Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
69	0.006739	0.3286	b2265	menF	-9.03	0.410924	65 -- 108	52 -- 101	isochorismate synthase 2	_____________64__________109\n_____________\|___________\|\n5'-ACU...CGGGU___________CUUUC...CUC-3'\n______________UAUCGAUAUUC\n______________:\|:\|:\|\|\|:\|\|\n______________GUGGUUAUGAG\n3'-UUU...AAAAU___________UCAGU...UAG-5'\n_____________\|___________\|\n_____________102_________51\n	285 -- 291	176 -- 182	-9.38108 kcal/mol	0.14396 kcal/mol	3.38772 kcal/mol	64 109@LB@ \| \|@LB@5'-ACU...CGGGU CUUUC...CUC-3'@LB@ UAUCGAUAUUC@LB@ :\|:\|:\|\|\|:\|\|@LB@ GUGGUUAUGAG@LB@3'-UUU...AAAAU UCAGU...UAG-5'@LB@ \| \|@LB@ 102 51@LB@@LB@@LB@Energy -9.03 kcal/mol@LB@Hybridization Energy -9.38108 kcal/mol@LB@Unfolding Energy - mRNA 0.14396 kcal/mol@LB@Unfolding Energy - sRNA 3.38772 kcal/mol@LB@@LB@Position - mRNA 65 -- 108@LB@Position - sRNA 52 -- 101@LB@Position Seed - mRNA 285 -- 291@LB@Position Seed - sRNA 176 -- 182@LB@
70	0.00686	0.3298	b0761	modE	-10.05	0.269682	248 -- 271	57 -- 77	transcriptional repressor for the molybdenum transport operon modABC	_____________247______272\n_____________\|________\|\n5'-ACC...GAAAA________CUUUU...CCA-3'\n______________GCACUCCC\n______________\|\|\|\|:\|\|\|\n______________CGUGGGGG\n3'-UUU...UACCC________AACGA...UAG-5'\n_____________\|________\|\n_____________78_______56\n	126 -- 132	11 -- 17	-14.7879 kcal/mol	0.633098 kcal/mol	5.13224 kcal/mol	247 272@LB@ \| \|@LB@5'-ACC...GAAAA CUUUU...CCA-3'@LB@ GCACUCCC@LB@ \|\|\|\|:\|\|\|@LB@ CGUGGGGG@LB@3'-UUU...UACCC AACGA...UAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -10.05 kcal/mol@LB@Hybridization Energy -14.7879 kcal/mol@LB@Unfolding Energy - mRNA 0.633098 kcal/mol@LB@Unfolding Energy - sRNA 5.13224 kcal/mol@LB@@LB@Position - mRNA 248 -- 271@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 11 -- 17@LB@
71	0.00726	0.3408	b2944	yggI	-9.32	0.365111	156 -- 174	1 -- 18	Zn-dependent metalloprotease-related protein	_____________155_____________175\n_____________\|_______________\|\n5'-GAA...AGCCA________AG_____UUUUC...ACC-3'\n______________CCUCUUGC__UCAUC\n______________\|\|:\|\|\|\|\|__\|\|\|\|\|\n______________GGGGAACG__AGUAG\n3'-UUU...CCGUG________A______-5'\n_____________\|______________\|\n_____________19_____________1\n	161 -- 167	7 -- 13	-18.0684 kcal/mol	1.30619 kcal/mol	6.71812 kcal/mol	155 175@LB@ \| \|@LB@5'-GAA...AGCCA AG UUUUC...ACC-3'@LB@ CCUCUUGC UCAUC@LB@ \|\|:\|\|\|\|\| \|\|\|\|\|@LB@ GGGGAACG AGUAG@LB@3'-UUU...CCGUG A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -9.32 kcal/mol@LB@Hybridization Energy -18.0684 kcal/mol@LB@Unfolding Energy - mRNA 1.30619 kcal/mol@LB@Unfolding Energy - sRNA 6.71812 kcal/mol@LB@@LB@Position - mRNA 156 -- 174@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 7 -- 13@LB@
72	0.007293	0.3408	b3240	aaeB	-15.57	0.020683	172 -- 248	45 -- 133	p-hydroxybenzoic acid efflux system component	_____________171________________249\n_____________\|__________________\|\n5'-ACU...ACAUA__________________CUGGC...UGG-3'\n______________UUCGCU_UUGCGGUAAAA\n______________\|\|\|\|\|\|_\|:\|\|\|\|\|\|\|\|\|\n______________AAGCGA_AGCGCCAUUUU\n3'-UUU...UGUUG______C___________AUCAC...UAG-5'\n_____________\|__________________\|\n_____________134________________44\n	240 -- 246	47 -- 53	-22.573 kcal/mol	5.7072 kcal/mol	6.14031 kcal/mol	171 249@LB@ \| \|@LB@5'-ACU...ACAUA CUGGC...UGG-3'@LB@ UUCGCU UUGCGGUAAAA@LB@ \|\|\|\|\|\| \|:\|\|\|\|\|\|\|\|\|@LB@ AAGCGA AGCGCCAUUUU@LB@3'-UUU...UGUUG C AUCAC...UAG-5'@LB@ \| \|@LB@ 134 44@LB@@LB@@LB@Energy -15.57 kcal/mol@LB@Hybridization Energy -22.573 kcal/mol@LB@Unfolding Energy - mRNA 5.7072 kcal/mol@LB@Unfolding Energy - sRNA 6.14031 kcal/mol@LB@@LB@Position - mRNA 172 -- 248@LB@Position - sRNA 45 -- 133@LB@Position Seed - mRNA 240 -- 246@LB@Position Seed - sRNA 47 -- 53@LB@
73	0.007584	0.3458	b0059	rapA	-13.35	0.058963	263 -- 277	46 -- 60	RNA polymerase remodeling/recycling factor ATPase; RNA polymerase-associated ATP-dependent RNA translocase	_____________262_____________278\n_____________\|_______________\|\n5'-GCU...GGAAC_______________UGCGC...UUU-3'\n______________CGUUGUCGCGGUGGA\n______________\|\|:\|\|\|\|\|\|\|\|\|::\|\n______________GCGACAGCGCCAUUU\n3'-UUU...UUGAA_______________UAUCA...UAG-5'\n_____________\|_______________\|\n_____________61______________45\n	269 -- 275	48 -- 54	-26.0749 kcal/mol	7.19742 kcal/mol	6.07408 kcal/mol	262 278@LB@ \| \|@LB@5'-GCU...GGAAC UGCGC...UUU-3'@LB@ CGUUGUCGCGGUGGA@LB@ \|\|:\|\|\|\|\|\|\|\|\|::\|@LB@ GCGACAGCGCCAUUU@LB@3'-UUU...UUGAA UAUCA...UAG-5'@LB@ \| \|@LB@ 61 45@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -26.0749 kcal/mol@LB@Unfolding Energy - mRNA 7.19742 kcal/mol@LB@Unfolding Energy - sRNA 6.07408 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 46 -- 60@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 48 -- 54@LB@
74	0.007724	0.3458	b1261	trpB	-16.40	0.014006	36 -- 47	195 -- 206	tryptophan synthase beta subunit	_____________35___________48\n_____________\|____________\|\n5'-UGG...AACGU____________GGGCU...UCA-3'\n______________UCUGCUGGCGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACGACCGCCC\n3'-UUU...AUAUU____________ACUAA...UAG-5'\n_____________\|____________\|\n_____________207__________194\n	41 -- 47	195 -- 201	-26.9412 kcal/mol	6.0368 kcal/mol	9.05854 kcal/mol	35 48@LB@ \| \|@LB@5'-UGG...AACGU GGGCU...UCA-3'@LB@ UCUGCUGGCGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACGACCGCCC@LB@3'-UUU...AUAUU ACUAA...UAG-5'@LB@ \| \|@LB@ 207 194@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -26.9412 kcal/mol@LB@Unfolding Energy - mRNA 6.0368 kcal/mol@LB@Unfolding Energy - sRNA 9.05854 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 195 -- 206@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 195 -- 201@LB@
75	0.007778	0.3458	b0766	ybhA	-9.49	0.341100	208 -- 245	124 -- 172	pyridoxal phosphate (PLP) phosphatase	_____________207___________________________246\n_____________\|_____________________________\|\n5'-GAA...UGGAA_______UG________________U___UCUCG...GCG-3'\n______________UACGCCA__AC_CA__CACGCGUGA_UGC\n______________\|\|\|:\|\|\|__\|\|_\|\|__\|\|\|:\|:\|\|\|_\|\|\|\n______________AUGUGGU__UG_GU__GUGUGUACU_ACG\n3'-UUU...CUAAA_______UA__A__CA_____________UCCGU...UAG-5'\n_____________\|_____________________________\|\n_____________173___________________________123\n	195 -- 201	182 -- 188	-28.0817 kcal/mol	7.23992 kcal/mol	7.72227 kcal/mol	207 246@LB@ \| \|@LB@5'-GAA...UGGAA UG U UCUCG...GCG-3'@LB@ UACGCCA AC CA CACGCGUGA UGC@LB@ \|\|\|:\|\|\| \|\| \|\| \|\|\|:\|:\|\|\| \|\|\|@LB@ AUGUGGU UG GU GUGUGUACU ACG@LB@3'-UUU...CUAAA UA A CA UCCGU...UAG-5'@LB@ \| \|@LB@ 173 123@LB@@LB@@LB@Energy -9.49 kcal/mol@LB@Hybridization Energy -28.0817 kcal/mol@LB@Unfolding Energy - mRNA 7.23992 kcal/mol@LB@Unfolding Energy - sRNA 7.72227 kcal/mol@LB@@LB@Position - mRNA 208 -- 245@LB@Position - sRNA 124 -- 172@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 182 -- 188@LB@
76	0.007832	0.3458	b1054	lpxL	-10.56	0.214918	224 -- 240	1 -- 17	lauryl-acyl carrier protein (ACP)-dependent acyltransferase	_____________223_______241\n_____________\|_________\|\n5'-AAA...CGCAC_________CGCGU...CCU-3'\n______________UGCUUCAUC\n______________\|\|\|\|\|\|\|\|\|\n______________ACGAAGUAG\n3'-UUU...GGGGA_________-5'\n_____________\|________\|\n_____________18_______1\n	234 -- 240	1 -- 7	-13.5925 kcal/mol	1.26369 kcal/mol	0.710349 kcal/mol	223 241@LB@ \| \|@LB@5'-AAA...CGCAC CGCGU...CCU-3'@LB@ UGCUUCAUC@LB@ \|\|\|\|\|\|\|\|\|@LB@ ACGAAGUAG@LB@3'-UUU...GGGGA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -13.5925 kcal/mol@LB@Unfolding Energy - mRNA 1.26369 kcal/mol@LB@Unfolding Energy - sRNA 0.710349 kcal/mol@LB@@LB@Position - mRNA 224 -- 240@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
77	0.007981	0.3458	b1738	chbB	-9.80	0.299184	58 -- 71	174 -- 187	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________57_______________________________72\n_____________\|________________________________\|\n5'-AAU...UAUAA___CAAAGAA______U_______G__U____CGUAU...CGG-3'\n______________GGU_______AUACUA_UGCUCAG_UC_AUAC\n______________\|\|\|_______\|:\|\|:\|_\|:\|\|\|\|\|_\|\|_\|:\|\|\n______________CCA_______UGUGGU_AUGAGUC_AG_UGUG\n3'-UUU...ACCGC___CUAAAA_______U_______________UACUA...UAG-5'\n_____________\|________________________________\|\n_____________188______________________________173\n	65 -- 71	174 -- 180	-20.4225 kcal/mol	4.13376 kcal/mol	5.03959 kcal/mol	57 72@LB@ \| \|@LB@5'-AAU...UAUAA CAAAGAA U G U CGUAU...CGG-3'@LB@ GGU AUACUA UGCUCAG UC AUAC@LB@ \|\|\| \|:\|\|:\| \|:\|\|\|\|\| \|\| \|:\|\|@LB@ CCA UGUGGU AUGAGUC AG UGUG@LB@3'-UUU...ACCGC CUAAAA U UACUA...UAG-5'@LB@ \| \|@LB@ 188 173@LB@@LB@@LB@Energy -9.80 kcal/mol@LB@Hybridization Energy -20.4225 kcal/mol@LB@Unfolding Energy - mRNA 4.13376 kcal/mol@LB@Unfolding Energy - sRNA 5.03959 kcal/mol@LB@@LB@Position - mRNA 58 -- 71@LB@Position - sRNA 174 -- 187@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 174 -- 180@LB@
78	0.008099	0.3458	b2810	csdA	-12.29	0.097398	132 -- 155	3 -- 23	cysteine sulfinate desulfinase	_____________131_______________156\n_____________\|_________________\|\n5'-CUU...GGUUA____U________A___AAGUG...AAG-3'\n______________GCAC_CUCCUUGU_UCA\n______________\|\|\|\|_\|:\|\|\|\|\|:_\|\|\|\n______________CGUG_GGGGAACG_AGU\n3'-UUU...UACCC_____________A___AG-5'\n_____________\|_________________\|\n_____________24________________2\n	145 -- 151	7 -- 13	-20.4088 kcal/mol	3.04417 kcal/mol	7.17675 kcal/mol	131 156@LB@ \| \|@LB@5'-CUU...GGUUA U A AAGUG...AAG-3'@LB@ GCAC CUCCUUGU UCA@LB@ \|\|\|\| \|:\|\|\|\|\|: \|\|\|@LB@ CGUG GGGGAACG AGU@LB@3'-UUU...UACCC A AG-5'@LB@ \| \|@LB@ 24 2@LB@@LB@@LB@Energy -12.29 kcal/mol@LB@Hybridization Energy -20.4088 kcal/mol@LB@Unfolding Energy - mRNA 3.04417 kcal/mol@LB@Unfolding Energy - sRNA 7.17675 kcal/mol@LB@@LB@Position - mRNA 132 -- 155@LB@Position - sRNA 3 -- 23@LB@Position Seed - mRNA 145 -- 151@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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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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