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
47	0.003448	0.2484	b0614	citX	-10.13	0.115098	76 -- 91	4 -- 17	apo-citrate lyase phosphoribosyl-dephospho-CoA transferase	_____________75_______________92\n_____________\|________________\|\n5'-UUA...GCUGC____AC__________GCUGA...UCA-3'\n______________GCGA__GUGCGCGUCU\n______________:\|:\|__:\|\|\|\|\|\|\|\|\|\n______________UGUU__UACGCGCAGA\n3'-UUU...ACUAU________________AAG-5'\n_____________\|________________\|\n_____________18_______________3\n	85 -- 91	4 -- 10	-19.1919 kcal/mol	7.83057 kcal/mol	1.22888 kcal/mol	75 92@LB@ \| \|@LB@5'-UUA...GCUGC AC GCUGA...UCA-3'@LB@ GCGA GUGCGCGUCU@LB@ :\|:\| :\|\|\|\|\|\|\|\|\|@LB@ UGUU UACGCGCAGA@LB@3'-UUU...ACUAU AAG-5'@LB@ \| \|@LB@ 18 3@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -19.1919 kcal/mol@LB@Unfolding Energy - mRNA 7.83057 kcal/mol@LB@Unfolding Energy - sRNA 1.22888 kcal/mol@LB@@LB@Position - mRNA 76 -- 91@LB@Position - sRNA 4 -- 17@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 4 -- 10@LB@
111	0.01125	0.3104	b0102	zapD	-10.07	0.117779	99 -- 113	8 -- 22	FtsZ stabilizer	_____________98______________114\n_____________\|_______________\|\n5'-ACC...GUCAU_________CG____ACCGG...CCA-3'\n______________UGAUAAUAA__GCGC\n______________\|\|\|\|\|\|:\|\|__\|\|\|\|\n______________ACUAUUGUU__CGCG\n3'-UUU...CUACU_________UA____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	101 -- 107	14 -- 20	-15.8633 kcal/mol	4.55182 kcal/mol	1.23838 kcal/mol	98 114@LB@ \| \|@LB@5'-ACC...GUCAU CG ACCGG...CCA-3'@LB@ UGAUAAUAA GCGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|@LB@ ACUAUUGUU CGCG@LB@3'-UUU...CUACU UA CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -10.07 kcal/mol@LB@Hybridization Energy -15.8633 kcal/mol@LB@Unfolding Energy - mRNA 4.55182 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 99 -- 113@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 14 -- 20@LB@
158	0.01496	0.3104	b4278	insG	-10.00	0.121023	32 -- 48	3 -- 20	IS4 transposase	_____________31_________________49\n_____________\|__________________\|\n5'-GUU...UCCAC________A_________GUUAC...CUC-3'\n______________AUAACAAA__CGCGUUUU\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|:\|\|\n______________UAUUGUUU__GCGCAGAA\n3'-UUU...ACUAC________AC________AG-5'\n_____________\|__________________\|\n_____________21_________________2\n	42 -- 48	3 -- 9	-15.3953 kcal/mol	4.13684 kcal/mol	1.25547 kcal/mol	31 49@LB@ \| \|@LB@5'-GUU...UCCAC A GUUAC...CUC-3'@LB@ AUAACAAA CGCGUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|:\|\|@LB@ UAUUGUUU GCGCAGAA@LB@3'-UUU...ACUAC AC AG-5'@LB@ \| \|@LB@ 21 2@LB@@LB@@LB@Energy -10.00 kcal/mol@LB@Hybridization Energy -15.3953 kcal/mol@LB@Unfolding Energy - mRNA 4.13684 kcal/mol@LB@Unfolding Energy - sRNA 1.25547 kcal/mol@LB@@LB@Position - mRNA 32 -- 48@LB@Position - sRNA 3 -- 20@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 3 -- 9@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@
44	0.003062	0.2325	b3847	pepQ	-9.98	0.122201	144 -- 157	8 -- 21	proline dipeptidase	_____________143____________158\n_____________\|______________\|\n5'-UUG...CUCUG_____AC_______UAAGA...UUC-3'\n______________GAUGA__GAUGUGC\n______________\|\|\|:\|__:\|\|\|:\|\|\n______________CUAUU__UUACGCG\n3'-UUU...UACUA_____GU_______CAGAAAG-5'\n_____________\|______________\|\n_____________22_____________7\n	151 -- 157	8 -- 14	-13.3112 kcal/mol	2.09686 kcal/mol	1.23638 kcal/mol	143 158@LB@ \| \|@LB@5'-UUG...CUCUG AC UAAGA...UUC-3'@LB@ GAUGA GAUGUGC@LB@ \|\|\|:\| :\|\|\|:\|\|@LB@ CUAUU UUACGCG@LB@3'-UUU...UACUA GU CAGAAAG-5'@LB@ \| \|@LB@ 22 7@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -13.3112 kcal/mol@LB@Unfolding Energy - mRNA 2.09686 kcal/mol@LB@Unfolding Energy - sRNA 1.23638 kcal/mol@LB@@LB@Position - mRNA 144 -- 157@LB@Position - sRNA 8 -- 21@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 8 -- 14@LB@
70	0.006501	0.3087	b3301	rplO	-9.96	0.122936	194 -- 206	8 -- 20	50S ribosomal subunit protein L15	_____________193___________207\n_____________\|_____________\|\n5'-UUC...GAGGA____G________UUAAA...GUG-3'\n______________GUAA_AGAUGCGU\n______________:\|\|\|_\|:\|\|\|\|\|:\n______________UAUU_UUUACGCG\n3'-UUU...ACUAC____G________CAGAAAG-5'\n_____________\|_____________\|\n_____________21____________7\n	200 -- 206	8 -- 14	-13.6668 kcal/mol	2.47062 kcal/mol	1.23367 kcal/mol	193 207@LB@ \| \|@LB@5'-UUC...GAGGA G UUAAA...GUG-3'@LB@ GUAA AGAUGCGU@LB@ :\|\|\| \|:\|\|\|\|\|:@LB@ UAUU UUUACGCG@LB@3'-UUU...ACUAC G CAGAAAG-5'@LB@ \| \|@LB@ 21 7@LB@@LB@@LB@Energy -9.96 kcal/mol@LB@Hybridization Energy -13.6668 kcal/mol@LB@Unfolding Energy - mRNA 2.47062 kcal/mol@LB@Unfolding Energy - sRNA 1.23367 kcal/mol@LB@@LB@Position - mRNA 194 -- 206@LB@Position - sRNA 8 -- 20@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
196	0.01921	0.3104	b2167	fruA	-9.92	0.125082	150 -- 163	5 -- 22	fused fructose-specific PTS enzymes: IIBcomponent/IIC components	_____________149________________164\n_____________\|__________________\|\n5'-CGC...CGCAA__________________GACUU...AAA-3'\n______________UGAUGGC____GCGCGUC\n______________\|\|\|\|::\|____\|\|\|\|\|\|\|\n______________ACUAUUG____CGCGCAG\n3'-UUU...CUACU_______UUUA_______AAAG-5'\n_____________\|__________________\|\n_____________23_________________4\n	157 -- 163	5 -- 11	-18.2874 kcal/mol	7.11819 kcal/mol	1.25155 kcal/mol	149 164@LB@ \| \|@LB@5'-CGC...CGCAA GACUU...AAA-3'@LB@ UGAUGGC GCGCGUC@LB@ \|\|\|\|::\| \|\|\|\|\|\|\|@LB@ ACUAUUG CGCGCAG@LB@3'-UUU...CUACU UUUA AAAG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -18.2874 kcal/mol@LB@Unfolding Energy - mRNA 7.11819 kcal/mol@LB@Unfolding Energy - sRNA 1.25155 kcal/mol@LB@@LB@Position - mRNA 150 -- 163@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 5 -- 11@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@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC	_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@LB@
84	0.008129	0.3104	b2579	grcA	-9.71	0.135356	279 -- 291	5 -- 18	autonomous glycyl radical cofactor	_____________278____________292\n_____________\|______________\|\n5'-UUG...AAAAA______________GCAUC...UUG-3'\n______________GGCGAA_GCGCGUU\n______________::\|:\|\|_\|\|\|\|\|\|:\n______________UUGUUU_CGCGCAG\n3'-UUU...UACUA______A_______AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	285 -- 291	5 -- 11	-16.0784 kcal/mol	5.14159 kcal/mol	1.2243 kcal/mol	278 292@LB@ \| \|@LB@5'-UUG...AAAAA GCAUC...UUG-3'@LB@ GGCGAA GCGCGUU@LB@ ::\|:\|\| \|\|\|\|\|\|:@LB@ UUGUUU CGCGCAG@LB@3'-UUU...UACUA A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -9.71 kcal/mol@LB@Hybridization Energy -16.0784 kcal/mol@LB@Unfolding Energy - mRNA 5.14159 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 279 -- 291@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 5 -- 11@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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