Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@LB@
136	0.00981	0.2504	b4063	soxR	-14.24	0.041834	39 -- 60	1 -- 21	redox-sensitive transcriptional activator of soxS; autorepressor		_____________38_____________________61\n_____________\|______________________\|\n5'-GCA...CGACU_______U_UU______C____CAAUA...GUA-3'\n______________ACAUCAA_G__AAGCGG_UGGU\n______________\|\|\|\|\|\|\|_\|__\|\|\|\|:\|_\|\|\|:\n______________UGUAGUU_C__UUCGUC_ACCG\n3'-UUU...ACCCC_______U_UU___________-5'\n_____________\|_____________________\|\n_____________22____________________1\n	39 -- 45	15 -- 21	-21.0533 kcal/mol	5.29766 kcal/mol	1.51103 kcal/mol	38 61@LB@ \| \|@LB@5'-GCA...CGACU U UU C CAAUA...GUA-3'@LB@ ACAUCAA G AAGCGG UGGU@LB@ \|\|\|\|\|\|\| \| \|\|\|\|:\| \|\|\|:@LB@ UGUAGUU C UUCGUC ACCG@LB@3'-UUU...ACCCC U UU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.24 kcal/mol@LB@Hybridization Energy -21.0533 kcal/mol@LB@Unfolding Energy - mRNA 5.29766 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 39 -- 60@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 39 -- 45@LB@Position Seed - sRNA 15 -- 21@LB@
145	0.01066	0.2504	b2153	folE	-11.37	0.162147	44 -- 68	1 -- 21	GTP cyclohydrolase I		_____________43________________________69\n_____________\|_________________________\|\n5'-CUG...UUUUA_____UGCU__U_________C___AAUUA...ACG-3'\n______________ACAUC____GA_GAAAGGCAG_GGC\n______________\|\|\|\|\|____:\|_\|\|\|\|:\|\|\|\|_\|\|\|\n______________UGUAG____UU_CUUUUCGUC_CCG\n3'-UUU...ACCCC___________U_________A___-5'\n_____________\|________________________\|\n_____________22_______________________1\n	58 -- 64	5 -- 11	-23.5216 kcal/mol	10.6442 kcal/mol	1.51103 kcal/mol	43 69@LB@ \| \|@LB@5'-CUG...UUUUA UGCU U C AAUUA...ACG-3'@LB@ ACAUC GA GAAAGGCAG GGC@LB@ \|\|\|\|\| :\| \|\|\|\|:\|\|\|\| \|\|\|@LB@ UGUAG UU CUUUUCGUC CCG@LB@3'-UUU...ACCCC U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -23.5216 kcal/mol@LB@Unfolding Energy - mRNA 10.6442 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 44 -- 68@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G		_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@LB@
141	0.01037	0.2504	b2161	nupX	-15.31	0.023296	54 -- 80	1 -- 26	nucleoside permease	b2164	_____________53____________________________81\n_____________\|_____________________________\|\n5'-UUG...GGUUC_______UA_________U_______C__GGCUA...GCG-3'\n______________UGGGGAU__GUCGAAGAG__GC_GUG_GC\n______________\|\|\|\|\|\|:__:\|\|:\|\|\|\|:__\|\|_\|\|\|_\|\|\n______________ACCCCUG__UAGUUUCUU__CG_CAC_CG\n3'-UUU...GUUUU__________________UU__U______-5'\n_____________\|____________________________\|\n_____________27___________________________1\n	65 -- 71	11 -- 17	-27.7009 kcal/mol	9.87339 kcal/mol	2.51842 kcal/mol	53 81@LB@ \| \|@LB@5'-UUG...GGUUC UA U C GGCUA...GCG-3'@LB@ UGGGGAU GUCGAAGAG GC GUG GC@LB@ \|\|\|\|\|\|: :\|\|:\|\|\|\|: \|\| \|\|\| \|\|@LB@ ACCCCUG UAGUUUCUU CG CAC CG@LB@3'-UUU...GUUUU UU U -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.7009 kcal/mol@LB@Unfolding Energy - mRNA 9.87339 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 11 -- 17@LB@
152	0.01123	0.2504	b1872	torZ	-17.40	0.006326	76 -- 107	1 -- 34	trimethylamine N-oxide reductase system III catalytic subunit	b0997 b3551	_____________75___________________________________108\n_____________\|____________________________________\|\n5'-ACG...CAUUG___AA_________________CC_________A__GAAAA...AGA-3'\n______________CCA__GGAAUGGGGGCA_CGAA____AGCA_UG_GC\n______________\|\|\|__::\|\|\|\|\|\|\|:\|\|_\|:\|\|____\|\|\|\|_\|\|_\|\|\n______________GGU__UUUUACCCCUGU_GUUU____UCGU_AC_CG\n3'-UUU...CCCGA___G_____________A____CUUU____C_____-5'\n_____________\|___________________________________\|\n_____________35__________________________________1\n	86 -- 92	19 -- 25	-29.6219 kcal/mol	7.95271 kcal/mol	4.26884 kcal/mol	75 108@LB@ \| \|@LB@5'-ACG...CAUUG AA CC A GAAAA...AGA-3'@LB@ CCA GGAAUGGGGGCA CGAA AGCA UG GC@LB@ \|\|\| ::\|\|\|\|\|\|\|:\|\| \|:\|\| \|\|\|\| \|\| \|\|@LB@ GGU UUUUACCCCUGU GUUU UCGU AC CG@LB@3'-UUU...CCCGA G A CUUU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -29.6219 kcal/mol@LB@Unfolding Energy - mRNA 7.95271 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 76 -- 107@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 19 -- 25@LB@
155	0.01136	0.2504	b2168	fruK	-7.75	0.545043	91 -- 105	7 -- 22	fructose-1-phosphate kinase		_____________90_______________106\n_____________\|________________\|\n5'-AAA...CACUU________________CAUCG...CCA-3'\n______________GGCGUU_AAGAAAGGU\n______________\|:\|:\|:_\|\|\|\|\|\|:\|:\n______________CUGUAG_UUCUUUUCG\n3'-UUU...UACCC______U_________UCACCG-5'\n_____________\|________________\|\n_____________23_______________6\n	99 -- 105	7 -- 13	-14.0922 kcal/mol	5.75103 kcal/mol	0.590875 kcal/mol	90 106@LB@ \| \|@LB@5'-AAA...CACUU CAUCG...CCA-3'@LB@ GGCGUU AAGAAAGGU@LB@ \|:\|:\|: \|\|\|\|\|\|:\|:@LB@ CUGUAG UUCUUUUCG@LB@3'-UUU...UACCC U UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -7.75 kcal/mol@LB@Hybridization Energy -14.0922 kcal/mol@LB@Unfolding Energy - mRNA 5.75103 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 91 -- 105@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 99 -- 105@LB@Position Seed - sRNA 7 -- 13@LB@
164	0.01206	0.2504	b0882	clpA	-9.12	0.369525	95 -- 107	48 -- 60	ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity		_____________94____________108\n_____________\|_____________\|\n5'-UUU...GCAGA____A________AUGGU...CGC-3'\n______________AACC_AAGUGGCG\n______________\|\|\|\|_\|\|:\|\|\|\|\|\n______________UUGG_UUUACCGC\n3'-UUU...GGAAC____C________CCCAA...CCG-5'\n_____________\|_____________\|\n_____________61____________47\n	101 -- 107	48 -- 54	-16.8445 kcal/mol	3.76103 kcal/mol	3.96136 kcal/mol	94 108@LB@ \| \|@LB@5'-UUU...GCAGA A AUGGU...CGC-3'@LB@ AACC AAGUGGCG@LB@ \|\|\|\| \|\|:\|\|\|\|\|@LB@ UUGG UUUACCGC@LB@3'-UUU...GGAAC C CCCAA...CCG-5'@LB@ \| \|@LB@ 61 47@LB@@LB@@LB@Energy -9.12 kcal/mol@LB@Hybridization Energy -16.8445 kcal/mol@LB@Unfolding Energy - mRNA 3.76103 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 48 -- 60@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 48 -- 54@LB@
183	0.01318	0.2504	b4483	tatD	-12.95	0.080004	100 -- 117	8 -- 25	quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase		_____________99__________________118\n_____________\|___________________\|\n5'-CUG...GUAAA___C__A____________GAAAA...UCA-3'\n______________GGG_GA_AUC_GGGAAGAG\n______________\|\|\|_\|\|_\|\|\|_::\|\|\|:\|\|\n______________CCC_CU_UAG_UUCUUUUC\n3'-UUU...UUUUA______G___U________GUCACCG-5'\n_____________\|___________________\|\n_____________26__________________7\n	111 -- 117	8 -- 14	-16.1661 kcal/mol	2.51597 kcal/mol	0.697717 kcal/mol	99 118@LB@ \| \|@LB@5'-CUG...GUAAA C A GAAAA...UCA-3'@LB@ GGG GA AUC GGGAAGAG@LB@ \|\|\| \|\| \|\|\| ::\|\|\|:\|\|@LB@ CCC CU UAG UUCUUUUC@LB@3'-UUU...UUUUA G U GUCACCG-5'@LB@ \| \|@LB@ 26 7@LB@@LB@@LB@Energy -12.95 kcal/mol@LB@Hybridization Energy -16.1661 kcal/mol@LB@Unfolding Energy - mRNA 2.51597 kcal/mol@LB@Unfolding Energy - sRNA 0.697717 kcal/mol@LB@@LB@Position - mRNA 100 -- 117@LB@Position - sRNA 8 -- 25@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 8 -- 14@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein		_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@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)

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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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