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
95	0.005084	0.1855	b3182	dacB	-12.18	0.052827	253 -- 263	2 -- 12	D-alanyl-D-alanine carboxypeptidase		_____________252_________264\n_____________\|___________\|\n5'-CCG...CAGUG___________AAUGU...GUG-3'\n______________UUCAGGCCGCA\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________AAGUCCGGCGU\n3'-UUU...ACAAA___________G-5'\n_____________\|___________\|\n_____________13__________1\n	257 -- 263	2 -- 8	-21.5619 kcal/mol	3.68722 kcal/mol	5.66926 kcal/mol	252 264@LB@ \| \|@LB@5'-CCG...CAGUG AAUGU...GUG-3'@LB@ UUCAGGCCGCA@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ AAGUCCGGCGU@LB@3'-UUU...ACAAA G-5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -21.5619 kcal/mol@LB@Unfolding Energy - mRNA 3.68722 kcal/mol@LB@Unfolding Energy - sRNA 5.66926 kcal/mol@LB@@LB@Position - mRNA 253 -- 263@LB@Position - sRNA 2 -- 12@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 2 -- 8@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@
94	0.005015	0.1855	b2703	srlE	-7.35	0.404948	254 -- 271	70 -- 86	glucitol/sorbitol-specific enzyme IIB component of PTS		_____________253_________________272\n_____________\|___________________\|\n5'-GAA...CUUGA____AAA____________AAAAA...GUA-3'\n______________GCUG___GCC_ACGCCGGG\n______________:\|\|\|___\|\|\|_\|\|:\|\|:\|\|\n______________UGAC___CGG_UGUGGUCC\n3'-UUU...GCUUA____G_____U________CUUUA...GUG-5'\n_____________\|___________________\|\n_____________87__________________69\n	265 -- 271	70 -- 76	-23.089 kcal/mol	8.46506 kcal/mol	7.27772 kcal/mol	253 272@LB@ \| \|@LB@5'-GAA...CUUGA AAA AAAAA...GUA-3'@LB@ GCUG GCC ACGCCGGG@LB@ :\|\|\| \|\|\| \|\|:\|\|:\|\|@LB@ UGAC CGG UGUGGUCC@LB@3'-UUU...GCUUA G U CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -7.35 kcal/mol@LB@Hybridization Energy -23.089 kcal/mol@LB@Unfolding Energy - mRNA 8.46506 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 254 -- 271@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 70 -- 76@LB@
134	0.007678	0.1993	b3139	agaC	-7.83	0.338422	255 -- 275	57 -- 74	N-acetylgalactosamine-specific enzyme IIC component of PTS		_____________254___________________276\n_____________\|_____________________\|\n5'-AAC...UUGUU_______UUGAU_________GAAGC...CGA-3'\n______________CUGGGGA_____UUUUGGCUG\n______________\|::\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________GGUCCCU_____AGAACCGAC\n3'-UUU...GUUGU_______UU____________GCGGC...GUG-5'\n_____________\|_____________________\|\n_____________75____________________56\n	269 -- 275	57 -- 63	-21.9136 kcal/mol	6.09668 kcal/mol	7.9843 kcal/mol	254 276@LB@ \| \|@LB@5'-AAC...UUGUU UUGAU GAAGC...CGA-3'@LB@ CUGGGGA UUUUGGCUG@LB@ \|::\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GGUCCCU AGAACCGAC@LB@3'-UUU...GUUGU UU GCGGC...GUG-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -21.9136 kcal/mol@LB@Unfolding Energy - mRNA 6.09668 kcal/mol@LB@Unfolding Energy - sRNA 7.9843 kcal/mol@LB@@LB@Position - mRNA 255 -- 275@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 57 -- 63@LB@
84	0.004676	0.1855	b0526	cysS	-14.43	0.019007	256 -- 269	64 -- 77	cysteinyl-tRNA synthetase		_____________255____________270\n_____________\|______________\|\n5'-GCC...UAUUC______________GGCAU...ACG-3'\n______________ACGCCGGGGAAGUC\n______________\|\|:\|\|:\|\|\|\|\|:\|\|\n______________UGUGGUCCCUUUAG\n3'-UUU...GCGGU______________AACCG...GUG-5'\n_____________\|______________\|\n_____________78_____________63\n	263 -- 269	64 -- 70	-23.2043 kcal/mol	4.03864 kcal/mol	4.72709 kcal/mol	255 270@LB@ \| \|@LB@5'-GCC...UAUUC GGCAU...ACG-3'@LB@ ACGCCGGGGAAGUC@LB@ \|\|:\|\|:\|\|\|\|\|:\|\|@LB@ UGUGGUCCCUUUAG@LB@3'-UUU...GCGGU AACCG...GUG-5'@LB@ \| \|@LB@ 78 63@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -23.2043 kcal/mol@LB@Unfolding Energy - mRNA 4.03864 kcal/mol@LB@Unfolding Energy - sRNA 4.72709 kcal/mol@LB@@LB@Position - mRNA 256 -- 269@LB@Position - sRNA 64 -- 77@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 64 -- 70@LB@
179	0.01058	0.208	b1325	ycjG	-11.81	0.062523	258 -- 297	32 -- 77	L-Ala-D/L-Glu epimerase		_____________257_______________________________________________298\n_____________\|_________________________________________________\|\n5'-AAG...UGAUU______________GCA__GAA____G______________________AAC-3'\n______________GC_CCGGGGAAGUC___GU___GCGC_CGUG_______GUGGUG_GUUG\n______________:\|_\|\|:\|\|\|\|\|:\|\|___\|:___\|\|\|\|_\|\|\|:_______:\|\|:\|\|_\|\|\|:\n______________UG_GGUCCCUUUAG___CG___CGCG_GCAU_______UACUAC_CAAU\n3'-UUU...GCGGU__U___________AAC__A___________UUAAUAA______U____GUUCC...GUG-5'\n_____________\|_________________________________________________\|\n_____________78________________________________________________31\n	264 -- 270	64 -- 70	-38.4326 kcal/mol	17.2613 kcal/mol	9.36253 kcal/mol	257 298@LB@ \| \|@LB@5'-AAG...UGAUU GCA GAA G AAC-3'@LB@ GC CCGGGGAAGUC GU GCGC CGUG GUGGUG GUUG@LB@ :\| \|\|:\|\|\|\|\|:\|\| \|: \|\|\|\| \|\|\|: :\|\|:\|\| \|\|\|:@LB@ UG GGUCCCUUUAG CG CGCG GCAU UACUAC CAAU@LB@3'-UUU...GCGGU U AAC A UUAAUAA U GUUCC...GUG-5'@LB@ \| \|@LB@ 78 31@LB@@LB@@LB@Energy -11.81 kcal/mol@LB@Hybridization Energy -38.4326 kcal/mol@LB@Unfolding Energy - mRNA 17.2613 kcal/mol@LB@Unfolding Energy - sRNA 9.36253 kcal/mol@LB@@LB@Position - mRNA 258 -- 297@LB@Position - sRNA 32 -- 77@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 64 -- 70@LB@
43	0.002187	0.1727	b2222	atoA	-7.38	0.400797	260 -- 273	68 -- 82	acetyl-CoA:acetoacetyl-CoA transferase beta subunit		_____________259_____________274\n_____________\|_______________\|\n5'-CGC...GACAU_______________UCGGU...AUU-3'\n______________CGUUAAC_UUAGGGA\n______________\|\|::\|\|\|_::\|\|\|\|\|\n______________GCGGUUG_GGUCCCU\n3'-UUU...AUGAC_______U_______UUAGA...GUG-5'\n_____________\|_______________\|\n_____________83______________67\n	267 -- 273	68 -- 74	-16.5153 kcal/mol	2.15948 kcal/mol	6.98098 kcal/mol	259 274@LB@ \| \|@LB@5'-CGC...GACAU UCGGU...AUU-3'@LB@ CGUUAAC UUAGGGA@LB@ \|\|::\|\|\| ::\|\|\|\|\|@LB@ GCGGUUG GGUCCCU@LB@3'-UUU...AUGAC U UUAGA...GUG-5'@LB@ \| \|@LB@ 83 67@LB@@LB@@LB@Energy -7.38 kcal/mol@LB@Hybridization Energy -16.5153 kcal/mol@LB@Unfolding Energy - mRNA 2.15948 kcal/mol@LB@Unfolding Energy - sRNA 6.98098 kcal/mol@LB@@LB@Position - mRNA 260 -- 273@LB@Position - sRNA 68 -- 82@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 68 -- 74@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent		_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@LB@
74	0.003792	0.1804	b2520	yfhM	-12.28	0.050623	263 -- 298	53 -- 91	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein		_____________262_____________________________________299\n_____________\|_______________________________________\|\n5'-CUC...AACAA___UA____________G___U____AAAGA________UU-3'\n______________CGA__AC_GCGCCAACA_CGG_GAAA_______UGCGCC\n______________\|\|\|__\|\|_\|\|\|\|\|\|\|\|\|_\|:\|_\|\|\|\|_______\|\|\|\|\|\|\n______________GCU__UG_CGCGGUUGU_GUC_CUUU_______ACGCGG\n3'-UUU...CACGC___UA__A_________G___C____AGAACCG______CAUUU...GUG-5'\n_____________\|_______________________________________\|\n_____________92______________________________________52\n	272 -- 278	75 -- 81	-39.9109 kcal/mol	10.9563 kcal/mol	16.677 kcal/mol	262 299@LB@ \| \|@LB@5'-CUC...AACAA UA G U AAAGA UU-3'@LB@ CGA AC GCGCCAACA CGG GAAA UGCGCC@LB@ \|\|\| \|\| \|\|\|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|\|\|\|\|@LB@ GCU UG CGCGGUUGU GUC CUUU ACGCGG@LB@3'-UUU...CACGC UA A G C AGAACCG CAUUU...GUG-5'@LB@ \| \|@LB@ 92 52@LB@@LB@@LB@Energy -12.28 kcal/mol@LB@Hybridization Energy -39.9109 kcal/mol@LB@Unfolding Energy - mRNA 10.9563 kcal/mol@LB@Unfolding Energy - sRNA 16.677 kcal/mol@LB@@LB@Position - mRNA 263 -- 298@LB@Position - sRNA 53 -- 91@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 75 -- 81@LB@
125	0.006795	0.1914	b3003	yghA	-11.52	0.071261	264 -- 274	70 -- 80	putative oxidoreductase	b2902	_____________263_________275\n_____________\|___________\|\n5'-AAC...AACAA___________CAUCC...UAC-3'\n______________CCGACGCCAGG\n______________\|\|:\|\|:\|\|\|\|\|\n______________GGUUGUGGUCC\n3'-UUU...GACGC___________CUUUA...GUG-5'\n_____________\|___________\|\n_____________81__________69\n	268 -- 274	70 -- 76	-20.3781 kcal/mol	2.1599 kcal/mol	6.70146 kcal/mol	263 275@LB@ \| \|@LB@5'-AAC...AACAA CAUCC...UAC-3'@LB@ CCGACGCCAGG@LB@ \|\|:\|\|:\|\|\|\|\|@LB@ GGUUGUGGUCC@LB@3'-UUU...GACGC CUUUA...GUG-5'@LB@ \| \|@LB@ 81 69@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -20.3781 kcal/mol@LB@Unfolding Energy - mRNA 2.1599 kcal/mol@LB@Unfolding Energy - sRNA 6.70146 kcal/mol@LB@@LB@Position - mRNA 264 -- 274@LB@Position - sRNA 70 -- 80@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 70 -- 76@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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