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
153	0.01124	0.2504	b0414	ribD	-14.78	0.031370	153 -- 170	1 -- 22	fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase	_____________152____________________171\n_____________\|______________________\|\n5'-AAA...UCGAA____________UU________GAAGA...AAG-3'\n______________GAUAUCAAAGAA______UGGC\n______________\|\|:\|\|\|\|\|\|\|\|\|______\|\|\|\|\n______________CUGUAGUUUCUU______ACCG\n3'-UUU...UACCC____________UUCGUC____-5'\n_____________\|_____________________\|\n_____________23____________________1\n	158 -- 164	11 -- 17	-19.3666 kcal/mol	3.04735 kcal/mol	1.54023 kcal/mol	152 171@LB@ \| \|@LB@5'-AAA...UCGAA UU GAAGA...AAG-3'@LB@ GAUAUCAAAGAA UGGC@LB@ \|\|:\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUGUAGUUUCUU ACCG@LB@3'-UUU...UACCC UUCGUC -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -19.3666 kcal/mol@LB@Unfolding Energy - mRNA 3.04735 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 153 -- 170@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 11 -- 17@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@
140	0.01029	0.2504	b3247	rng	-10.20	0.255190	49 -- 63	1 -- 14	ribonuclease G	_____________48______________64\n_____________\|_______________\|\n5'-GUU...CCGUU___U_______GU__AUACG...CGC-3'\n______________AGA_AAAGCAG__GC\n______________\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________UCU_UUUCGUC__CG\n3'-UUU...UAGUU___________AC__-5'\n_____________\|______________\|\n_____________15_____________1\n	53 -- 59	5 -- 11	-13.7724 kcal/mol	2.22711 kcal/mol	1.34059 kcal/mol	48 64@LB@ \| \|@LB@5'-GUU...CCGUU U GU AUACG...CGC-3'@LB@ AGA AAAGCAG GC@LB@ \|\|\| \|\|\|\|\|\|\| \|\|@LB@ UCU UUUCGUC CG@LB@3'-UUU...UAGUU AC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -13.7724 kcal/mol@LB@Unfolding Energy - mRNA 2.22711 kcal/mol@LB@Unfolding Energy - sRNA 1.34059 kcal/mol@LB@@LB@Position - mRNA 49 -- 63@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@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@
55	0.002823	0.1778	b3319	rplD	-12.54	0.096993	18 -- 45	1 -- 32	50S ribosomal subunit protein L4	_____________17________________________________46\n_____________\|_________________________________\|\n5'-UCA...UCCGG________U____________C___AAAA____AGGUC...UUG-3'\n______________GCAAAGUG______UCAAAGG_AAG____UGGC\n______________:\|\|\|\|:\|\|______\|\|\|\|\|\|:_\|\|\|____\|\|\|\|\n______________UGUUUUAC______AGUUUCU_UUC____ACCG\n3'-UUU...CGAGG________CCCUGU_______U___GUC_____-5'\n_____________\|________________________________\|\n_____________33_______________________________1\n	27 -- 33	12 -- 18	-19.13 kcal/mol	4.04955 kcal/mol	2.53929 kcal/mol	17 46@LB@ \| \|@LB@5'-UCA...UCCGG U C AAAA AGGUC...UUG-3'@LB@ GCAAAGUG UCAAAGG AAG UGGC@LB@ :\|\|\|\|:\|\| \|\|\|\|\|\|: \|\|\| \|\|\|\|@LB@ UGUUUUAC AGUUUCU UUC ACCG@LB@3'-UUU...CGAGG CCCUGU U GUC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -12.54 kcal/mol@LB@Hybridization Energy -19.13 kcal/mol@LB@Unfolding Energy - mRNA 4.04955 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 18 -- 45@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 27 -- 33@LB@Position Seed - sRNA 12 -- 18@LB@
23	0.0008148	0.1243	b2573	rpoE	-12.22	0.112158	248 -- 284	1 -- 24	RNA polymerase sigma E factor	_____________247___________________________________285\n_____________\|_____________________________________\|\n5'-ACA...CAGAA____G______AAGCCUUUAACUUACU_______C__UAUCA...UGG-3'\n______________GGGA_AUCAGA________________GGUAGUG_GC\n______________\|\|\|\|_\|\|\|\|:\|________________:\|:\|\|\|\|_\|\|\n______________CCCU_UAGUUU________________UCGUCAC_CG\n3'-UUU...UUUAC____G______CUUU______________________-5'\n_____________\|____________________________________\|\n_____________25___________________________________1\n	275 -- 281	3 -- 9	-22.4239 kcal/mol	7.75978 kcal/mol	2.44282 kcal/mol	247 285@LB@ \| \|@LB@5'-ACA...CAGAA G AAGCCUUUAACUUACU C UAUCA...UGG-3'@LB@ GGGA AUCAGA GGUAGUG GC@LB@ \|\|\|\| \|\|\|\|:\| :\|:\|\|\|\| \|\|@LB@ CCCU UAGUUU UCGUCAC CG@LB@3'-UUU...UUUAC G CUUU -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -12.22 kcal/mol@LB@Hybridization Energy -22.4239 kcal/mol@LB@Unfolding Energy - mRNA 7.75978 kcal/mol@LB@Unfolding Energy - sRNA 2.44282 kcal/mol@LB@@LB@Position - mRNA 248 -- 284@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 3 -- 9@LB@
82	0.005087	0.2147	b2741	rpoS	-15.46	0.021295	2 -- 28	1 -- 25	RNA polymerase sigma S (sigma 38) factor	_____________1____________________________29\n_____________\|____________________________\|\n__________5'-C___A___ACAA____UU___________AAAAA...AGG-3'\n______________GGG_ACA____GAAG__AAGGCGG_GGC\n______________\|\|\|_\|\|\|____:\|\|\|__\|\|:\|\|:\|_\|\|\|\n______________CCC_UGU____UUUC__UUUCGUC_CCG\n3'-UUU...UUUUA___C___AG______U________A___-5'\n_____________\|___________________________\|\n_____________26__________________________1\n	19 -- 25	5 -- 11	-23.9329 kcal/mol	5.95047 kcal/mol	2.51748 kcal/mol	1 29@LB@ \| \|@LB@ 5'-C A ACAA UU AAAAA...AGG-3'@LB@ GGG ACA GAAG AAGGCGG GGC@LB@ \|\|\| \|\|\| :\|\|\| \|\|:\|\|:\| \|\|\|@LB@ CCC UGU UUUC UUUCGUC CCG@LB@3'-UUU...UUUUA C AG U A -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -15.46 kcal/mol@LB@Hybridization Energy -23.9329 kcal/mol@LB@Unfolding Energy - mRNA 5.95047 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 2 -- 28@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 5 -- 11@LB@
149	0.01096	0.2504	b3230	rpsI	-12.23	0.111717	165 -- 205	1 -- 34	30S ribosomal subunit protein S9	_____________164_______________________________________206\n_____________\|_________________________________________\|\n5'-GUG...AGCAA_______UUCUU______UAAUC____UUAU_____A____UGAAA...GUU-3'\n______________CCGCAAG_____GACAUC_____GGGA____AGGCA_UGGC\n______________\|\|:\|\|\|:_____\|\|\|\|\|\|_____:\|:\|____\|:\|\|\|_\|\|\|\|\n______________GGUGUUU_____CUGUAG_____UCUU____UUCGU_ACCG\n3'-UUU...CCCGA_______UACCC______UU________________C____-5'\n_____________\|________________________________________\|\n_____________35_______________________________________1\n	165 -- 171	28 -- 34	-26.3465 kcal/mol	9.84752 kcal/mol	4.26884 kcal/mol	164 206@LB@ \| \|@LB@5'-GUG...AGCAA UUCUU UAAUC UUAU A UGAAA...GUU-3'@LB@ CCGCAAG GACAUC GGGA AGGCA UGGC@LB@ \|\|:\|\|\|: \|\|\|\|\|\| :\|:\| \|:\|\|\| \|\|\|\|@LB@ GGUGUUU CUGUAG UCUU UUCGU ACCG@LB@3'-UUU...CCCGA UACCC UU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -12.23 kcal/mol@LB@Hybridization Energy -26.3465 kcal/mol@LB@Unfolding Energy - mRNA 9.84752 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 28 -- 34@LB@
4	1.99e-05	0.01653	b4255	rraB	-17.36	0.006479	180 -- 205	1 -- 23	protein inhibitor of RNase E	_____________179________________________206\n_____________\|__________________________\|\n5'-GAG...CGGCA_________GA____U____CA____AAACC...CCA-3'\n______________GGACAUUAA__GGAA_GAGC__UGGC\n______________\|\|\|\|\|\|:\|\|__:\|\|\|_:\|\|\|__\|\|\|\|\n______________CCUGUAGUU__UCUU_UUCG__ACCG\n3'-UUU...UUACC____________________UC____-5'\n_____________\|_________________________\|\n_____________24________________________1\n	182 -- 188	15 -- 21	-24.3176 kcal/mol	5.37332 kcal/mol	1.57928 kcal/mol	179 206@LB@ \| \|@LB@5'-GAG...CGGCA GA U CA AAACC...CCA-3'@LB@ GGACAUUAA GGAA GAGC UGGC@LB@ \|\|\|\|\|\|:\|\| :\|\|\| :\|\|\| \|\|\|\|@LB@ CCUGUAGUU UCUU UUCG ACCG@LB@3'-UUU...UUACC UC -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.36 kcal/mol@LB@Hybridization Energy -24.3176 kcal/mol@LB@Unfolding Energy - mRNA 5.37332 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 180 -- 205@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 15 -- 21@LB@
148	0.01095	0.2504	b0082	rsmH	-17.59	0.005541	130 -- 156	1 -- 25	16S rRNA m(4)C1402 methyltransferase SAM-dependent	_____________129_________________________157\n_____________\|___________________________\|\n5'-UGG...GUCAA__AA________C_C________U___UACCG...GUC-3'\n______________GG__GAUAUCGA_G_AGAGCAGU_GGC\n______________\|\|__\|\|:\|\|\|:\|_\|_\|:\|\|\|\|\|\|_\|\|\|\n______________CC__CUGUAGUU_C_UUUCGUCA_CCG\n3'-UUU...UUUUA__C_________U_U____________-5'\n_____________\|__________________________\|\n_____________26_________________________1\n	146 -- 152	4 -- 10	-26.6505 kcal/mol	6.5392 kcal/mol	2.51748 kcal/mol	129 157@LB@ \| \|@LB@5'-UGG...GUCAA AA C C U UACCG...GUC-3'@LB@ GG GAUAUCGA G AGAGCAGU GGC@LB@ \|\| \|\|:\|\|\|:\| \| \|:\|\|\|\|\|\| \|\|\|@LB@ CC CUGUAGUU C UUUCGUCA CCG@LB@3'-UUU...UUUUA C U U -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -17.59 kcal/mol@LB@Hybridization Energy -26.6505 kcal/mol@LB@Unfolding Energy - mRNA 6.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 130 -- 156@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 4 -- 10@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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