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
20	0.0007622	0.1243	b1507	hipA	-19.17	0.001718	1 -- 29	1 -- 31	inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase		______________1________________________________30\n______________\|________________________________\|\n___________5'-________CU___________C___________GAAAA...UAG-3'\n______________CAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________GUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...GAGGU_______________A_____UU____UC____-5'\n_____________\|________________________________\|\n_____________32_______________________________1\n	2 -- 8	24 -- 30	-30.0086 kcal/mol	8.29611 kcal/mol	2.53929 kcal/mol	1 30@LB@ \| \|@LB@ 5'- CU C GAAAA...UAG-3'@LB@ CAAAAUGG GGACG CAGAG GAGC UGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ GUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...GAGGU A UU UC -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -19.17 kcal/mol@LB@Hybridization Energy -30.0086 kcal/mol@LB@Unfolding Energy - mRNA 8.29611 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 2 -- 8@LB@Position Seed - sRNA 24 -- 30@LB@
64	0.003422	0.1851	b4238	nrdD	-18.31	0.003326	69 -- 106	1 -- 34	anaerobic ribonucleoside-triphosphate reductase		_____________68_____________________________________107\n_____________\|______________________________________\|\n5'-UAU...GCUCC________AA__U_C_______U___U______A____GAUUG...UCG-3'\n______________CCACGAAA__GG_G_GGCGUUG_GGA_AAGCGG_UGGC\n______________\|\|\|\|:\|\|\|__\|\|_\|_\|:\|:\|::_:\|\|_\|\|\|\|:\|_\|\|\|\|\n______________GGUGUUUU__CC_C_CUGUAGU_UCU_UUCGUC_ACCG\n3'-UUU...CCCGA________A_____________U___U___________-5'\n_____________\|_____________________________________\|\n_____________35____________________________________1\n	84 -- 90	16 -- 22	-34.2754 kcal/mol	11.6957 kcal/mol	4.26884 kcal/mol	68 107@LB@ \| \|@LB@5'-UAU...GCUCC AA U C U U A GAUUG...UCG-3'@LB@ CCACGAAA GG G GGCGUUG GGA AAGCGG UGGC@LB@ \|\|\|\|:\|\|\| \|\| \| \|:\|:\|:: :\|\| \|\|\|\|:\| \|\|\|\|@LB@ GGUGUUUU CC C CUGUAGU UCU UUCGUC ACCG@LB@3'-UUU...CCCGA A U U -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -18.31 kcal/mol@LB@Hybridization Energy -34.2754 kcal/mol@LB@Unfolding Energy - mRNA 11.6957 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 69 -- 106@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
78	0.004634	0.2062	b1601	tqsA	-18.27	0.003423	191 -- 205	1 -- 25	pheromone AI-2 transporter		_____________190_______________________206\n_____________\|_________________________\|\n5'-AUU...AAAAC_________________________AAAGC...UCA-3'\n______________GGGGACA_________AGCA_UGGC\n______________\|\|\|\|\|\|\|_________\|\|\|\|_\|\|\|\|\n______________CCCCUGU_________UCGU_ACCG\n3'-UUU...UUUUA_______AGUUUCUUU____C____-5'\n_____________\|________________________\|\n_____________26_______________________1\n	191 -- 197	19 -- 25	-23.2822 kcal/mol	2.49324 kcal/mol	2.51748 kcal/mol	190 206@LB@ \| \|@LB@5'-AUU...AAAAC AAAGC...UCA-3'@LB@ GGGGACA AGCA UGGC@LB@ \|\|\|\|\|\|\| \|\|\|\| \|\|\|\|@LB@ CCCCUGU UCGU ACCG@LB@3'-UUU...UUUUA AGUUUCUUU C -5'@LB@ \| \|@LB@ 26 1@LB@@LB@@LB@Energy -18.27 kcal/mol@LB@Hybridization Energy -23.2822 kcal/mol@LB@Unfolding Energy - mRNA 2.49324 kcal/mol@LB@Unfolding Energy - sRNA 2.51748 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 1 -- 25@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 19 -- 25@LB@
67	0.003548	0.1858	b4412	hokC	-18.22	0.003564	16 -- 36	7 -- 32	toxic membrane protein small	b1562 b0018	_____________15_________________________37\n_____________\|__________________________\|\n5'-AUU...AUAAA__________________________GAUAU...ACA-3'\n______________ACAAAAUGGG____UUAAAGAGA_GC\n______________\|\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\|_\|\|\n______________UGUUUUACCC____AGUUUCUUU_CG\n3'-UUU...CGAGG__________CUGU_________U__UCACCG-5'\n_____________\|__________________________\|\n_____________33_________________________6\n	28 -- 34	10 -- 16	-22.2189 kcal/mol	1.46836 kcal/mol	2.53437 kcal/mol	15 37@LB@ \| \|@LB@5'-AUU...AUAAA GAUAU...ACA-3'@LB@ ACAAAAUGGG UUAAAGAGA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:\| \|\|@LB@ UGUUUUACCC AGUUUCUUU CG@LB@3'-UUU...CGAGG CUGU U UCACCG-5'@LB@ \| \|@LB@ 33 6@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -22.2189 kcal/mol@LB@Unfolding Energy - mRNA 1.46836 kcal/mol@LB@Unfolding Energy - sRNA 2.53437 kcal/mol@LB@@LB@Position - mRNA 16 -- 36@LB@Position - sRNA 7 -- 32@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 10 -- 16@LB@
51	0.00253	0.1729	b0699	ybfA	-18.06	0.004001	182 -- 204	2 -- 32	DUF2517 family protein		_____________181_____________________________205\n_____________\|_______________________________\|\n5'-AUG...UAGAU_______________________________AACUC...GGA-3'\n______________ACAAAA_GGGG______GAGAAAAGUA_UGG\n______________\|\|\|\|\|\|_\|\|\|\|______:\|\|\|\|\|\|\|:\|_\|\|\|\n______________UGUUUU_CCCC______UUCUUUUCGU_ACC\n3'-UUU...CGAGG______A____UGUAGU__________C___G-5'\n_____________\|_______________________________\|\n_____________33______________________________1\n	195 -- 201	6 -- 12	-23.7835 kcal/mol	3.18782 kcal/mol	2.53929 kcal/mol	181 205@LB@ \| \|@LB@5'-AUG...UAGAU AACUC...GGA-3'@LB@ ACAAAA GGGG GAGAAAAGUA UGG@LB@ \|\|\|\|\|\| \|\|\|\| :\|\|\|\|\|\|\|:\| \|\|\|@LB@ UGUUUU CCCC UUCUUUUCGU ACC@LB@3'-UUU...CGAGG A UGUAGU C G-5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.06 kcal/mol@LB@Hybridization Energy -23.7835 kcal/mol@LB@Unfolding Energy - mRNA 3.18782 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 182 -- 204@LB@Position - sRNA 2 -- 32@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
19	0.000738	0.1243	b1508	hipB	-18.00	0.004180	266 -- 295	1 -- 32	antitoxin of HipAB toxin-antitoxin system	b1299 b1434	_____________265________________________________296\n_____________\|__________________________________\|\n5'-AUG...CGCCA_________CU___________C___________GAAAA-3'\n______________GCAAAAUGG__GGACG_CAGAG__GAGC__UGGC\n______________:\|\|\|\|\|\|\|\|__\|\|\|\|:_\|\|:\|\|__:\|\|\|__\|\|\|\|\n______________UGUUUUACC__CCUGU_GUUUC__UUCG__ACCG\n3'-UUU...CGAGG________________A_____UU____UC____-5'\n_____________\|_________________________________\|\n_____________33________________________________1\n	268 -- 274	24 -- 30	-30.0826 kcal/mol	9.54799 kcal/mol	2.53929 kcal/mol	265 296@LB@ \| \|@LB@5'-AUG...CGCCA CU C GAAAA-3'@LB@ GCAAAAUGG GGACG CAGAG GAGC UGGC@LB@ :\|\|\|\|\|\|\|\| \|\|\|\|: \|\|:\|\| :\|\|\| \|\|\|\|@LB@ UGUUUUACC CCUGU GUUUC UUCG ACCG@LB@3'-UUU...CGAGG A UU UC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -18.00 kcal/mol@LB@Hybridization Energy -30.0826 kcal/mol@LB@Unfolding Energy - mRNA 9.54799 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 266 -- 295@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 24 -- 30@LB@
21	0.0007937	0.1243	b3055	ygiM	-17.78	0.004866	75 -- 99	1 -- 23	SH3 domain protein		_____________74________________________100\n_____________\|_________________________\|\n5'-GGC...UUGAC______A____UUU___________AAGAC...AUA-3'\n______________GGGCGU_AAAG___GAAGCAGUGGC\n______________\|\|:\|:\|_\|\|\|\|___:\|\|\|\|\|\|\|\|\|\|\n______________CCUGUA_UUUC___UUUCGUCACCG\n3'-UUU...UUACC______G____U_____________-5'\n_____________\|________________________\|\n_____________24_______________________1\n	93 -- 99	1 -- 7	-29.8569 kcal/mol	10.4968 kcal/mol	1.57928 kcal/mol	74 100@LB@ \| \|@LB@5'-GGC...UUGAC A UUU AAGAC...AUA-3'@LB@ GGGCGU AAAG GAAGCAGUGGC@LB@ \|\|:\|:\| \|\|\|\| :\|\|\|\|\|\|\|\|\|\|@LB@ CCUGUA UUUC UUUCGUCACCG@LB@3'-UUU...UUACC G U -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -17.78 kcal/mol@LB@Hybridization Energy -29.8569 kcal/mol@LB@Unfolding Energy - mRNA 10.4968 kcal/mol@LB@Unfolding Energy - sRNA 1.57928 kcal/mol@LB@@LB@Position - mRNA 75 -- 99@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 93 -- 99@LB@Position Seed - sRNA 1 -- 7@LB@
46	0.002205	0.1648	b1662	ribC	-17.71	0.005126	34 -- 61	2 -- 29	riboflavin synthase alpha subunit		_____________33_____________________________62\n_____________\|______________________________\|\n5'-UUU...CGCCU_______CA___A_____A___________GAAAU...UGG-3'\n______________GAAUGGG__GCA__AAAG_AGAAGCAG_GG\n______________:\|\|\|\|\|\|__:\|\|__\|\|\|\|_\|:\|\|\|\|\|\|_\|\|\n______________UUUACCC__UGU__UUUC_UUUUCGUC_CC\n3'-UUU...GGUGU_______C____AG_____________A__G-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	53 -- 59	5 -- 11	-25.8778 kcal/mol	5.65259 kcal/mol	2.51906 kcal/mol	33 62@LB@ \| \|@LB@5'-UUU...CGCCU CA A A GAAAU...UGG-3'@LB@ GAAUGGG GCA AAAG AGAAGCAG GG@LB@ :\|\|\|\|\|\| :\|\| \|\|\|\| \|:\|\|\|\|\|\| \|\|@LB@ UUUACCC UGU UUUC UUUUCGUC CC@LB@3'-UUU...GGUGU C AG A G-5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -17.71 kcal/mol@LB@Hybridization Energy -25.8778 kcal/mol@LB@Unfolding Energy - mRNA 5.65259 kcal/mol@LB@Unfolding Energy - sRNA 2.51906 kcal/mol@LB@@LB@Position - mRNA 34 -- 61@LB@Position - sRNA 2 -- 29@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 5 -- 11@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@
152	0.01123	0.2504	b1872	torZ	-17.40	0.006326	76 -- 107	1 -- 34	trimethylamine N-oxide reductase system III catalytic subunit	b0997 b3551	_____________75___________________________________108\n_____________\|____________________________________\|\n5'-ACG...CAUUG___AA_________________CC_________A__GAAAA...AGA-3'\n______________CCA__GGAAUGGGGGCA_CGAA____AGCA_UG_GC\n______________\|\|\|__::\|\|\|\|\|\|\|:\|\|_\|:\|\|____\|\|\|\|_\|\|_\|\|\n______________GGU__UUUUACCCCUGU_GUUU____UCGU_AC_CG\n3'-UUU...CCCGA___G_____________A____CUUU____C_____-5'\n_____________\|___________________________________\|\n_____________35__________________________________1\n	86 -- 92	19 -- 25	-29.6219 kcal/mol	7.95271 kcal/mol	4.26884 kcal/mol	75 108@LB@ \| \|@LB@5'-ACG...CAUUG AA CC A GAAAA...AGA-3'@LB@ CCA GGAAUGGGGGCA CGAA AGCA UG GC@LB@ \|\|\| ::\|\|\|\|\|\|\|:\|\| \|:\|\| \|\|\|\| \|\| \|\|@LB@ GGU UUUUACCCCUGU GUUU UCGU AC CG@LB@3'-UUU...CCCGA G A CUUU C -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -17.40 kcal/mol@LB@Hybridization Energy -29.6219 kcal/mol@LB@Unfolding Energy - mRNA 7.95271 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 76 -- 107@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 19 -- 25@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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