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
49	0.002324	0.1648	b1119	nagK	-12.21	0.112661	180 -- 199	1 -- 21	N-acetyl-D-glucosamine kinase		_____________179___________________200\n_____________\|_____________________\|\n5'-UCA...GCAGU________AC____G__C___AAUGU...GUG-3'\n______________ACAUUAAA___AAG_AG_GGC\n______________\|\|\|\|:\|\|\|___\|\|\|_\|\|_\|\|\|\n______________UGUAGUUU___UUC_UC_CCG\n3'-UUU...ACCCC________CUU___G__A___-5'\n_____________\|____________________\|\n_____________22___________________1\n	181 -- 187	14 -- 20	-16.408 kcal/mol	2.6857 kcal/mol	1.51103 kcal/mol	179 200@LB@ \| \|@LB@5'-UCA...GCAGU AC G C AAUGU...GUG-3'@LB@ ACAUUAAA AAG AG GGC@LB@ \|\|\|\|:\|\|\| \|\|\| \|\| \|\|\|@LB@ UGUAGUUU UUC UC CCG@LB@3'-UUU...ACCCC CUU G A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -16.408 kcal/mol@LB@Unfolding Energy - mRNA 2.6857 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 180 -- 199@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 181 -- 187@LB@Position Seed - sRNA 14 -- 20@LB@
193	0.01407	0.2529	b3582	sgbU	-12.18	0.114391	219 -- 241	1 -- 24	putative L-xylulose 5-phosphate 3-epimerase		_____________218______________________242\n_____________\|________________________\|\n5'-UCU...AGUUA_________UGA_______C____GAAAG...UUG-3'\n______________GGGAU_UUA___AAAAGCG_UGGC\n______________\|\|\|\|:_\|:\|___\|\|\|\|\|\|:_\|\|\|\|\n______________CCCUG_AGU___UUUUCGU_ACCG\n3'-UUU...UUUAC_____U___UUC_______C____-5'\n_____________\|_______________________\|\n_____________25______________________1\n	230 -- 236	6 -- 12	-20.9157 kcal/mol	6.29567 kcal/mol	2.44282 kcal/mol	218 242@LB@ \| \|@LB@5'-UCU...AGUUA UGA C GAAAG...UUG-3'@LB@ GGGAU UUA AAAAGCG UGGC@LB@ \|\|\|\|: \|:\| \|\|\|\|\|\|: \|\|\|\|@LB@ CCCUG AGU UUUUCGU ACCG@LB@3'-UUU...UUUAC U UUC C -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.18 kcal/mol@LB@Hybridization Energy -20.9157 kcal/mol@LB@Unfolding Energy - mRNA 6.29567 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 219 -- 241@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 230 -- 236@LB@Position Seed - sRNA 6 -- 12@LB@
132	0.00937	0.2491	b1120	cobB	-12.17	0.114836	175 -- 191	3 -- 18	deacetylase of acs and cheY chemotaxis regulator		_____________174_______________192\n_____________\|_________________\|\n5'-CGC...UUUUU_______U_________CCGGA...AUC-3'\n______________UCAGAGA_AAAGUGGUG\n______________\|\|\|:\|\|\|_\|\|\|\|::\|\|\|\n______________AGUUUCU_UUUCGUCAC\n3'-UUU...CCUGU_________________CG-5'\n_____________\|_________________\|\n_____________19________________2\n	185 -- 191	3 -- 9	-17.0979 kcal/mol	3.47557 kcal/mol	1.45388 kcal/mol	174 192@LB@ \| \|@LB@5'-CGC...UUUUU U CCGGA...AUC-3'@LB@ UCAGAGA AAAGUGGUG@LB@ \|\|\|:\|\|\| \|\|\|\|::\|\|\|@LB@ AGUUUCU UUUCGUCAC@LB@3'-UUU...CCUGU CG-5'@LB@ \| \|@LB@ 19 2@LB@@LB@@LB@Energy -12.17 kcal/mol@LB@Hybridization Energy -17.0979 kcal/mol@LB@Unfolding Energy - mRNA 3.47557 kcal/mol@LB@Unfolding Energy - sRNA 1.45388 kcal/mol@LB@@LB@Position - mRNA 175 -- 191@LB@Position - sRNA 3 -- 18@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 3 -- 9@LB@
84	0.005241	0.2147	b2513	yfgM	-12.13	0.116945	176 -- 204	2 -- 26	ancillary SecYEG translocon subunit; putative anti-RcsB factor		_____________175___________________________205\n_____________\|_____________________________\|\n5'-GGC...GUUAC____UUAAGG_________G_CAGC____AAAUU...UUG-3'\n______________UGGG______AAGGAGAAG_A____GUGG\n______________\|\|\|\|______\|\|:\|\|:\|\|\|_\|____\|\|\|\|\n______________ACCC______UUUCUUUUC_U____CACC\n3'-UUU...GUUUU____CUGUAG_________G_________G-5'\n_____________\|_____________________________\|\n_____________27____________________________1\n	188 -- 194	8 -- 14	-19.1762 kcal/mol	4.53021 kcal/mol	2.5184 kcal/mol	175 205@LB@ \| \|@LB@5'-GGC...GUUAC UUAAGG G CAGC AAAUU...UUG-3'@LB@ UGGG AAGGAGAAG A GUGG@LB@ \|\|\|\| \|\|:\|\|:\|\|\| \| \|\|\|\|@LB@ ACCC UUUCUUUUC U CACC@LB@3'-UUU...GUUUU CUGUAG G G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -19.1762 kcal/mol@LB@Unfolding Energy - mRNA 4.53021 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 176 -- 204@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 8 -- 14@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@
186	0.01333	0.2514	b0084	ftsI	-11.80	0.135121	196 -- 214	1 -- 22	transpeptidase involved in septal peptidoglycan synthesis; penicillin-binding protein 3		_____________195____________________215\n_____________\|______________________\|\n5'-GUU...AACGC_______U__________C___GAAAA...UGG-3'\n______________GACG_CA___GAAAGCAG_GGC\n______________\|\|\|:_\|\|___:\|\|\|\|\|\|\|_\|\|\|\n______________CUGU_GU___UUUUCGUC_CCG\n3'-UUU...UACCC____A__UUC________A___-5'\n_____________\|_____________________\|\n_____________23____________________1\n	204 -- 210	5 -- 11	-21.3841 kcal/mol	8.04628 kcal/mol	1.54023 kcal/mol	195 215@LB@ \| \|@LB@5'-GUU...AACGC U C GAAAA...UGG-3'@LB@ GACG CA GAAAGCAG GGC@LB@ \|\|\|: \|\| :\|\|\|\|\|\|\| \|\|\|@LB@ CUGU GU UUUUCGUC CCG@LB@3'-UUU...UACCC A UUC A -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -21.3841 kcal/mol@LB@Unfolding Energy - mRNA 8.04628 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 196 -- 214@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
165	0.01211	0.2504	b3642	pyrE	-11.74	0.138291	22 -- 41	7 -- 25	orotate phosphoribosyltransferase		_____________21___________________42\n_____________\|____________________\|\n5'-CGG...GUGCA_______GCA_____C____CGUUC...AUU-3'\n______________GGGGACG___GAAGG_GAGC\n______________\|\|\|\|\|\|:___:\|\|\|:_:\|\|\|\n______________CCCCUGU___UUUCU_UUCG\n3'-UUU...UUUUA_______AG______U____UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	22 -- 28	19 -- 25	-22.5653 kcal/mol	10.1153 kcal/mol	0.70626 kcal/mol	21 42@LB@ \| \|@LB@5'-CGG...GUGCA GCA C CGUUC...AUU-3'@LB@ GGGGACG GAAGG GAGC@LB@ \|\|\|\|\|\|: :\|\|\|: :\|\|\|@LB@ CCCCUGU UUUCU UUCG@LB@3'-UUU...UUUUA AG U UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -11.74 kcal/mol@LB@Hybridization Energy -22.5653 kcal/mol@LB@Unfolding Energy - mRNA 10.1153 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 22 -- 41@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 22 -- 28@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@
142	0.01047	0.2504	b3998	nfi	-11.68	0.142276	34 -- 51	5 -- 21	endonuclease V; deoxyinosine 3' endonuclease		_____________33_________________52\n_____________\|__________________\|\n5'-UGG...UGCCC_________A________CGACU...GAG-3'\n______________GCAUUGAAG_AGAAGUAG\n______________:\|\|\|::\|\|\|_\|:\|\|\|:\|\|\n______________UGUAGUUUC_UUUUCGUC\n3'-UUU...ACCCC__________________ACCG-5'\n_____________\|__________________\|\n_____________22_________________4\n	45 -- 51	5 -- 11	-17.0993 kcal/mol	3.91468 kcal/mol	1.5073 kcal/mol	33 52@LB@ \| \|@LB@5'-UGG...UGCCC A CGACU...GAG-3'@LB@ GCAUUGAAG AGAAGUAG@LB@ :\|\|\|::\|\|\| \|:\|\|\|:\|\|@LB@ UGUAGUUUC UUUUCGUC@LB@3'-UUU...ACCCC ACCG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.68 kcal/mol@LB@Hybridization Energy -17.0993 kcal/mol@LB@Unfolding Energy - mRNA 3.91468 kcal/mol@LB@Unfolding Energy - sRNA 1.5073 kcal/mol@LB@@LB@Position - mRNA 34 -- 51@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 45 -- 51@LB@Position Seed - sRNA 5 -- 11@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@

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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