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
64	0.003339	0.1645	b3166	truB	-7.27	0.093914	187 -- 199	36 -- 48	tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase	_____________186___________200\n_____________\|_____________\|\n5'-GGC...ACGAC_________G___AAUGA...AAC-3'\n______________AGCAAGGAG_ACU\n______________\|\|\|\|\|\|:\|\|_\|\|\|\n______________UCGUUCUUC_UGA\n3'-UUU...CGAAU_________G___AUUUU...CAA-5'\n_____________\|_____________\|\n_____________49____________35\n	189 -- 195	40 -- 46	-16.8762 kcal/mol	3.76451 kcal/mol	5.83861 kcal/mol	186 200@LB@ \| \|@LB@5'-GGC...ACGAC G AAUGA...AAC-3'@LB@ AGCAAGGAG ACU@LB@ \|\|\|\|\|\|:\|\| \|\|\|@LB@ UCGUUCUUC UGA@LB@3'-UUU...CGAAU G AUUUU...CAA-5'@LB@ \| \|@LB@ 49 35@LB@@LB@@LB@Energy -7.27 kcal/mol@LB@Hybridization Energy -16.8762 kcal/mol@LB@Unfolding Energy - mRNA 3.76451 kcal/mol@LB@Unfolding Energy - sRNA 5.83861 kcal/mol@LB@@LB@Position - mRNA 187 -- 199@LB@Position - sRNA 36 -- 48@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 40 -- 46@LB@
191	0.02253	0.38	b3186	rplU	-5.10	0.305418	95 -- 102	34 -- 41	50S ribosomal subunit protein L21	_____________94_______103\n_____________\|________\|\n5'-UUA...ACUGU________UCAAA...UUG-3'\n______________AGCACUUG\n______________\|\|\|\|\|\|\|:\n______________UCGUGAAU\n3'-UUU...GUUCU________UUUUU...CAA-5'\n_____________\|________\|\n_____________42_______33\n	96 -- 102	34 -- 40	-9.60207 kcal/mol	2.88333 kcal/mol	1.6155 kcal/mol	94 103@LB@ \| \|@LB@5'-UUA...ACUGU UCAAA...UUG-3'@LB@ AGCACUUG@LB@ \|\|\|\|\|\|\|:@LB@ UCGUGAAU@LB@3'-UUU...GUUCU UUUUU...CAA-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -5.10 kcal/mol@LB@Hybridization Energy -9.60207 kcal/mol@LB@Unfolding Energy - mRNA 2.88333 kcal/mol@LB@Unfolding Energy - sRNA 1.6155 kcal/mol@LB@@LB@Position - mRNA 95 -- 102@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 96 -- 102@LB@Position Seed - sRNA 34 -- 40@LB@
89	0.006302	0.2266	b3208	mtgA	-4.90	0.336213	28 -- 47	28 -- 47	biosynthetic peptidoglycan transglycosylase	_____________27____________________48\n_____________\|_____________________\|\n5'-UUG...AUACC____________GG_______GGGCG...UGU-3'\n______________GC_AGAAGUGCU__AAGAGAU\n______________\|\|_\|\|\|\|\|::\|\|__\|\|:\|:\|\|\n______________CG_UCUUCGUGA__UUUUUUA\n3'-UUU...GAAUU__U_________A________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________48____________________27\n	32 -- 38	36 -- 42	-15.6239 kcal/mol	4.50128 kcal/mol	6.22212 kcal/mol	27 48@LB@ \| \|@LB@5'-UUG...AUACC GG GGGCG...UGU-3'@LB@ GC AGAAGUGCU AAGAGAU@LB@ \|\| \|\|\|\|\|::\|\| \|\|:\|:\|\|@LB@ CG UCUUCGUGA UUUUUUA@LB@3'-UUU...GAAUU U A AGCAA...CAA-5'@LB@ \| \|@LB@ 48 27@LB@@LB@@LB@Energy -4.90 kcal/mol@LB@Hybridization Energy -15.6239 kcal/mol@LB@Unfolding Energy - mRNA 4.50128 kcal/mol@LB@Unfolding Energy - sRNA 6.22212 kcal/mol@LB@@LB@Position - mRNA 28 -- 47@LB@Position - sRNA 28 -- 47@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 36 -- 42@LB@
48	0.002202	0.1465	b3209	elbB	-11.61	0.005163	95 -- 137	2 -- 41	isoprenoid biosynthesis protein with amidotransferase-like domain	_____________94__________________________________________138\n_____________\|___________________________________________\|\n5'-GCG...AAGAU___AAA_______U____________G_AUC____AA______GAUGC...GUG-3'\n______________AGC___ACUUAAA_GAUUUGUUACAU_A___AGUU__AUGUGU\n______________\|\|\|___\|\|\|\|\|\|\|_:\|\|\|:\|\|\|\|\|\|:_\|___\|:\|:__\|\|\|\|\|\|\n______________UCG___UGAAUUU_UUAAGCAAUGUG_U___UUAG__UACACA\n3'-UUU...GUUCU_____________U____________G_CCU____AC______A-5'\n_____________\|___________________________________________\|\n_____________42__________________________________________1\n	101 -- 107	32 -- 38	-29.0989 kcal/mol	8.27062 kcal/mol	9.22136 kcal/mol	94 138@LB@ \| \|@LB@5'-GCG...AAGAU AAA U G AUC AA GAUGC...GUG-3'@LB@ AGC ACUUAAA GAUUUGUUACAU A AGUU AUGUGU@LB@ \|\|\| \|\|\|\|\|\|\| :\|\|\|:\|\|\|\|\|\|: \| \|:\|: \|\|\|\|\|\|@LB@ UCG UGAAUUU UUAAGCAAUGUG U UUAG UACACA@LB@3'-UUU...GUUCU U G CCU AC A-5'@LB@ \| \|@LB@ 42 1@LB@@LB@@LB@Energy -11.61 kcal/mol@LB@Hybridization Energy -29.0989 kcal/mol@LB@Unfolding Energy - mRNA 8.27062 kcal/mol@LB@Unfolding Energy - sRNA 9.22136 kcal/mol@LB@@LB@Position - mRNA 95 -- 137@LB@Position - sRNA 2 -- 41@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 32 -- 38@LB@
179	0.02107	0.3768	b3226	nanR	-7.22	0.096643	281 -- 296	26 -- 41	sialic acid-inducible nan operon repressor	_____________280______________297\n_____________\|________________\|\n5'-AUU...CCGCU_____G_______C__UCCG-3'\n______________GGCGC_UAAAAAA_UC\n______________:\|\|:\|_\|\|\|\|\|\|\|_\|\|\n______________UCGUG_AUUUUUU_AG\n3'-UUU...GUUCU_____A_______A__CAAUG...CAA-5'\n_____________\|________________\|\n_____________42_______________25\n	287 -- 293	29 -- 35	-11.6683 kcal/mol	2.7952 kcal/mol	1.64829 kcal/mol	280 297@LB@ \| \|@LB@5'-AUU...CCGCU G C UCCG-3'@LB@ GGCGC UAAAAAA UC@LB@ :\|\|:\| \|\|\|\|\|\|\| \|\|@LB@ UCGUG AUUUUUU AG@LB@3'-UUU...GUUCU A A CAAUG...CAA-5'@LB@ \| \|@LB@ 42 25@LB@@LB@@LB@Energy -7.22 kcal/mol@LB@Hybridization Energy -11.6683 kcal/mol@LB@Unfolding Energy - mRNA 2.7952 kcal/mol@LB@Unfolding Energy - sRNA 1.64829 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 26 -- 41@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 29 -- 35@LB@
113	0.009602	0.2693	b3237	argR	-14.05	0.000763	205 -- 250	27 -- 60	l-arginine-responsive arginine metabolism regulon transcriptional regulator	_____________204_____________________________________________251\n_____________\|_______________________________________________\|\n5'-ACA...UAUGC______CG____________AGAACUAGUUAA___________C___ACUUA...UGC-3'\n______________GAAGCU__GC_UAAGCAAGA____________AGCAUUUAAAG_AUU\n______________\|\|\|:\|\|__\|\|_\|\|\|\|\|\|\|\|\|____________\|\|\|\|:\|\|\|\|\|:_\|\|\|\n______________CUUUGA__CG_AUUCGUUCU____________UCGUGAAUUUU_UAA\n3'-UUU...CCCUA______A___A________________________________U___GCAAU...CAA-5'\n_____________\|_______________________________________________\|\n_____________61______________________________________________26\n	238 -- 244	33 -- 39	-28.1986 kcal/mol	7.87477 kcal/mol	6.27096 kcal/mol	204 251@LB@ \| \|@LB@5'-ACA...UAUGC CG AGAACUAGUUAA C ACUUA...UGC-3'@LB@ GAAGCU GC UAAGCAAGA AGCAUUUAAAG AUU@LB@ \|\|\|:\|\| \|\| \|\|\|\|\|\|\|\|\| \|\|\|\|:\|\|\|\|\|: \|\|\|@LB@ CUUUGA CG AUUCGUUCU UCGUGAAUUUU UAA@LB@3'-UUU...CCCUA A A U GCAAU...CAA-5'@LB@ \| \|@LB@ 61 26@LB@@LB@@LB@Energy -14.05 kcal/mol@LB@Hybridization Energy -28.1986 kcal/mol@LB@Unfolding Energy - mRNA 7.87477 kcal/mol@LB@Unfolding Energy - sRNA 6.27096 kcal/mol@LB@@LB@Position - mRNA 205 -- 250@LB@Position - sRNA 27 -- 60@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 33 -- 39@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@
38	0.00143	0.1212	b3315	rplV	-7.95	0.062235	2 -- 19	23 -- 40	50S ribosomal subunit protein L22	_____________1__________________20\n_____________\|__________________\|\n__________5'-C________UCCCG_____CAACG...UGG-3'\n______________GCACUUGG_____UCGUU\n______________\|\|\|\|\|\|::_____\|\|\|\|\|\n______________CGUGAAUU_____AGCAA\n3'-UUU...UUCUU________UUUUA_____UGUGG...CAA-5'\n_____________\|__________________\|\n_____________41_________________22\n	3 -- 9	33 -- 39	-14.4443 kcal/mol	4.84591 kcal/mol	1.64885 kcal/mol	1 20@LB@ \| \|@LB@ 5'-C UCCCG CAACG...UGG-3'@LB@ GCACUUGG UCGUU@LB@ \|\|\|\|\|\|:: \|\|\|\|\|@LB@ CGUGAAUU AGCAA@LB@3'-UUU...UUCUU UUUUA UGUGG...CAA-5'@LB@ \| \|@LB@ 41 22@LB@@LB@@LB@Energy -7.95 kcal/mol@LB@Hybridization Energy -14.4443 kcal/mol@LB@Unfolding Energy - mRNA 4.84591 kcal/mol@LB@Unfolding Energy - sRNA 1.64885 kcal/mol@LB@@LB@Position - mRNA 2 -- 19@LB@Position - sRNA 23 -- 40@LB@Position Seed - mRNA 3 -- 9@LB@Position Seed - sRNA 33 -- 39@LB@
134	0.01281	0.308	b3316	rpsS	-8.71	0.038435	274 -- 288	39 -- 53	30S ribosomal subunit protein S19	_____________273______________289\n_____________\|________________\|\n5'-GCG...GGAAA__G____A________CCCUG...CUU-3'\n______________GC__GAG_CAAGAAGC\n______________\|\|__:\|\|_\|\|\|\|\|\|\|\|\n______________CG__UUC_GUUCUUCG\n3'-UUU...UUGAA__AA____________UGAAU...CAA-5'\n_____________\|________________\|\n_____________54_______________38\n	282 -- 288	39 -- 45	-16.1876 kcal/mol	1.46049 kcal/mol	6.01745 kcal/mol	273 289@LB@ \| \|@LB@5'-GCG...GGAAA G A CCCUG...CUU-3'@LB@ GC GAG CAAGAAGC@LB@ \|\| :\|\| \|\|\|\|\|\|\|\|@LB@ CG UUC GUUCUUCG@LB@3'-UUU...UUGAA AA UGAAU...CAA-5'@LB@ \| \|@LB@ 54 38@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -16.1876 kcal/mol@LB@Unfolding Energy - mRNA 1.46049 kcal/mol@LB@Unfolding Energy - sRNA 6.01745 kcal/mol@LB@@LB@Position - mRNA 274 -- 288@LB@Position - sRNA 39 -- 53@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 39 -- 45@LB@
106	0.009044	0.2693	b3360	pabA	-9.65	0.020637	134 -- 165	7 -- 41	aminodeoxychorismate synthase subunit II	_____________133_________________________________166\n_____________\|___________________________________\|\n5'-GCG...UAUUU____AAGUGGUAAG___AA________________GUAAA...CGU-3'\n______________AGCA___________CG____GCCGGGGAAUCUGA\n______________\|\|\|\|___________\|\|____:\|\|:\|\|:\|\|\|\|\|\|\|\n______________UCGU___________GC____UGGUCCUUUAGACU\n3'-UUU...GUUCU____GAAUUUUUUAA__AAUG______________ACACAA-5'\n_____________\|___________________________________\|\n_____________42__________________________________6\n	156 -- 162	10 -- 16	-26.3396 kcal/mol	7.46958 kcal/mol	9.22092 kcal/mol	133 166@LB@ \| \|@LB@5'-GCG...UAUUU AAGUGGUAAG AA GUAAA...CGU-3'@LB@ AGCA CG GCCGGGGAAUCUGA@LB@ \|\|\|\| \|\| :\|\|:\|\|:\|\|\|\|\|\|\|@LB@ UCGU GC UGGUCCUUUAGACU@LB@3'-UUU...GUUCU GAAUUUUUUAA AAUG ACACAA-5'@LB@ \| \|@LB@ 42 6@LB@@LB@@LB@Energy -9.65 kcal/mol@LB@Hybridization Energy -26.3396 kcal/mol@LB@Unfolding Energy - mRNA 7.46958 kcal/mol@LB@Unfolding Energy - sRNA 9.22092 kcal/mol@LB@@LB@Position - mRNA 134 -- 165@LB@Position - sRNA 7 -- 41@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 10 -- 16@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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