Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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	0.004045	0.1176	b1738	chbB	-6.64	0.311906	2 -- 15	34 -- 50	N N'-diacetylchitobiose-specific enzyme IIB component of PTS	_____________1_________________16\n_____________\|_________________\|\n__________5'-A_________________AUAAC...CGG-3'\n______________AUGUGAAG___AGGGUC\n______________\|:\|\|\|\|\|\|___\|:\|\|\|\|\n______________UGCACUUC___UUCCAG\n3'-AUU...GCUAA________AUU______ACUUU...AUG-5'\n_____________\|_________________\|\n_____________51________________33\n	3 -- 9	43 -- 49	-17.276 kcal/mol	2.8636 kcal/mol	7.69543 kcal/mol	1 16@LB@ \| \|@LB@ 5'-A AUAAC...CGG-3'@LB@ AUGUGAAG AGGGUC@LB@ \|:\|\|\|\|\|\| \|:\|\|\|\|@LB@ UGCACUUC UUCCAG@LB@3'-AUU...GCUAA AUU ACUUU...AUG-5'@LB@ \| \|@LB@ 51 33@LB@@LB@@LB@Energy -6.64 kcal/mol@LB@Hybridization Energy -17.276 kcal/mol@LB@Unfolding Energy - mRNA 2.8636 kcal/mol@LB@Unfolding Energy - sRNA 7.69543 kcal/mol@LB@@LB@Position - mRNA 2 -- 15@LB@Position - sRNA 34 -- 50@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 43 -- 49@LB@
122	0.004081	0.1177	b3940	metL	-10.48	0.032541	261 -- 280	41 -- 59	Bifunctional aspartokinase/homoserine dehydrogenase 2	_____________260__________________281\n_____________\|____________________\|\n5'-ACG...GCAGU_______CUG__________UUAUU...GCA-3'\n______________AGUCUGG___AUGUGAAGUG\n______________\|:\|\|:\|:___\|:\|\|\|\|\|\|\|:\n______________UUAGGCU___UGCACUUCAU\n3'-AUU...UCGGU_______AA___________UUUCC...AUG-5'\n_____________\|____________________\|\n_____________60___________________40\n	274 -- 280	41 -- 47	-17.3741 kcal/mol	3.59224 kcal/mol	3.31634 kcal/mol	260 281@LB@ \| \|@LB@5'-ACG...GCAGU CUG UUAUU...GCA-3'@LB@ AGUCUGG AUGUGAAGUG@LB@ \|:\|\|:\|: \|:\|\|\|\|\|\|\|:@LB@ UUAGGCU UGCACUUCAU@LB@3'-AUU...UCGGU AA UUUCC...AUG-5'@LB@ \| \|@LB@ 60 40@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.3741 kcal/mol@LB@Unfolding Energy - mRNA 3.59224 kcal/mol@LB@Unfolding Energy - sRNA 3.31634 kcal/mol@LB@@LB@Position - mRNA 261 -- 280@LB@Position - sRNA 41 -- 59@LB@Position Seed - mRNA 274 -- 280@LB@Position Seed - sRNA 41 -- 47@LB@
123	0.004171	0.1178	b2989	yghU	-8.31	0.130595	46 -- 54	49 -- 57	putative S-transferase	_____________45________55\n_____________\|_________\|\n5'-UUA...UGUGC_________CUGCU...CGC-3'\n______________UCUGAUUAC\n______________\|\|:\|\|\|\|\|\|\n______________AGGCUAAUG\n3'-AUU...GGUUU_________CACUU...AUG-5'\n_____________\|_________\|\n_____________58________48\n	48 -- 54	49 -- 55	-9.38135 kcal/mol	0.766517 kcal/mol	0.318327 kcal/mol	45 55@LB@ \| \|@LB@5'-UUA...UGUGC CUGCU...CGC-3'@LB@ UCUGAUUAC@LB@ \|\|:\|\|\|\|\|\|@LB@ AGGCUAAUG@LB@3'-AUU...GGUUU CACUU...AUG-5'@LB@ \| \|@LB@ 58 48@LB@@LB@@LB@Energy -8.31 kcal/mol@LB@Hybridization Energy -9.38135 kcal/mol@LB@Unfolding Energy - mRNA 0.766517 kcal/mol@LB@Unfolding Energy - sRNA 0.318327 kcal/mol@LB@@LB@Position - mRNA 46 -- 54@LB@Position - sRNA 49 -- 57@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 49 -- 55@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase	_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@LB@
125	0.004186	0.1178	b0781	moaA	-8.90	0.091954	79 -- 99	4 -- 23	molybdopterin biosynthesis protein A	_____________78____________________100\n_____________\|_____________________\|\n5'-ACG...CACUA____C___A_______C____GGGUC...CGG-3'\n______________AACA_UCU_GCCUCUG_ACCU\n______________\|\|\|\|_\|\|\|_:\|\|\|\|\|\|_\|\|\|:\n______________UUGU_AGA_UGGAGAC_UGGG\n3'-AUU...CUAUC________A_______A____AUG-5'\n_____________\|_____________________\|\n_____________24____________________3\n	88 -- 94	9 -- 15	-21.7522 kcal/mol	4.86496 kcal/mol	8.01134 kcal/mol	78 100@LB@ \| \|@LB@5'-ACG...CACUA C A C GGGUC...CGG-3'@LB@ AACA UCU GCCUCUG ACCU@LB@ \|\|\|\| \|\|\| :\|\|\|\|\|\| \|\|\|:@LB@ UUGU AGA UGGAGAC UGGG@LB@3'-AUU...CUAUC A A AUG-5'@LB@ \| \|@LB@ 24 3@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -21.7522 kcal/mol@LB@Unfolding Energy - mRNA 4.86496 kcal/mol@LB@Unfolding Energy - sRNA 8.01134 kcal/mol@LB@@LB@Position - mRNA 79 -- 99@LB@Position - sRNA 4 -- 23@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 9 -- 15@LB@
126	0.00422	0.1178	b1621	malX	-14.96	0.000732	43 -- 87	1 -- 56	maltose and glucose-specific PTS enzyme IIB component and IIC component	_____________42__________________________________________________________88\n_____________\|___________________________________________________________\|\n5'-AUG...ACUCC____________C___________________A______________UAUU________ACCCG...GCA-3'\n______________CUGAUUAUGUGA_______________AGAUA_AACGUUUUACCUUU____UAUCUUAU\n______________\|:\|\|\|\|\|:\|\|\|\|_______________\|\|\|\|\|_\|\|\|:\|:\|\|\|\|\|\|:\|____\|\|:\|:\|\|:\n______________GGCUAAUGCACU_______________UCUAU_UUGUAGAAUGGAGA____AUGGGAUG\n3'-AUU...GUUUA____________UCAUUUUCCAGACUU_____C______________C___________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	81 -- 87	1 -- 7	-37.7188 kcal/mol	10.08 kcal/mol	12.7022 kcal/mol	42 88@LB@ \| \|@LB@5'-AUG...ACUCC C A UAUU ACCCG...GCA-3'@LB@ CUGAUUAUGUGA AGAUA AACGUUUUACCUUU UAUCUUAU@LB@ \|:\|\|\|\|\|:\|\|\|\| \|\|\|\|\| \|\|\|:\|:\|\|\|\|\|\|:\| \|\|:\|:\|\|:@LB@ GGCUAAUGCACU UCUAU UUGUAGAAUGGAGA AUGGGAUG@LB@3'-AUU...GUUUA UCAUUUUCCAGACUU C C -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -14.96 kcal/mol@LB@Hybridization Energy -37.7188 kcal/mol@LB@Unfolding Energy - mRNA 10.08 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 43 -- 87@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 1 -- 7@LB@
127	0.004255	0.1179	b2838	lysA	-9.87	0.049362	214 -- 233	52 -- 69	diaminopimelate decarboxylase PLP-binding	_____________213__________________234\n_____________\|____________________\|\n5'-GGU...UUCAC________A_C___A_____CUCAC...CGC-3'\n______________UGUUCAGC_C_GAU_CCGAU\n______________\|:\|\|\|\|\|\|_\|_:\|\|_\|\|\|\|\|\n______________AUAAGUCG_G_UUA_GGCUA\n3'-AUU...AUUUU__________U_________AUGCA...AUG-5'\n_____________\|____________________\|\n_____________70___________________51\n	215 -- 221	62 -- 68	-18.1264 kcal/mol	2.0842 kcal/mol	6.19243 kcal/mol	213 234@LB@ \| \|@LB@5'-GGU...UUCAC A C A CUCAC...CGC-3'@LB@ UGUUCAGC C GAU CCGAU@LB@ \|:\|\|\|\|\|\| \| :\|\| \|\|\|\|\|@LB@ AUAAGUCG G UUA GGCUA@LB@3'-AUU...AUUUU U AUGCA...AUG-5'@LB@ \| \|@LB@ 70 51@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -18.1264 kcal/mol@LB@Unfolding Energy - mRNA 2.0842 kcal/mol@LB@Unfolding Energy - sRNA 6.19243 kcal/mol@LB@@LB@Position - mRNA 214 -- 233@LB@Position - sRNA 52 -- 69@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 62 -- 68@LB@
128	0.004347	0.1195	b3690	cbrA	-9.56	0.060736	197 -- 211	17 -- 31	colicin M resistance protein; FAD-binding protein putative oxidoreductase	_____________196_____________212\n_____________\|_______________\|\n5'-CAG...AGUGA_______________CGACG...AAA-3'\n______________AAAGAUGGAACAUUU\n______________\|\|\|\|\|\|:\|\|\|\|\|\|:\|\n______________UUUCUAUCUUGUAGA\n3'-AUU...CAGAC_______________AUGGA...AUG-5'\n_____________\|_______________\|\n_____________32______________16\n	204 -- 210	18 -- 24	-17.0326 kcal/mol	3.22818 kcal/mol	4.26586 kcal/mol	196 212@LB@ \| \|@LB@5'-CAG...AGUGA CGACG...AAA-3'@LB@ AAAGAUGGAACAUUU@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|:\|@LB@ UUUCUAUCUUGUAGA@LB@3'-AUU...CAGAC AUGGA...AUG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -9.56 kcal/mol@LB@Hybridization Energy -17.0326 kcal/mol@LB@Unfolding Energy - mRNA 3.22818 kcal/mol@LB@Unfolding Energy - sRNA 4.26586 kcal/mol@LB@@LB@Position - mRNA 197 -- 211@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 18 -- 24@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase	_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
130	0.004431	0.1199	b3355	prkB	-7.29	0.227256	214 -- 220	52 -- 58	putative phosphoribulokinase	_____________213_____221\n_____________\|_______\|\n5'-GGC...CAAAC_______CAUUG...AUC-3'\n______________AUCCGGU\n______________\|\|\|\|\|:\|\n______________UAGGCUA\n3'-AUU...CGGUU_______AUGCA...AUG-5'\n_____________\|_______\|\n_____________59______51\n	214 -- 220	52 -- 58	-8.26146 kcal/mol	0.695321 kcal/mol	0.296688 kcal/mol	213 221@LB@ \| \|@LB@5'-GGC...CAAAC CAUUG...AUC-3'@LB@ AUCCGGU@LB@ \|\|\|\|\|:\|@LB@ UAGGCUA@LB@3'-AUU...CGGUU AUGCA...AUG-5'@LB@ \| \|@LB@ 59 51@LB@@LB@@LB@Energy -7.29 kcal/mol@LB@Hybridization Energy -8.26146 kcal/mol@LB@Unfolding Energy - mRNA 0.695321 kcal/mol@LB@Unfolding Energy - sRNA 0.296688 kcal/mol@LB@@LB@Position - mRNA 214 -- 220@LB@Position - sRNA 52 -- 58@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 52 -- 58@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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