Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
167	0.01599	0.3104	b4220	tamA	-9.57	0.142740	193 -- 207	4 -- 21	translocation and assembly module for autotransporter export outer membrane subunit		_____________192________________208\n_____________\|__________________\|\n5'-CGC...UUCAG__GA______________AUAUC...GAC-3'\n______________GA____AAAUGUGCG_CU\n______________\|\|____\|\|\|\|\|:\|\|\|_\|\|\n______________CU____UUUACGCGC_GA\n3'-UUU...UACUA__AUUG_________A__AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	199 -- 205	7 -- 13	-13.0971 kcal/mol	2.26836 kcal/mol	1.2552 kcal/mol	192 208@LB@ \| \|@LB@5'-CGC...UUCAG GA AUAUC...GAC-3'@LB@ GA AAAUGUGCG CU@LB@ \|\| \|\|\|\|\|:\|\|\| \|\|@LB@ CU UUUACGCGC GA@LB@3'-UUU...UACUA AUUG A AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.0971 kcal/mol@LB@Unfolding Energy - mRNA 2.26836 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@LB@
176	0.01748	0.3104	b0435	bolA	-9.78	0.131850	202 -- 220	4 -- 22	stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC		_____________201_________________221\n_____________\|___________________\|\n5'-UGA...UUUCA________C___A___GA_AGAAG...CCG-3'\n______________UGAUGAUA_GUG_GCG__U\n______________\|\|\|\|:\|:\|_:\|\|_\|\|\|__\|\n______________ACUAUUGU_UAC_CGC__A\n3'-UUU...CUACU________U___G___AG_AAG-5'\n_____________\|___________________\|\n_____________23__________________3\n	203 -- 209	15 -- 21	-14.8727 kcal/mol	3.8346 kcal/mol	1.2572 kcal/mol	201 221@LB@ \| \|@LB@5'-UGA...UUUCA C A GA AGAAG...CCG-3'@LB@ UGAUGAUA GUG GCG U@LB@ \|\|\|\|:\|:\| :\|\| \|\|\| \|@LB@ ACUAUUGU UAC CGC A@LB@3'-UUU...CUACU U G AG AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -14.8727 kcal/mol@LB@Unfolding Energy - mRNA 3.8346 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 202 -- 220@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 15 -- 21@LB@
180	0.01774	0.3104	b0593	entC	-14.03	0.023631	112 -- 128	4 -- 19	isochorismate synthase 1		_____________111_______________129\n_____________\|_________________\|\n5'-GGC...AGAGU_____U___________GCUUU...CAG-3'\n______________UGACA_AGUGCGCGUUU\n______________\|:\|\|\|_\|:\|\|\|\|\|\|\|:\|\n______________AUUGU_UUACGCGCAGA\n3'-UUU...CUACU_________________AAG-5'\n_____________\|_________________\|\n_____________20________________3\n	122 -- 128	4 -- 10	-18.4725 kcal/mol	3.19872 kcal/mol	1.2406 kcal/mol	111 129@LB@ \| \|@LB@5'-GGC...AGAGU U GCUUU...CAG-3'@LB@ UGACA AGUGCGCGUUU@LB@ \|:\|\|\| \|:\|\|\|\|\|\|\|:\|@LB@ AUUGU UUACGCGCAGA@LB@3'-UUU...CUACU AAG-5'@LB@ \| \|@LB@ 20 3@LB@@LB@@LB@Energy -14.03 kcal/mol@LB@Hybridization Energy -18.4725 kcal/mol@LB@Unfolding Energy - mRNA 3.19872 kcal/mol@LB@Unfolding Energy - sRNA 1.2406 kcal/mol@LB@@LB@Position - mRNA 112 -- 128@LB@Position - sRNA 4 -- 19@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 4 -- 10@LB@
184	0.01824	0.3104	b2055	wcaE	-6.17	0.461247	221 -- 230	4 -- 12	putative glycosyl transferase		_____________220________231\n_____________\|__________\|\n5'-ACU...AUCAC__U_______CGUAA...GCU-3'\n______________UG_CGCGUUU\n______________\|\|_\|\|\|\|\|:\|\n______________AC_GCGCAGA\n3'-UUU...UGUUU__________AAG-5'\n_____________\|__________\|\n_____________13_________3\n	224 -- 230	4 -- 10	-10.1102 kcal/mol	2.78254 kcal/mol	1.16019 kcal/mol	220 231@LB@ \| \|@LB@5'-ACU...AUCAC U CGUAA...GCU-3'@LB@ UG CGCGUUU@LB@ \|\| \|\|\|\|\|:\|@LB@ AC GCGCAGA@LB@3'-UUU...UGUUU AAG-5'@LB@ \| \|@LB@ 13 3@LB@@LB@@LB@Energy -6.17 kcal/mol@LB@Hybridization Energy -10.1102 kcal/mol@LB@Unfolding Energy - mRNA 2.78254 kcal/mol@LB@Unfolding Energy - sRNA 1.16019 kcal/mol@LB@@LB@Position - mRNA 221 -- 230@LB@Position - sRNA 4 -- 12@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 4 -- 10@LB@
200	0.0195	0.3104	b3183	obgE	-7.01	0.355777	76 -- 83	4 -- 11	GTPase involved in cell partioning and DNA repair		_____________75_______84\n_____________\|________\|\n5'-UUU...UCUCG________GUCGU...GCC-3'\n______________GUGCGUUU\n______________\|:\|\|\|\|:\|\n______________CGCGCAGA\n3'-UUU...GUUUA________AAG-5'\n_____________\|________\|\n_____________12_______3\n	77 -- 83	4 -- 10	-11.428 kcal/mol	3.26207 kcal/mol	1.15639 kcal/mol	75 84@LB@ \| \|@LB@5'-UUU...UCUCG GUCGU...GCC-3'@LB@ GUGCGUUU@LB@ \|:\|\|\|\|:\|@LB@ CGCGCAGA@LB@3'-UUU...GUUUA AAG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.01 kcal/mol@LB@Hybridization Energy -11.428 kcal/mol@LB@Unfolding Energy - mRNA 3.26207 kcal/mol@LB@Unfolding Energy - sRNA 1.15639 kcal/mol@LB@@LB@Position - mRNA 76 -- 83@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 4 -- 10@LB@
3	3.559e-05	0.03436	b0168	map	-14.62	0.018437	228 -- 248	5 -- 21	methionine aminopeptidase		_____________227___________________249\n_____________\|_____________________\|\n5'-CUU...CAGAA____UCGAAA___________GCUGG...AAC-3'\n______________GAUA______AAAUGCGCGUC\n______________\|\|\|\|______\|\|\|\|\|\|\|\|\|\|\|\n______________CUAU______UUUACGCGCAG\n3'-UUU...UACUA____UG_______________AAAG-5'\n_____________\|_____________________\|\n_____________22____________________4\n	242 -- 248	5 -- 11	-19.3611 kcal/mol	3.48659 kcal/mol	1.24955 kcal/mol	227 249@LB@ \| \|@LB@5'-CUU...CAGAA UCGAAA GCUGG...AAC-3'@LB@ GAUA AAAUGCGCGUC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|\|\|@LB@ CUAU UUUACGCGCAG@LB@3'-UUU...UACUA UG AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -14.62 kcal/mol@LB@Hybridization Energy -19.3611 kcal/mol@LB@Unfolding Energy - mRNA 3.48659 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 228 -- 248@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 5 -- 11@LB@
6	9.655e-05	0.04801	b4175	hflC	-9.47	0.148653	186 -- 211	5 -- 32	HflB protease modulator specific for phage lambda cII repressor		_____________185____________________________212\n_____________\|______________________________\|\n5'-UUA...CAGCG_________________________AA___AGUUA...GUU-3'\n______________UCAGGGG_GA__AUAAC_GAUGCGU__GUC\n______________\|\|\|\|\|\|:_\|\|__\|\|\|\|\|_:\|\|\|\|\|:__\|\|\|\n______________AGUCCCU_CU__UAUUG_UUACGCG__CAG\n3'-UUU...ACUUA_______A__AC_____U____________AAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________4\n	200 -- 206	8 -- 14	-26.2754 kcal/mol	8.97237 kcal/mol	7.8362 kcal/mol	185 212@LB@ \| \|@LB@5'-UUA...CAGCG AA AGUUA...GUU-3'@LB@ UCAGGGG GA AUAAC GAUGCGU GUC@LB@ \|\|\|\|\|\|: \|\| \|\|\|\|\| :\|\|\|\|\|: \|\|\|@LB@ AGUCCCU CU UAUUG UUACGCG CAG@LB@3'-UUU...ACUUA A AC U AAAG-5'@LB@ \| \|@LB@ 33 4@LB@@LB@@LB@Energy -9.47 kcal/mol@LB@Hybridization Energy -26.2754 kcal/mol@LB@Unfolding Energy - mRNA 8.97237 kcal/mol@LB@Unfolding Energy - sRNA 7.8362 kcal/mol@LB@@LB@Position - mRNA 186 -- 211@LB@Position - sRNA 5 -- 32@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 8 -- 14@LB@
10	0.0002413	0.08171	b2594	rluD	-15.70	0.011720	48 -- 64	5 -- 21	23S rRNA pseudouridine(1911 1915 1917) synthase		_____________47________________65\n_____________\|_________________\|\n5'-CCC...CACCA____UUUC_________AUGAC...GUU-3'\n______________GAUA____AUGCGCGUC\n______________\|\|\|\|____\|\|\|\|\|\|\|\|\|\n______________CUAU____UACGCGCAG\n3'-UUU...UACUA____UGUU_________AAAG-5'\n_____________\|_________________\|\n_____________22________________4\n	58 -- 64	5 -- 11	-19.7285 kcal/mol	2.7828 kcal/mol	1.24955 kcal/mol	47 65@LB@ \| \|@LB@5'-CCC...CACCA UUUC AUGAC...GUU-3'@LB@ GAUA AUGCGCGUC@LB@ \|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CUAU UACGCGCAG@LB@3'-UUU...UACUA UGUU AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -15.70 kcal/mol@LB@Hybridization Energy -19.7285 kcal/mol@LB@Unfolding Energy - mRNA 2.7828 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 48 -- 64@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 5 -- 11@LB@
11	0.0003246	0.08948	b2299	yfcD	-11.11	0.078371	283 -- 295	5 -- 18	putative NUDIX hydrolase		_____________282____________296\n_____________\|______________\|\n5'-AGA...CCGGG__________G___ACAGU-3'\n______________AACAAAUGCG_G_C\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\n______________UUGUUUACGC_C_G\n3'-UUU...UACUA__________G_A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	286 -- 292	9 -- 15	-15.7313 kcal/mol	3.39963 kcal/mol	1.2243 kcal/mol	282 296@LB@ \| \|@LB@5'-AGA...CCGGG G ACAGU-3'@LB@ AACAAAUGCG G C@LB@ \|\|\|\|\|\|\|\|\|\| \| \|@LB@ UUGUUUACGC C G@LB@3'-UUU...UACUA G A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.7313 kcal/mol@LB@Unfolding Energy - mRNA 3.39963 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 9 -- 15@LB@
21	0.0009524	0.1536	b0241	phoE	-11.39	0.070016	174 -- 180	5 -- 11	outer membrane phosphoporin protein E	b0929 b2215 b1377	_____________173_____181\n_____________\|_______\|\n5'-AGC...UAUUC_______AAUUA...AUG-3'\n______________GCGCGUU\n______________\|\|\|\|\|\|:\n______________CGCGCAG\n3'-UUU...GUUUA_______AAAG-5'\n_____________\|_______\|\n_____________12______4\n	174 -- 180	5 -- 11	-12.879 kcal/mol	0.378776 kcal/mol	1.11145 kcal/mol	173 181@LB@ \| \|@LB@5'-AGC...UAUUC AAUUA...AUG-3'@LB@ GCGCGUU@LB@ \|\|\|\|\|\|:@LB@ CGCGCAG@LB@3'-UUU...GUUUA AAAG-5'@LB@ \| \|@LB@ 12 4@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -12.879 kcal/mol@LB@Unfolding Energy - mRNA 0.378776 kcal/mol@LB@Unfolding Energy - sRNA 1.11145 kcal/mol@LB@@LB@Position - mRNA 174 -- 180@LB@Position - sRNA 5 -- 11@LB@Position Seed - mRNA 174 -- 180@LB@Position Seed - sRNA 5 -- 11@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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