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
156	0.01139	0.2504	b0197	metQ	-9.46	0.330846	169 -- 205	1 -- 33	DL-methionine transporter subunit	_____________168_____________________________________206\n_____________\|_______________________________________\|\n5'-GUG...UUCAA_____CAUAAAUA___________GAAUAA_________GUUCA...UUA-3'\n______________CACAA_________AUUGAAGAAG______GGUA_UGGC\n______________\|\|\|\|\|_________\|\|::\|\|\|\|\|:______:\|:\|_\|\|\|\|\n______________GUGUU_________UAGUUUCUUU______UCGU_ACCG\n3'-UUU...CCGAG_____UUACCCCUG____________________C____-5'\n_____________\|______________________________________\|\n_____________34_____________________________________1\n	185 -- 191	10 -- 16	-16.9822 kcal/mol	4.44131 kcal/mol	3.07861 kcal/mol	168 206@LB@ \| \|@LB@5'-GUG...UUCAA CAUAAAUA GAAUAA GUUCA...UUA-3'@LB@ CACAA AUUGAAGAAG GGUA UGGC@LB@ \|\|\|\|\| \|\|::\|\|\|\|\|: :\|:\| \|\|\|\|@LB@ GUGUU UAGUUUCUUU UCGU ACCG@LB@3'-UUU...CCGAG UUACCCCUG C -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.46 kcal/mol@LB@Hybridization Energy -16.9822 kcal/mol@LB@Unfolding Energy - mRNA 4.44131 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 169 -- 205@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 10 -- 16@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@
34	0.001647	0.1648	b1218	chaC	-13.74	0.054411	171 -- 189	1 -- 17	cation transport regulator	_____________170_________________190\n_____________\|___________________\|\n5'-AUA...UGUCG________UAU________GGAAG...CGC-3'\n______________CAGGGAAG___GCAGUGGC\n______________\|\|::\|\|\|:___\|\|\|\|\|\|\|\|\n______________GUUUCUUU___CGUCACCG\n3'-UUU...CUGUA________U__________-5'\n_____________\|__________________\|\n_____________18_________________1\n	183 -- 189	1 -- 7	-23.3292 kcal/mol	8.15416 kcal/mol	1.43853 kcal/mol	170 190@LB@ \| \|@LB@5'-AUA...UGUCG UAU GGAAG...CGC-3'@LB@ CAGGGAAG GCAGUGGC@LB@ \|\|::\|\|\|: \|\|\|\|\|\|\|\|@LB@ GUUUCUUU CGUCACCG@LB@3'-UUU...CUGUA U -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -13.74 kcal/mol@LB@Hybridization Energy -23.3292 kcal/mol@LB@Unfolding Energy - mRNA 8.15416 kcal/mol@LB@Unfolding Energy - sRNA 1.43853 kcal/mol@LB@@LB@Position - mRNA 171 -- 189@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 1 -- 7@LB@
169	0.01228	0.2504	b3386	rpe	-13.36	0.065831	171 -- 203	3 -- 33	D-ribulose-5-phosphate 3-epimerase	_____________170_______________________________204\n_____________\|_________________________________\|\n5'-CGC...UCACC_______AAAUAAUUC______________A__AAACA...UGC-3'\n______________CGCGAAA_________UCAAGGAGAAGCGG_UG\n______________\|:\|:\|\|\|_________\|\|\|\|:\|\|:\|\|\|\|:\|_\|\|\n______________GUGUUUU_________AGUUUCUUUUCGUC_AC\n3'-UUU...CCGAG_______ACCCCUGU__________________CG-5'\n_____________\|_________________________________\|\n_____________34________________________________2\n	194 -- 200	5 -- 11	-23.2607 kcal/mol	6.82691 kcal/mol	3.0786 kcal/mol	170 204@LB@ \| \|@LB@5'-CGC...UCACC AAAUAAUUC A AAACA...UGC-3'@LB@ CGCGAAA UCAAGGAGAAGCGG UG@LB@ \|:\|:\|\|\| \|\|\|\|:\|\|:\|\|\|\|:\| \|\|@LB@ GUGUUUU AGUUUCUUUUCGUC AC@LB@3'-UUU...CCGAG ACCCCUGU CG-5'@LB@ \| \|@LB@ 34 2@LB@@LB@@LB@Energy -13.36 kcal/mol@LB@Hybridization Energy -23.2607 kcal/mol@LB@Unfolding Energy - mRNA 6.82691 kcal/mol@LB@Unfolding Energy - sRNA 3.0786 kcal/mol@LB@@LB@Position - mRNA 171 -- 203@LB@Position - sRNA 3 -- 33@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@LB@
3	3.973e-07	0.0004647	b0081	mraZ	-16.47	0.011640	172 -- 200	1 -- 32	RsmH methytransferase inhibitor	_____________171______________________________201\n_____________\|________________________________\|\n5'-GAU...GUGGG__________A___A_____U___________AUGUU...AAA-3'\n______________GCAAAGUGGG_AUA__GGGG_GAGGC__UGGC\n______________:\|\|\|\|:\|\|\|\|_\|:\|__:::\|_:\|:\|\|__\|\|\|\|\n______________UGUUUUACCC_UGU__UUUC_UUUCG__ACCG\n3'-UUU...CGAGG__________C___AG____U_____UC____-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	175 -- 181	23 -- 29	-28.2943 kcal/mol	9.28897 kcal/mol	2.53929 kcal/mol	171 201@LB@ \| \|@LB@5'-GAU...GUGGG A A U AUGUU...AAA-3'@LB@ GCAAAGUGGG AUA GGGG GAGGC UGGC@LB@ :\|\|\|\|:\|\|\|\| \|:\| :::\| :\|:\|\| \|\|\|\|@LB@ UGUUUUACCC UGU UUUC UUUCG ACCG@LB@3'-UUU...CGAGG C AG U UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -16.47 kcal/mol@LB@Hybridization Energy -28.2943 kcal/mol@LB@Unfolding Energy - mRNA 9.28897 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 172 -- 200@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 23 -- 29@LB@
29	0.00125	0.1512	b2499	purM	-15.92	0.016248	173 -- 203	3 -- 34	phosphoribosylaminoimidazole synthetase	_____________172____________________________________204\n_____________\|______________________________________\|\n5'-UAU...UUCUA_______UAACGC________CC_______________ACCGA...CGC-3'\n______________CCGCAAG______GUGGGGAC_________AAGCAGUG\n______________\|\|:\|\|\|:______:\|\|\|\|\|\|\|_________\|\|\|\|\|\|\|\|\n______________GGUGUUU______UACCCCUG_________UUCGUCAC\n3'-UUU...CCCGA_____________________UAGUUUCUU________CG-5'\n_____________\|______________________________________\|\n_____________35_____________________________________2\n	197 -- 203	3 -- 9	-29.7141 kcal/mol	9.52212 kcal/mol	4.26884 kcal/mol	172 204@LB@ \| \|@LB@5'-UAU...UUCUA UAACGC CC ACCGA...CGC-3'@LB@ CCGCAAG GUGGGGAC AAGCAGUG@LB@ \|\|:\|\|\|: :\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ GGUGUUU UACCCCUG UUCGUCAC@LB@3'-UUU...CCCGA UAGUUUCUU CG-5'@LB@ \| \|@LB@ 35 2@LB@@LB@@LB@Energy -15.92 kcal/mol@LB@Hybridization Energy -29.7141 kcal/mol@LB@Unfolding Energy - mRNA 9.52212 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 173 -- 203@LB@Position - sRNA 3 -- 34@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 3 -- 9@LB@
135	0.009724	0.2504	b1387	paaZ	-12.57	0.095542	174 -- 198	5 -- 30	oxepin-CoA hydrolase and 3-oxo-5 6-dehydrosuberyl-CoA semialdehyde dehydrogenase	_____________173_________________________199\n_____________\|___________________________\|\n5'-UAA...CAACA______U_AA_____U___________CGAUG...AAG-3'\n______________GAAAUG_G__ACAUC___GGAGAGUAG\n______________:\|\|\|\|\|_\|__\|\|\|\|\|___\|:\|:\|\|:\|\|\n______________UUUUAC_C__UGUAG___CUUUUCGUC\n3'-UUU...AGGUG________CC_____UUU_________ACCG-5'\n_____________\|___________________________\|\n_____________31__________________________4\n	192 -- 198	5 -- 11	-19.0129 kcal/mol	3.93627 kcal/mol	2.50278 kcal/mol	173 199@LB@ \| \|@LB@5'-UAA...CAACA U AA U CGAUG...AAG-3'@LB@ GAAAUG G ACAUC GGAGAGUAG@LB@ :\|\|\|\|\| \| \|\|\|\|\| \|:\|:\|\|:\|\|@LB@ UUUUAC C UGUAG CUUUUCGUC@LB@3'-UUU...AGGUG CC UUU ACCG-5'@LB@ \| \|@LB@ 31 4@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -19.0129 kcal/mol@LB@Unfolding Energy - mRNA 3.93627 kcal/mol@LB@Unfolding Energy - sRNA 2.50278 kcal/mol@LB@@LB@Position - mRNA 174 -- 198@LB@Position - sRNA 5 -- 30@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 5 -- 11@LB@
144	0.01052	0.2504	b1066	rimJ	-12.60	0.094480	174 -- 195	1 -- 22	ribosomal-protein-S5-alanine N-acetyltransferase	_____________173_____________________196\n_____________\|_______________________\|\n5'-AUU...UUAAA_______C___________A___AUAGA...AUU-3'\n______________GACGUUA_GGGAAGG_AGU_GGU\n______________\|\|\|:\|:\|_:\|:\|\|:\|_\|\|\|_\|\|:\n______________CUGUAGU_UCUUUUC_UCA_CCG\n3'-UUU...UACCC_______U_______G_______-5'\n_____________\|______________________\|\n_____________23_____________________1\n	182 -- 188	8 -- 14	-20.3318 kcal/mol	6.19349 kcal/mol	1.54023 kcal/mol	173 196@LB@ \| \|@LB@5'-AUU...UUAAA C A AUAGA...AUU-3'@LB@ GACGUUA GGGAAGG AGU GGU@LB@ \|\|\|:\|:\| :\|:\|\|:\| \|\|\| \|\|:@LB@ CUGUAGU UCUUUUC UCA CCG@LB@3'-UUU...UACCC U G -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -20.3318 kcal/mol@LB@Unfolding Energy - mRNA 6.19349 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 174 -- 195@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 8 -- 14@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@
2	5.107e-11	8.961e-08	b2314	dedD	-25.37	0.000001	176 -- 205	1 -- 30	membrane-anchored periplasmic protein involved in septation	_____________175_____________________________206\n_____________\|_______________________________\|\n5'-UUG...UCAUG______AUU______________________AAGUA...AUU-3'\n______________GAAGUG___GACG_CGAGGAGAAGCGGUGGC\n______________:\|\|:\|\|___\|\|\|:_\|:\|:\|\|:\|\|\|\|:\|\|\|\|\|\n______________UUUUAC___CUGU_GUUUCUUUUCGUCACCG\n3'-UUU...AGGUG______CC_____A_________________-5'\n_____________\|______________________________\|\n_____________31_____________________________1\n	199 -- 205	1 -- 7	-36.5756 kcal/mol	8.68219 kcal/mol	2.51911 kcal/mol	175 206@LB@ \| \|@LB@5'-UUG...UCAUG AUU AAGUA...AUU-3'@LB@ GAAGUG GACG CGAGGAGAAGCGGUGGC@LB@ :\|\|:\|\| \|\|\|: \|:\|:\|\|:\|\|\|\|:\|\|\|\|\|@LB@ UUUUAC CUGU GUUUCUUUUCGUCACCG@LB@3'-UUU...AGGUG CC A -5'@LB@ \| \|@LB@ 31 1@LB@@LB@@LB@Energy -25.37 kcal/mol@LB@Hybridization Energy -36.5756 kcal/mol@LB@Unfolding Energy - mRNA 8.68219 kcal/mol@LB@Unfolding Energy - sRNA 2.51911 kcal/mol@LB@@LB@Position - mRNA 176 -- 205@LB@Position - sRNA 1 -- 30@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 1 -- 7@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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service.

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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