Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
121	0.01057	0.2813	b0452	tesB	-8.75	0.037433	210 -- 223	26 -- 40	acyl-CoA thioesterase 2	_____________209_____________224\n_____________\|_______________\|\n5'-CAA...GUCAG_______________ACUGA...AGG-3'\n______________GCGC_UAAAAAAUUU\n______________\|\|:\|_\|\|\|\|\|\|\|\|\|:\n______________CGUG_AUUUUUUAAG\n3'-UUU...UUCUU____A__________CAAUG...CAA-5'\n_____________\|_______________\|\n_____________41______________25\n	217 -- 223	26 -- 32	-10.9054 kcal/mol	0.50684 kcal/mol	1.64811 kcal/mol	209 224@LB@ \| \|@LB@5'-CAA...GUCAG ACUGA...AGG-3'@LB@ GCGC UAAAAAAUUU@LB@ \|\|:\| \|\|\|\|\|\|\|\|\|:@LB@ CGUG AUUUUUUAAG@LB@3'-UUU...UUCUU A CAAUG...CAA-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -10.9054 kcal/mol@LB@Unfolding Energy - mRNA 0.50684 kcal/mol@LB@Unfolding Energy - sRNA 1.64811 kcal/mol@LB@@LB@Position - mRNA 210 -- 223@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 26 -- 32@LB@
122	0.01076	0.2828	b1908	yecA	-7.65	0.074805	79 -- 96	18 -- 40	UPF0149 family protein	_____________78_______________________97\n_____________\|________________________\|\n5'-UAC...UGCCU__A_____________________CUCCU...UGG-3'\n______________GC_ACUUG______UCGUUACACC\n______________\|\|_\|\|\|\|:______\|\|\|\|\|\|\|\|\|\|\n______________CG_UGAAU______AGCAAUGUGG\n3'-UUU...UUCUU________UUUUUA__________UCCUU...CAA-5'\n_____________\|________________________\|\n_____________41_______________________17\n	90 -- 96	18 -- 24	-19.1188 kcal/mol	2.30438 kcal/mol	9.1639 kcal/mol	78 97@LB@ \| \|@LB@5'-UAC...UGCCU A CUCCU...UGG-3'@LB@ GC ACUUG UCGUUACACC@LB@ \|\| \|\|\|\|: \|\|\|\|\|\|\|\|\|\|@LB@ CG UGAAU AGCAAUGUGG@LB@3'-UUU...UUCUU UUUUUA UCCUU...CAA-5'@LB@ \| \|@LB@ 41 17@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -19.1188 kcal/mol@LB@Unfolding Energy - mRNA 2.30438 kcal/mol@LB@Unfolding Energy - sRNA 9.1639 kcal/mol@LB@@LB@Position - mRNA 79 -- 96@LB@Position - sRNA 18 -- 40@LB@Position Seed - mRNA 90 -- 96@LB@Position Seed - sRNA 18 -- 24@LB@
123	0.0108	0.2828	b2606	rplS	-6.81	0.122900	220 -- 252	37 -- 58	50S ribosomal subunit protein L19	_____________219_______________________________253\n_____________\|_________________________________\|\n5'-AUA...UAAGC______AACAAGAGCAGAUG________C____CUUCC...UUG-3'\n______________AACUUG______________AAGCAGGA_GUAC\n______________\|\|\|\|\|\|______________\|\|\|\|\|:\|\|_\|:\|\|\n______________UUGAAC______________UUCGUUCU_CGUG\n3'-UUU...CUACU______GAA___________________U____AAUUU...CAA-5'\n_____________\|_________________________________\|\n_____________59________________________________36\n	241 -- 247	42 -- 48	-17.5998 kcal/mol	4.54246 kcal/mol	6.24354 kcal/mol	219 253@LB@ \| \|@LB@5'-AUA...UAAGC AACAAGAGCAGAUG C CUUCC...UUG-3'@LB@ AACUUG AAGCAGGA GUAC@LB@ \|\|\|\|\|\| \|\|\|\|\|:\|\| \|:\|\|@LB@ UUGAAC UUCGUUCU CGUG@LB@3'-UUU...CUACU GAA U AAUUU...CAA-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -17.5998 kcal/mol@LB@Unfolding Energy - mRNA 4.54246 kcal/mol@LB@Unfolding Energy - sRNA 6.24354 kcal/mol@LB@@LB@Position - mRNA 220 -- 252@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 42 -- 48@LB@
124	0.01089	0.2829	b0186	ldcC	-10.51	0.011388	34 -- 66	24 -- 58	lysine decarboxylase 2 constitutive	_____________33___________________________________67\n_____________\|____________________________________\|\n5'-AAA...AUCUC___G__________CU____________________CGUUA...UUA-3'\n______________GAC_UG_UUAAGCA__GAAG_AUUUAAAAAA_UCGU\n______________:\|\|_\|\|_\|\|\|\|\|\|\|__\|\|\|\|_\|:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UUG_AC_AAUUCGU__CUUC_UGAAUUUUUU_AGCA\n3'-UUU...CUACU___A__G_______U_____G__________A____AUGUG...CAA-5'\n_____________\|____________________________________\|\n_____________59___________________________________23\n	53 -- 59	32 -- 38	-24.2219 kcal/mol	7.43557 kcal/mol	6.27608 kcal/mol	33 67@LB@ \| \|@LB@5'-AAA...AUCUC G CU CGUUA...UUA-3'@LB@ GAC UG UUAAGCA GAAG AUUUAAAAAA UCGU@LB@ :\|\| \|\| \|\|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUG AC AAUUCGU CUUC UGAAUUUUUU AGCA@LB@3'-UUU...CUACU A G U G A AUGUG...CAA-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -24.2219 kcal/mol@LB@Unfolding Energy - mRNA 7.43557 kcal/mol@LB@Unfolding Energy - sRNA 6.27608 kcal/mol@LB@@LB@Position - mRNA 34 -- 66@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 32 -- 38@LB@
125	0.01132	0.2916	b4152	frdC	-8.74	0.037729	137 -- 154	25 -- 41	fumarate reductase (anaerobic) membrane anchor subunit	_____________136________________155\n_____________\|__________________\|\n5'-AGA...AGCAG____AAG___________AAAGA...CGG-3'\n______________GGCA___UAGAAAGUUCG\n______________:\|\|\|___\|\|:\|\|\|:\|\|\|\|\n______________UCGU___AUUUUUUAAGC\n3'-UUU...GUUCU____GA____________AAUGU...CAA-5'\n_____________\|__________________\|\n_____________42_________________24\n	148 -- 154	25 -- 31	-13.3883 kcal/mol	3.00162 kcal/mol	1.64839 kcal/mol	136 155@LB@ \| \|@LB@5'-AGA...AGCAG AAG AAAGA...CGG-3'@LB@ GGCA UAGAAAGUUCG@LB@ :\|\|\| \|\|:\|\|\|:\|\|\|\|@LB@ UCGU AUUUUUUAAGC@LB@3'-UUU...GUUCU GA AAUGU...CAA-5'@LB@ \| \|@LB@ 42 24@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -13.3883 kcal/mol@LB@Unfolding Energy - mRNA 3.00162 kcal/mol@LB@Unfolding Energy - sRNA 1.64839 kcal/mol@LB@@LB@Position - mRNA 137 -- 154@LB@Position - sRNA 25 -- 41@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 25 -- 31@LB@
126	0.01159	0.2964	b3693	dgoK	-8.44	0.045823	138 -- 160	34 -- 54	2-oxo-3-deoxygalactonate kinase	_____________137_____________________161\n_____________\|_______________________\|\n5'-CAG...GGCGA___GGCA_______C________CCAUG...CAG-3'\n______________UGC____GAGCAGG_GGCGCUUA\n______________\|\|\|____:\|\|\|\|:\|_:\|\|:\|\|\|\|\n______________ACG____UUCGUUC_UCGUGAAU\n3'-UUU...UUUGA___AA_________U________UUUUU...CAA-5'\n_____________\|_______________________\|\n_____________55______________________33\n	154 -- 160	34 -- 40	-23.026 kcal/mol	8.41527 kcal/mol	6.17478 kcal/mol	137 161@LB@ \| \|@LB@5'-CAG...GGCGA GGCA C CCAUG...CAG-3'@LB@ UGC GAGCAGG GGCGCUUA@LB@ \|\|\| :\|\|\|\|:\| :\|\|:\|\|\|\|@LB@ ACG UUCGUUC UCGUGAAU@LB@3'-UUU...UUUGA AA U UUUUU...CAA-5'@LB@ \| \|@LB@ 55 33@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -23.026 kcal/mol@LB@Unfolding Energy - mRNA 8.41527 kcal/mol@LB@Unfolding Energy - sRNA 6.17478 kcal/mol@LB@@LB@Position - mRNA 138 -- 160@LB@Position - sRNA 34 -- 54@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 34 -- 40@LB@
127	0.01193	0.3024	b3625	waaY	-10.33	0.012897	24 -- 38	26 -- 41	lipopolysaccharide core biosynthesis protein	_____________23_______________39\n_____________\|________________\|\n5'-CCA...AAAAU________________CCCCU...UAA-3'\n______________AGC_UUUAGAAAAUUC\n______________\|\|\|_:\|\|\|:\|\|\|\|\|\|\|\n______________UCG_GAAUUUUUUAAG\n3'-UUU...GUUCU___U____________CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	32 -- 38	26 -- 32	-12.5754 kcal/mol	0.594404 kcal/mol	1.64829 kcal/mol	23 39@LB@ \| \|@LB@5'-CCA...AAAAU CCCCU...UAA-3'@LB@ AGC UUUAGAAAAUUC@LB@ \|\|\| :\|\|\|:\|\|\|\|\|\|\|@LB@ UCG GAAUUUUUUAAG@LB@3'-UUU...GUUCU U CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -10.33 kcal/mol@LB@Hybridization Energy -12.5754 kcal/mol@LB@Unfolding Energy - mRNA 0.594404 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 24 -- 38@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 26 -- 32@LB@
128	0.01225	0.3033	b3299	rpmJ	-5.94	0.199813	193 -- 212	24 -- 42	50S ribosomal subunit protein L36	_____________192__________________213\n_____________\|____________________\|\n5'-GGA...ACGGA_____AAAAU__________GCUUC...AUA-3'\n______________GAGUA_____GAAAGUUCGU\n______________:\|\|:\|_____:\|\|\|:\|\|\|\|\|\n______________UUCGU_____UUUUUAAGCA\n3'-UUU...CGUUC_____GAAU___________AUGUG...CAA-5'\n_____________\|____________________\|\n_____________43___________________23\n	206 -- 212	24 -- 30	-12.4383 kcal/mol	4.85088 kcal/mol	1.64896 kcal/mol	192 213@LB@ \| \|@LB@5'-GGA...ACGGA AAAAU GCUUC...AUA-3'@LB@ GAGUA GAAAGUUCGU@LB@ :\|\|:\| :\|\|\|:\|\|\|\|\|@LB@ UUCGU UUUUUAAGCA@LB@3'-UUU...CGUUC GAAU AUGUG...CAA-5'@LB@ \| \|@LB@ 43 23@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -12.4383 kcal/mol@LB@Unfolding Energy - mRNA 4.85088 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 193 -- 212@LB@Position - sRNA 24 -- 42@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 24 -- 30@LB@
129	0.01228	0.3033	b2249	yfaY	-6.27	0.166554	88 -- 102	6 -- 22	inactive PncC family protein	_____________87________________103\n_____________\|_________________\|\n5'-UUG...GGUUA_______UU________CCCUU...AGG-3'\n______________ACGCCAG____UCUGAU\n______________\|\|:\|\|\|\|____\|\|\|\|\|\|\n______________UGUGGUC____AGACUA\n3'-UUU...AGCAA_______CUUU______CACAA-5'\n_____________\|_________________\|\n_____________23________________5\n	88 -- 94	16 -- 22	-16.5501 kcal/mol	2.71406 kcal/mol	7.56159 kcal/mol	87 103@LB@ \| \|@LB@5'-UUG...GGUUA UU CCCUU...AGG-3'@LB@ ACGCCAG UCUGAU@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|@LB@ UGUGGUC AGACUA@LB@3'-UUU...AGCAA CUUU CACAA-5'@LB@ \| \|@LB@ 23 5@LB@@LB@@LB@Energy -6.27 kcal/mol@LB@Hybridization Energy -16.5501 kcal/mol@LB@Unfolding Energy - mRNA 2.71406 kcal/mol@LB@Unfolding Energy - sRNA 7.56159 kcal/mol@LB@@LB@Position - mRNA 88 -- 102@LB@Position - sRNA 6 -- 22@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 16 -- 22@LB@
130	0.01234	0.3033	b2958	yggN	-5.61	0.236844	227 -- 233	35 -- 41	DUF2884 family putative periplasmic protein	_____________226_____234\n_____________\|_______\|\n5'-ACG...GCGGC_______UCAGU...UUG-3'\n______________AGCACUU\n______________\|\|\|\|\|\|\|\n______________UCGUGAA\n3'-UUU...GUUCU_______UUUUU...CAA-5'\n_____________\|_______\|\n_____________42______34\n	227 -- 233	35 -- 41	-8.1936 kcal/mol	0.976472 kcal/mol	1.6033 kcal/mol	226 234@LB@ \| \|@LB@5'-ACG...GCGGC UCAGU...UUG-3'@LB@ AGCACUU@LB@ \|\|\|\|\|\|\|@LB@ UCGUGAA@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 34@LB@@LB@@LB@Energy -5.61 kcal/mol@LB@Hybridization Energy -8.1936 kcal/mol@LB@Unfolding Energy - mRNA 0.976472 kcal/mol@LB@Unfolding Energy - sRNA 1.6033 kcal/mol@LB@@LB@Position - mRNA 227 -- 233@LB@Position - sRNA 35 -- 41@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 35 -- 41@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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