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
8	0.0001267	0.05555	b2697	alaS	-16.66	0.010303	247 -- 274	1 -- 35	alanyl-tRNA synthetase	_____________246_________________________________275\n_____________\|___________________________________\|\n5'-CCA...CUUUU_______UAA______________________U__CAGCA...ACG-3'\n______________UCCAUAG____GGGACAUCA______GGUAGU_GC\n______________\|\|\|\|:\|:____\|\|\|\|\|\|\|\|\|______:\|:\|\|\|_\|\|\n______________AGGUGUU____CCCUGUAGU______UCGUCA_CG\n3'-UUU...ACCCG_______UUAC_________UUCUUU______C__-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	259 -- 265	16 -- 22	-29.5579 kcal/mol	7.86268 kcal/mol	5.03645 kcal/mol	246 275@LB@ \| \|@LB@5'-CCA...CUUUU UAA U CAGCA...ACG-3'@LB@ UCCAUAG GGGACAUCA GGUAGU GC@LB@ \|\|\|\|:\|: \|\|\|\|\|\|\|\|\| :\|:\|\|\| \|\|@LB@ AGGUGUU CCCUGUAGU UCGUCA CG@LB@3'-UUU...ACCCG UUAC UUCUUU C -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -16.66 kcal/mol@LB@Hybridization Energy -29.5579 kcal/mol@LB@Unfolding Energy - mRNA 7.86268 kcal/mol@LB@Unfolding Energy - sRNA 5.03645 kcal/mol@LB@@LB@Position - mRNA 247 -- 274@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 259 -- 265@LB@Position Seed - sRNA 16 -- 22@LB@
23	0.0008148	0.1243	b2573	rpoE	-12.22	0.112158	248 -- 284	1 -- 24	RNA polymerase sigma E factor	_____________247___________________________________285\n_____________\|_____________________________________\|\n5'-ACA...CAGAA____G______AAGCCUUUAACUUACU_______C__UAUCA...UGG-3'\n______________GGGA_AUCAGA________________GGUAGUG_GC\n______________\|\|\|\|_\|\|\|\|:\|________________:\|:\|\|\|\|_\|\|\n______________CCCU_UAGUUU________________UCGUCAC_CG\n3'-UUU...UUUAC____G______CUUU______________________-5'\n_____________\|____________________________________\|\n_____________25___________________________________1\n	275 -- 281	3 -- 9	-22.4239 kcal/mol	7.75978 kcal/mol	2.44282 kcal/mol	247 285@LB@ \| \|@LB@5'-ACA...CAGAA G AAGCCUUUAACUUACU C UAUCA...UGG-3'@LB@ GGGA AUCAGA GGUAGUG GC@LB@ \|\|\|\| \|\|\|\|:\| :\|:\|\|\|\| \|\|@LB@ CCCU UAGUUU UCGUCAC CG@LB@3'-UUU...UUUAC G CUUU -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.4239 kcal/mol@LB@Unfolding Energy - mRNA 7.75978 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 248 -- 284@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
178	0.01293	0.2504	b4258	valS	-13.78	0.053235	248 -- 266	1 -- 21	valyl-tRNA synthetase	_____________247___________________267\n_____________\|_____________________\|\n5'-AUC...UACGA_____U_______________UACUU...AAA-3'\n______________GCA_C_GGGAAAAGCAG_GGC\n______________:\|\|_\|_::\|\|\|\|\|\|\|\|\|_\|\|\|\n______________UGU_G_UUCUUUUCGUC_CCG\n3'-UUU...ACCCC___A_U___________A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	257 -- 263	5 -- 11	-22.196 kcal/mol	6.90555 kcal/mol	1.51103 kcal/mol	247 267@LB@ \| \|@LB@5'-AUC...UACGA U UACUU...AAA-3'@LB@ GCA C GGGAAAAGCAG GGC@LB@ :\|\| \| ::\|\|\|\|\|\|\|\|\| \|\|\|@LB@ UGU G UUCUUUUCGUC CCG@LB@3'-UUU...ACCCC A U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.78 kcal/mol@LB@Hybridization Energy -22.196 kcal/mol@LB@Unfolding Energy - mRNA 6.90555 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 248 -- 266@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 257 -- 263@LB@Position Seed - sRNA 5 -- 11@LB@
197	0.0142	0.2529	b2295	yfbV	-14.79	0.031139	250 -- 276	1 -- 25	UPF0208 family inner membrane protein	_____________249_________________________277\n_____________\|___________________________\|\n5'-AUG...UCGCC_______G__UUACUC____AC_____CGCUG...CGG-3'\n______________GGGGACA_CA______AAAG__GUGGC\n______________\|\|\|\|\|\|\|_\|\|______\|\|\|\|__\|\|\|\|\|\n______________CCCCUGU_GU______UUUC__CACCG\n3'-UUU...UUUUA_______A__UUCU______GU_____-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	250 -- 256	19 -- 25	-25.4481 kcal/mol	8.13822 kcal/mol	2.51748 kcal/mol	249 277@LB@ \| \|@LB@5'-AUG...UCGCC G UUACUC AC CGCUG...CGG-3'@LB@ GGGGACA CA AAAG GUGGC@LB@ \|\|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|@LB@ CCCCUGU GU UUUC CACCG@LB@3'-UUU...UUUUA A UUCU GU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -14.79 kcal/mol@LB@Hybridization Energy -25.4481 kcal/mol@LB@Unfolding Energy - mRNA 8.13822 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 250 -- 276@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 19 -- 25@LB@
71	0.003993	0.1953	b2347	yfdC	-11.68	0.141997	251 -- 269	1 -- 17	putative inner membrane protein	_____________250__________________270\n_____________\|____________________\|\n5'-GCA...GAGAG_______AAA______C___AAAAA...UCC-3'\n______________CGAAGAA___GAGC_G_GGC\n______________\|:\|\|\|\|\|___:\|\|\|_\|_\|\|\|\n______________GUUUCUU___UUCG_C_CCG\n3'-UUU...CUGUA______________U_A___-5'\n_____________\|___________________\|\n_____________18__________________1\n	251 -- 257	11 -- 17	-16.1242 kcal/mol	3.00377 kcal/mol	1.43853 kcal/mol	250 270@LB@ \| \|@LB@5'-GCA...GAGAG AAA C AAAAA...UCC-3'@LB@ CGAAGAA GAGC G GGC@LB@ \|:\|\|\|\|\| :\|\|\| \| \|\|\|@LB@ GUUUCUU UUCG C CCG@LB@3'-UUU...CUGUA U A -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -16.1242 kcal/mol@LB@Unfolding Energy - mRNA 3.00377 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 251 -- 269@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 251 -- 257@LB@Position Seed - sRNA 11 -- 17@LB@
38	0.001836	0.1648	b3188	sfsB	-13.60	0.058336	253 -- 274	1 -- 32	malPQ operon transcriptional activator	_____________252______________________________275\n_____________\|________________________________\|\n5'-CGG...UUUGC______A___A_____________________GGCGG...UGA-3'\n______________GCAAGA_GGG_ACGUCAA__________UGGC\n______________:\|\|\|:\|_\|\|\|_\|\|:\|\|\|\|__________\|\|\|\|\n______________UGUUUU_CCC_UGUAGUU__________ACCG\n3'-UUU...CGAGG______A___C_______UCUUUUCGUC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	264 -- 270	15 -- 21	-21.5209 kcal/mol	5.38314 kcal/mol	2.53929 kcal/mol	252 275@LB@ \| \|@LB@5'-CGG...UUUGC A A GGCGG...UGA-3'@LB@ GCAAGA GGG ACGUCAA UGGC@LB@ :\|\|\|:\| \|\|\| \|\|:\|\|\|\| \|\|\|\|@LB@ UGUUUU CCC UGUAGUU ACCG@LB@3'-UUU...CGAGG A C UCUUUUCGUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -13.60 kcal/mol@LB@Hybridization Energy -21.5209 kcal/mol@LB@Unfolding Energy - mRNA 5.38314 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 253 -- 274@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 264 -- 270@LB@Position Seed - sRNA 15 -- 21@LB@
33	0.001538	0.1635	b4141	yjeH	-13.95	0.048780	254 -- 275	1 -- 22	putative transporter	_____________253____________________276\n_____________\|______________________\|\n5'-CAG...CUAUC_______UUAUU_____C____GUGUU...CUG-3'\n______________GACGUCA_____AGGCA_UGGC\n______________\|\|\|:\|\|\|_____\|:\|\|\|_\|\|\|\|\n______________CUGUAGU_____UUCGU_ACCG\n3'-UUU...UACCC_______UUCUU_____C____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	254 -- 260	16 -- 22	-22.2624 kcal/mol	6.77205 kcal/mol	1.54023 kcal/mol	253 276@LB@ \| \|@LB@5'-CAG...CUAUC UUAUU C GUGUU...CUG-3'@LB@ GACGUCA AGGCA UGGC@LB@ \|\|\|:\|\|\| \|:\|\|\| \|\|\|\|@LB@ CUGUAGU UUCGU ACCG@LB@3'-UUU...UACCC UUCUU C -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -13.95 kcal/mol@LB@Hybridization Energy -22.2624 kcal/mol@LB@Unfolding Energy - mRNA 6.77205 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 254 -- 275@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 16 -- 22@LB@
116	0.007938	0.2401	b0008	talB	-12.38	0.104625	254 -- 276	7 -- 26	transaldolase B	_____________253_____________________277\n_____________\|_______________________\|\n5'-AGG...GACAC___________C__CAAU_____UGUAU...CAA-3'\n______________UGGGGACAUCG_GG____GAAGC\n______________\|\|\|\|\|\|\|\|\|\|:_:\|____:\|\|\|\|\n______________ACCCCUGUAGU_UC____UUUCG\n3'-UUU...GUUUU___________U__U________UCACCG-5'\n_____________\|_______________________\|\n_____________27______________________6\n	258 -- 264	16 -- 22	-23.5048 kcal/mol	10.4229 kcal/mol	0.706388 kcal/mol	253 277@LB@ \| \|@LB@5'-AGG...GACAC C CAAU UGUAU...CAA-3'@LB@ UGGGGACAUCG GG GAAGC@LB@ \|\|\|\|\|\|\|\|\|\|: :\| :\|\|\|\|@LB@ ACCCCUGUAGU UC UUUCG@LB@3'-UUU...GUUUU U U UCACCG-5'@LB@ \| \|@LB@ 27 6@LB@@LB@@LB@Energy -12.38 kcal/mol@LB@Hybridization Energy -23.5048 kcal/mol@LB@Unfolding Energy - mRNA 10.4229 kcal/mol@LB@Unfolding Energy - sRNA 0.706388 kcal/mol@LB@@LB@Position - mRNA 254 -- 276@LB@Position - sRNA 7 -- 26@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 16 -- 22@LB@
59	0.003042	0.1789	b4132	cadB	-12.03	0.121895	256 -- 272	4 -- 32	putative lysine/cadaverine transporter	_____________255___________________________273\n_____________\|_____________________________\|\n5'-UCA...CGGUA___U_________________________AUUGC...CAA-3'\n______________AUA_GAUGGGGA____________GCGGU\n______________\|:\|_:\|\|\|\|\|\|\|____________\|\|:\|\|\n______________UGU_UUACCCCU____________CGUCA\n3'-UUU...CGAGG___U________GUAGUUUCUUUU_____CCG-5'\n_____________\|_____________________________\|\n_____________33____________________________3\n	261 -- 267	21 -- 27	-16.7324 kcal/mol	2.16267 kcal/mol	2.53583 kcal/mol	255 273@LB@ \| \|@LB@5'-UCA...CGGUA U AUUGC...CAA-3'@LB@ AUA GAUGGGGA GCGGU@LB@ \|:\| :\|\|\|\|\|\|\| \|\|:\|\|@LB@ UGU UUACCCCU CGUCA@LB@3'-UUU...CGAGG U GUAGUUUCUUUU CCG-5'@LB@ \| \|@LB@ 33 3@LB@@LB@@LB@Energy -12.03 kcal/mol@LB@Hybridization Energy -16.7324 kcal/mol@LB@Unfolding Energy - mRNA 2.16267 kcal/mol@LB@Unfolding Energy - sRNA 2.53583 kcal/mol@LB@@LB@Position - mRNA 256 -- 272@LB@Position - sRNA 4 -- 32@LB@Position Seed - mRNA 261 -- 267@LB@Position Seed - sRNA 21 -- 27@LB@
73	0.004089	0.1966	b3857	mobA	-16.43	0.011914	256 -- 282	7 -- 29	molybdopterin-guanine dinucleotide synthase	_____________255_________________________283\n_____________\|___________________________\|\n5'-UCC...CAGAC_______C_____AGA_______UU__UUGAA...AAC-3'\n______________GAAUGGG_GGCGU___UAAAGGA__GC\n______________:\|\|\|\|\|\|_\|:\|:\|___:\|\|\|\|:\|__\|\|\n______________UUUACCC_CUGUA___GUUUCUU__CG\n3'-UUU...GGUGU_______________________UU__UCACCG-5'\n_____________\|___________________________\|\n_____________30__________________________6\n	272 -- 278	11 -- 17	-21.4093 kcal/mol	4.27411 kcal/mol	0.706428 kcal/mol	255 283@LB@ \| \|@LB@5'-UCC...CAGAC C AGA UU UUGAA...AAC-3'@LB@ GAAUGGG GGCGU UAAAGGA GC@LB@ :\|\|\|\|\|\| \|:\|:\| :\|\|\|\|:\| \|\|@LB@ UUUACCC CUGUA GUUUCUU CG@LB@3'-UUU...GGUGU UU UCACCG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -16.43 kcal/mol@LB@Hybridization Energy -21.4093 kcal/mol@LB@Unfolding Energy - mRNA 4.27411 kcal/mol@LB@Unfolding Energy - sRNA 0.706428 kcal/mol@LB@@LB@Position - mRNA 256 -- 282@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 11 -- 17@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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