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
178	0.02044	0.3833	b3433	asd	-8.72	0.462346	170 -- 185	58 -- 71	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________169__________________186\n_____________\|____________________\|\n5'-UCA...UUAUA___________CUU______AAAAA...UCU-3'\n______________CAG_CACACAU___UGCAGG\n______________\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________GUC_GUGUGUA___ACGUCC\n3'-UUU...UAUGA___A_______CU_______GUUCA...UAG-5'\n_____________\|____________________\|\n_____________72___________________57\n	173 -- 179	166 -- 172	-22.5694 kcal/mol	4.04779 kcal/mol	7.34152 kcal/mol	169 186@LB@ \| \|@LB@5'-UCA...UUAUA CUU AAAAA...UCU-3'@LB@ CAG CACACAU UGCAGG@LB@ \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ GUC GUGUGUA ACGUCC@LB@3'-UUU...UAUGA A CU GUUCA...UAG-5'@LB@ \| \|@LB@ 72 57@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -22.5694 kcal/mol@LB@Unfolding Energy - mRNA 4.04779 kcal/mol@LB@Unfolding Energy - sRNA 7.34152 kcal/mol@LB@@LB@Position - mRNA 170 -- 185@LB@Position - sRNA 58 -- 71@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 166 -- 172@LB@
42	0.003683	0.2912	b2221	atoD	-14.87	0.028783	141 -- 155	6 -- 19	acetyl-CoA:acetoacetyl-CoA transferase alpha subunit	_____________140_____________156\n_____________\|_______________\|\n5'-UAU...AUUCU_____U_________AUUGC...CCC-3'\n______________GGCAC_CCCCUUGCU\n______________\|\|\|\|\|_\|\|\|\|\|\|\|\|\|\n______________CCGUG_GGGGAACGA\n3'-UUU...GUACC_______________AGUAG-5'\n_____________\|_______________\|\n_____________20______________5\n	149 -- 155	6 -- 12	-27.0081 kcal/mol	4.79018 kcal/mol	8.30673 kcal/mol	140 156@LB@ \| \|@LB@5'-UAU...AUUCU U AUUGC...CCC-3'@LB@ GGCAC CCCCUUGCU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|\|@LB@ CCGUG GGGGAACGA@LB@3'-UUU...GUACC AGUAG-5'@LB@ \| \|@LB@ 20 5@LB@@LB@@LB@Energy -14.87 kcal/mol@LB@Hybridization Energy -27.0081 kcal/mol@LB@Unfolding Energy - mRNA 4.79018 kcal/mol@LB@Unfolding Energy - sRNA 8.30673 kcal/mol@LB@@LB@Position - mRNA 141 -- 155@LB@Position - sRNA 6 -- 19@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 6 -- 12@LB@
157	0.01768	0.3749	b1216	chaA	-11.60	0.134178	242 -- 292	18 -- 65	calcium/sodium:proton antiporter	_____________241_______________293\n_____________\|_________________\|\n5'-AUU...AAUGU_________C___A___UUUCU...GCC-3'\n______________UACCGAUAU_CAG_CAC\n______________:\|\|\|:\|\|\|:_\|\|\|_\|\|\|\n______________GUGGUUAUG_GUC_GUG\n3'-UUU...AAAAU_________A___A___UGUAC...UAG-5'\n_____________\|_________________\|\n_____________66________________17\n	120 -- 126	178 -- 184	-16.2011 kcal/mol	3.68451 kcal/mol	4.86651 kcal/mol	241 293@LB@ \| \|@LB@5'-AUU...AAUGU C A UUUCU...GCC-3'@LB@ UACCGAUAU CAG CAC@LB@ :\|\|\|:\|\|\|: \|\|\| \|\|\|@LB@ GUGGUUAUG GUC GUG@LB@3'-UUU...AAAAU A A UGUAC...UAG-5'@LB@ \| \|@LB@ 66 17@LB@@LB@@LB@Energy -11.60 kcal/mol@LB@Hybridization Energy -16.2011 kcal/mol@LB@Unfolding Energy - mRNA 3.68451 kcal/mol@LB@Unfolding Energy - sRNA 4.86651 kcal/mol@LB@@LB@Position - mRNA 242 -- 292@LB@Position - sRNA 18 -- 65@LB@Position Seed - mRNA 120 -- 126@LB@Position Seed - sRNA 178 -- 184@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@
101	0.01097	0.3575	b1882	cheY	-8.64	0.475467	226 -- 255	72 -- 99	chemotaxis regulator transmitting signal to flagellar motor component	_____________225_______________256\n_____________\|_________________\|\n5'-GCG...AGGCG_______GGA_______GCAAA...UUG-3'\n______________GGGGCAU___CCCUUGC\n______________\|\|\|\|\|\|:___\|\|\|\|\|\|\|\n______________CCCCGUG___GGGAACG\n3'-UUU...GCGUA_______G_________AAGUAG-5'\n_____________\|_________________\|\n_____________100_______________71\n	38 -- 44	7 -- 13	-25.3164 kcal/mol	8.48869 kcal/mol	10.1447 kcal/mol	225 256@LB@ \| \|@LB@5'-GCG...AGGCG GGA GCAAA...UUG-3'@LB@ GGGGCAU CCCUUGC@LB@ \|\|\|\|\|\|: \|\|\|\|\|\|\|@LB@ CCCCGUG GGGAACG@LB@3'-UUU...GCGUA G AAGUAG-5'@LB@ \| \|@LB@ 100 71@LB@@LB@@LB@Energy -8.64 kcal/mol@LB@Hybridization Energy -25.3164 kcal/mol@LB@Unfolding Energy - mRNA 8.48869 kcal/mol@LB@Unfolding Energy - sRNA 10.1447 kcal/mol@LB@@LB@Position - mRNA 226 -- 255@LB@Position - sRNA 72 -- 99@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 7 -- 13@LB@
135	0.01453	0.3575	b2934	cmtB	-15.85	0.018111	229 -- 275	145 -- 186	putative mannitol-specific enzyme IIA component of PTS	_____________228___________________276\n_____________\|_____________________\|\n5'-AUA...AGAAU_____________________UCAGC...UGG-3'\n______________CAUCAAU_CUCAGUUAUACAU\n______________\|\|:\|\|\|\|_\|\|\|\|\|\|:\|:\|\|\|\|\n______________GUGGUUA_GAGUCAGUGUGUA\n3'-UUU...AAAAU_______U_____________CUACG...UAG-5'\n_____________\|_____________________\|\n_____________187___________________144\n	242 -- 248	166 -- 172	-24.8158 kcal/mol	1.5387 kcal/mol	5.06797 kcal/mol	228 276@LB@ \| \|@LB@5'-AUA...AGAAU UCAGC...UGG-3'@LB@ CAUCAAU CUCAGUUAUACAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|@LB@ GUGGUUA GAGUCAGUGUGUA@LB@3'-UUU...AAAAU U CUACG...UAG-5'@LB@ \| \|@LB@ 187 144@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -24.8158 kcal/mol@LB@Unfolding Energy - mRNA 1.5387 kcal/mol@LB@Unfolding Energy - sRNA 5.06797 kcal/mol@LB@@LB@Position - mRNA 229 -- 275@LB@Position - sRNA 145 -- 186@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 166 -- 172@LB@
170	0.01941	0.3812	b3911	cpxA	-13.13	0.065341	265 -- 299	168 -- 204	sensory histidine kinase in two-component regulatory system with CpxR	_____________264______300\n_____________\|________\|\n5'-UAU...GUUUC________GAUAG...GCC-3'\n______________UGCUUCAU\n______________\|\|\|\|\|\|\|\|\n______________ACGAAGUA\n3'-UUU...GGGGA________G-5'\n_____________\|________\|\n_____________205______167\n	196 -- 202	2 -- 8	-10.3801 kcal/mol	3.0426 kcal/mol	0.709873 kcal/mol	264 300@LB@ \| \|@LB@5'-UAU...GUUUC GAUAG...GCC-3'@LB@ UGCUUCAU@LB@ \|\|\|\|\|\|\|\|@LB@ ACGAAGUA@LB@3'-UUU...GGGGA G-5'@LB@ \| \|@LB@ 205 167@LB@@LB@@LB@Energy -13.13 kcal/mol@LB@Hybridization Energy -10.3801 kcal/mol@LB@Unfolding Energy - mRNA 3.0426 kcal/mol@LB@Unfolding Energy - sRNA 0.709873 kcal/mol@LB@@LB@Position - mRNA 265 -- 299@LB@Position - sRNA 168 -- 204@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 2 -- 8@LB@
188	0.0218	0.3833	b3357	crp	-15.41	0.022266	196 -- 257	123 -- 172	cAMP-activated global transcription factor mediator of catabolite repression	_____________195_________________258\n_____________\|___________________\|\n5'-GAC...AUAAC____________UU_____ACCGC...AGG-3'\n______________CGCGCAUGGUGC__GGCAA\n______________\|:\|:\|\|\|\|:\|\|\|__\|\|\|\|\|\n______________GUGUGUACUACG__CCGUU\n3'-UUU...AGUCA____________U______CAGUU...UAG-5'\n_____________\|___________________\|\n_____________173_________________122\n	201 -- 207	161 -- 167	-26.7729 kcal/mol	8.17538 kcal/mol	7.52835 kcal/mol	195 258@LB@ \| \|@LB@5'-GAC...AUAAC UU ACCGC...AGG-3'@LB@ CGCGCAUGGUGC GGCAA@LB@ \|:\|:\|\|\|\|:\|\|\| \|\|\|\|\|@LB@ GUGUGUACUACG CCGUU@LB@3'-UUU...AGUCA U CAGUU...UAG-5'@LB@ \| \|@LB@ 173 122@LB@@LB@@LB@Energy -15.41 kcal/mol@LB@Hybridization Energy -26.7729 kcal/mol@LB@Unfolding Energy - mRNA 8.17538 kcal/mol@LB@Unfolding Energy - sRNA 7.52835 kcal/mol@LB@@LB@Position - mRNA 196 -- 257@LB@Position - sRNA 123 -- 172@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 161 -- 167@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@
179	0.02059	0.3833	b2535	csiE	-10.55	0.216292	103 -- 142	58 -- 90	stationary phase inducible protein	_____________102___________143\n_____________\|_____________\|\n5'-GCA...GAUUA__________C__CAUUU...UGG-3'\n______________GCAUUCCCUU_GC\n______________\|\|\|::\|\|\|\|\|_\|\|\n______________CGUGGGGGAA_CG\n3'-UUU...UACCC_____________AAGUAG-5'\n_____________\|_____________\|\n_____________91____________57\n	133 -- 139	9 -- 15	-16.9052 kcal/mol	2.85301 kcal/mol	6.64496 kcal/mol	102 143@LB@ \| \|@LB@5'-GCA...GAUUA C CAUUU...UGG-3'@LB@ GCAUUCCCUU GC@LB@ \|\|\|::\|\|\|\|\| \|\|@LB@ CGUGGGGGAA CG@LB@3'-UUU...UACCC AAGUAG-5'@LB@ \| \|@LB@ 91 57@LB@@LB@@LB@Energy -10.55 kcal/mol@LB@Hybridization Energy -16.9052 kcal/mol@LB@Unfolding Energy - mRNA 2.85301 kcal/mol@LB@Unfolding Energy - sRNA 6.64496 kcal/mol@LB@@LB@Position - mRNA 103 -- 142@LB@Position - sRNA 58 -- 90@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 9 -- 15@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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