Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 24 -- 30@LB@
14	0.0004762	0.1198	b2286	nuoC	-13.55	0.028468	156 -- 179	68 -- 87	NADH:ubiquinone oxidoreductase fused CD subunit		_____________155______________________180\n_____________\|________________________\|\n5'-AGG...AAGCU_____________GUCA___C___CCAUU...CCU-3'\n______________UACUGCGCCGACA____CCA_GGA\n______________\|\|\|\|\|\|\|\|\|:\|\|\|____\|\|\|_\|\|\|\n______________AUGACGCGGUUGU____GGU_CCU\n3'-UUU...CGCUU____________________C___UUAGA...GUG-5'\n_____________\|________________________\|\n_____________88_______________________67\n	162 -- 168	75 -- 81	-29.2495 kcal/mol	8.32219 kcal/mol	7.38006 kcal/mol	155 180@LB@ \| \|@LB@5'-AGG...AAGCU GUCA C CCAUU...CCU-3'@LB@ UACUGCGCCGACA CCA GGA@LB@ \|\|\|\|\|\|\|\|\|:\|\|\| \|\|\| \|\|\|@LB@ AUGACGCGGUUGU GGU CCU@LB@3'-UUU...CGCUU C UUAGA...GUG-5'@LB@ \| \|@LB@ 88 67@LB@@LB@@LB@Energy -13.55 kcal/mol@LB@Hybridization Energy -29.2495 kcal/mol@LB@Unfolding Energy - mRNA 8.32219 kcal/mol@LB@Unfolding Energy - sRNA 7.38006 kcal/mol@LB@@LB@Position - mRNA 156 -- 179@LB@Position - sRNA 68 -- 87@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 75 -- 81@LB@
55	0.002731	0.1727	b2480	bcp	-8.89	0.222722	156 -- 187	28 -- 56	peroxiredoxin; thiol peroxidase thioredoxin-dependent		_____________155_________________________________188\n_____________\|___________________________________\|\n5'-GAG...AUUAA______C_______CCCAAC_______________AUGGA...UUC-3'\n______________CGUCGU_AAUUAUU______AUGAUGA___ACAGG\n______________\|\|:\|\|\|_\|\|\|\|\|\|\|______\|\|\|\|\|\|\|___\|\|\|:\|\n______________GCGGCA_UUAAUAA______UACUACU___UGUUC\n3'-UUU...CCGAC______U____________________CAA_____CCGUG...GUG-5'\n_____________\|___________________________________\|\n_____________57__________________________________27\n	176 -- 182	36 -- 42	-21.7802 kcal/mol	6.3273 kcal/mol	6.56571 kcal/mol	155 188@LB@ \| \|@LB@5'-GAG...AUUAA C CCCAAC AUGGA...UUC-3'@LB@ CGUCGU AAUUAUU AUGAUGA ACAGG@LB@ \|\|:\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|:\|@LB@ GCGGCA UUAAUAA UACUACU UGUUC@LB@3'-UUU...CCGAC U CAA CCGUG...GUG-5'@LB@ \| \|@LB@ 57 27@LB@@LB@@LB@Energy -8.89 kcal/mol@LB@Hybridization Energy -21.7802 kcal/mol@LB@Unfolding Energy - mRNA 6.3273 kcal/mol@LB@Unfolding Energy - sRNA 6.56571 kcal/mol@LB@@LB@Position - mRNA 156 -- 187@LB@Position - sRNA 28 -- 56@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 36 -- 42@LB@
124	0.006738	0.1913	b2533	suhB	-10.44	0.114821	158 -- 166	51 -- 59	inositol monophosphatase		_____________157_______167\n_____________\|_________\|\n5'-UUG...AUACU_________UUUCC...AGA-3'\n______________CUGCGCCGU\n______________\|\|\|\|\|\|\|\|\|\n______________GACGCGGCA\n3'-UUU...GAACC_________UUUAA...GUG-5'\n_____________\|_________\|\n_____________60________50\n	160 -- 166	51 -- 57	-17.2912 kcal/mol	2.02049 kcal/mol	4.83013 kcal/mol	157 167@LB@ \| \|@LB@5'-UUG...AUACU UUUCC...AGA-3'@LB@ CUGCGCCGU@LB@ \|\|\|\|\|\|\|\|\|@LB@ GACGCGGCA@LB@3'-UUU...GAACC UUUAA...GUG-5'@LB@ \| \|@LB@ 60 50@LB@@LB@@LB@Energy -10.44 kcal/mol@LB@Hybridization Energy -17.2912 kcal/mol@LB@Unfolding Energy - mRNA 2.02049 kcal/mol@LB@Unfolding Energy - sRNA 4.83013 kcal/mol@LB@@LB@Position - mRNA 158 -- 166@LB@Position - sRNA 51 -- 59@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 51 -- 57@LB@
140	0.008117	0.2031	b3221	yhcH	-13.19	0.033484	158 -- 212	34 -- 73	DUF386 family protein cupin superfamily		_____________157_____________________________________________________213\n_____________\|_______________________________________________________\|\n5'-AUC...UGAUG____UUUAC__GG___________UGGCCCAGGGAGAA_______G_________GAAGU...AAG-3'\n______________CAGG_____UU__GGCUGCGCUGU______________AAAUUAU_AUGAUGGGU\n______________\|\|\|\|_____\|:__\|\|\|\|\|\|\|\|:\|\|______________\|\|\|\|\|\|\|_\|\|\|\|\|\|:\|\|\n______________GUCC_____AG__CCGACGCGGCA______________UUUAAUA_UACUACUCA\n3'-UUU...UUGUG____CUUU___AA________________________________A_________AUGUU...GUG-5'\n_____________\|_______________________________________________________\|\n_____________74______________________________________________________33\n	206 -- 212	34 -- 40	-41.3429 kcal/mol	18.8865 kcal/mol	9.26614 kcal/mol	157 213@LB@ \| \|@LB@5'-AUC...UGAUG UUUAC GG UGGCCCAGGGAGAA G GAAGU...AAG-3'@LB@ CAGG UU GGCUGCGCUGU AAAUUAU AUGAUGGGU@LB@ \|\|\|\| \|: \|\|\|\|\|\|\|\|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|:\|\|@LB@ GUCC AG CCGACGCGGCA UUUAAUA UACUACUCA@LB@3'-UUU...UUGUG CUUU AA A AUGUU...GUG-5'@LB@ \| \|@LB@ 74 33@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -41.3429 kcal/mol@LB@Unfolding Energy - mRNA 18.8865 kcal/mol@LB@Unfolding Energy - sRNA 9.26614 kcal/mol@LB@@LB@Position - mRNA 158 -- 212@LB@Position - sRNA 34 -- 73@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 34 -- 40@LB@
154	0.009082	0.2059	b2676	nrdF	-13.94	0.023769	159 -- 176	53 -- 69	ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein		_____________158________________177\n_____________\|__________________\|\n5'-AAG...GCACU______GAA_________UCCUG...CAG-3'\n______________GAAAUU___GGCUGCGUC\n______________\|\|\|\|\|:___\|\|\|\|\|\|\|:\|\n______________CUUUAG___CCGACGCGG\n3'-UUU...GGUCC______AA__________CAUUU...GUG-5'\n_____________\|__________________\|\n_____________70_________________52\n	170 -- 176	53 -- 59	-23.1658 kcal/mol	2.38862 kcal/mol	6.83371 kcal/mol	158 177@LB@ \| \|@LB@5'-AAG...GCACU GAA UCCUG...CAG-3'@LB@ GAAAUU GGCUGCGUC@LB@ \|\|\|\|\|: \|\|\|\|\|\|\|:\|@LB@ CUUUAG CCGACGCGG@LB@3'-UUU...GGUCC AA CAUUU...GUG-5'@LB@ \| \|@LB@ 70 52@LB@@LB@@LB@Energy -13.94 kcal/mol@LB@Hybridization Energy -23.1658 kcal/mol@LB@Unfolding Energy - mRNA 2.38862 kcal/mol@LB@Unfolding Energy - sRNA 6.83371 kcal/mol@LB@@LB@Position - mRNA 159 -- 176@LB@Position - sRNA 53 -- 69@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 53 -- 59@LB@
148	0.008708	0.2059	b1754	ynjB	-13.35	0.031185	160 -- 171	50 -- 61	putative ABC transporter periplasmic binding protein		_____________159__________172\n_____________\|____________\|\n5'-CCG...UCAGG____________UUCCU...AAA-3'\n______________GGCUGUGCCGUA\n______________\|\|\|\|\|:\|\|\|\|\|\|\n______________CCGACGCGGCAU\n3'-UUU...UAGAA____________UUAAU...GUG-5'\n_____________\|____________\|\n_____________62___________49\n	165 -- 171	50 -- 56	-23.078 kcal/mol	3.86799 kcal/mol	5.86332 kcal/mol	159 172@LB@ \| \|@LB@5'-CCG...UCAGG UUCCU...AAA-3'@LB@ GGCUGUGCCGUA@LB@ \|\|\|\|\|:\|\|\|\|\|\|@LB@ CCGACGCGGCAU@LB@3'-UUU...UAGAA UUAAU...GUG-5'@LB@ \| \|@LB@ 62 49@LB@@LB@@LB@Energy -13.35 kcal/mol@LB@Hybridization Energy -23.078 kcal/mol@LB@Unfolding Energy - mRNA 3.86799 kcal/mol@LB@Unfolding Energy - sRNA 5.86332 kcal/mol@LB@@LB@Position - mRNA 160 -- 171@LB@Position - sRNA 50 -- 61@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 50 -- 56@LB@
15	0.000767	0.1666	b2497	uraA	-16.56	0.007223	161 -- 232	28 -- 90	uracil permease		_____________160_________________________________________________________________________233\n_____________\|___________________________________________________________________________\|\n5'-AGC...UUUUU_____AA_____UAU_____AUAAUA___A___U___A__AU_AC________C_____CGG_______GA____ACCGC...UCC-3'\n______________GAGUA__GCGCC___AACAC______CAG_GGA_AAU_CU__G__GCGCCGUG___UAU___GGUGAGU___AAG\n______________\|\|:\|\|__\|\|\|\|\|___\|\|\|\|\|______\|\|\|_\|\|\|_\|\|\|_\|\|__\|__\|\|\|\|\|\|\|:___\|\|\|___\|:\|\|\|\|\|___\|\|\|\n______________CUUAU__CGCGG___UUGUG______GUC_CCU_UUA_GA__C__CGCGGCAU___AUA___CUACUCA___UUC\n3'-UUU...ACGCG_____GA_________________________________AC_GA________UUA___AUA_______AUG___CCGUG...GUG-5'\n_____________\|___________________________________________________________________________\|\n_____________91__________________________________________________________________________27\n	221 -- 227	34 -- 40	-48.784 kcal/mol	15.1604 kcal/mol	17.0677 kcal/mol	160 233@LB@ \| \|@LB@5'-AGC...UUUUU AA UAU AUAAUA A U A AU AC C CGG GA ACCGC...UCC-3'@LB@ GAGUA GCGCC AACAC CAG GGA AAU CU G GCGCCGUG UAU GGUGAGU AAG@LB@ \|\|:\|\| \|\|\|\|\| \|\|\|\|\| \|\|\| \|\|\| \|\|\| \|\| \| \|\|\|\|\|\|\|: \|\|\| \|:\|\|\|\|\| \|\|\|@LB@ CUUAU CGCGG UUGUG GUC CCU UUA GA C CGCGGCAU AUA CUACUCA UUC@LB@3'-UUU...ACGCG GA AC GA UUA AUA AUG CCGUG...GUG-5'@LB@ \| \|@LB@ 91 27@LB@@LB@@LB@Energy -16.56 kcal/mol@LB@Hybridization Energy -48.784 kcal/mol@LB@Unfolding Energy - mRNA 15.1604 kcal/mol@LB@Unfolding Energy - sRNA 17.0677 kcal/mol@LB@@LB@Position - mRNA 161 -- 232@LB@Position - sRNA 28 -- 90@LB@Position Seed - mRNA 221 -- 227@LB@Position Seed - sRNA 34 -- 40@LB@
26	0.001553	0.1727	b0853	ybjN	-8.94	0.217650	161 -- 169	52 -- 60	negative regulator of motility; multicopy suppressor of coaA(Ts)		_____________160_______170\n_____________\|_________\|\n5'-CGC...CGUAA_________GUCUU...AUC-3'\n______________GCUGUGCCG\n______________\|\|\|\|:\|\|\|\|\n______________CGACGCGGC\n3'-UUU...AGAAC_________AUUUA...GUG-5'\n_____________\|_________\|\n_____________61________51\n	163 -- 169	52 -- 58	-18.9448 kcal/mol	5.13325 kcal/mol	4.86882 kcal/mol	160 170@LB@ \| \|@LB@5'-CGC...CGUAA GUCUU...AUC-3'@LB@ GCUGUGCCG@LB@ \|\|\|\|:\|\|\|\|@LB@ CGACGCGGC@LB@3'-UUU...AGAAC AUUUA...GUG-5'@LB@ \| \|@LB@ 61 51@LB@@LB@@LB@Energy -8.94 kcal/mol@LB@Hybridization Energy -18.9448 kcal/mol@LB@Unfolding Energy - mRNA 5.13325 kcal/mol@LB@Unfolding Energy - sRNA 4.86882 kcal/mol@LB@@LB@Position - mRNA 161 -- 169@LB@Position - sRNA 52 -- 60@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 52 -- 58@LB@
190	0.01143	0.2119	b3233	yhcB	-11.72	0.064941	161 -- 178	66 -- 81	DUF1043 family inner membrane-anchored protein		_____________160________________179\n_____________\|__________________\|\n5'-UUU...CUGAA_________CUAC_____CAAAA...CGU-3'\n______________GCCAACACC____GGAAA\n______________\|\|\|\|\|\|\|\|\|____\|\|\|\|\|\n______________CGGUUGUGG____CCUUU\n3'-UUU...UGACG_________UC_______AGAAC...GUG-5'\n_____________\|__________________\|\n_____________82_________________65\n	163 -- 169	73 -- 79	-21.1167 kcal/mol	2.37182 kcal/mol	7.0207 kcal/mol	160 179@LB@ \| \|@LB@5'-UUU...CUGAA CUAC CAAAA...CGU-3'@LB@ GCCAACACC GGAAA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CGGUUGUGG CCUUU@LB@3'-UUU...UGACG UC AGAAC...GUG-5'@LB@ \| \|@LB@ 82 65@LB@@LB@@LB@Energy -11.72 kcal/mol@LB@Hybridization Energy -21.1167 kcal/mol@LB@Unfolding Energy - mRNA 2.37182 kcal/mol@LB@Unfolding Energy - sRNA 7.0207 kcal/mol@LB@@LB@Position - mRNA 161 -- 178@LB@Position - sRNA 66 -- 81@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 73 -- 79@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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