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
141	0.01037	0.2504	b2161	nupX	-15.31	0.023296	54 -- 80	1 -- 26	nucleoside permease	b2164	_____________53____________________________81\n_____________\|_____________________________\|\n5'-UUG...GGUUC_______UA_________U_______C__GGCUA...GCG-3'\n______________UGGGGAU__GUCGAAGAG__GC_GUG_GC\n______________\|\|\|\|\|\|:__:\|\|:\|\|\|\|:__\|\|_\|\|\|_\|\|\n______________ACCCCUG__UAGUUUCUU__CG_CAC_CG\n3'-UUU...GUUUU__________________UU__U______-5'\n_____________\|____________________________\|\n_____________27___________________________1\n	65 -- 71	11 -- 17	-27.7009 kcal/mol	9.87339 kcal/mol	2.51842 kcal/mol	53 81@LB@ \| \|@LB@5'-UUG...GGUUC UA U C GGCUA...GCG-3'@LB@ UGGGGAU GUCGAAGAG GC GUG GC@LB@ \|\|\|\|\|\|: :\|\|:\|\|\|\|: \|\| \|\|\| \|\|@LB@ ACCCCUG UAGUUUCUU CG CAC CG@LB@3'-UUU...GUUUU UU U -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -27.7009 kcal/mol@LB@Unfolding Energy - mRNA 9.87339 kcal/mol@LB@Unfolding Energy - sRNA 2.51842 kcal/mol@LB@@LB@Position - mRNA 54 -- 80@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 11 -- 17@LB@
66	0.003537	0.1858	b0411	tsx	-15.28	0.023631	170 -- 194	1 -- 34	nucleoside channel receptor of phage T6 and colicin K		_____________169_________________________________195\n_____________\|___________________________________\|\n5'-AGG...CACUC_______________UU__________________AUACA...ACU-3'\n______________CCGCAA____GGGAU__UCAAA______CAGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GGUGUU____CCCUG__AGUUU______GUCACCG\n3'-UUU...CCCGA______UUAC_____U______CUUUUC_______-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	188 -- 194	1 -- 7	-27.9509 kcal/mol	8.39787 kcal/mol	4.26884 kcal/mol	169 195@LB@ \| \|@LB@5'-AGG...CACUC UU AUACA...ACU-3'@LB@ CCGCAA GGGAU UCAAA CAGUGGC@LB@ \|\|:\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGUGUU CCCUG AGUUU GUCACCG@LB@3'-UUU...CCCGA UUAC U CUUUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -27.9509 kcal/mol@LB@Unfolding Energy - mRNA 8.39787 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 1 -- 7@LB@
70	0.003861	0.1936	b3559	glyS	-15.28	0.023738	120 -- 130	1 -- 11	glycine tRNA synthetase beta subunit		_____________119_________131\n_____________\|___________\|\n5'-CGC...UGACC___________AGAAG...CGG-3'\n______________AAAGCAGUGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	124 -- 130	1 -- 7	-20.0617 kcal/mol	3.50787 kcal/mol	1.27751 kcal/mol	119 131@LB@ \| \|@LB@5'-CGC...UGACC AGAAG...CGG-3'@LB@ AAAGCAGUGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -20.0617 kcal/mol@LB@Unfolding Energy - mRNA 3.50787 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 120 -- 130@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 124 -- 130@LB@Position Seed - sRNA 1 -- 7@LB@
123	0.008923	0.2491	b3243	aaeR	-15.21	0.024673	72 -- 99	1 -- 34	transcriptional regulator for aaeXAB operon		_____________71_________________________________100\n_____________\|__________________________________\|\n5'-AAC...UGUCG________AA__________________C_____GAGAG...UCA-3'\n______________CCGCAGAG___GGGCAU____GGAAAGC_G_GGC\n______________\|\|:\|\|:\|:___\|\|:\|\|\|____\|:\|\|\|\|\|_\|_\|\|\|\n______________GGUGUUUU___CCUGUA____CUUUUCG_C_CCG\n3'-UUU...CCCGA________ACC______GUUU_______U_A___-5'\n_____________\|_________________________________\|\n_____________35________________________________1\n	88 -- 94	7 -- 13	-28.4227 kcal/mol	8.94529 kcal/mol	4.26884 kcal/mol	71 100@LB@ \| \|@LB@5'-AAC...UGUCG AA C GAGAG...UCA-3'@LB@ CCGCAGAG GGGCAU GGAAAGC G GGC@LB@ \|\|:\|\|:\|: \|\|:\|\|\| \|:\|\|\|\|\| \| \|\|\|@LB@ GGUGUUUU CCUGUA CUUUUCG C CCG@LB@3'-UUU...CCCGA ACC GUUU U A -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.21 kcal/mol@LB@Hybridization Energy -28.4227 kcal/mol@LB@Unfolding Energy - mRNA 8.94529 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 72 -- 99@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 7 -- 13@LB@
48	0.002302	0.1648	b3460	livJ	-15.11	0.026091	183 -- 229	1 -- 30	branched-chain amino acid ABC transporter periplasmic binding protein		_____________182_____________________________________________230\n_____________\|_______________________________________________\|\n5'-AAU...CCAGA___________UC___GGAUGAACAUAA____U______UUAC____AGGAU...CAA-3'\n______________AGAAUGGGGAU__UCA____________AGGG_AAAGCG____UGGC\n______________\|:\|\|\|\|\|\|\|\|:__\|\|\|____________\|:\|:_\|\|\|\|\|:____\|\|\|\|\n______________UUUUACCCCUG__AGU____________UUCU_UUUCGU____ACCG\n3'-UUU...AGGUG___________U___________________________C_______-5'\n_____________\|______________________________________________\|\n_____________31_____________________________________________1\n	187 -- 193	20 -- 26	-27.0033 kcal/mol	9.37443 kcal/mol	2.51911 kcal/mol	182 230@LB@ \| \|@LB@5'-AAU...CCAGA UC GGAUGAACAUAA U UUAC AGGAU...CAA-3'@LB@ AGAAUGGGGAU UCA AGGG AAAGCG UGGC@LB@ \|:\|\|\|\|\|\|\|\|: \|\|\| \|:\|: \|\|\|\|\|: \|\|\|\|@LB@ UUUUACCCCUG AGU UUCU UUUCGU ACCG@LB@3'-UUU...AGGUG U C -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -15.11 kcal/mol@LB@Hybridization Energy -27.0033 kcal/mol@LB@Unfolding Energy - mRNA 9.37443 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 183 -- 229@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@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@
45	0.002187	0.1648	b3391	hofQ	-14.99	0.027914	2 -- 20	1 -- 20	DNA catabolic putative fimbrial transporter		_____________1____________________21\n_____________\|____________________\|\n__________5'-C__________U_________GAGGC...UAG-3'\n______________UAUCAGGGGA_GGUAG_GGC\n______________:\|\|\|\|::\|:\|_:\|:\|\|_\|\|\|\n______________GUAGUUUCUU_UCGUC_CCG\n3'-UUU...CCCCU__________U_____A___-5'\n_____________\|___________________\|\n_____________21__________________1\n	5 -- 11	11 -- 17	-22.4478 kcal/mol	5.99969 kcal/mol	1.45855 kcal/mol	1 21@LB@ \| \|@LB@ 5'-C U GAGGC...UAG-3'@LB@ UAUCAGGGGA GGUAG GGC@LB@ :\|\|\|\|::\|:\| :\|:\|\| \|\|\|@LB@ GUAGUUUCUU UCGUC CCG@LB@3'-UUU...CCCCU U A -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -22.4478 kcal/mol@LB@Unfolding Energy - mRNA 5.99969 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 2 -- 20@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 11 -- 17@LB@
101	0.006298	0.2188	b3549	tag	-14.94	0.028658	147 -- 165	3 -- 21	3-methyl-adenine DNA glycosylase I constitutive		_____________146__________________166\n_____________\|____________________\|\n5'-GCA...CCGAU_________________C__AAAUU...AAA-3'\n______________GCGUC_AAGAAAAGCGG_UG\n______________:\|:\|\|_\|\|\|\|\|\|\|\|\|:\|_\|\|\n______________UGUAG_UUCUUUUCGUC_AC\n3'-UUU...ACCCC_____U______________CG-5'\n_____________\|____________________\|\n_____________22___________________2\n	156 -- 162	5 -- 11	-20.7072 kcal/mol	4.25403 kcal/mol	1.5107 kcal/mol	146 166@LB@ \| \|@LB@5'-GCA...CCGAU C AAAUU...AAA-3'@LB@ GCGUC AAGAAAAGCGG UG@LB@ :\|:\|\| \|\|\|\|\|\|\|\|\|:\| \|\|@LB@ UGUAG UUCUUUUCGUC AC@LB@3'-UUU...ACCCC U CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -14.94 kcal/mol@LB@Hybridization Energy -20.7072 kcal/mol@LB@Unfolding Energy - mRNA 4.25403 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 147 -- 165@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 5 -- 11@LB@
11	0.0003708	0.1087	b4201	priB	-14.90	0.029310	176 -- 193	6 -- 26	primosomal protein N		_____________175___________________194\n_____________\|_____________________\|\n5'-AGG...GAAGC__________U__________AUUUC...AUC-3'\n______________UGGGGAU_UC___GAAGAGUA\n______________\|\|\|\|\|\|:_\|\|___\|\|\|:\|\|:\|\n______________ACCCCUG_AG___CUUUUCGU\n3'-UUU...GUUUU_______U__UUU________CACCG-5'\n_____________\|_____________________\|\n_____________27____________________5\n	187 -- 193	6 -- 12	-19.0189 kcal/mol	3.41067 kcal/mol	0.706421 kcal/mol	175 194@LB@ \| \|@LB@5'-AGG...GAAGC U AUUUC...AUC-3'@LB@ UGGGGAU UC GAAGAGUA@LB@ \|\|\|\|\|\|: \|\| \|\|\|:\|\|:\|@LB@ ACCCCUG AG CUUUUCGU@LB@3'-UUU...GUUUU U UUU CACCG-5'@LB@ \| \|@LB@ 27 5@LB@@LB@@LB@Energy -14.90 kcal/mol@LB@Hybridization Energy -19.0189 kcal/mol@LB@Unfolding Energy - mRNA 3.41067 kcal/mol@LB@Unfolding Energy - sRNA 0.706421 kcal/mol@LB@@LB@Position - mRNA 176 -- 193@LB@Position - sRNA 6 -- 26@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 6 -- 12@LB@
147	0.01091	0.2504	b2720	hycF	-14.84	0.030299	116 -- 133	1 -- 16	formate hydrogenlyase complex iron-sulfur protein		_____________115________________134\n_____________\|__________________\|\n5'-CGA...CGUAA___________AA_____GCCGU...CAG-3'\n______________GAAGAAGAGCA__GUGGU\n______________:\|\|\|\|\|:\|\|\|\|__\|\|\|\|:\n______________UUUCUUUUCGU__CACCG\n3'-UUU...UGUAG__________________-5'\n_____________\|_________________\|\n_____________17________________1\n	120 -- 126	6 -- 12	-19.8629 kcal/mol	3.67538 kcal/mol	1.34555 kcal/mol	115 134@LB@ \| \|@LB@5'-CGA...CGUAA AA GCCGU...CAG-3'@LB@ GAAGAAGAGCA GUGGU@LB@ :\|\|\|\|\|:\|\|\|\| \|\|\|\|:@LB@ UUUCUUUUCGU CACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -14.84 kcal/mol@LB@Hybridization Energy -19.8629 kcal/mol@LB@Unfolding Energy - mRNA 3.67538 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 116 -- 133@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 6 -- 12@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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