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
74	0.004177	0.1979	b2155	cirA	-15.75	0.017995	130 -- 157	1 -- 33	colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter		_____________129________________________________158\n_____________\|__________________________________\|\n5'-GGA...CCGUA_________________________U_____A__GAUAA...UGG-3'\n______________CGCAA___GGGGACGU_GAAGAAGA___GUG_GC\n______________\|:\|\|\|___\|\|\|\|\|\|:\|_:\|\|\|\|\|:\|___\|\|\|_\|\|\n______________GUGUU___CCCCUGUA_UUUCUUUU___CAC_CG\n3'-UUU...CCGAG_____UUA________G________CGU______-5'\n_____________\|_________________________________\|\n_____________34________________________________1\n	144 -- 150	9 -- 15	-28.6012 kcal/mol	9.77062 kcal/mol	3.07861 kcal/mol	129 158@LB@ \| \|@LB@5'-GGA...CCGUA U A GAUAA...UGG-3'@LB@ CGCAA GGGGACGU GAAGAAGA GUG GC@LB@ \|:\|\|\| \|\|\|\|\|\|:\| :\|\|\|\|\|:\| \|\|\| \|\|@LB@ GUGUU CCCCUGUA UUUCUUUU CAC CG@LB@3'-UUU...CCGAG UUA G CGU -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -28.6012 kcal/mol@LB@Unfolding Energy - mRNA 9.77062 kcal/mol@LB@Unfolding Energy - sRNA 3.07861 kcal/mol@LB@@LB@Position - mRNA 130 -- 157@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 9 -- 15@LB@
185	0.0132	0.2504	b2009	sbmC	-15.75	0.018057	263 -- 294	1 -- 27	DNA gyrase inhibitor		_____________262______________________________295\n_____________\|________________________________\|\n5'-CUG...GGCCC_____AACA____G___________UU__A__AGUUGA-3'\n______________GUGGG____GACG_UAAAGAAAGGC__UG_GC\n______________:\|\|\|\|____\|\|\|:_:\|\|\|\|\|\|\|:\|\|__\|\|_\|\|\n______________UACCC____CUGU_GUUUCUUUUCG__AC_CG\n3'-UUU...UGUUU_____________A___________UC_____-5'\n_____________\|_______________________________\|\n_____________28______________________________1\n	281 -- 287	7 -- 13	-27.1244 kcal/mol	8.85955 kcal/mol	2.51867 kcal/mol	262 295@LB@ \| \|@LB@5'-CUG...GGCCC AACA G UU A AGUUGA-3'@LB@ GUGGG GACG UAAAGAAAGGC UG GC@LB@ :\|\|\|\| \|\|\|: :\|\|\|\|\|\|\|:\|\| \|\| \|\|@LB@ UACCC CUGU GUUUCUUUUCG AC CG@LB@3'-UUU...UGUUU A UC -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -15.75 kcal/mol@LB@Hybridization Energy -27.1244 kcal/mol@LB@Unfolding Energy - mRNA 8.85955 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 263 -- 294@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 7 -- 13@LB@
37	0.001785	0.1648	b3933	ftsN	-15.64	0.019200	24 -- 52	1 -- 29	essential cell division protein		_____________23______________________________53\n_____________\|_______________________________\|\n5'-AGC...UGAUC_____CA______A__CGUU___________UCUCG...CUC-3'\n______________AAAUG__GGGGCA_CA______GGCAGUGGC\n______________\|\|\|\|\|__\|\|\|:\|\|_\|\|______:\|\|\|\|\|\|\|\|\n______________UUUAC__CCCUGU_GU______UCGUCACCG\n3'-UUU...GGUGU_____________A__UUCUUU_________-5'\n_____________\|______________________________\|\n_____________30_____________________________1\n	46 -- 52	1 -- 7	-29.0551 kcal/mol	10.8938 kcal/mol	2.51907 kcal/mol	23 53@LB@ \| \|@LB@5'-AGC...UGAUC CA A CGUU UCUCG...CUC-3'@LB@ AAAUG GGGGCA CA GGCAGUGGC@LB@ \|\|\|\|\| \|\|\|:\|\| \|\| :\|\|\|\|\|\|\|\|@LB@ UUUAC CCCUGU GU UCGUCACCG@LB@3'-UUU...GGUGU A UUCUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.64 kcal/mol@LB@Hybridization Energy -29.0551 kcal/mol@LB@Unfolding Energy - mRNA 10.8938 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 24 -- 52@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 1 -- 7@LB@
162	0.012	0.2504	b2079	baeR	-15.58	0.019969	182 -- 201	6 -- 24	response regulator in two-component regulatory system with BaeS		_____________181__________________202\n_____________\|____________________\|\n5'-CAG...GGAAC_____UUA____________UGACC...CGA-3'\n______________GGGAU___CAGAGAGAAGUA\n______________\|\|\|\|:___\|\|:\|\|\|:\|\|\|:\|\n______________CCCUG___GUUUCUUUUCGU\n3'-UUU...UUUAC_____UA_____________CACCG-5'\n_____________\|____________________\|\n_____________25___________________5\n	195 -- 201	6 -- 12	-20.602 kcal/mol	4.32458 kcal/mol	0.702143 kcal/mol	181 202@LB@ \| \|@LB@5'-CAG...GGAAC UUA UGACC...CGA-3'@LB@ GGGAU CAGAGAGAAGUA@LB@ \|\|\|\|: \|\|:\|\|\|:\|\|\|:\|@LB@ CCCUG GUUUCUUUUCGU@LB@3'-UUU...UUUAC UA CACCG-5'@LB@ \| \|@LB@ 25 5@LB@@LB@@LB@Energy -15.58 kcal/mol@LB@Hybridization Energy -20.602 kcal/mol@LB@Unfolding Energy - mRNA 4.32458 kcal/mol@LB@Unfolding Energy - sRNA 0.702143 kcal/mol@LB@@LB@Position - mRNA 182 -- 201@LB@Position - sRNA 6 -- 24@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 6 -- 12@LB@
187	0.01374	0.2529	b1344	ttcA	-15.51	0.020761	46 -- 73	1 -- 29	tRNA s(2)C32 thioltransferase iron sulfur cluster protein		_____________45_____________________________74\n_____________\|______________________________\|\n5'-GCU...CAGCC____________G___CUGC_____A____GUAUG...UCA-3'\n______________AAAUGGGG_CAU_AAA_____GCAG_UGGU\n______________\|\|\|\|\|\|\|\|_\|\|\|_\|\|\|_____\|\|\|\|_\|\|\|:\n______________UUUACCCC_GUA_UUU_____CGUC_ACCG\n3'-UUU...GGUGU________U___G___CUUUU_________-5'\n_____________\|_____________________________\|\n_____________30____________________________1\n	47 -- 53	22 -- 28	-26.0543 kcal/mol	8.02666 kcal/mol	2.51907 kcal/mol	45 74@LB@ \| \|@LB@5'-GCU...CAGCC G CUGC A GUAUG...UCA-3'@LB@ AAAUGGGG CAU AAA GCAG UGGU@LB@ \|\|\|\|\|\|\|\| \|\|\| \|\|\| \|\|\|\| \|\|\|:@LB@ UUUACCCC GUA UUU CGUC ACCG@LB@3'-UUU...GGUGU U G CUUUU -5'@LB@ \| \|@LB@ 30 1@LB@@LB@@LB@Energy -15.51 kcal/mol@LB@Hybridization Energy -26.0543 kcal/mol@LB@Unfolding Energy - mRNA 8.02666 kcal/mol@LB@Unfolding Energy - sRNA 2.51907 kcal/mol@LB@@LB@Position - mRNA 46 -- 73@LB@Position - sRNA 1 -- 29@LB@Position Seed - mRNA 47 -- 53@LB@Position Seed - sRNA 22 -- 28@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@
182	0.01317	0.2504	b2101	yegW	-15.40	0.022099	126 -- 162	3 -- 28	putative DNA-binding transcriptional regulator		_____________125______________________________________163\n_____________\|________________________________________\|\n5'-CGG...UCGUU_________________AACGCCUUAAAUAA_________AUAUA...AAA-3'\n______________GAUGGG___AUUAAAGA______________GAAGCAGUG\n______________:\|\|\|\|\|___\|\|:\|\|\|\|\|______________:\|\|\|\|\|\|\|\|\n______________UUACCC___UAGUUUCU______________UUUCGUCAC\n3'-UUU...GUGUU______CUG_______________________________CG-5'\n_____________\|________________________________________\|\n_____________29_______________________________________2\n	156 -- 162	3 -- 9	-24.3736 kcal/mol	6.45453 kcal/mol	2.51813 kcal/mol	125 163@LB@ \| \|@LB@5'-CGG...UCGUU AACGCCUUAAAUAA AUAUA...AAA-3'@LB@ GAUGGG AUUAAAGA GAAGCAGUG@LB@ :\|\|\|\|\| \|\|:\|\|\|\|\| :\|\|\|\|\|\|\|\|@LB@ UUACCC UAGUUUCU UUUCGUCAC@LB@3'-UUU...GUGUU CUG CG-5'@LB@ \| \|@LB@ 29 2@LB@@LB@@LB@Energy -15.40 kcal/mol@LB@Hybridization Energy -24.3736 kcal/mol@LB@Unfolding Energy - mRNA 6.45453 kcal/mol@LB@Unfolding Energy - sRNA 2.51813 kcal/mol@LB@@LB@Position - mRNA 126 -- 162@LB@Position - sRNA 3 -- 28@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 3 -- 9@LB@
181	0.01309	0.2504	b2799	fucO	-15.36	0.022654	183 -- 205	1 -- 21	L-1 2-propanediol oxidoreductase		_____________182_____________________206\n_____________\|_______________________\|\n5'-CUU...GUAAA___A__________G_U_A____UAACA...CGC-3'\n______________GCA_CAAGGAGAAG_A_G_UGGC\n______________:\|\|_\|\|\|:\|\|:\|\|\|_\|_\|_\|\|\|\|\n______________UGU_GUUUCUUUUC_U_C_ACCG\n3'-UUU...ACCCC___A__________G________-5'\n_____________\|______________________\|\n_____________22_____________________1\n	190 -- 196	8 -- 14	-20.3858 kcal/mol	3.51699 kcal/mol	1.51103 kcal/mol	182 206@LB@ \| \|@LB@5'-CUU...GUAAA A G U A UAACA...CGC-3'@LB@ GCA CAAGGAGAAG A G UGGC@LB@ :\|\| \|\|\|:\|\|:\|\|\| \| \| \|\|\|\|@LB@ UGU GUUUCUUUUC U C ACCG@LB@3'-UUU...ACCCC A G -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.36 kcal/mol@LB@Hybridization Energy -20.3858 kcal/mol@LB@Unfolding Energy - mRNA 3.51699 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 8 -- 14@LB@
97	0.005972	0.2161	b0768	ybhD	-15.34	0.022873	51 -- 78	6 -- 32	putative DNA-binding transcriptional regulator	b2409	_____________50___________________________79\n_____________\|____________________________\|\n5'-CAG...UUAUU____U____UU__________C______UCUCU...CAU-3'\n______________GCGA_AUGG__ACAUUAAGGG_AAAGCA\n______________:\|:\|_\|\|\|\|__\|\|\|\|:\|\|:\|:_\|\|\|\|\|\|\n______________UGUU_UACC__UGUAGUUUCU_UUUCGU\n3'-UUU...CGAGG____U____CC_________________CACCG-5'\n_____________\|____________________________\|\n_____________33___________________________5\n	64 -- 70	13 -- 19	-24.2506 kcal/mol	6.37495 kcal/mol	2.53457 kcal/mol	50 79@LB@ \| \|@LB@5'-CAG...UUAUU U UU C UCUCU...CAU-3'@LB@ GCGA AUGG ACAUUAAGGG AAAGCA@LB@ :\|:\| \|\|\|\| \|\|\|\|:\|\|:\|: \|\|\|\|\|\|@LB@ UGUU UACC UGUAGUUUCU UUUCGU@LB@3'-UUU...CGAGG U CC CACCG-5'@LB@ \| \|@LB@ 33 5@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -24.2506 kcal/mol@LB@Unfolding Energy - mRNA 6.37495 kcal/mol@LB@Unfolding Energy - sRNA 2.53457 kcal/mol@LB@@LB@Position - mRNA 51 -- 78@LB@Position - sRNA 6 -- 32@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 13 -- 19@LB@
35	0.00168	0.1648	b2231	gyrA	-15.33	0.023033	230 -- 249	7 -- 25	DNA gyrase (type II topoisomerase) subunit A		_____________229__________________250\n_____________\|____________________\|\n5'-AGC...ACACC__UCA_______________UGAAG...CGC-3'\n______________GG___ACAUUGAGGAAGAGC\n______________\|\|___\|\|\|\|::\|:\|\|\|:\|\|\|\n______________CC___UGUAGUUUCUUUUCG\n3'-UUU...UUUUA__CC________________UCACCG-5'\n_____________\|____________________\|\n_____________26___________________6\n	243 -- 249	7 -- 13	-19.3394 kcal/mol	3.30418 kcal/mol	0.70626 kcal/mol	229 250@LB@ \| \|@LB@5'-AGC...ACACC UCA UGAAG...CGC-3'@LB@ GG ACAUUGAGGAAGAGC@LB@ \|\| \|\|\|\|::\|:\|\|\|:\|\|\|@LB@ CC UGUAGUUUCUUUUCG@LB@3'-UUU...UUUUA CC UCACCG-5'@LB@ \| \|@LB@ 26 6@LB@@LB@@LB@Energy -15.33 kcal/mol@LB@Hybridization Energy -19.3394 kcal/mol@LB@Unfolding Energy - mRNA 3.30418 kcal/mol@LB@Unfolding Energy - sRNA 0.70626 kcal/mol@LB@@LB@Position - mRNA 230 -- 249@LB@Position - sRNA 7 -- 25@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 7 -- 13@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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