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
158	0.01161	0.2504	b3907	rhaT	-15.90	0.016445	218 -- 234	1 -- 28	L-rhamnose:proton symporter		_____________217__________________________235\n_____________\|____________________________\|\n5'-AUG...AUUAC____________U_______________AUUUG...CAU-3'\n______________GAUGGGGAUAUU____________UGGC\n______________:\|\|\|\|\|\|\|:\|\|:____________\|\|\|\|\n______________UUACCCCUGUAG____________ACCG\n3'-UUU...GUGUU____________UUUCUUUUCGUC____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	223 -- 229	17 -- 23	-20.3321 kcal/mol	1.91011 kcal/mol	2.519 kcal/mol	217 235@LB@ \| \|@LB@5'-AUG...AUUAC U AUUUG...CAU-3'@LB@ GAUGGGGAUAUU UGGC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|@LB@ UUACCCCUGUAG ACCG@LB@3'-UUU...GUGUU UUUCUUUUCGUC -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -20.3321 kcal/mol@LB@Unfolding Energy - mRNA 1.91011 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 218 -- 234@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 17 -- 23@LB@
160	0.0118	0.2504	b0078	ilvH	-13.58	0.059018	151 -- 175	1 -- 25	acetolactate synthase 3 small subunit valine-sensitive		_____________150_______________________176\n_____________\|_________________________\|\n5'-GCC...UUCGC_______GAAU___UGAAAU_____UAAGC...UGA-3'\n______________GGGGGCG____GGA______GUGGU\n______________\|\|\|\|:\|:____:\|\|______\|\|\|\|:\n______________CCCCUGU____UCU______CACCG\n3'-UUU...UUUUA_______AGUU___UUUCGU_____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	151 -- 157	19 -- 25	-21.9405 kcal/mol	5.84786 kcal/mol	2.51748 kcal/mol	150 176@LB@ \| \|@LB@5'-GCC...UUCGC GAAU UGAAAU UAAGC...UGA-3'@LB@ GGGGGCG GGA GUGGU@LB@ \|\|\|\|:\|: :\|\| \|\|\|\|:@LB@ CCCCUGU UCU CACCG@LB@3'-UUU...UUUUA AGUU UUUCGU -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -13.58 kcal/mol@LB@Hybridization Energy -21.9405 kcal/mol@LB@Unfolding Energy - mRNA 5.84786 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 151 -- 175@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 19 -- 25@LB@
163	0.01202	0.2504	b1482	osmC	-10.53	0.225653	203 -- 226	1 -- 22	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin		_____________202_______________________227\n_____________\|_________________________\|\n5'-UAG...ACAAU___A___CAU_________CA____ACACU...CGU-3'\n______________GAC_AUC___AAGAAAGGU___GGC\n______________\|\|\|_\|\|\|___\|\|\|\|\|\|:\|:___\|\|\|\n______________CUG_UAG___UUCUUUUCG___CCG\n3'-UUU...UACCC_______U___________UCA___-5'\n_____________\|________________________\|\n_____________23_______________________1\n	215 -- 221	7 -- 13	-17.1921 kcal/mol	5.11752 kcal/mol	1.54023 kcal/mol	202 227@LB@ \| \|@LB@5'-UAG...ACAAU A CAU CA ACACU...CGU-3'@LB@ GAC AUC AAGAAAGGU GGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\|:\|: \|\|\|@LB@ CUG UAG UUCUUUUCG CCG@LB@3'-UUU...UACCC U UCA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -17.1921 kcal/mol@LB@Unfolding Energy - mRNA 5.11752 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 7 -- 13@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@
172	0.01269	0.2504	b0571	cusR	-10.48	0.230388	14 -- 48	1 -- 33	response regulator in two-component regulatory system with CusS	b1969	_____________13___________________________________49\n_____________\|____________________________________\|\n5'-AGC...GGCCA__________CA__A___UAC__________UA___UCAUA...GGC-3'\n______________CACAAAAUGG__GA_GUU___AAGGAGA_CA__GGC\n______________\|\|\|\|\|\|\|\|\|\|__\|\|_:\|:___\|\|\|:\|:\|_\|\|__\|\|\|\n______________GUGUUUUACC__CU_UAG___UUCUUUU_GU__CCG\n3'-UUU...CCGAG__________C___G___U_________C__CA___-5'\n_____________\|___________________________________\|\n_____________34__________________________________1\n	35 -- 41	9 -- 15	-22.821 kcal/mol	9.26274 kcal/mol	3.07861 kcal/mol	13 49@LB@ \| \|@LB@5'-AGC...GGCCA CA A UAC UA UCAUA...GGC-3'@LB@ CACAAAAUGG GA GUU AAGGAGA CA GGC@LB@ \|\|\|\|\|\|\|\|\|\| \|\| :\|: \|\|\|:\|:\| \|\| \|\|\|@LB@ GUGUUUUACC CU UAG UUCUUUU GU CCG@LB@3'-UUU...CCGAG C G U C CA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -22.821 kcal/mol@LB@Unfolding Energy - mRNA 9.26274 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 14 -- 48@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 9 -- 15@LB@
173	0.01269	0.2504	b4172	hfq	-12.44	0.101529	181 -- 205	1 -- 21	global sRNA chaperone; HF-I host factor for RNA phage Q beta replication		_____________180_______________________206\n_____________\|_________________________\|\n5'-GAA...AAUAA____A__________AG__AA____UAAGG...AAG-3'\n______________GCAU_UAAGGAAAAG__AG__UGGC\n______________:\|\|\|_:\|\|:\|\|\|\|\|\|__\|\|__\|\|\|\|\n______________UGUA_GUUUCUUUUC__UC__ACCG\n3'-UUU...ACCCC_______________G_________-5'\n_____________\|________________________\|\n_____________22_______________________1\n	189 -- 195	8 -- 14	-17.6301 kcal/mol	3.67752 kcal/mol	1.51103 kcal/mol	180 206@LB@ \| \|@LB@5'-GAA...AAUAA A AG AA UAAGG...AAG-3'@LB@ GCAU UAAGGAAAAG AG UGGC@LB@ :\|\|\| :\|\|:\|\|\|\|\|\| \|\| \|\|\|\|@LB@ UGUA GUUUCUUUUC UC ACCG@LB@3'-UUU...ACCCC G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -12.44 kcal/mol@LB@Hybridization Energy -17.6301 kcal/mol@LB@Unfolding Energy - mRNA 3.67752 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 181 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 8 -- 14@LB@
174	0.0127	0.2504	b1960	vsr	-15.05	0.027057	161 -- 177	1 -- 19	DNA mismatch endonuclease of very short patch repair		_____________160_________________178\n_____________\|___________________\|\n5'-UCG...CAAAA______C____________GUUGC...CCG-3'\n______________AUCAAA___AGGCGGUGGC\n______________\|\|\|\|\|\|___\|:\|\|:\|\|\|\|\|\n______________UAGUUU___UUCGUCACCG\n3'-UUU...CCCUG______CUU__________-5'\n_____________\|__________________\|\n_____________20_________________1\n	171 -- 177	1 -- 7	-22.0844 kcal/mol	5.58177 kcal/mol	1.45734 kcal/mol	160 178@LB@ \| \|@LB@5'-UCG...CAAAA C GUUGC...CCG-3'@LB@ AUCAAA AGGCGGUGGC@LB@ \|\|\|\|\|\| \|:\|\|:\|\|\|\|\|@LB@ UAGUUU UUCGUCACCG@LB@3'-UUU...CCCUG CUU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -15.05 kcal/mol@LB@Hybridization Energy -22.0844 kcal/mol@LB@Unfolding Energy - mRNA 5.58177 kcal/mol@LB@Unfolding Energy - sRNA 1.45734 kcal/mol@LB@@LB@Position - mRNA 161 -- 177@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 171 -- 177@LB@Position Seed - sRNA 1 -- 7@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@
180	0.01303	0.2504	b3487	yhiI	-13.61	0.058128	230 -- 256	1 -- 27	putative membrane fusion protein (MFP) of efflux pump		_____________229__________________________257\n_____________\|____________________________\|\n5'-UUU...GCGUG_____U________UUACU_________GGCUA...CGG-3'\n______________GUGGG__UGUCGGG_____GGCGGUGGC\n______________:\|\|\|\|__::\|\|:::_____:\|\|:\|\|\|\|\|\n______________UACCC__GUAGUUU_____UCGUCACCG\n3'-UUU...UGUUU_____CU_______CUUU__________-5'\n_____________\|___________________________\|\n_____________28__________________________1\n	250 -- 256	1 -- 7	-27.1902 kcal/mol	11.0661 kcal/mol	2.51867 kcal/mol	229 257@LB@ \| \|@LB@5'-UUU...GCGUG U UUACU GGCUA...CGG-3'@LB@ GUGGG UGUCGGG GGCGGUGGC@LB@ :\|\|\|\| ::\|\|::: :\|\|:\|\|\|\|\|@LB@ UACCC GUAGUUU UCGUCACCG@LB@3'-UUU...UGUUU CU CUUU -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.61 kcal/mol@LB@Hybridization Energy -27.1902 kcal/mol@LB@Unfolding Energy - mRNA 11.0661 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 230 -- 256@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 1 -- 7@LB@
181	0.01309	0.2504	b2799	fucO	-15.36	0.022654	183 -- 205	1 -- 21	L-1 2-propanediol oxidoreductase		_____________182_____________________206\n_____________\|_______________________\|\n5'-CUU...GUAAA___A__________G_U_A____UAACA...CGC-3'\n______________GCA_CAAGGAGAAG_A_G_UGGC\n______________:\|\|_\|\|\|:\|\|:\|\|\|_\|_\|_\|\|\|\|\n______________UGU_GUUUCUUUUC_U_C_ACCG\n3'-UUU...ACCCC___A__________G________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-20.3858 kcal/mol	3.51699 kcal/mol	1.51103 kcal/mol	182 206@LB@ \| \|@LB@5'-CUU...GUAAA A G U A UAACA...CGC-3'@LB@ GCA CAAGGAGAAG A G UGGC@LB@ :\|\| \|\|\|:\|\|:\|\|\| \| \| \|\|\|\|@LB@ UGU GUUUCUUUUC U C ACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -20.3858 kcal/mol@LB@Unfolding Energy - mRNA 3.51699 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@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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