UUCAG__GA______________AUAUC...GAC-3'\n______________GA____AAAUGUGCG_CU\n______________\|\|____\|\|\|\|\|:\|\|\|_\|\|\n______________CU____UUUACGCGC_GA\n3'-UUU...UACUA__AUUG_________A__AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	199 -- 205	7 -- 13	-13.0971 kcal/mol	2.26836 kcal/mol	1.2552 kcal/mol	192 208@LB@ \| \|@LB@5'-CGC...UUCAG GA AUAUC...GAC-3'@LB@ GA AAAUGUGCG CU@LB@ \|\| \|\|\|\|\|:\|\|\| \|\|@LB@ CU UUUACGCGC GA@LB@3'-UUU...UACUA AUUG A AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.0971 kcal/mol@LB@Unfolding Energy - mRNA 2.26836 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@LB@
59	0.005538	0.3084	b2812	tcdA	-16.71	0.007603	29 -- 48	1 -- 19	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA	_____________28___________________49\n_____________\|____________________\|\n5'-GUG...AUUAU____U___________G___AUGCC...UUU-3'\n______________UGAC_AAGUGCGCGUU_UUC\n______________\|:\|\|_\|\|:\|\|\|\|\|\|\|:_\|\|\|\n______________AUUG_UUUACGCGCAG_AAG\n3'-UUU...CUACU________________A___-5'\n_____________\|___________________\|\n_____________20__________________1\n	38 -- 44	5 -- 11	-22.1898 kcal/mol	4.2278 kcal/mol	1.25156 kcal/mol	28 49@LB@ \| \|@LB@5'-GUG...AUUAU U G AUGCC...UUU-3'@LB@ UGAC AAGUGCGCGUU UUC@LB@ \|:\|\| \|\|:\|\|\|\|\|\|\|: \|\|\|@LB@ AUUG UUUACGCGCAG AAG@LB@3'-UUU...CUACU A -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -22.1898 kcal/mol@LB@Unfolding Energy - mRNA 4.2278 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 29 -- 48@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 5 -- 11@LB@
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@LB@
74	0.006875	0.3087	b2474	tmcA	-10.30	0.108021	196 -- 222	5 -- 31	elongator methionine tRNA (ac4C34) acetyltransferase	_____________195____________________________223\n_____________\|______________________________\|\n5'-GAU...CGGGG_________C___AC____________U__ACACA...UUG-3'\n______________CAGGGAUGG_UGA__UGAC___UGCGC_UC\n______________\|\|\|\|\|\|\|\|:_\|\|\|__\|:\|\|___\|\|\|\|\|_\|\|\n______________GUCCCUACU_ACU__AUUG___ACGCG_AG\n3'-UUU...CUUAA___________________UUU_____C__AAAG-5'\n_____________\|______________________________\|\n_____________32_____________________________4\n	198 -- 204	23 -- 29	-27.934 kcal/mol	9.88036 kcal/mol	7.7585 kcal/mol	195 223@LB@ \| \|@LB@5'-GAU...CGGGG C AC U ACACA...UUG-3'@LB@ CAGGGAUGG UGA UGAC UGCGC UC@LB@ \|\|\|\|\|\|\|\|: \|\|\| \|:\|\| \|\|\|\|\| \|\|@LB@ GUCCCUACU ACU AUUG ACGCG AG@LB@3'-UUU...CUUAA UUU C AAAG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -10.30 kcal/mol@LB@Hybridization Energy -27.934 kcal/mol@LB@Unfolding Energy - mRNA 9.88036 kcal/mol@LB@Unfolding Energy - sRNA 7.7585 kcal/mol@LB@@LB@Position - mRNA 196 -- 222@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@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@
100	0.01004	0.3104	b3166	truB	-9.42	0.151044	113 -- 128	5 -- 18	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________112______________129\n_____________\|________________\|\n5'-GGC...GGUUG__G________AU___AAACC...AAC-3'\n______________AA_GGAUGCGC__GUC\n______________\|\|_::\|\|\|\|\|\|__\|\|\|\n______________UU_UUUACGCG__CAG\n3'-UUU...UACUA__G_____________AAAG-5'\n_____________\|________________\|\n_____________19_______________4\n	117 -- 123	8 -- 14	-15.4757 kcal/mol	4.82661 kcal/mol	1.2243 kcal/mol	112 129@LB@ \| \|@LB@5'-GGC...GGUUG G AU AAACC...AAC-3'@LB@ AA GGAUGCGC GUC@LB@ \|\| ::\|\|\|\|\|\| \|\|\|@LB@ UU UUUACGCG CAG@LB@3'-UUU...UACUA G AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -15.4757 kcal/mol@LB@Unfolding Energy - mRNA 4.82661 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 113 -- 128@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 117 -- 123@LB@Position Seed - sRNA 8 -- 14@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

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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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