Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
92	0.006692	0.2343	b2421	cysM	-10.79	0.009324	40 -- 63	37 -- 60	cysteine synthase B (O-acetylserine sulfhydrolase B)	_____________39_______________________64\n_____________\|________________________\|\n5'-GCU...GAUGA__________CUC___CA______CUGAU...GCA-3'\n______________GGAACUUGCU___GCA__AAGCGC\n______________\|:\|\|\|\|\|\|\|\|___\|\|\|__\|\|\|\|:\|\n______________CUUUGAACGA___CGU__UUCGUG\n3'-UUU...CCCUA__________AUU___UC______AAUUU...CAA-5'\n_____________\|________________________\|\n_____________61_______________________36\n	43 -- 49	51 -- 57	-24.0401 kcal/mol	7.00094 kcal/mol	6.24651 kcal/mol	39 64@LB@ \| \|@LB@5'-GCU...GAUGA CUC CA CUGAU...GCA-3'@LB@ GGAACUUGCU GCA AAGCGC@LB@ \|:\|\|\|\|\|\|\|\| \|\|\| \|\|\|\|:\|@LB@ CUUUGAACGA CGU UUCGUG@LB@3'-UUU...CCCUA AUU UC AAUUU...CAA-5'@LB@ \| \|@LB@ 61 36@LB@@LB@@LB@Energy -10.79 kcal/mol@LB@Hybridization Energy -24.0401 kcal/mol@LB@Unfolding Energy - mRNA 7.00094 kcal/mol@LB@Unfolding Energy - sRNA 6.24651 kcal/mol@LB@@LB@Position - mRNA 40 -- 63@LB@Position - sRNA 37 -- 60@LB@Position Seed - mRNA 43 -- 49@LB@Position Seed - sRNA 51 -- 57@LB@
102	0.008217	0.2595	b4220	tamA	-7.38	0.088103	40 -- 47	39 -- 46	translocation and assembly module for autotransporter export outer membrane subunit	_____________39_______48\n_____________\|________\|\n5'-CGC...UGUAA________GUAUU...GAC-3'\n______________CAAGAGGC\n______________\|\|\|\|\|:\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	41 -- 47	39 -- 45	-10.989 kcal/mol	0.983473 kcal/mol	2.62555 kcal/mol	39 48@LB@ \| \|@LB@5'-CGC...UGUAA GUAUU...GAC-3'@LB@ CAAGAGGC@LB@ \|\|\|\|\|:\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -10.989 kcal/mol@LB@Unfolding Energy - mRNA 0.983473 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 40 -- 47@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 39 -- 45@LB@
98	0.007325	0.239	b4171	miaA	-8.40	0.046782	42 -- 58	5 -- 24	delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase	_____________41___________________59\n_____________\|____________________\|\n5'-GAA...GUGGA____________________AGCGA...UUU-3'\n______________UUGCAC___GAAAUCUGAUG\n______________\|\|:\|\|\|___\|\|\|\|\|\|\|\|\|\|\|\n______________AAUGUG___CUUUAGACUAC\n3'-UUU...UAAGC______GUC___________ACAA-5'\n_____________\|____________________\|\n_____________25___________________4\n	52 -- 58	5 -- 11	-19.996 kcal/mol	4.00751 kcal/mol	7.58501 kcal/mol	41 59@LB@ \| \|@LB@5'-GAA...GUGGA AGCGA...UUU-3'@LB@ UUGCAC GAAAUCUGAUG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ AAUGUG CUUUAGACUAC@LB@3'-UUU...UAAGC GUC ACAA-5'@LB@ \| \|@LB@ 25 4@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -19.996 kcal/mol@LB@Unfolding Energy - mRNA 4.00751 kcal/mol@LB@Unfolding Energy - sRNA 7.58501 kcal/mol@LB@@LB@Position - mRNA 42 -- 58@LB@Position - sRNA 5 -- 24@LB@Position Seed - mRNA 52 -- 58@LB@Position Seed - sRNA 5 -- 11@LB@
108	0.009338	0.2693	b0639	nadD	-9.48	0.023112	42 -- 61	34 -- 53	nicotinic acid mononucleotide adenylyltransferase NAD(P)-dependent	_____________41___________________62\n_____________\|____________________\|\n5'-AUG...AAAUC________C___C___G___CGUCA...CGC-3'\n______________GCUUAAGU_AGA_GCA_UUA\n______________\|\|\|\|\|\|\|:_\|\|\|_\|\|\|_\|\|\|\n______________CGAAUUCG_UCU_CGU_AAU\n3'-UUU...UUGAA________U___U___G___UUUUU...CAA-5'\n_____________\|____________________\|\n_____________54___________________33\n	42 -- 48	47 -- 53	-20.1483 kcal/mol	4.55179 kcal/mol	6.11529 kcal/mol	41 62@LB@ \| \|@LB@5'-AUG...AAAUC C C G CGUCA...CGC-3'@LB@ GCUUAAGU AGA GCA UUA@LB@ \|\|\|\|\|\|\|: \|\|\| \|\|\| \|\|\|@LB@ CGAAUUCG UCU CGU AAU@LB@3'-UUU...UUGAA U U G UUUUU...CAA-5'@LB@ \| \|@LB@ 54 33@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -20.1483 kcal/mol@LB@Unfolding Energy - mRNA 4.55179 kcal/mol@LB@Unfolding Energy - sRNA 6.11529 kcal/mol@LB@@LB@Position - mRNA 42 -- 61@LB@Position - sRNA 34 -- 53@LB@Position Seed - mRNA 42 -- 48@LB@Position Seed - sRNA 47 -- 53@LB@
120	0.01039	0.2788	b2314	dedD	-6.27	0.167184	42 -- 54	45 -- 58	membrane-anchored periplasmic protein involved in septation	_____________41_____________55\n_____________\|______________\|\n5'-UUG...AGAAC______________UUUGG...AUU-3'\n______________AAC_UGCUUGAGCA\n______________\|\|\|_\|\|\|\|\|:\|\|\|\|\n______________UUG_ACGAAUUCGU\n3'-UUU...CUACU___A__________UCUUC...CAA-5'\n_____________\|______________\|\n_____________59_____________44\n	47 -- 53	46 -- 52	-15.7533 kcal/mol	3.46622 kcal/mol	6.01947 kcal/mol	41 55@LB@ \| \|@LB@5'-UUG...AGAAC UUUGG...AUU-3'@LB@ AAC UGCUUGAGCA@LB@ \|\|\| \|\|\|\|\|:\|\|\|\|@LB@ UUG ACGAAUUCGU@LB@3'-UUU...CUACU A UCUUC...CAA-5'@LB@ \| \|@LB@ 59 44@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -15.7533 kcal/mol@LB@Unfolding Energy - mRNA 3.46622 kcal/mol@LB@Unfolding Energy - sRNA 6.01947 kcal/mol@LB@@LB@Position - mRNA 42 -- 54@LB@Position - sRNA 45 -- 58@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 46 -- 52@LB@
33	0.001071	0.1045	b2058	wcaB	-10.41	0.012241	46 -- 64	25 -- 42	putative acyl transferase	_____________45__________________65\n_____________\|___________________\|\n5'-ACC...ACCGC______AA___C_______ACCGC...AGA-3'\n______________AAGCAC__AGA_AAAUUCG\n______________\|\|\|\|\|\|__\|:\|_\|\|\|\|\|\|\|\n______________UUCGUG__UUU_UUUAAGC\n3'-UUU...CGUUC______AA___________AAUGU...CAA-5'\n_____________\|___________________\|\n_____________43__________________24\n	58 -- 64	25 -- 31	-12.8013 kcal/mol	0.745291 kcal/mol	1.64855 kcal/mol	45 65@LB@ \| \|@LB@5'-ACC...ACCGC AA C ACCGC...AGA-3'@LB@ AAGCAC AGA AAAUUCG@LB@ \|\|\|\|\|\| \|:\| \|\|\|\|\|\|\|@LB@ UUCGUG UUU UUUAAGC@LB@3'-UUU...CGUUC AA AAUGU...CAA-5'@LB@ \| \|@LB@ 43 24@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -12.8013 kcal/mol@LB@Unfolding Energy - mRNA 0.745291 kcal/mol@LB@Unfolding Energy - sRNA 1.64855 kcal/mol@LB@@LB@Position - mRNA 46 -- 64@LB@Position - sRNA 25 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 25 -- 31@LB@
119	0.01022	0.2766	b0123	cueO	-7.29	0.093095	47 -- 59	29 -- 41	multicopper oxidase (laccase)	_____________46____________60\n_____________\|_____________\|\n5'-CUG...UACCA__G__________GAUAA...CGU-3'\n______________GG_GCUUAAAGAA\n______________:\|_:\|\|\|\|\|\|:\|\|\n______________UC_UGAAUUUUUU\n3'-UUU...GUUCU__G__________AAGCA...CAA-5'\n_____________\|_____________\|\n_____________42____________28\n	53 -- 59	29 -- 35	-11.0144 kcal/mol	2.10364 kcal/mol	1.62306 kcal/mol	46 60@LB@ \| \|@LB@5'-CUG...UACCA G GAUAA...CGU-3'@LB@ GG GCUUAAAGAA@LB@ :\| :\|\|\|\|\|\|:\|\|@LB@ UC UGAAUUUUUU@LB@3'-UUU...GUUCU G AAGCA...CAA-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -11.0144 kcal/mol@LB@Unfolding Energy - mRNA 2.10364 kcal/mol@LB@Unfolding Energy - sRNA 1.62306 kcal/mol@LB@@LB@Position - mRNA 47 -- 59@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 29 -- 35@LB@
200	0.02417	0.3893	b1747	astA	-6.36	0.159223	49 -- 56	39 -- 46	arginine succinyltransferase	_____________48_______57\n_____________\|________\|\n5'-GGC...UCUCU________GGCGA...AAG-3'\n______________CAGGAAGC\n______________\|\|:\|\|\|\|\|\n______________GUUCUUCG\n3'-UUU...AAUUC________UGAAU...CAA-5'\n_____________\|________\|\n_____________47_______38\n	50 -- 56	39 -- 45	-10.5455 kcal/mol	1.56403 kcal/mol	2.62555 kcal/mol	48 57@LB@ \| \|@LB@5'-GGC...UCUCU GGCGA...AAG-3'@LB@ CAGGAAGC@LB@ \|\|:\|\|\|\|\|@LB@ GUUCUUCG@LB@3'-UUU...AAUUC UGAAU...CAA-5'@LB@ \| \|@LB@ 47 38@LB@@LB@@LB@Energy -6.36 kcal/mol@LB@Hybridization Energy -10.5455 kcal/mol@LB@Unfolding Energy - mRNA 1.56403 kcal/mol@LB@Unfolding Energy - sRNA 2.62555 kcal/mol@LB@@LB@Position - mRNA 49 -- 56@LB@Position - sRNA 39 -- 46@LB@Position Seed - mRNA 50 -- 56@LB@Position Seed - sRNA 39 -- 45@LB@
24	0.000694	0.09021	b2531	iscR	-7.21	0.097486	53 -- 65	27 -- 41	isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor	_____________52______________66\n_____________\|_______________\|\n5'-AUG...AAAAU_______________AAAUA...AAC-3'\n______________GGCACU__GAAGGUU\n______________:\|\|\|\|\|__:\|\|::\|\|\n______________UCGUGA__UUUUUAA\n3'-UUU...GUUCU______AU_______GCAAU...CAA-5'\n_____________\|_______________\|\n_____________42______________26\n	59 -- 65	27 -- 33	-10.1429 kcal/mol	1.29 kcal/mol	1.6427 kcal/mol	52 66@LB@ \| \|@LB@5'-AUG...AAAAU AAAUA...AAC-3'@LB@ GGCACU GAAGGUU@LB@ :\|\|\|\|\| :\|\|::\|\|@LB@ UCGUGA UUUUUAA@LB@3'-UUU...GUUCU AU GCAAU...CAA-5'@LB@ \| \|@LB@ 42 26@LB@@LB@@LB@Energy -7.21 kcal/mol@LB@Hybridization Energy -10.1429 kcal/mol@LB@Unfolding Energy - mRNA 1.29 kcal/mol@LB@Unfolding Energy - sRNA 1.6427 kcal/mol@LB@@LB@Position - mRNA 53 -- 65@LB@Position - sRNA 27 -- 41@LB@Position Seed - mRNA 59 -- 65@LB@Position Seed - sRNA 27 -- 33@LB@
58	0.002968	0.1645	b0421	ispA	-9.70	0.019970	54 -- 76	25 -- 47	geranyltranstransferase	_____________53______________________77\n_____________\|_______________________\|\n5'-CUG...CCGCU_G__________GAAC_______AACGC...UCG-3'\n______________G_AAGAGGCGCU____GAGUUCG\n______________\|_\|\|\|\|:\|\|:\|\|____:\|:\|\|\|\|\n______________C_UUCUUCGUGA____UUUAAGC\n3'-UUU...GAAUU_G__________AUUU_______AAUGU...CAA-5'\n_____________\|_______________________\|\n_____________48______________________24\n	70 -- 76	25 -- 31	-22.3845 kcal/mol	6.43631 kcal/mol	6.25056 kcal/mol	53 77@LB@ \| \|@LB@5'-CUG...CCGCU G GAAC AACGC...UCG-3'@LB@ G AAGAGGCGCU GAGUUCG@LB@ \| \|\|\|\|:\|\|:\|\| :\|:\|\|\|\|@LB@ C UUCUUCGUGA UUUAAGC@LB@3'-UUU...GAAUU G AUUU AAUGU...CAA-5'@LB@ \| \|@LB@ 48 24@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -22.3845 kcal/mol@LB@Unfolding Energy - mRNA 6.43631 kcal/mol@LB@Unfolding Energy - sRNA 6.25056 kcal/mol@LB@@LB@Position - mRNA 54 -- 76@LB@Position - sRNA 25 -- 47@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 25 -- 31@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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