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
81	0.004478	0.1855	b3327	gspF	-8.77	0.233220	243 -- 251	26 -- 34	general secretory pathway component cryptic	_____________242_______252\n_____________\|_________\|\n5'-AUG...AAAAA_________AUCAU...AAG-3'\n______________UUGCAAGGG\n______________\|\|:\|\|\|\|\|\|\n______________AAUGUUCCC\n3'-UUU...UACUC_________GUGUC...GUG-5'\n_____________\|_________\|\n_____________35________25\n	245 -- 251	26 -- 32	-12.3281 kcal/mol	0.874927 kcal/mol	2.67841 kcal/mol	242 252@LB@ \| \|@LB@5'-AUG...AAAAA AUCAU...AAG-3'@LB@ UUGCAAGGG@LB@ \|\|:\|\|\|\|\|\|@LB@ AAUGUUCCC@LB@3'-UUU...UACUC GUGUC...GUG-5'@LB@ \| \|@LB@ 35 25@LB@@LB@@LB@Energy -8.77 kcal/mol@LB@Hybridization Energy -12.3281 kcal/mol@LB@Unfolding Energy - mRNA 0.874927 kcal/mol@LB@Unfolding Energy - sRNA 2.67841 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 26 -- 34@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 26 -- 32@LB@
104	0.005642	0.1855	b1476	fdnI	-8.74	0.236866	280 -- 291	51 -- 62	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________279__________292\n_____________\|____________\|\n5'-CGU...CUUCC____G_______CCGGG...UUU-3'\n______________UGGU_GCGCUGU\n______________\|\|\|:_\|\|\|\|:\|\|\n______________ACCG_CGCGGCA\n3'-UUU...UUAGA____A_______UUUAA...GUG-5'\n_____________\|____________\|\n_____________63___________50\n	285 -- 291	51 -- 57	-16.7644 kcal/mol	3.14516 kcal/mol	4.8826 kcal/mol	279 292@LB@ \| \|@LB@5'-CGU...CUUCC G CCGGG...UUU-3'@LB@ UGGU GCGCUGU@LB@ \|\|\|: \|\|\|\|:\|\|@LB@ ACCG CGCGGCA@LB@3'-UUU...UUAGA A UUUAA...GUG-5'@LB@ \| \|@LB@ 63 50@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -16.7644 kcal/mol@LB@Unfolding Energy - mRNA 3.14516 kcal/mol@LB@Unfolding Energy - sRNA 4.8826 kcal/mol@LB@@LB@Position - mRNA 280 -- 291@LB@Position - sRNA 51 -- 62@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 51 -- 57@LB@
64	0.003238	0.1727	b2578	eamB	-8.70	0.240388	240 -- 262	70 -- 85	cysteine and O-acetylserine exporter	_____________239_____________________263\n_____________\|_______________________\|\n5'-GUC...ACACC___AUUAC____AU_________ACCGA...CGC-3'\n______________CUG_____CGCU__GACGCCAGG\n______________\|\|\|_____\|\|\|:__:\|\|:\|\|\|\|\|\n______________GAC_____GCGG__UUGUGGUCC\n3'-UUU...CUUAU_______________________CUUUA...GUG-5'\n_____________\|_______________________\|\n_____________86______________________69\n	256 -- 262	70 -- 76	-20.6717 kcal/mol	4.69447 kcal/mol	7.27689 kcal/mol	239 263@LB@ \| \|@LB@5'-GUC...ACACC AUUAC AU ACCGA...CGC-3'@LB@ CUG CGCU GACGCCAGG@LB@ \|\|\| \|\|\|: :\|\|:\|\|\|\|\|@LB@ GAC GCGG UUGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -20.6717 kcal/mol@LB@Unfolding Energy - mRNA 4.69447 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 70 -- 76@LB@
162	0.009519	0.2068	b4167	nnr	-8.70	0.240671	167 -- 176	76 -- 85	bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase	_____________166________177\n_____________\|__________\|\n5'-ACU...AUUUU__________UGAUU...UGC-3'\n______________UUGCGCUAAC\n______________:\|\|\|\|\|:\|\|\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	170 -- 176	76 -- 82	-14.3794 kcal/mol	0.586298 kcal/mol	5.09564 kcal/mol	166 177@LB@ \| \|@LB@5'-ACU...AUUUU UGAUU...UGC-3'@LB@ UUGCGCUAAC@LB@ :\|\|\|\|\|:\|\|\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -14.3794 kcal/mol@LB@Unfolding Energy - mRNA 0.586298 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 167 -- 176@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 76 -- 82@LB@
101	0.005473	0.1855	b1129	phoQ	-8.66	0.244665	211 -- 219	79 -- 87	sensory histidine kinase in two-component regulatory system with PhoP	_____________210_______220\n_____________\|_________\|\n5'-AUG...AAAAU_________UUUUU...GAA-3'\n______________UACUGCGUC\n______________\|\|\|\|\|\|\|:\|\n______________AUGACGCGG\n3'-UUU...CGCUU_________UUGUG...GUG-5'\n_____________\|_________\|\n_____________88________78\n	213 -- 219	79 -- 85	-14.7172 kcal/mol	1.01485 kcal/mol	5.0453 kcal/mol	210 220@LB@ \| \|@LB@5'-AUG...AAAAU UUUUU...GAA-3'@LB@ UACUGCGUC@LB@ \|\|\|\|\|\|\|:\|@LB@ AUGACGCGG@LB@3'-UUU...CGCUU UUGUG...GUG-5'@LB@ \| \|@LB@ 88 78@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -14.7172 kcal/mol@LB@Unfolding Energy - mRNA 1.01485 kcal/mol@LB@Unfolding Energy - sRNA 5.0453 kcal/mol@LB@@LB@Position - mRNA 211 -- 219@LB@Position - sRNA 79 -- 87@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 79 -- 85@LB@
136	0.007706	0.1993	b2188	yejM	-8.60	0.250530	107 -- 119	70 -- 83	essential inner membrane DUF3413 domain-containing protein; lipid A production and membrane permeability factor	_____________106____________120\n_____________\|______________\|\n5'-CGC...CCCCG______________CAAUU...UUG-3'\n______________GC_CCAACGCCAGG\n______________\|\|_\|\|\|\|\|:\|\|\|\|\|\n______________CG_GGUUGUGGUCC\n3'-UUU...UAUGA__C___________CUUUA...GUG-5'\n_____________\|______________\|\n_____________84_____________69\n	113 -- 119	70 -- 76	-22.9581 kcal/mol	7.21499 kcal/mol	7.14463 kcal/mol	106 120@LB@ \| \|@LB@5'-CGC...CCCCG CAAUU...UUG-3'@LB@ GC CCAACGCCAGG@LB@ \|\| \|\|\|\|\|:\|\|\|\|\|@LB@ CG GGUUGUGGUCC@LB@3'-UUU...UAUGA C CUUUA...GUG-5'@LB@ \| \|@LB@ 84 69@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -22.9581 kcal/mol@LB@Unfolding Energy - mRNA 7.21499 kcal/mol@LB@Unfolding Energy - sRNA 7.14463 kcal/mol@LB@@LB@Position - mRNA 107 -- 119@LB@Position - sRNA 70 -- 83@LB@Position Seed - mRNA 113 -- 119@LB@Position Seed - sRNA 70 -- 76@LB@
137	0.007754	0.1993	b4024	lysC	-8.53	0.257132	131 -- 141	73 -- 85	lysine-sensitive aspartokinase 3	_____________130___________142\n_____________\|_____________\|\n5'-UGA...UCGCU_____________CGUCU...UGC-3'\n______________CUGCGCC__CACC\n______________\|\|\|\|\|\|\|__\|\|\|\|\n______________GACGCGG__GUGG\n3'-UUU...CUUAU_______UU____UCCCU...GUG-5'\n_____________\|_____________\|\n_____________86____________72\n	131 -- 137	79 -- 85	-18.3373 kcal/mol	2.85158 kcal/mol	6.95176 kcal/mol	130 142@LB@ \| \|@LB@5'-UGA...UCGCU CGUCU...UGC-3'@LB@ CUGCGCC CACC@LB@ \|\|\|\|\|\|\| \|\|\|\|@LB@ GACGCGG GUGG@LB@3'-UUU...CUUAU UU UCCCU...GUG-5'@LB@ \| \|@LB@ 86 72@LB@@LB@@LB@Energy -8.53 kcal/mol@LB@Hybridization Energy -18.3373 kcal/mol@LB@Unfolding Energy - mRNA 2.85158 kcal/mol@LB@Unfolding Energy - sRNA 6.95176 kcal/mol@LB@@LB@Position - mRNA 131 -- 141@LB@Position - sRNA 73 -- 85@LB@Position Seed - mRNA 131 -- 137@LB@Position Seed - sRNA 79 -- 85@LB@
147	0.008705	0.2059	b0071	leuD	-8.42	0.269085	76 -- 114	1 -- 54	3-isopropylmalate dehydratase small subunit	_____________75_____________________________________________________115\n_____________\|______________________________________________________\|\n5'-GCC...AGCAA______C_________A__CCGC_________________________G_____GCAUC...AAG-3'\n______________CCGUAA_UU____UGA_GG____CAGGGGCGCGGC___________GG_CGCAC\n______________\|\|\|\|\|\|_\|\|____\|\|\|_\|:____\|\|:\|\|\|\|:\|:\|\|___________\|\|_\|\|\|\|\|\n______________GGCAUU_AA____ACU_CU____GUUCCCGUGUCG___________CC_GCGUG\n3'-UUU...GACGC______U__UAAU___A__CAAU____________UGACAAAAAGU__G_____-5'\n_____________\|_____________________________________________________\|\n_____________55____________________________________________________1\n	98 -- 104	22 -- 28	-40.9174 kcal/mol	15.4198 kcal/mol	17.077 kcal/mol	75 115@LB@ \| \|@LB@5'-GCC...AGCAA C A CCGC G GCAUC...AAG-3'@LB@ CCGUAA UU UGA GG CAGGGGCGCGGC GG CGCAC@LB@ \|\|\|\|\|\| \|\| \|\|\| \|: \|\|:\|\|\|\|:\|:\|\| \|\| \|\|\|\|\|@LB@ GGCAUU AA ACU CU GUUCCCGUGUCG CC GCGUG@LB@3'-UUU...GACGC U UAAU A CAAU UGACAAAAAGU G -5'@LB@ \| \|@LB@ 55 1@LB@@LB@@LB@Energy -8.42 kcal/mol@LB@Hybridization Energy -40.9174 kcal/mol@LB@Unfolding Energy - mRNA 15.4198 kcal/mol@LB@Unfolding Energy - sRNA 17.077 kcal/mol@LB@@LB@Position - mRNA 76 -- 114@LB@Position - sRNA 1 -- 54@LB@Position Seed - mRNA 98 -- 104@LB@Position Seed - sRNA 22 -- 28@LB@
107	0.005754	0.1855	b3447	ggt	-8.41	0.270031	252 -- 270	52 -- 70	gamma-glutamyltranspeptidase	_____________251_________________271\n_____________\|___________________\|\n5'-GUU...UCUCA_______GUUUUA______CCGCC...CGU-3'\n______________GGAAGUU______GCGCCG\n______________\|\|\|\|:\|:______\|\|\|\|\|\|\n______________CCUUUAG______CGCGGC\n3'-UUU...UGGUC_______AACCGA______AUUUA...GUG-5'\n_____________\|___________________\|\n_____________71__________________51\n	252 -- 258	64 -- 70	-19.4063 kcal/mol	4.14766 kcal/mol	6.84683 kcal/mol	251 271@LB@ \| \|@LB@5'-GUU...UCUCA GUUUUA CCGCC...CGU-3'@LB@ GGAAGUU GCGCCG@LB@ \|\|\|\|:\|: \|\|\|\|\|\|@LB@ CCUUUAG CGCGGC@LB@3'-UUU...UGGUC AACCGA AUUUA...GUG-5'@LB@ \| \|@LB@ 71 51@LB@@LB@@LB@Energy -8.41 kcal/mol@LB@Hybridization Energy -19.4063 kcal/mol@LB@Unfolding Energy - mRNA 4.14766 kcal/mol@LB@Unfolding Energy - sRNA 6.84683 kcal/mol@LB@@LB@Position - mRNA 252 -- 270@LB@Position - sRNA 52 -- 70@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 64 -- 70@LB@
149	0.008735	0.2059	b3088	alx	-8.37	0.274530	278 -- 288	25 -- 35	putative membrane-bound redox modulator	_____________277_________289\n_____________\|___________\|\n5'-GGG...CUGUU___________GUCGU...CAC-3'\n______________GUUGCAGGGGC\n______________\|\|\|:\|\|:\|\|\|\|\n______________CAAUGUUCCCG\n3'-UUU...CUACU___________UGUCG...GUG-5'\n_____________\|___________\|\n_____________36__________24\n	282 -- 288	25 -- 31	-18.295 kcal/mol	6.20791 kcal/mol	3.71635 kcal/mol	277 289@LB@ \| \|@LB@5'-GGG...CUGUU GUCGU...CAC-3'@LB@ GUUGCAGGGGC@LB@ \|\|\|:\|\|:\|\|\|\|@LB@ CAAUGUUCCCG@LB@3'-UUU...CUACU UGUCG...GUG-5'@LB@ \| \|@LB@ 36 24@LB@@LB@@LB@Energy -8.37 kcal/mol@LB@Hybridization Energy -18.295 kcal/mol@LB@Unfolding Energy - mRNA 6.20791 kcal/mol@LB@Unfolding Energy - sRNA 3.71635 kcal/mol@LB@@LB@Position - mRNA 278 -- 288@LB@Position - sRNA 25 -- 35@LB@Position Seed - mRNA 282 -- 288@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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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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