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
118	0.008241	0.2451	b3394	hofN	-17.25	0.007000	1 -- 22	2 -- 26	DNA catabolic putative fimbrial assembly protein	______________1________________________23\n______________\|________________________\|\n___________5'-_____________CU__________GGAUG...CCG-3'\n______________UGGGGGCG_CAAA____GGCGGUGG\n______________\|\|\|\|\|:\|:_\|\|\|\|____:\|\|:\|\|\|\|\n______________ACCCCUGU_GUUU____UCGUCACC\n3'-UUU...GUUUU________A____CUUU________G-5'\n_____________\|_________________________\|\n_____________27________________________1\n	16 -- 22	2 -- 8	-29.7277 kcal/mol	9.95926 kcal/mol	2.5184 kcal/mol	1 23@LB@ \| \|@LB@ 5'- CU GGAUG...CCG-3'@LB@ UGGGGGCG CAAA GGCGGUGG@LB@ \|\|\|\|\|:\|: \|\|\|\| :\|\|:\|\|\|\|@LB@ ACCCCUGU GUUU UCGUCACC@LB@3'-UUU...GUUUU A CUUU G-5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -17.25 kcal/mol@LB@Hybridization Energy -29.7277 kcal/mol@LB@Unfolding Energy - mRNA 9.95926 kcal/mol@LB@Unfolding Energy - sRNA 2.5184 kcal/mol@LB@@LB@Position - mRNA 1 -- 22@LB@Position - sRNA 2 -- 26@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 2 -- 8@LB@
130	0.009344	0.2491	b2840	ygeA	-9.74	0.301486	266 -- 295	2 -- 29	Asp/Glu_racemase family protein	_____________265____________________________296\n_____________\|______________________________\|\n5'-AAA...UUGAU_____AA_________C__C___UU_____GCUUC-3'\n______________AAAUG__GGCAUUAAA_AG_GGC__GGUGG\n______________\|\|\|\|\|__\|:\|\|\|:\|\|\|_\|:_:\|\|__:\|\|\|\|\n______________UUUAC__CUGUAGUUU_UU_UCG__UCACC\n3'-UUU...GGUGU_____CC_________C__U__________G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	275 -- 281	14 -- 20	-20.8158 kcal/mol	8.56062 kcal/mol	2.51906 kcal/mol	265 296@LB@ \| \|@LB@5'-AAA...UUGAU AA C C UU GCUUC-3'@LB@ AAAUG GGCAUUAAA AG GGC GGUGG@LB@ \|\|\|\|\| \|:\|\|\|:\|\|\| \|: :\|\| :\|\|\|\|@LB@ UUUAC CUGUAGUUU UU UCG UCACC@LB@3'-UUU...GGUGU CC C U G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -9.74 kcal/mol@LB@Hybridization Energy -20.8158 kcal/mol@LB@Unfolding Energy - mRNA 8.56062 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 275 -- 281@LB@Position Seed - sRNA 14 -- 20@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@
13	0.0004028	0.1087	b1107	nagZ	-16.35	0.012500	184 -- 201	3 -- 21	beta N-acetyl-glucosaminidase	_____________183_________________202\n_____________\|___________________\|\n5'-AUU...AUAAA___AU______________UGGGU...CGC-3'\n______________ACA___AAGGAGAGCAGUG\n______________\|\|\|___\|\|\|:\|:\|\|\|\|\|\|\|\n______________UGU___UUCUUUUCGUCAC\n3'-UUU...ACCCC___AGU_____________CG-5'\n_____________\|___________________\|\n_____________22__________________2\n	195 -- 201	3 -- 9	-19.0842 kcal/mol	1.22154 kcal/mol	1.5107 kcal/mol	183 202@LB@ \| \|@LB@5'-AUU...AUAAA AU UGGGU...CGC-3'@LB@ ACA AAGGAGAGCAGUG@LB@ \|\|\| \|\|\|:\|:\|\|\|\|\|\|\|@LB@ UGU UUCUUUUCGUCAC@LB@3'-UUU...ACCCC AGU CG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -16.35 kcal/mol@LB@Hybridization Energy -19.0842 kcal/mol@LB@Unfolding Energy - mRNA 1.22154 kcal/mol@LB@Unfolding Energy - sRNA 1.5107 kcal/mol@LB@@LB@Position - mRNA 184 -- 201@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 3 -- 9@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@
50	0.002349	0.1648	b2040	rfbD	-20.63	0.000491	127 -- 157	3 -- 32	dTDP-L-rhamnose synthase NAD(P)-dependent dTDP-4-dehydrorhamnose reductase subunit	_____________126______________________________158\n_____________\|________________________________\|\n5'-GAU...CCAAU__________UU____AUGU____________CCUAU...CUA-3'\n______________ACAAAAUGGG__GAUA_____GAAAAGUGGUG\n______________\|\|\|\|\|\|\|\|\|\|__\|\|:\|_____\|\|\|\|\|\|::\|\|\|\n______________UGUUUUACCC__CUGU_____CUUUUCGUCAC\n3'-UUU...CGAGG________________AGUUU___________CG-5'\n_____________\|________________________________\|\n_____________33_______________________________2\n	151 -- 157	3 -- 9	-27.2371 kcal/mol	4.0691 kcal/mol	2.53925 kcal/mol	126 158@LB@ \| \|@LB@5'-GAU...CCAAU UU AUGU CCUAU...CUA-3'@LB@ ACAAAAUGGG GAUA GAAAAGUGGUG@LB@ \|\|\|\|\|\|\|\|\|\| \|\|:\| \|\|\|\|\|\|::\|\|\|@LB@ UGUUUUACCC CUGU CUUUUCGUCAC@LB@3'-UUU...CGAGG AGUUU CG-5'@LB@ \| \|@LB@ 33 2@LB@@LB@@LB@Energy -20.63 kcal/mol@LB@Hybridization Energy -27.2371 kcal/mol@LB@Unfolding Energy - mRNA 4.0691 kcal/mol@LB@Unfolding Energy - sRNA 2.53925 kcal/mol@LB@@LB@Position - mRNA 127 -- 157@LB@Position - sRNA 3 -- 32@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 3 -- 9@LB@
58	0.00302	0.1789	b0556	rzpD	-16.79	0.009474	64 -- 103	3 -- 36	DLP12 prophage; putative murein endopeptidase	_____________63_________________________________________104\n_____________\|__________________________________________\|\n5'-CGC...CGCUU___________AAACCA___C___________C_____U___AUCAG...ACA-3'\n______________CUUCGCAAAAU______GGG_GAUAUCAAAGG___GCA_GUG\n______________\|\|:\|:\|\|\|\|\|\|______\|\|\|_\|\|:\|\|\|\|\|\|\|:___\|\|\|_\|\|\|\n______________GAGGUGUUUUA______CCC_CUGUAGUUUCU___CGU_CAC\n3'-UUU...UACCC________________________________UUU_______CG-5'\n_____________\|__________________________________________\|\n_____________37_________________________________________2\n	89 -- 95	12 -- 18	-34.1904 kcal/mol	10.724 kcal/mol	6.67685 kcal/mol	63 104@LB@ \| \|@LB@5'-CGC...CGCUU AAACCA C C U AUCAG...ACA-3'@LB@ CUUCGCAAAAU GGG GAUAUCAAAGG GCA GUG@LB@ \|\|:\|:\|\|\|\|\|\| \|\|\| \|\|:\|\|\|\|\|\|\|: \|\|\| \|\|\|@LB@ GAGGUGUUUUA CCC CUGUAGUUUCU CGU CAC@LB@3'-UUU...UACCC UUU CG-5'@LB@ \| \|@LB@ 37 2@LB@@LB@@LB@Energy -16.79 kcal/mol@LB@Hybridization Energy -34.1904 kcal/mol@LB@Unfolding Energy - mRNA 10.724 kcal/mol@LB@Unfolding Energy - sRNA 6.67685 kcal/mol@LB@@LB@Position - mRNA 64 -- 103@LB@Position - sRNA 3 -- 36@LB@Position Seed - mRNA 89 -- 95@LB@Position Seed - sRNA 12 -- 18@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@
110	0.007401	0.2348	b0784	moaD	-14.78	0.031320	178 -- 203	3 -- 25	molybdopterin synthase small subunit	_____________177________________________204\n_____________\|__________________________\|\n5'-GCA...AAGUC___U___U______U________A__AUUAA...AGC-3'\n______________GGG_GAC_UUAAGG_GGAAGCGG_UG\n______________\|\|\|_\|\|\|_\|:\|\|:\|_::\|\|\|\|:\|_\|\|\n______________CCC_CUG_AGUUUC_UUUUCGUC_AC\n3'-UUU...UUUUA_______U__________________CG-5'\n_____________\|__________________________\|\n_____________26_________________________2\n	194 -- 200	5 -- 11	-23.9822 kcal/mol	6.68375 kcal/mol	2.5166 kcal/mol	177 204@LB@ \| \|@LB@5'-GCA...AAGUC U U U A AUUAA...AGC-3'@LB@ GGG GAC UUAAGG GGAAGCGG UG@LB@ \|\|\| \|\|\| \|:\|\|:\| ::\|\|\|\|:\| \|\|@LB@ CCC CUG AGUUUC UUUUCGUC AC@LB@3'-UUU...UUUUA U CG-5'@LB@ \| \|@LB@ 26 2@LB@@LB@@LB@Energy -14.78 kcal/mol@LB@Hybridization Energy -23.9822 kcal/mol@LB@Unfolding Energy - mRNA 6.68375 kcal/mol@LB@Unfolding Energy - sRNA 2.5166 kcal/mol@LB@@LB@Position - mRNA 178 -- 203@LB@Position - sRNA 3 -- 25@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 5 -- 11@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@

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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