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
194	0.01408	0.2529	b0952	pqiC	-11.52	0.151794	181 -- 195	48 -- 61	DUF330 family putative lipoprotein	_____________180_____________196\n_____________\|_______________\|\n5'-ACG...AUCCA_________AG____AAACA...GCG-3'\n______________GAGCCGAAG__GGCG\n______________\|\|:\|\|\|\|\|:__\|\|\|\|\n______________CUUGGCUUU__CCGC\n3'-UUU...UGGAA_________A_____CCCAA...CCG-5'\n_____________\|_______________\|\n_____________62______________47\n	183 -- 189	53 -- 59	-21.1549 kcal/mol	5.66908 kcal/mol	3.96136 kcal/mol	180 196@LB@ \| \|@LB@5'-ACG...AUCCA AG AAACA...GCG-3'@LB@ GAGCCGAAG GGCG@LB@ \|\|:\|\|\|\|\|: \|\|\|\|@LB@ CUUGGCUUU CCGC@LB@3'-UUU...UGGAA A CCCAA...CCG-5'@LB@ \| \|@LB@ 62 47@LB@@LB@@LB@Energy -11.52 kcal/mol@LB@Hybridization Energy -21.1549 kcal/mol@LB@Unfolding Energy - mRNA 5.66908 kcal/mol@LB@Unfolding Energy - sRNA 3.96136 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 48 -- 61@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 53 -- 59@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@
170	0.01232	0.2504	b2580	ung	-11.45	0.156876	183 -- 205	1 -- 22	uracil-DNA-glycosylase	_____________182______________________206\n_____________\|________________________\|\n5'-UCU...UUGAA_______C________G__A____UAACG...CCG-3'\n______________GAU_UCG_AGGAGAGC_AG_UGGC\n______________\|\|:_\|\|:_\|\|:\|:\|\|\|_\|\|_\|\|\|\|\n______________CUG_AGU_UCUUUUCG_UC_ACCG\n3'-UUU...UACCC___U___U________________-5'\n_____________\|_______________________\|\n_____________23______________________1\n	191 -- 197	7 -- 13	-20.4372 kcal/mol	7.45123 kcal/mol	1.54023 kcal/mol	182 206@LB@ \| \|@LB@5'-UCU...UUGAA C G A UAACG...CCG-3'@LB@ GAU UCG AGGAGAGC AG UGGC@LB@ \|\|: \|\|: \|\|:\|:\|\|\| \|\| \|\|\|\|@LB@ CUG AGU UCUUUUCG UC ACCG@LB@3'-UUU...UACCC U U -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -20.4372 kcal/mol@LB@Unfolding Energy - mRNA 7.45123 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 7 -- 13@LB@
86	0.005461	0.2147	b0002	thrA	-11.41	0.159352	219 -- 235	1 -- 25	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________218_________________________236\n_____________\|___________________________\|\n5'-CCA...AGUUC__C__U_____________________AAAUG...UGG-3'\n______________GG_GG_ACAU__________CAGUGGC\n______________\|\|_\|\|_\|\|\|\|__________\|\|\|\|\|\|\|\n______________CC_CC_UGUA__________GUCACCG\n3'-UUU...UUUUA__________GUUUCUUUUC_______-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	229 -- 235	1 -- 7	-18.4664 kcal/mol	4.54068 kcal/mol	2.51748 kcal/mol	218 236@LB@ \| \|@LB@5'-CCA...AGUUC C U AAAUG...UGG-3'@LB@ GG GG ACAU CAGUGGC@LB@ \|\| \|\| \|\|\|\| \|\|\|\|\|\|\|@LB@ CC CC UGUA GUCACCG@LB@3'-UUU...UUUUA GUUUCUUUUC -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -18.4664 kcal/mol@LB@Unfolding Energy - mRNA 4.54068 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 219 -- 235@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
145	0.01066	0.2504	b2153	folE	-11.37	0.162147	44 -- 68	1 -- 21	GTP cyclohydrolase I	_____________43________________________69\n_____________\|_________________________\|\n5'-CUG...UUUUA_____UGCU__U_________C___AAUUA...ACG-3'\n______________ACAUC____GA_GAAAGGCAG_GGC\n______________\|\|\|\|\|____:\|_\|\|\|\|:\|\|\|\|_\|\|\|\n______________UGUAG____UU_CUUUUCGUC_CCG\n3'-UUU...ACCCC___________U_________A___-5'\n_____________\|________________________\|\n_____________22_______________________1\n	58 -- 64	5 -- 11	-23.5216 kcal/mol	10.6442 kcal/mol	1.51103 kcal/mol	43 69@LB@ \| \|@LB@5'-CUG...UUUUA UGCU U C AAUUA...ACG-3'@LB@ ACAUC GA GAAAGGCAG GGC@LB@ \|\|\|\|\| :\| \|\|\|\|:\|\|\|\| \|\|\|@LB@ UGUAG UU CUUUUCGUC CCG@LB@3'-UUU...ACCCC U A -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -11.37 kcal/mol@LB@Hybridization Energy -23.5216 kcal/mol@LB@Unfolding Energy - mRNA 10.6442 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 44 -- 68@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon	_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
75	0.00423	0.1979	b1917	yecC	-10.99	0.188691	288 -- 298	1 -- 11	putative ABC transporter ATPase	_____________287_________299\n_____________\|___________\|\n5'-CUG...CUGGC___________AA-3'\n______________GAAGUGGUGGC\n______________:\|\|\|::\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	292 -- 298	1 -- 7	-16.6045 kcal/mol	4.33348 kcal/mol	1.27751 kcal/mol	287 299@LB@ \| \|@LB@5'-CUG...CUGGC AA-3'@LB@ GAAGUGGUGGC@LB@ :\|\|\|::\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -10.99 kcal/mol@LB@Hybridization Energy -16.6045 kcal/mol@LB@Unfolding Energy - mRNA 4.33348 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 288 -- 298@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 1 -- 7@LB@
17	0.0006839	0.1243	b1247	oppF	-10.96	0.191014	264 -- 288	1 -- 22	oligopeptide ABC transporter ATPase	_____________263________________________289\n_____________\|__________________________\|\n5'-GCG...ACUUU__A________U____AAAC______UCUGG...CGC-3'\n______________GA_AUCAAAGA__GGC____AGUGGU\n______________\|\|_\|\|\|\|\|\|\|\|__:\|\|____\|\|\|\|\|:\n______________CU_UAGUUUCU__UCG____UCACCG\n3'-UUU...UACCC__G________UU_____________-5'\n_____________\|_________________________\|\n_____________23________________________1\n	268 -- 274	12 -- 18	-19.2479 kcal/mol	6.74487 kcal/mol	1.54023 kcal/mol	263 289@LB@ \| \|@LB@5'-GCG...ACUUU A U AAAC UCUGG...CGC-3'@LB@ GA AUCAAAGA GGC AGUGGU@LB@ \|\| \|\|\|\|\|\|\|\| :\|\| \|\|\|\|\|:@LB@ CU UAGUUUCU UCG UCACCG@LB@3'-UUU...UACCC G UU -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.96 kcal/mol@LB@Hybridization Energy -19.2479 kcal/mol@LB@Unfolding Energy - mRNA 6.74487 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 264 -- 288@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 12 -- 18@LB@
188	0.01388	0.2529	b4198	ulaF	-10.93	0.193396	24 -- 37	2 -- 17	L-ribulose 5-phosphate 4-epimerase	_____________23_______________38\n_____________\|________________\|\n5'-GUC...UUUGG______U_________AUUUC...GCG-3'\n______________CGAAGG___GUAGUGG\n______________\|:\|\|\|:___\|:\|\|\|\|\|\n______________GUUUCU___CGUCACC\n3'-UUU...CUGUA______UUU_______G-5'\n_____________\|________________\|\n_____________18_______________1\n	31 -- 37	2 -- 8	-15.3961 kcal/mol	3.02615 kcal/mol	1.43836 kcal/mol	23 38@LB@ \| \|@LB@5'-GUC...UUUGG U AUUUC...GCG-3'@LB@ CGAAGG GUAGUGG@LB@ \|:\|\|\|: \|:\|\|\|\|\|@LB@ GUUUCU CGUCACC@LB@3'-UUU...CUGUA UUU G-5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.93 kcal/mol@LB@Hybridization Energy -15.3961 kcal/mol@LB@Unfolding Energy - mRNA 3.02615 kcal/mol@LB@Unfolding Energy - sRNA 1.43836 kcal/mol@LB@@LB@Position - mRNA 24 -- 37@LB@Position - sRNA 2 -- 17@LB@Position Seed - mRNA 31 -- 37@LB@Position Seed - sRNA 2 -- 8@LB@
60	0.003101	0.1789	b1849	purT	-10.92	0.194410	188 -- 196	17 -- 25	phosphoribosylglycinamide formyltransferase 2	_____________187_______197\n_____________\|_________\|\n5'-UUU...AAUCA_________CGUUA...GUC-3'\n______________GGGGAUAUU\n______________\|\|\|\|\|:\|\|:\n______________CCCCUGUAG\n3'-UUU...UUUUA_________UUUCU...CCG-5'\n_____________\|_________\|\n_____________26________16\n	190 -- 196	17 -- 23	-14.1846 kcal/mol	2.60139 kcal/mol	0.664736 kcal/mol	187 197@LB@ \| \|@LB@5'-UUU...AAUCA CGUUA...GUC-3'@LB@ GGGGAUAUU@LB@ \|\|\|\|\|:\|\|:@LB@ CCCCUGUAG@LB@3'-UUU...UUUUA UUUCU...CCG-5'@LB@ \| \|@LB@ 26 16@LB@@LB@@LB@Energy -10.92 kcal/mol@LB@Hybridization Energy -14.1846 kcal/mol@LB@Unfolding Energy - mRNA 2.60139 kcal/mol@LB@Unfolding Energy - sRNA 0.664736 kcal/mol@LB@@LB@Position - mRNA 188 -- 196@LB@Position - sRNA 17 -- 25@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 17 -- 23@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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