Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
102	0.005508	0.1855	b0659	ybeY	-7.73	0.351978	30 -- 54	64 -- 89	ssRNA-specific endoribonuclease; 16S rRNA 3' end maturation and quality control co-endoribonuclease working with RNase R; rRNA transcription antitermination factor		_____________29_________________________55\n_____________\|__________________________\|\n5'-ACU...AUCGA__________________AA______AGCUU...CGC-3'\n______________AGUGCUG_GCCGAUGUCG__GAGAUC\n______________\|:\|:\|\|\|_\|\|\|:\|:::\|:__\|\|:\|\|\|\n______________UUAUGAC_CGGUUGUGGU__CUUUAG\n3'-UUU...CGCGC_______G__________CC______AACCG...GUG-5'\n_____________\|__________________________\|\n_____________90_________________________63\n	30 -- 36	83 -- 89	-23.8058 kcal/mol	8.19456 kcal/mol	7.88317 kcal/mol	29 55@LB@ \| \|@LB@5'-ACU...AUCGA AA AGCUU...CGC-3'@LB@ AGUGCUG GCCGAUGUCG GAGAUC@LB@ \|:\|:\|\|\| \|\|\|:\|:::\|: \|\|:\|\|\|@LB@ UUAUGAC CGGUUGUGGU CUUUAG@LB@3'-UUU...CGCGC G CC AACCG...GUG-5'@LB@ \| \|@LB@ 90 63@LB@@LB@@LB@Energy -7.73 kcal/mol@LB@Hybridization Energy -23.8058 kcal/mol@LB@Unfolding Energy - mRNA 8.19456 kcal/mol@LB@Unfolding Energy - sRNA 7.88317 kcal/mol@LB@@LB@Position - mRNA 30 -- 54@LB@Position - sRNA 64 -- 89@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 83 -- 89@LB@
157	0.009216	0.2062	b3361	fic	-9.77	0.153316	103 -- 112	5 -- 14	stationary phase-induced protein putative toxin		_____________102________113\n_____________\|__________\|\n5'-CGC...CGUAA__________AGUCG...AAC-3'\n______________UUUUCAGGCC\n______________\|\|\|\|\|\|\|\|\|\|\n______________AAAAGUCCGG\n3'-UUU...UGACA__________CGUG-5'\n_____________\|__________\|\n_____________15_________4\n	106 -- 112	5 -- 11	-15.6889 kcal/mol	1.64573 kcal/mol	4.24834 kcal/mol	102 113@LB@ \| \|@LB@5'-CGC...CGUAA AGUCG...AAC-3'@LB@ UUUUCAGGCC@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ AAAAGUCCGG@LB@3'-UUU...UGACA CGUG-5'@LB@ \| \|@LB@ 15 4@LB@@LB@@LB@Energy -9.77 kcal/mol@LB@Hybridization Energy -15.6889 kcal/mol@LB@Unfolding Energy - mRNA 1.64573 kcal/mol@LB@Unfolding Energy - sRNA 4.24834 kcal/mol@LB@@LB@Position - mRNA 103 -- 112@LB@Position - sRNA 5 -- 14@LB@Position Seed - mRNA 106 -- 112@LB@Position Seed - sRNA 5 -- 11@LB@
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit		_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
27	0.001577	0.1727	b1679	sufE	-9.94	0.142549	247 -- 262	68 -- 86	sulfur acceptor protein		_____________246_________________263\n_____________\|___________________\|\n5'-AUG...UUUAC___________U_______AGAGA...GUC-3'\n______________GCUGCGCCAAC____GGGA\n______________:\|\|\|\|\|\|\|\|\|\|____\|\|\|\|\n______________UGACGCGGUUG____CCCU\n3'-UUU...GCUUA___________UGGU____UUAGA...GUG-5'\n_____________\|___________________\|\n_____________87__________________67\n	251 -- 257	76 -- 82	-25.4399 kcal/mol	8.12138 kcal/mol	7.37523 kcal/mol	246 263@LB@ \| \|@LB@5'-AUG...UUUAC U AGAGA...GUC-3'@LB@ GCUGCGCCAAC GGGA@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UGACGCGGUUG CCCU@LB@3'-UUU...GCUUA UGGU UUAGA...GUG-5'@LB@ \| \|@LB@ 87 67@LB@@LB@@LB@Energy -9.94 kcal/mol@LB@Hybridization Energy -25.4399 kcal/mol@LB@Unfolding Energy - mRNA 8.12138 kcal/mol@LB@Unfolding Energy - sRNA 7.37523 kcal/mol@LB@@LB@Position - mRNA 247 -- 262@LB@Position - sRNA 68 -- 86@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 76 -- 82@LB@
167	0.009922	0.2071	b0367	tauC	-5.98	0.628340	152 -- 162	85 -- 95	taurine ABC transporter permease		_____________151_________163\n_____________\|___________\|\n5'-AUA...CGCCA___________GUUUU...UUU-3'\n______________UGCGCGAAUAU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________ACGCGCUUAUG\n3'-UUU...GCCCC___________ACGCG...GUG-5'\n_____________\|___________\|\n_____________96__________84\n	154 -- 160	87 -- 93	-16.0697 kcal/mol	4.17782 kcal/mol	5.90856 kcal/mol	151 163@LB@ \| \|@LB@5'-AUA...CGCCA GUUUU...UUU-3'@LB@ UGCGCGAAUAU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ ACGCGCUUAUG@LB@3'-UUU...GCCCC ACGCG...GUG-5'@LB@ \| \|@LB@ 96 84@LB@@LB@@LB@Energy -5.98 kcal/mol@LB@Hybridization Energy -16.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.17782 kcal/mol@LB@Unfolding Energy - sRNA 5.90856 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 85 -- 95@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 87 -- 93@LB@
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit		_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
145	0.008374	0.2033	b0068	thiB	-7.61	0.367750	229 -- 244	73 -- 87	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein		_____________228______________245\n_____________\|________________\|\n5'-UUU...GCUGU________A_______CGUUU...ACU-3'\n______________UGCUGUGC_CAGCGCC\n______________\|:\|\|\|:\|\|_\|\|:\|:\|\|\n______________AUGACGCG_GUUGUGG\n3'-UUU...CGCUU________________UCCCU...GUG-5'\n_____________\|________________\|\n_____________88_______________72\n	230 -- 236	80 -- 86	-23.483 kcal/mol	8.91653 kcal/mol	6.95602 kcal/mol	228 245@LB@ \| \|@LB@5'-UUU...GCUGU A CGUUU...ACU-3'@LB@ UGCUGUGC CAGCGCC@LB@ \|:\|\|\|:\|\| \|\|:\|:\|\|@LB@ AUGACGCG GUUGUGG@LB@3'-UUU...CGCUU UCCCU...GUG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -7.61 kcal/mol@LB@Hybridization Energy -23.483 kcal/mol@LB@Unfolding Energy - mRNA 8.91653 kcal/mol@LB@Unfolding Energy - sRNA 6.95602 kcal/mol@LB@@LB@Position - mRNA 229 -- 244@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 80 -- 86@LB@
79	0.004357	0.1855	b0008	talB	-10.61	0.106795	240 -- 280	50 -- 88	transaldolase B		_____________239________________________________________281\n_____________\|__________________________________________\|\n5'-AGG...CCACC___G_________________C___GC___AAUGAA______UCAAC...CAA-3'\n______________GUA_UG_GCCGACACUGGGGA_AUC__GGC______GCUGUA\n______________:\|\|_\|\|_\|\|\|:\|\|\|\|::\|\|\|\|_\|\|\|__\|\|\|______\|\|:\|\|\|\n______________UAU_AC_CGGUUGUGGUCCCU_UAG__CCG______CGGCAU\n3'-UUU...GCGCU___G__G______________U___AA___ACG_________UUAAU...GUG-5'\n_____________\|__________________________________________\|\n_____________89_________________________________________49\n	253 -- 259	68 -- 74	-44.9099 kcal/mol	17.4497 kcal/mol	16.8544 kcal/mol	239 281@LB@ \| \|@LB@5'-AGG...CCACC G C GC AAUGAA UCAAC...CAA-3'@LB@ GUA UG GCCGACACUGGGGA AUC GGC GCUGUA@LB@ :\|\| \|\| \|\|\|:\|\|\|\|::\|\|\|\| \|\|\| \|\|\| \|\|:\|\|\|@LB@ UAU AC CGGUUGUGGUCCCU UAG CCG CGGCAU@LB@3'-UUU...GCGCU G G U AA ACG UUAAU...GUG-5'@LB@ \| \|@LB@ 89 49@LB@@LB@@LB@Energy -10.61 kcal/mol@LB@Hybridization Energy -44.9099 kcal/mol@LB@Unfolding Energy - mRNA 17.4497 kcal/mol@LB@Unfolding Energy - sRNA 16.8544 kcal/mol@LB@@LB@Position - mRNA 240 -- 280@LB@Position - sRNA 50 -- 88@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 68 -- 74@LB@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
71	0.003482	0.1727	b4046	zur	-8.96	0.216158	254 -- 300	53 -- 94	transcriptional repressor Zn(II)-binding		_____________253__________________________________________________300\n_____________\|____________________________________________________\|\n5'-UAA...UGCGC__A___U___________UGACCCCAC______U___________________-3'\n______________GC_GCG_AAUG_UGCGCC_________AGCGCC__GGAAGU____GUUGCGCC\n______________\|\|_\|\|\|_\|\|\|:_\|\|\|\|\|\|_________\|:\|:\|\|__\|\|\|\|:\|____\|:\|\|\|\|\|\|\n______________CG_CGC_UUAU_ACGCGG_________UUGUGG__CCUUUA____CGACGCGG\n3'-UUU...CCCCA___________G_____________________UC______GAAC________CAUUU...GUG-5'\n_____________\|_____________________________________________________\|\n_____________95____________________________________________________52\n	294 -- 300	53 -- 59	-43.5981 kcal/mol	17.5702 kcal/mol	17.0684 kcal/mol	253 300@LB@ \| \|@LB@5'-UAA...UGCGC A U UGACCCCAC U -3'@LB@ GC GCG AAUG UGCGCC AGCGCC GGAAGU GUUGCGCC@LB@ \|\| \|\|\| \|\|\|: \|\|\|\|\|\| \|:\|:\|\| \|\|\|\|:\| \|:\|\|\|\|\|\|@LB@ CG CGC UUAU ACGCGG UUGUGG CCUUUA CGACGCGG@LB@3'-UUU...CCCCA G UC GAAC CAUUU...GUG-5'@LB@ \| \|@LB@ 95 52@LB@@LB@@LB@Energy -8.96 kcal/mol@LB@Hybridization Energy -43.5981 kcal/mol@LB@Unfolding Energy - mRNA 17.5702 kcal/mol@LB@Unfolding Energy - sRNA 17.0684 kcal/mol@LB@@LB@Position - mRNA 254 -- 300@LB@Position - sRNA 53 -- 94@LB@Position Seed - mRNA 294 -- 300@LB@Position Seed - sRNA 53 -- 59@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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