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
171	0.01687	0.3104	b1512	lsrR	-11.43	0.068975	231 -- 262	7 -- 31	lsr operon transcriptional repressor	b4295	_____________230______________________________263\n_____________\|________________________________\|\n5'-GCU...CAGAA______AUGUG___A__AG_______C_____GAUCG...AGA-3'\n______________CAGGGA_____UGA_GA__AACAGGU_GCGCG\n______________\|\|\|\|\|\|_____\|\|\|_\|\|__\|\|\|\|::\|_\|\|\|\|\|\n______________GUCCCU_____ACU_CU__UUGUUUA_CGCGC\n3'-UUU...CUUAA______________A__A______________AGAAAG-5'\n_____________\|________________________________\|\n_____________32_______________________________6\n	250 -- 256	12 -- 18	-27.0439 kcal/mol	7.86672 kcal/mol	7.75103 kcal/mol	230 263@LB@ \| \|@LB@5'-GCU...CAGAA AUGUG A AG C GAUCG...AGA-3'@LB@ CAGGGA UGA GA AACAGGU GCGCG@LB@ \|\|\|\|\|\| \|\|\| \|\| \|\|\|\|::\| \|\|\|\|\|@LB@ GUCCCU ACU CU UUGUUUA CGCGC@LB@3'-UUU...CUUAA A A AGAAAG-5'@LB@ \| \|@LB@ 32 6@LB@@LB@@LB@Energy -11.43 kcal/mol@LB@Hybridization Energy -27.0439 kcal/mol@LB@Unfolding Energy - mRNA 7.86672 kcal/mol@LB@Unfolding Energy - sRNA 7.75103 kcal/mol@LB@@LB@Position - mRNA 231 -- 262@LB@Position - sRNA 7 -- 31@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 12 -- 18@LB@
172	0.01719	0.3104	b0678	nagB	-13.42	0.030481	5 -- 26	1 -- 17	glucosamine-6-phosphate deaminase		_____________4______________________27\n_____________\|______________________\|\n_______5'-UAUC______UAAAC___________GUGAG...GUC-3'\n______________GCAAAU_____GCGUGUCUUUU\n______________:\|\|\|\|\|_____\|\|\|:\|\|\|\|\|\|:\n______________UGUUUA_____CGCGCAGAAAG\n3'-UUU...ACUAU______________________-5'\n_____________\|_____________________\|\n_____________18____________________1\n	20 -- 26	1 -- 7	-18.2092 kcal/mol	3.54695 kcal/mol	1.23994 kcal/mol	4 27@LB@ \| \|@LB@ 5'-UAUC UAAAC GUGAG...GUC-3'@LB@ GCAAAU GCGUGUCUUUU@LB@ :\|\|\|\|\| \|\|\|:\|\|\|\|\|\|:@LB@ UGUUUA CGCGCAGAAAG@LB@3'-UUU...ACUAU -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.42 kcal/mol@LB@Hybridization Energy -18.2092 kcal/mol@LB@Unfolding Energy - mRNA 3.54695 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 5 -- 26@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 1 -- 7@LB@
173	0.0173	0.3104	b0145	dksA	-10.49	0.099910	175 -- 187	5 -- 21	transcriptional regulator of rRNA transcription; DnaK suppressor protein		_____________174_______________188\n_____________\|_________________\|\n5'-AAU...GGAUC_________________AAGGA...AUG-3'\n______________GAUA____GUGCGUGUU\n______________\|\|\|\|____:\|\|\|\|:\|\|:\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	181 -- 187	5 -- 11	-14.603 kcal/mol	2.85898 kcal/mol	1.24955 kcal/mol	174 188@LB@ \| \|@LB@5'-AAU...GGAUC AAGGA...AUG-3'@LB@ GAUA GUGCGUGUU@LB@ \|\|\|\| :\|\|\|\|:\|\|:@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -10.49 kcal/mol@LB@Hybridization Energy -14.603 kcal/mol@LB@Unfolding Energy - mRNA 2.85898 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 175 -- 187@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 5 -- 11@LB@
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@
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@
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@
177	0.01751	0.3104	b2900	yqfB	-9.18	0.165418	52 -- 70	1 -- 17	UPF0267 family protein		_____________51__________________71\n_____________\|___________________\|\n5'-UUC...ACGUC________U__GCC_____CCGCC...UCA-3'\n______________ACAAAUGC_CG___CUUUU\n______________\|\|\|\|\|\|\|\|_\|\|___\|\|\|\|:\n______________UGUUUACG_GC___GAAAG\n3'-UUU...ACUAU________C__A_______-5'\n_____________\|__________________\|\n_____________18_________________1\n	53 -- 59	10 -- 16	-13.5578 kcal/mol	3.13415 kcal/mol	1.23994 kcal/mol	51 71@LB@ \| \|@LB@5'-UUC...ACGUC U GCC CCGCC...UCA-3'@LB@ ACAAAUGC CG CUUUU@LB@ \|\|\|\|\|\|\|\| \|\| \|\|\|\|:@LB@ UGUUUACG GC GAAAG@LB@3'-UUU...ACUAU C A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -9.18 kcal/mol@LB@Hybridization Energy -13.5578 kcal/mol@LB@Unfolding Energy - mRNA 3.13415 kcal/mol@LB@Unfolding Energy - sRNA 1.23994 kcal/mol@LB@@LB@Position - mRNA 52 -- 70@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 10 -- 16@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@
179	0.01766	0.3104	b0377	sbmA	-9.49	0.147268	6 -- 15	3 -- 12	peptide antibiotic transporter	b1496	_____________5__________16\n_____________\|__________\|\n______5'-GAUCC_______G__AAUCC...ACU-3'\n______________UGCGCGU_UU\n______________\|\|\|\|\|\|\|_\|\|\n______________ACGCGCA_AA\n3'-UUU...UGUUU_______G__AG-5'\n_____________\|__________\|\n_____________13_________2\n	6 -- 12	6 -- 12	-14.1156 kcal/mol	3.45883 kcal/mol	1.16529 kcal/mol	5 16@LB@ \| \|@LB@ 5'-GAUCC G AAUCC...ACU-3'@LB@ UGCGCGU UU@LB@ \|\|\|\|\|\|\| \|\|@LB@ ACGCGCA AA@LB@3'-UUU...UGUUU G AG-5'@LB@ \| \|@LB@ 13 2@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -14.1156 kcal/mol@LB@Unfolding Energy - mRNA 3.45883 kcal/mol@LB@Unfolding Energy - sRNA 1.16529 kcal/mol@LB@@LB@Position - mRNA 6 -- 15@LB@Position - sRNA 3 -- 12@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 6 -- 12@LB@
180	0.01774	0.3104	b0593	entC	-14.03	0.023631	112 -- 128	4 -- 19	isochorismate synthase 1		_____________111_______________129\n_____________\|_________________\|\n5'-GGC...AGAGU_____U___________GCUUU...CAG-3'\n______________UGACA_AGUGCGCGUUU\n______________\|:\|\|\|_\|:\|\|\|\|\|\|\|:\|\n______________AUUGU_UUACGCGCAGA\n3'-UUU...CUACU_________________AAG-5'\n_____________\|_________________\|\n_____________20________________3\n	122 -- 128	4 -- 10	-18.4725 kcal/mol	3.19872 kcal/mol	1.2406 kcal/mol	111 129@LB@ \| \|@LB@5'-GGC...AGAGU U GCUUU...CAG-3'@LB@ UGACA AGUGCGCGUUU@LB@ \|:\|\|\| \|:\|\|\|\|\|\|\|:\|@LB@ AUUGU UUACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -18.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.19872 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 112 -- 128@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 4 -- 10@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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