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
121	0.01226	0.3104	b3209	elbB	-12.57	0.043302	225 -- 240	4 -- 18	isoprenoid biosynthesis protein with amidotransferase-like domain		_____________224______________241\n_____________\|________________\|\n5'-GCG...UUCUG__________G_____AUGAC...GUG-3'\n______________AGCGGAUGCG_CGUCU\n______________\|:\|::\|\|\|\|\|_\|\|\|\|\|\n______________UUGUUUACGC_GCAGA\n3'-UUU...UACUA________________AAG-5'\n_____________\|________________\|\n_____________19_______________3\n	228 -- 234	9 -- 15	-20.315 kcal/mol	6.5132 kcal/mol	1.22995 kcal/mol	224 241@LB@ \| \|@LB@5'-GCG...UUCUG G AUGAC...GUG-3'@LB@ AGCGGAUGCG CGUCU@LB@ \|:\|::\|\|\|\|\| \|\|\|\|\|@LB@ UUGUUUACGC GCAGA@LB@3'-UUU...UACUA AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -20.315 kcal/mol@LB@Unfolding Energy - mRNA 6.5132 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 225 -- 240@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 9 -- 15@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@
7	9.926e-05	0.04801	b1113	ldtC	-15.69	0.011765	184 -- 223	1 -- 45	L D-transpeptidase linking Lpp to murein		_____________183___________________________________________224\n_____________\|_____________________________________________\|\n5'-CGU...UUAUA______A________UU________________A___________UCGCU...UGC-3'\n______________UUUAUU__UGGAUUU___GGUGAUGAU__CAAA__CGCGUUUUUC\n______________\|\|:\|\|:__\|\|:\|\|\|:___\|:\|\|\|\|\|\|\|__\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________AAGUAG__ACUUAAG___CUACUACUA__GUUU__GCGCAGAAAG\n3'-UUU...UUUUA______AG_______UCC_________UU____AC__________-5'\n_____________\|____________________________________________\|\n_____________46___________________________________________1\n	217 -- 223	1 -- 7	-33.7876 kcal/mol	8.63912 kcal/mol	9.46113 kcal/mol	183 224@LB@ \| \|@LB@5'-CGU...UUAUA A UU A UCGCU...UGC-3'@LB@ UUUAUU UGGAUUU GGUGAUGAU CAAA CGCGUUUUUC@LB@ \|\|:\|\|: \|\|:\|\|\|: \|:\|\|\|\|\|\|\| \|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ AAGUAG ACUUAAG CUACUACUA GUUU GCGCAGAAAG@LB@3'-UUU...UUUUA AG UCC UU AC -5'@LB@ \| \|@LB@ 46 1@LB@@LB@@LB@Energy -15.69 kcal/mol@LB@Hybridization Energy -33.7876 kcal/mol@LB@Unfolding Energy - mRNA 8.63912 kcal/mol@LB@Unfolding Energy - sRNA 9.46113 kcal/mol@LB@@LB@Position - mRNA 184 -- 223@LB@Position - sRNA 1 -- 45@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 1 -- 7@LB@
64	0.005939	0.3087	b3237	argR	-9.39	0.153279	85 -- 104	1 -- 19	l-arginine-responsive arginine metabolism regulon transcriptional regulator		_____________84____________________105\n_____________\|_____________________\|\n5'-ACA...AAAUU_______AUCC__________AUAAC...UGC-3'\n______________UGAUAAA____CGC_UCUUUC\n______________\|:\|:\|\|\|____\|\|\|_\|\|\|\|\|\|\n______________AUUGUUU____GCG_AGAAAG\n3'-UUU...CUACU_______AC_____C______-5'\n_____________\|____________________\|\n_____________20___________________1\n	85 -- 91	13 -- 19	-12.1021 kcal/mol	1.46458 kcal/mol	1.25156 kcal/mol	84 105@LB@ \| \|@LB@5'-ACA...AAAUU AUCC AUAAC...UGC-3'@LB@ UGAUAAA CGC UCUUUC@LB@ \|:\|:\|\|\| \|\|\| \|\|\|\|\|\|@LB@ AUUGUUU GCG AGAAAG@LB@3'-UUU...CUACU AC C -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -12.1021 kcal/mol@LB@Unfolding Energy - mRNA 1.46458 kcal/mol@LB@Unfolding Energy - sRNA 1.25156 kcal/mol@LB@@LB@Position - mRNA 85 -- 104@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 13 -- 19@LB@
79	0.007292	0.3087	b0063	araB	-12.45	0.045578	14 -- 28	6 -- 20	L-ribulokinase		_____________13______________29\n_____________\|_______________\|\n5'-CGG...AAGCC________AA_____AACAA...GGU-3'\n______________AUGACAAA__CGCGU\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________UAUUGUUU__GCGCA\n3'-UUU...ACUAC________AC_____GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	15 -- 21	13 -- 19	-14.5023 kcal/mol	0.813134 kcal/mol	1.24244 kcal/mol	13 29@LB@ \| \|@LB@5'-CGG...AAGCC AA AACAA...GGU-3'@LB@ AUGACAAA CGCGU@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ UAUUGUUU GCGCA@LB@3'-UUU...ACUAC AC GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -14.5023 kcal/mol@LB@Unfolding Energy - mRNA 0.813134 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 14 -- 28@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 15 -- 21@LB@Position Seed - sRNA 13 -- 19@LB@
94	0.009498	0.3104	b4198	ulaF	-10.74	0.090813	136 -- 150	6 -- 20	L-ribulose 5-phosphate 4-epimerase		_____________135_____________151\n_____________\|_______________\|\n5'-GUC...CAGAA________A______GAUUG...GCG-3'\n______________GUGGCGAA_GCGCGU\n______________:\|::\|:\|\|_\|\|\|\|\|\|\n______________UAUUGUUU_CGCGCA\n3'-UUU...ACUAC________A______GAAAG-5'\n_____________\|_______________\|\n_____________21______________5\n	137 -- 143	13 -- 19	-18.1084 kcal/mol	6.12954 kcal/mol	1.24244 kcal/mol	135 151@LB@ \| \|@LB@5'-GUC...CAGAA A GAUUG...GCG-3'@LB@ GUGGCGAA GCGCGU@LB@ :\|::\|:\|\| \|\|\|\|\|\|@LB@ UAUUGUUU CGCGCA@LB@3'-UUU...ACUAC A GAAAG-5'@LB@ \| \|@LB@ 21 5@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.1084 kcal/mol@LB@Unfolding Energy - mRNA 6.12954 kcal/mol@LB@Unfolding Energy - sRNA 1.24244 kcal/mol@LB@@LB@Position - mRNA 136 -- 150@LB@Position - sRNA 6 -- 20@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 13 -- 19@LB@
41	0.00276	0.2279	b0889	lrp	-10.49	0.100208	207 -- 221	8 -- 21	leucine-responsive global transcriptional regulator		_____________206_____________222\n_____________\|_______________\|\n5'-GUG...UGGUA_________AA____CCUGG...AGC-3'\n______________GAUAGCAAG__GCGC\n______________\|\|\|\|:\|\|\|:__\|\|\|\|\n______________CUAUUGUUU__CGCG\n3'-UUU...UACUA_________A_____CAGAAAG-5'\n_____________\|_______________\|\n_____________22______________7\n	209 -- 215	13 -- 19	-15.2704 kcal/mol	3.5472 kcal/mol	1.23638 kcal/mol	206 222@LB@ \| \|@LB@5'-GUG...UGGUA AA CCUGG...AGC-3'@LB@ GAUAGCAAG GCGC@LB@ \|\|\|\|:\|\|\|: \|\|\|\|@LB@ CUAUUGUUU CGCG@LB@3'-UUU...UACUA A CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -15.2704 kcal/mol@LB@Unfolding Energy - mRNA 3.5472 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 207 -- 221@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 13 -- 19@LB@
61	0.005608	0.3084	b2174	lpxT	-9.09	0.171357	170 -- 179	1 -- 10	lipid A 1-diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase		_____________169________180\n_____________\|__________\|\n5'-GAA...UUGCC__________AGUAA...CGA-3'\n______________UGCGUUUUUC\n______________:\|\|\|\|:\|\|\|\|\n______________GCGCAGAAAG\n3'-UUU...UUUAC__________-5'\n_____________\|_________\|\n_____________11________1\n	173 -- 179	1 -- 7	-13.1644 kcal/mol	2.90849 kcal/mol	1.16635 kcal/mol	169 180@LB@ \| \|@LB@5'-GAA...UUGCC AGUAA...CGA-3'@LB@ UGCGUUUUUC@LB@ :\|\|\|\|:\|\|\|\|@LB@ GCGCAGAAAG@LB@3'-UUU...UUUAC -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -9.09 kcal/mol@LB@Hybridization Energy -13.1644 kcal/mol@LB@Unfolding Energy - mRNA 2.90849 kcal/mol@LB@Unfolding Energy - sRNA 1.16635 kcal/mol@LB@@LB@Position - mRNA 170 -- 179@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
85	0.008151	0.3104	b0914	msbA	-12.09	0.052799	181 -- 198	1 -- 18	lipid ABC transporter permease/ATPase		_____________180________________199\n_____________\|__________________\|\n5'-AGC...AUUUC_________UG_______GAAUG...CGU-3'\n______________AACAAAUGC__GUUUUUU\n______________\|\|\|\|\|\|\|\|\|__\|\|:\|\|\|:\n______________UUGUUUACG__CAGAAAG\n3'-UUU...UACUA_________CG_______-5'\n_____________\|_________________\|\n_____________19________________1\n	192 -- 198	1 -- 7	-16.7201 kcal/mol	3.39277 kcal/mol	1.24077 kcal/mol	180 199@LB@ \| \|@LB@5'-AGC...AUUUC UG GAAUG...CGU-3'@LB@ AACAAAUGC GUUUUUU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|\|\|:@LB@ UUGUUUACG CAGAAAG@LB@3'-UUU...UACUA CG -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -16.7201 kcal/mol@LB@Unfolding Energy - mRNA 3.39277 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 181 -- 198@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 1 -- 7@LB@
78	0.007118	0.3087	b1118	lolE	-12.65	0.041861	19 -- 36	6 -- 21	lipoprotein-releasing system transmembrane protein		_____________18_________________37\n_____________\|__________________\|\n5'-CUG...CUACC______CUC_________AACGC...GCA-3'\n______________GGUAAC___GAUGCGCGU\n______________\|:\|\|\|\|___:\|\|\|\|\|\|\|\|\n______________CUAUUG___UUACGCGCA\n3'-UUU...UACUA______U___________GAAAG-5'\n_____________\|__________________\|\n_____________22_________________5\n	30 -- 36	6 -- 12	-20.2716 kcal/mol	6.37224 kcal/mol	1.24519 kcal/mol	18 37@LB@ \| \|@LB@5'-CUG...CUACC CUC AACGC...GCA-3'@LB@ GGUAAC GAUGCGCGU@LB@ \|:\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ CUAUUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -12.65 kcal/mol@LB@Hybridization Energy -20.2716 kcal/mol@LB@Unfolding Energy - mRNA 6.37224 kcal/mol@LB@Unfolding Energy - sRNA 1.24519 kcal/mol@LB@@LB@Position - mRNA 19 -- 36@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 6 -- 12@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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