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
61	0.003042	0.1727	b0104	guaC	-6.79	0.490983	117 -- 124	52 -- 59	GMP reductase	_____________116______125\n_____________\|________\|\n5'-AUG...CAGUC________CAUUG...GUC-3'\n______________UUGCGCCG\n______________:\|\|\|\|\|\|\|\n______________GACGCGGC\n3'-UUU...GAACC________AUUUA...GUG-5'\n_____________\|________\|\n_____________60_______51\n	118 -- 124	52 -- 58	-14.4979 kcal/mol	2.89251 kcal/mol	4.81798 kcal/mol	116 125@LB@ \| \|@LB@5'-AUG...CAGUC CAUUG...GUC-3'@LB@ UUGCGCCG@LB@ :\|\|\|\|\|\|\|@LB@ GACGCGGC@LB@3'-UUU...GAACC AUUUA...GUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -6.79 kcal/mol@LB@Hybridization Energy -14.4979 kcal/mol@LB@Unfolding Energy - mRNA 2.89251 kcal/mol@LB@Unfolding Energy - sRNA 4.81798 kcal/mol@LB@@LB@Position - mRNA 117 -- 124@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 52 -- 58@LB@
62	0.003053	0.1727	b3812	yigB	-11.80	0.062766	182 -- 199	65 -- 83	5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase; pyrimidine phosphatase; riboflavin synthesis	_____________181_________________200\n_____________\|___________________\|\n5'-CUG...UCCAC__________G________AAUGC...GAG-3'\n______________GCGCCAA_AC_GGGGAAAU\n______________\|\|\|\|\|\|\|_\|\|_:\|\|\|\|\|\|\|\n______________CGCGGUU_UG_UCCCUUUA\n3'-UUU...UAUGA_______G__G________GAACC...GUG-5'\n_____________\|___________________\|\n_____________84__________________64\n	193 -- 199	65 -- 71	-28.1563 kcal/mol	8.99645 kcal/mol	7.35968 kcal/mol	181 200@LB@ \| \|@LB@5'-CUG...UCCAC G AAUGC...GAG-3'@LB@ GCGCCAA AC GGGGAAAU@LB@ \|\|\|\|\|\|\| \|\| :\|\|\|\|\|\|\|@LB@ CGCGGUU UG UCCCUUUA@LB@3'-UUU...UAUGA G G GAACC...GUG-5'@LB@ \| \|@LB@ 84 64@LB@@LB@@LB@Energy -11.80 kcal/mol@LB@Hybridization Energy -28.1563 kcal/mol@LB@Unfolding Energy - mRNA 8.99645 kcal/mol@LB@Unfolding Energy - sRNA 7.35968 kcal/mol@LB@@LB@Position - mRNA 182 -- 199@LB@Position - sRNA 65 -- 83@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 65 -- 71@LB@
63	0.003148	0.1727	b0131	panD	-12.33	0.049519	276 -- 291	70 -- 84	aspartate 1-decarboxylase	_____________275______________292\n_____________\|________________\|\n5'-AUU...GUUCU_______UUG______AUUUU...UUG-3'\n______________UGCGCCA___ACCAGG\n______________\|\|\|\|\|\|\|___\|\|\|\|\|\|\n______________ACGCGGU___UGGUCC\n3'-UUU...UUAUG_______UG_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________85_______________69\n	276 -- 282	78 -- 84	-24.0598 kcal/mol	4.4848 kcal/mol	7.24859 kcal/mol	275 292@LB@ \| \|@LB@5'-AUU...GUUCU UUG AUUUU...UUG-3'@LB@ UGCGCCA ACCAGG@LB@ \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ ACGCGGU UGGUCC@LB@3'-UUU...UUAUG UG CUUUA...GUG-5'@LB@ \| \|@LB@ 85 69@LB@@LB@@LB@Energy -12.33 kcal/mol@LB@Hybridization Energy -24.0598 kcal/mol@LB@Unfolding Energy - mRNA 4.4848 kcal/mol@LB@Unfolding Energy - sRNA 7.24859 kcal/mol@LB@@LB@Position - mRNA 276 -- 291@LB@Position - sRNA 70 -- 84@LB@Position Seed - mRNA 276 -- 282@LB@Position Seed - sRNA 78 -- 84@LB@
64	0.003238	0.1727	b2578	eamB	-8.70	0.240388	240 -- 262	70 -- 85	cysteine and O-acetylserine exporter	_____________239_____________________263\n_____________\|_______________________\|\n5'-GUC...ACACC___AUUAC____AU_________ACCGA...CGC-3'\n______________CUG_____CGCU__GACGCCAGG\n______________\|\|\|_____\|\|\|:__:\|\|:\|\|\|\|\|\n______________GAC_____GCGG__UUGUGGUCC\n3'-UUU...CUUAU_______________________CUUUA...GUG-5'\n_____________\|_______________________\|\n_____________86______________________69\n	256 -- 262	70 -- 76	-20.6717 kcal/mol	4.69447 kcal/mol	7.27689 kcal/mol	239 263@LB@ \| \|@LB@5'-GUC...ACACC AUUAC AU ACCGA...CGC-3'@LB@ CUG CGCU GACGCCAGG@LB@ \|\|\| \|\|\|: :\|\|:\|\|\|\|\|@LB@ GAC GCGG UUGUGGUCC@LB@3'-UUU...CUUAU CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -20.6717 kcal/mol@LB@Unfolding Energy - mRNA 4.69447 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 240 -- 262@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 256 -- 262@LB@Position Seed - sRNA 70 -- 76@LB@
65	0.003263	0.1727	b2584	pka	-7.67	0.359085	49 -- 62	69 -- 82	protein lysine acetyltransferase	_____________48_____________63\n_____________\|______________\|\n5'-AGG...AUGGC__G___________CGGCG...GUA-3'\n______________CG_CGAUACCGGGG\n______________\|\|_\|:\|:\|\|\|:\|\|\|\n______________GC_GUUGUGGUCCC\n3'-UUU...AUGAC__G___________UUUAG...GUG-5'\n_____________\|______________\|\n_____________83_____________68\n	56 -- 62	69 -- 75	-21.7159 kcal/mol	7.18281 kcal/mol	6.85849 kcal/mol	48 63@LB@ \| \|@LB@5'-AGG...AUGGC G CGGCG...GUA-3'@LB@ CG CGAUACCGGGG@LB@ \|\| \|:\|:\|\|\|:\|\|\|@LB@ GC GUUGUGGUCCC@LB@3'-UUU...AUGAC G UUUAG...GUG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -7.67 kcal/mol@LB@Hybridization Energy -21.7159 kcal/mol@LB@Unfolding Energy - mRNA 7.18281 kcal/mol@LB@Unfolding Energy - sRNA 6.85849 kcal/mol@LB@@LB@Position - mRNA 49 -- 62@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 56 -- 62@LB@Position Seed - sRNA 69 -- 75@LB@
66	0.003275	0.1727	b0394	mak	-8.12	0.303293	18 -- 92	5 -- 77	manno(fructo)kinase	_____________17_______________________________________________________________________________93\n_____________\|________________________________________________________________________________\|\n5'-GUU...CUUCU____G___C_______CGC____AA_A_G_____CC____AAUUUUUGA_______________GAUAA____CAC____UUGUC...GUG-3'\n______________GCAC_CAG_GAAAUCU___GGCU__G_C_GUAAA__AUUA_________AC_____CACAGCAU_____UUUC___GGCC\n______________:\|\|\|_\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|__\|_\|_\|\|\|\|\|__\|\|\|\|_________\|\|_____\|\|\|\|\|\|\|:_____\|\|\|\|___\|\|\|\|\n______________UGUG_GUC_CUUUAGA___CCGA__C_G_CAUUU__UAAU_________UG_____GUGUCGUG_____AAAG___CCGG\n3'-UUU...GCGGU________C_______A______CG___G_____AA____ACUACUCAA__UUCCC________ACAA_____U______CGUG-5'\n_____________\|________________________________________________________________________________\|\n_____________78_______________________________________________________________________________4\n	70 -- 76	18 -- 24	-46.4183 kcal/mol	15.5654 kcal/mol	22.7286 kcal/mol	17 93@LB@ \| \|@LB@5'-GUU...CUUCU G C CGC AA A G CC AAUUUUUGA GAUAA CAC UUGUC...GUG-3'@LB@ GCAC CAG GAAAUCU GGCU G C GUAAA AUUA AC CACAGCAU UUUC GGCC@LB@ :\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| \| \| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ UGUG GUC CUUUAGA CCGA C G CAUUU UAAU UG GUGUCGUG AAAG CCGG@LB@3'-UUU...GCGGU C A CG G AA ACUACUCAA UUCCC ACAA U CGUG-5'@LB@ \| \|@LB@ 78 4@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -46.4183 kcal/mol@LB@Unfolding Energy - mRNA 15.5654 kcal/mol@LB@Unfolding Energy - sRNA 22.7286 kcal/mol@LB@@LB@Position - mRNA 18 -- 92@LB@Position - sRNA 5 -- 77@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 18 -- 24@LB@
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit	_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
68	0.00345	0.1727	b3168	infB	-10.64	0.105292	126 -- 148	49 -- 77	translation initiation factor IF-2	_____________125___________________________149\n_____________\|_____________________________\|\n5'-AAG...CCGGA______________A______________UAUUU...CUG-3'\n______________GCACU_____GAUU_UGGCUGC_CCGUAA\n______________:\|\|\|:_____:\|\|:_\|\|\|\|\|\|\|_\|\|\|\|\|\|\n______________UGUGG_____UUAG_ACCGACG_GGCAUU\n3'-UUU...GCGGU_____UCCCU____A_______C______UAAUA...GUG-5'\n_____________\|_____________________________\|\n_____________78____________________________48\n	136 -- 142	56 -- 62	-27.6009 kcal/mol	7.61735 kcal/mol	9.34562 kcal/mol	125 149@LB@ \| \|@LB@5'-AAG...CCGGA A UAUUU...CUG-3'@LB@ GCACU GAUU UGGCUGC CCGUAA@LB@ :\|\|\|: :\|\|: \|\|\|\|\|\|\| \|\|\|\|\|\|@LB@ UGUGG UUAG ACCGACG GGCAUU@LB@3'-UUU...GCGGU UCCCU A C UAAUA...GUG-5'@LB@ \| \|@LB@ 78 48@LB@@LB@@LB@Energy -10.64 kcal/mol@LB@Hybridization Energy -27.6009 kcal/mol@LB@Unfolding Energy - mRNA 7.61735 kcal/mol@LB@Unfolding Energy - sRNA 9.34562 kcal/mol@LB@@LB@Position - mRNA 126 -- 148@LB@Position - sRNA 49 -- 77@LB@Position Seed - mRNA 136 -- 142@LB@Position Seed - sRNA 56 -- 62@LB@
69	0.003463	0.1727	b2346	mlaA	-10.50	0.111973	167 -- 195	66 -- 86	ABC transporter maintaining OM lipid asymmetry OM lipoprotein component	_____________166___________________________196\n_____________\|_____________________________\|\n5'-GCG...GGCAA_____AUAA____UAAAAAAA________CAUUU...AAG-3'\n______________ACUGC____GCCA________CAGGGAGA\n______________\|\|\|\|\|____\|\|\|\|________\|\|\|\|\|\|:\|\n______________UGACG____CGGU________GUCCCUUU\n3'-UUU...GCUUA_____________UGUG____________AGAAC...GUG-5'\n_____________\|_____________________________\|\n_____________87____________________________65\n	189 -- 195	66 -- 72	-21.8219 kcal/mol	3.94189 kcal/mol	7.38216 kcal/mol	166 196@LB@ \| \|@LB@5'-GCG...GGCAA AUAA UAAAAAAA CAUUU...AAG-3'@LB@ ACUGC GCCA CAGGGAGA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UGACG CGGU GUCCCUUU@LB@3'-UUU...GCUUA UGUG AGAAC...GUG-5'@LB@ \| \|@LB@ 87 65@LB@@LB@@LB@Energy -10.50 kcal/mol@LB@Hybridization Energy -21.8219 kcal/mol@LB@Unfolding Energy - mRNA 3.94189 kcal/mol@LB@Unfolding Energy - sRNA 7.38216 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 66 -- 86@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 66 -- 72@LB@
70	0.003478	0.1727	b1919	dcyD	-7.16	0.432573	249 -- 279	53 -- 83	D-cysteine desulfhydrase PLP-dependent	_____________248_______________________________280\n_____________\|_________________________________\|\n5'-CUG...UCGGC____________CUC___U________C_____UUUCU...GGG-3'\n______________GCGCCAACGCCG___GAA_AUCU__GC_GCGCU\n______________\|\|\|\|\|\|\|\|:\|\|:___\|\|\|_\|\|\|\|__\|\|_\|\|\|\|:\n______________CGCGGUUGUGGU___CUU_UAGA__CG_CGCGG\n3'-UUU...UAUGA____________CC_________AC__A_____CAUUU...GUG-5'\n_____________\|_________________________________\|\n_____________84________________________________52\n	252 -- 258	74 -- 80	-36.5845 kcal/mol	12.956 kcal/mol	16.4685 kcal/mol	248 280@LB@ \| \|@LB@5'-CUG...UCGGC CUC U C UUUCU...GGG-3'@LB@ GCGCCAACGCCG GAA AUCU GC GCGCU@LB@ \|\|\|\|\|\|\|\|:\|\|: \|\|\| \|\|\|\| \|\| \|\|\|\|:@LB@ CGCGGUUGUGGU CUU UAGA CG CGCGG@LB@3'-UUU...UAUGA CC AC A CAUUU...GUG-5'@LB@ \| \|@LB@ 84 52@LB@@LB@@LB@Energy -7.16 kcal/mol@LB@Hybridization Energy -36.5845 kcal/mol@LB@Unfolding Energy - mRNA 12.956 kcal/mol@LB@Unfolding Energy - sRNA 16.4685 kcal/mol@LB@@LB@Position - mRNA 249 -- 279@LB@Position - sRNA 53 -- 83@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 74 -- 80@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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