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
174	0.01734	0.3104	b3470	tusA	-9.03	0.174990	268 -- 281	8 -- 22	mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase	_____________267_____________282\n_____________\|_______________\|\n5'-CAU...ACCGG_______________AAAAC...UGC-3'\n______________UGAUGAU_GGUGCGC\n______________\|\|\|\|:\|:_::\|\|\|\|\|\n______________ACUAUUG_UUACGCG\n3'-UUU...CUACU_______U_______CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	275 -- 281	8 -- 14	-15.1295 kcal/mol	4.85785 kcal/mol	1.23838 kcal/mol	267 282@LB@ \| \|@LB@5'-CAU...ACCGG AAAAC...UGC-3'@LB@ UGAUGAU GGUGCGC@LB@ \|\|\|\|:\|: ::\|\|\|\|\|@LB@ ACUAUUG UUACGCG@LB@3'-UUU...CUACU U CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -15.1295 kcal/mol@LB@Unfolding Energy - mRNA 4.85785 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 268 -- 281@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 8 -- 14@LB@
191	0.01886	0.3104	b3494	uspB	-6.32	0.440313	280 -- 286	5 -- 11	universal stress (ethanol tolerance) protein B	_____________279_____287\n_____________\|_______\|\n5'-AAU...ACUAC_______GUUAG...UGC-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	280 -- 286	5 -- 11	-11.0709 kcal/mol	3.63469 kcal/mol	1.11145 kcal/mol	279 287@LB@ \| \|@LB@5'-AAU...ACUAC GUUAG...UGC-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -6.32 kcal/mol@LB@Hybridization Energy -11.0709 kcal/mol@LB@Unfolding Energy - mRNA 3.63469 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 280 -- 286@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 5 -- 11@LB@
102	0.01008	0.3104	b3500	gor	-8.16	0.240292	285 -- 295	4 -- 15	glutathione oxidoreductase	_____________284__________296\n_____________\|____________\|\n5'-GGC...GCCAG____________GAUUG-3'\n______________AAAUGUGCG_CU\n______________\|\|\|\|\|:\|\|\|_\|\|\n______________UUUACGCGC_GA\n3'-UUU...UAUUG_________A__AAG-5'\n_____________\|____________\|\n_____________16___________3\n	287 -- 293	7 -- 13	-12.6909 kcal/mol	3.32128 kcal/mol	1.20666 kcal/mol	284 296@LB@ \| \|@LB@5'-GGC...GCCAG GAUUG-3'@LB@ AAAUGUGCG CU@LB@ \|\|\|\|\|:\|\|\| \|\|@LB@ UUUACGCGC GA@LB@3'-UUU...UAUUG A AAG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -8.16 kcal/mol@LB@Hybridization Energy -12.6909 kcal/mol@LB@Unfolding Energy - mRNA 3.32128 kcal/mol@LB@Unfolding Energy - sRNA 1.20666 kcal/mol@LB@@LB@Position - mRNA 285 -- 295@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 7 -- 13@LB@
186	0.01836	0.3104	b3521	yhjC	-9.62	0.140197	158 -- 166	5 -- 13	LysR family putative transcriptional regulator	_____________157_______167\n_____________\|_________\|\n5'-UUU...GCGAU_________ACUGU...UUU-3'\n______________AUGCGCGUU\n______________\|\|\|\|\|\|\|\|:\n______________UACGCGCAG\n3'-UUU...UUGUU_________AAAG-5'\n_____________\|_________\|\n_____________14________4\n	160 -- 166	5 -- 11	-14.2497 kcal/mol	3.47777 kcal/mol	1.15134 kcal/mol	157 167@LB@ \| \|@LB@5'-UUU...GCGAU ACUGU...UUU-3'@LB@ AUGCGCGUU@LB@ \|\|\|\|\|\|\|\|:@LB@ UACGCGCAG@LB@3'-UUU...UUGUU AAAG-5'@LB@ \| \|@LB@ 14 4@LB@@LB@@LB@Energy -9.62 kcal/mol@LB@Hybridization Energy -14.2497 kcal/mol@LB@Unfolding Energy - mRNA 3.47777 kcal/mol@LB@Unfolding Energy - sRNA 1.15134 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 5 -- 13@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 5 -- 11@LB@
51	0.004574	0.3024	b3529	yhjK	-9.99	0.121635	195 -- 213	1 -- 18	cyclic-di-GMP phosphodiesterase	_____________194_________________214\n_____________\|___________________\|\n5'-AGC...GGGGA_____UU_______AAG__GCUCG...AUC-3'\n______________GACAA__UGCGCGU___UC\n______________:\|\|\|\|__\|\|\|\|\|\|\|___\|\|\n______________UUGUU__ACGCGCA___AG\n3'-UUU...UACUA_____U________GAA__-5'\n_____________\|__________________\|\n_____________19_________________1\n	202 -- 208	6 -- 12	-16.8324 kcal/mol	5.6017 kcal/mol	1.24077 kcal/mol	194 214@LB@ \| \|@LB@5'-AGC...GGGGA UU AAG GCUCG...AUC-3'@LB@ GACAA UGCGCGU UC@LB@ :\|\|\|\| \|\|\|\|\|\|\| \|\|@LB@ UUGUU ACGCGCA AG@LB@3'-UUU...UACUA U GAA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.99 kcal/mol@LB@Hybridization Energy -16.8324 kcal/mol@LB@Unfolding Energy - mRNA 5.6017 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 195 -- 213@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
166	0.01595	0.3104	b3560	glyQ	-10.24	0.110293	22 -- 29	7 -- 14	glycine tRNA synthetase alpha subunit	_____________21_______30\n_____________\|________\|\n5'-ACA...UAUGA________GUUAU...UGG-3'\n______________AAUGCGCG\n______________\|\|\|\|\|\|\|\|\n______________UUACGCGC\n3'-UUU...AUUGU________AGAAAG-5'\n_____________\|________\|\n_____________15_______6\n	23 -- 29	7 -- 13	-12.7168 kcal/mol	1.35517 kcal/mol	1.11978 kcal/mol	21 30@LB@ \| \|@LB@5'-ACA...UAUGA GUUAU...UGG-3'@LB@ AAUGCGCG@LB@ \|\|\|\|\|\|\|\|@LB@ UUACGCGC@LB@3'-UUU...AUUGU AGAAAG-5'@LB@ \| \|@LB@ 15 6@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -12.7168 kcal/mol@LB@Unfolding Energy - mRNA 1.35517 kcal/mol@LB@Unfolding Energy - sRNA 1.11978 kcal/mol@LB@@LB@Position - mRNA 22 -- 29@LB@Position - sRNA 7 -- 14@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 7 -- 13@LB@
169	0.01667	0.3104	b3575	yiaK	-9.90	0.125874	198 -- 219	8 -- 29	2 3-diketo-L-gulonate reductase NADH-dependent	_____________197____________________220\n_____________\|______________________\|\n5'-UUU...AGCCU_______AA______UU__A__AGUUA...UCG-3'\n______________GGGAUGA__GUGACA__UG_GC\n______________\|\|\|\|\|\|\|__:\|:\|\|\|__\|\|_\|\|\n______________CCCUACU__UAUUGU__AC_CG\n3'-UUU...UAAGU_______AC______UU__G__CAGAAAG-5'\n_____________\|______________________\|\n_____________30_____________________7\n	198 -- 204	23 -- 29	-23.0827 kcal/mol	5.7681 kcal/mol	7.41331 kcal/mol	197 220@LB@ \| \|@LB@5'-UUU...AGCCU AA UU A AGUUA...UCG-3'@LB@ GGGAUGA GUGACA UG GC@LB@ \|\|\|\|\|\|\| :\|:\|\|\| \|\| \|\|@LB@ CCCUACU UAUUGU AC CG@LB@3'-UUU...UAAGU AC UU G CAGAAAG-5'@LB@ \| \|@LB@ 30 7@LB@@LB@@LB@Energy -9.90 kcal/mol@LB@Hybridization Energy -23.0827 kcal/mol@LB@Unfolding Energy - mRNA 5.7681 kcal/mol@LB@Unfolding Energy - sRNA 7.41331 kcal/mol@LB@@LB@Position - mRNA 198 -- 219@LB@Position - sRNA 8 -- 29@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 23 -- 29@LB@
122	0.01233	0.3104	b3599	mtlA	-8.56	0.208645	247 -- 281	4 -- 32	mannitol-specific PTS enzyme: IIA IIB and IIC components	_____________246_________________________________282\n_____________\|___________________________________\|\n5'-GAU...UUUCC____CAAC_________C_____AUCG________AUCGC...UCA-3'\n______________UCAG____AUGGUGAUG_CAAAU____GCGCGUUU\n______________\|\|\|\|____\|\|\|:\|\|\|\|:_\|\|\|\|\|____\|\|\|\|\|\|:\|\n______________AGUC____UACUACUAU_GUUUA____CGCGCAGA\n3'-UUU...ACUUA____CC___________U_________________AAG-5'\n_____________\|___________________________________\|\n_____________33__________________________________3\n	275 -- 281	4 -- 10	-27.4972 kcal/mol	11.1013 kcal/mol	7.84022 kcal/mol	246 282@LB@ \| \|@LB@5'-GAU...UUUCC CAAC C AUCG AUCGC...UCA-3'@LB@ UCAG AUGGUGAUG CAAAU GCGCGUUU@LB@ \|\|\|\| \|\|\|:\|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ AGUC UACUACUAU GUUUA CGCGCAGA@LB@3'-UUU...ACUUA CC U AAG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -8.56 kcal/mol@LB@Hybridization Energy -27.4972 kcal/mol@LB@Unfolding Energy - mRNA 11.1013 kcal/mol@LB@Unfolding Energy - sRNA 7.84022 kcal/mol@LB@@LB@Position - mRNA 247 -- 281@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 4 -- 10@LB@
92	0.009361	0.3104	b3652	recG	-7.88	0.265686	265 -- 278	7 -- 20	ATP-dependent DNA helicase	_____________264_____________279\n_____________\|_______________\|\n5'-CAA...ACUUA________C______AAAAU...UGC-3'\n______________GUAACAAA_UG_GCG\n______________:\|\|\|\|\|\|\|_\|\|_\|\|\|\n______________UAUUGUUU_AC_CGC\n3'-UUU...ACUAC___________G___AGAAAG-5'\n_____________\|_______________\|\n_____________21______________6\n	266 -- 272	13 -- 19	-11.4583 kcal/mol	2.34189 kcal/mol	1.23906 kcal/mol	264 279@LB@ \| \|@LB@5'-CAA...ACUUA C AAAAU...UGC-3'@LB@ GUAACAAA UG GCG@LB@ :\|\|\|\|\|\|\| \|\| \|\|\|@LB@ UAUUGUUU AC CGC@LB@3'-UUU...ACUAC G AGAAAG-5'@LB@ \| \|@LB@ 21 6@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -11.4583 kcal/mol@LB@Unfolding Energy - mRNA 2.34189 kcal/mol@LB@Unfolding Energy - sRNA 1.23906 kcal/mol@LB@@LB@Position - mRNA 265 -- 278@LB@Position - sRNA 7 -- 20@LB@Position Seed - mRNA 266 -- 272@LB@Position Seed - sRNA 13 -- 19@LB@
199	0.01944	0.3104	b3657	yicJ	-13.22	0.033173	129 -- 161	8 -- 45	putative transporter	_____________128_____________________________________162\n_____________\|_______________________________________\|\n5'-CAG...GAAUA_________CA_____________UU____A________UAUCG...UGU-3'\n______________UUCG_CUCU_____CAGGGAUGGU____AC_AAAUGCGU\n______________\|\|\|:_\|\|\|\|_____\|\|\|\|\|\|\|\|:\|____\|\|_\|\|\|\|\|\|\|:\n______________AAGU_GAGA_____GUCCCUACUA____UG_UUUACGCG\n3'-UUU...UUUUA____A____CUUAA__________CUAU___________CAGAAAG-5'\n_____________\|_______________________________________\|\n_____________46______________________________________7\n	155 -- 161	8 -- 14	-30.3918 kcal/mol	7.7216 kcal/mol	9.45195 kcal/mol	128 162@LB@ \| \|@LB@5'-CAG...GAAUA CA UU A UAUCG...UGU-3'@LB@ UUCG CUCU CAGGGAUGGU AC AAAUGCGU@LB@ \|\|\|: \|\|\|\| \|\|\|\|\|\|\|\|:\| \|\| \|\|\|\|\|\|\|:@LB@ AAGU GAGA GUCCCUACUA UG UUUACGCG@LB@3'-UUU...UUUUA A CUUAA CUAU CAGAAAG-5'@LB@ \| \|@LB@ 46 7@LB@@LB@@LB@Energy -13.22 kcal/mol@LB@Hybridization Energy -30.3918 kcal/mol@LB@Unfolding Energy - mRNA 7.7216 kcal/mol@LB@Unfolding Energy - sRNA 9.45195 kcal/mol@LB@@LB@Position - mRNA 129 -- 161@LB@Position - sRNA 8 -- 45@LB@Position Seed - mRNA 155 -- 161@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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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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