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
111	0.007434	0.2348	b0103	coaE	-19.66	0.001155	224 -- 242	1 -- 25	dephospho-CoA kinase		_____________223________________________243\n_____________\|__________________________\|\n5'-UAU...UUAAC___A______________________AAGAG...AUA-3'\n______________GGG_GGCAUU_______GGCAGUGGC\n______________\|\|\|_\|:\|\|\|:_______:\|\|\|\|\|\|\|\|\n______________CCC_CUGUAG_______UCGUCACCG\n3'-UUU...UUUUA__________UUUCUUU_________-5'\n_____________\|_________________________\|\n_____________26________________________1\n	236 -- 242	1 -- 7	-28.3462 kcal/mol	6.16994 kcal/mol	2.51748 kcal/mol	223 243@LB@ \| \|@LB@5'-UAU...UUAAC A AAGAG...AUA-3'@LB@ GGG GGCAUU GGCAGUGGC@LB@ \|\|\| \|:\|\|\|: :\|\|\|\|\|\|\|\|@LB@ CCC CUGUAG UCGUCACCG@LB@3'-UUU...UUUUA UUUCUUU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -19.66 kcal/mol@LB@Hybridization Energy -28.3462 kcal/mol@LB@Unfolding Energy - mRNA 6.16994 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 224 -- 242@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 1 -- 7@LB@
112	0.007494	0.2348	b2529	iscU	-11.51	0.152972	152 -- 183	2 -- 33	iron-sulfur cluster assembly scaffold protein		_____________151______________________________184\n_____________\|________________________________\|\n5'-UGG...AACAG___C_______CU_____UUAAUC____UC__AAUCA...GGG-3'\n______________CAU_GAAUGGG__CAUCA______GGUA__GG\n______________\|\|:_:\|\|\|\|\|\|__\|\|\|\|\|______:\|:\|__\|\|\n______________GUG_UUUACCC__GUAGU______UCGU__CC\n3'-UUU...CCGAG___U_______CU_____UUCUUU____CA__G-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	156 -- 162	23 -- 29	-21.7 kcal/mol	7.11537 kcal/mol	3.07861 kcal/mol	151 184@LB@ \| \|@LB@5'-UGG...AACAG C CU UUAAUC UC AAUCA...GGG-3'@LB@ CAU GAAUGGG CAUCA GGUA GG@LB@ \|\|: :\|\|\|\|\|\| \|\|\|\|\| :\|:\| \|\|@LB@ GUG UUUACCC GUAGU UCGU CC@LB@3'-UUU...CCGAG U CU UUCUUU CA G-5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -21.7 kcal/mol@LB@Unfolding Energy - mRNA 7.11537 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 152 -- 183@LB@Position - sRNA 2 -- 33@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 23 -- 29@LB@
113	0.00768	0.2368	b1923	fliC	-14.29	0.040892	38 -- 54	4 -- 25	flagellar filament structural protein (flagellin)		_____________37_____________________55\n_____________\|______________________\|\n5'-GUU...AAUAA______________________AUUUC...CUU-3'\n______________GGGG____CAGAGAAAAG_AGU\n______________\|\|\|\|____\|\|:\|\|\|\|\|\|\|_\|\|\|\n______________CCCC____GUUUCUUUUC_UCA\n3'-UUU...UUUUA____UGUA__________G___CCG-5'\n_____________\|______________________\|\n_____________26_____________________3\n	45 -- 51	8 -- 14	-19.9416 kcal/mol	3.14092 kcal/mol	2.51306 kcal/mol	37 55@LB@ \| \|@LB@5'-GUU...AAUAA AUUUC...CUU-3'@LB@ GGGG CAGAGAAAAG AGU@LB@ \|\|\|\| \|\|:\|\|\|\|\|\|\| \|\|\|@LB@ CCCC GUUUCUUUUC UCA@LB@3'-UUU...UUUUA UGUA G CCG-5'@LB@ \| \|@LB@ 26 3@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -19.9416 kcal/mol@LB@Unfolding Energy - mRNA 3.14092 kcal/mol@LB@Unfolding Energy - sRNA 2.51306 kcal/mol@LB@@LB@Position - mRNA 38 -- 54@LB@Position - sRNA 4 -- 25@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 8 -- 14@LB@
114	0.007692	0.2368	b0584	fepA	-13.71	0.055244	241 -- 265	1 -- 26	ferrienterobactin outer membrane transporter		_____________240________________________266\n_____________\|__________________________\|\n5'-GAA...CAAUC___________U____U____CA___ACAAG...ACG-3'\n______________UGGGGAU_UUA_GGGG_AGCG__GGC\n______________\|\|\|\|\|\|:_\|:\|_:\|::_\|\|\|:__\|\|\|\n______________ACCCCUG_AGU_UCUU_UCGU__CCG\n3'-UUU...GUUUU_______U___U____U____CA___-5'\n_____________\|_________________________\|\n_____________27________________________1\n	241 -- 247	20 -- 26	-24.8633 kcal/mol	8.63835 kcal/mol	2.51842 kcal/mol	240 266@LB@ \| \|@LB@5'-GAA...CAAUC U U CA ACAAG...ACG-3'@LB@ UGGGGAU UUA GGGG AGCG GGC@LB@ \|\|\|\|\|\|: \|:\| :\|:: \|\|\|: \|\|\|@LB@ ACCCCUG AGU UCUU UCGU CCG@LB@3'-UUU...GUUUU U U U CA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -13.71 kcal/mol@LB@Hybridization Energy -24.8633 kcal/mol@LB@Unfolding Energy - mRNA 8.63835 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 241 -- 265@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 20 -- 26@LB@
115	0.007886	0.2401	b2890	lysS	-11.64	0.144658	161 -- 186	1 -- 20	lysine tRNA synthetase constitutive	b4129	_____________160_________________________187\n_____________\|___________________________\|\n5'-AAA...CAAUU________CAAGUUU____________UAUGA...GGA-3'\n______________UAUCGAAG_______GAAAGCAG_GGU\n______________:\|\|\|:\|\|\|_______:\|\|\|\|\|\|\|_\|\|:\n______________GUAGUUUC_______UUUUCGUC_CCG\n3'-UUU...CCCCU_______________________A___-5'\n_____________\|__________________________\|\n_____________21_________________________1\n	177 -- 183	5 -- 11	-18.6981 kcal/mol	5.60124 kcal/mol	1.45855 kcal/mol	160 187@LB@ \| \|@LB@5'-AAA...CAAUU CAAGUUU UAUGA...GGA-3'@LB@ UAUCGAAG GAAAGCAG GGU@LB@ :\|\|\|:\|\|\| :\|\|\|\|\|\|\| \|\|:@LB@ GUAGUUUC UUUUCGUC CCG@LB@3'-UUU...CCCCU A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -11.64 kcal/mol@LB@Hybridization Energy -18.6981 kcal/mol@LB@Unfolding Energy - mRNA 5.60124 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 161 -- 186@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 5 -- 11@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@
117	0.008014	0.2404	b3052	hldE	-12.77	0.087254	132 -- 161	1 -- 30	heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase		_____________131______________________________162\n_____________\|________________________________\|\n5'-GCG...UGGCA_______CUG___G_____AU___________AUUAU...CGC-3'\n______________GAAGUGG____GU_GAAGA__GAAGUA_UGGU\n______________:\|\|:\|\|\|____:\|_:\|\|\|\|__:\|\|\|:\|_\|\|\|:\n______________UUUUACC____UA_UUUCU__UUUCGU_ACCG\n3'-UUU...AGGUG_______CCUG__G_____________C____-5'\n_____________\|_______________________________\|\n_____________31______________________________1\n	132 -- 138	24 -- 30	-21.0542 kcal/mol	5.76621 kcal/mol	2.51911 kcal/mol	131 162@LB@ \| \|@LB@5'-GCG...UGGCA CUG G AU AUUAU...CGC-3'@LB@ GAAGUGG GU GAAGA GAAGUA UGGU@LB@ :\|\|:\|\|\| :\| :\|\|\|\| :\|\|\|:\| \|\|\|:@LB@ UUUUACC UA UUUCU UUUCGU ACCG@LB@3'-UUU...AGGUG CCUG G C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -12.77 kcal/mol@LB@Hybridization Energy -21.0542 kcal/mol@LB@Unfolding Energy - mRNA 5.76621 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 132 -- 161@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 132 -- 138@LB@Position Seed - sRNA 24 -- 30@LB@
118	0.008241	0.2451	b3394	hofN	-17.25	0.007000	1 -- 22	2 -- 26	DNA catabolic putative fimbrial assembly protein		______________1________________________23\n______________\|________________________\|\n___________5'-_____________CU__________GGAUG...CCG-3'\n______________UGGGGGCG_CAAA____GGCGGUGG\n______________\|\|\|\|\|:\|:_\|\|\|\|____:\|\|:\|\|\|\|\n______________ACCCCUGU_GUUU____UCGUCACC\n3'-UUU...GUUUU________A____CUUU________G-5'\n_____________\|_________________________\|\n_____________27________________________1\n	16 -- 22	2 -- 8	-29.7277 kcal/mol	9.95926 kcal/mol	2.5184 kcal/mol	1 23@LB@ \| \|@LB@ 5'- CU GGAUG...CCG-3'@LB@ UGGGGGCG CAAA GGCGGUGG@LB@ \|\|\|\|\|:\|: \|\|\|\| :\|\|:\|\|\|\|@LB@ ACCCCUGU GUUU UCGUCACC@LB@3'-UUU...GUUUU A CUUU G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -17.25 kcal/mol@LB@Hybridization Energy -29.7277 kcal/mol@LB@Unfolding Energy - mRNA 9.95926 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 1 -- 22@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 2 -- 8@LB@
119	0.008338	0.2459	b0123	cueO	-14.31	0.040489	47 -- 61	9 -- 24	multicopper oxidase (laccase)		_____________46_______________62\n_____________\|________________\|\n5'-CUG...UACCA________________UAAAC...CGU-3'\n______________GGGGC_UUAAAGAAGA\n______________\|\|\|:\|_\|:\|\|\|\|\|\|:\|\n______________CCCUG_AGUUUCUUUU\n3'-UUU...UUUAC_____U__________CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	55 -- 61	9 -- 15	-17.0719 kcal/mol	2.10565 kcal/mol	0.659805 kcal/mol	46 62@LB@ \| \|@LB@5'-CUG...UACCA UAAAC...CGU-3'@LB@ GGGGC UUAAAGAAGA@LB@ \|\|\|:\| \|:\|\|\|\|\|\|:\|@LB@ CCCUG AGUUUCUUUU@LB@3'-UUU...UUUAC U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -14.31 kcal/mol@LB@Hybridization Energy -17.0719 kcal/mol@LB@Unfolding Energy - mRNA 2.10565 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 47 -- 61@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 55 -- 61@LB@Position Seed - sRNA 9 -- 15@LB@
120	0.00842	0.2462	b1068	yceM	-12.88	0.082928	190 -- 205	9 -- 24	putative oxidoreductase		_____________189______________206\n_____________\|________________\|\n5'-GCG...CAUCU____G_______U___AAAAU...GAG-3'\n______________GGGA_AUUAAAG_GAA\n______________\|\|\|\|_\|\|:\|\|\|\|_:\|\|\n______________CCCU_UAGUUUC_UUU\n3'-UUU...UUUAC____G_______U___CGUCACCG-5'\n_____________\|________________\|\n_____________25_______________8\n	195 -- 201	13 -- 19	-15.5519 kcal/mol	2.0153 kcal/mol	0.659805 kcal/mol	189 206@LB@ \| \|@LB@5'-GCG...CAUCU G U AAAAU...GAG-3'@LB@ GGGA AUUAAAG GAA@LB@ \|\|\|\| \|\|:\|\|\|\| :\|\|@LB@ CCCU UAGUUUC UUU@LB@3'-UUU...UUUAC G U CGUCACCG-5'@LB@ \| \|@LB@ 25 8@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -15.5519 kcal/mol@LB@Unfolding Energy - mRNA 2.0153 kcal/mol@LB@Unfolding Energy - sRNA 0.659805 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 9 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 13 -- 19@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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