Input and runtime details for job 6527768 (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 6527768 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:51 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:20 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:38:58 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:39:05 CET 2018
	Job Completed		@ Fri Feb 16 20:39:38 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicA

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
11	0.0003246	0.08948	b2299	yfcD	-11.11	0.078371	283 -- 295	5 -- 18	putative NUDIX hydrolase	_____________282____________296\n_____________\|______________\|\n5'-AGA...CCGGG__________G___ACAGU-3'\n______________AACAAAUGCG_G_C\n______________\|\|\|\|\|\|\|\|\|\|_\|_\|\n______________UUGUUUACGC_C_G\n3'-UUU...UACUA__________G_A_AAAG-5'\n_____________\|______________\|\n_____________19_____________4\n	286 -- 292	9 -- 15	-15.7313 kcal/mol	3.39963 kcal/mol	1.2243 kcal/mol	282 296@LB@ \| \|@LB@5'-AGA...CCGGG G ACAGU-3'@LB@ AACAAAUGCG G C@LB@ \|\|\|\|\|\|\|\|\|\| \| \|@LB@ UUGUUUACGC C G@LB@3'-UUU...UACUA G A AAAG-5'@LB@ \| \|@LB@ 19 4@LB@@LB@@LB@Energy -11.11 kcal/mol@LB@Hybridization Energy -15.7313 kcal/mol@LB@Unfolding Energy - mRNA 3.39963 kcal/mol@LB@Unfolding Energy - sRNA 1.2243 kcal/mol@LB@@LB@Position - mRNA 283 -- 295@LB@Position - sRNA 5 -- 18@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 9 -- 15@LB@
12	0.0003263	0.08948	b4036	lamB	-12.21	0.050157	189 -- 218	8 -- 32	maltose outer membrane porin (maltoporin)	_____________188____________________________219\n_____________\|______________________________\|\n5'-CGC...AUGAC_____A___A_A________UACUC_____AAACU...GUU-3'\n______________UCAGG_GAU_G_AUGAUGAU_____UGCGC\n______________\|\|\|\|\|_\|\|\|_\|_\|\|\|\|\|:\|:_____\|\|\|\|\|\n______________AGUCC_CUA_C_UACUAUUG_____ACGCG\n3'-UUU...ACUUA____________________UUU_______CAGAAAG-5'\n_____________\|______________________________\|\n_____________33_____________________________7\n	202 -- 208	16 -- 22	-24.7132 kcal/mol	4.6775 kcal/mol	7.82314 kcal/mol	188 219@LB@ \| \|@LB@5'-CGC...AUGAC A A A UACUC AAACU...GUU-3'@LB@ UCAGG GAU G AUGAUGAU UGCGC@LB@ \|\|\|\|\| \|\|\| \| \|\|\|\|\|:\|: \|\|\|\|\|@LB@ AGUCC CUA C UACUAUUG ACGCG@LB@3'-UUU...ACUUA UUU CAGAAAG-5'@LB@ \| \|@LB@ 33 7@LB@@LB@@LB@Energy -12.21 kcal/mol@LB@Hybridization Energy -24.7132 kcal/mol@LB@Unfolding Energy - mRNA 4.6775 kcal/mol@LB@Unfolding Energy - sRNA 7.82314 kcal/mol@LB@@LB@Position - mRNA 189 -- 218@LB@Position - sRNA 8 -- 32@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 16 -- 22@LB@
13	0.0003435	0.08948	b2551	glyA	-14.51	0.019315	147 -- 213	7 -- 69	serine hydroxymethyltransferase	_____________146____________________________________________________________________214\n_____________\|______________________________________________________________________\|\n5'-CAA...CCAAC___A______UAUAAA_______A________GUUAG___________A____CG____U__________AAAUG...UCG-3'\n______________AGG_CCGC_C______GGCCAAA_AUUUUAUU_____CUGAG_UCAGG_GAUG__GAUG_UAAA_GCGUG\n______________\|\|\|_\|\|:\|_\|______\|\|\|\|\|\|\|_\|\|\|\|:\|\|:_____\|\|\|\|:_\|\|\|\|\|_\|\|\|\|__\|\|\|:_:\|\|\|_\|\|\|:\|\n______________UCC_GGUG_G______CCGGUUU_UAAAGUAG_____GACUU_AGUCC_CUAC__CUAU_GUUU_CGCGC\n________3'-UUU________A_CACUCA________________A_________A__________UA____U____A_____AGAAAG-5'\n_____________\|______________________________________________________________________\|\n_____________70_____________________________________________________________________6\n	162 -- 168	48 -- 54	-52.4461 kcal/mol	16.168 kcal/mol	21.7638 kcal/mol	146 214@LB@ \| \|@LB@5'-CAA...CCAAC A UAUAAA A GUUAG A CG U AAAUG...UCG-3'@LB@ AGG CCGC C GGCCAAA AUUUUAUU CUGAG UCAGG GAUG GAUG UAAA GCGUG@LB@ \|\|\| \|\|:\| \| \|\|\|\|\|\|\| \|\|\|\|:\|\|: \|\|\|\|: \|\|\|\|\| \|\|\|\| \|\|\|: :\|\|\| \|\|\|:\|@LB@ UCC GGUG G CCGGUUU UAAAGUAG GACUU AGUCC CUAC CUAU GUUU CGCGC@LB@ 3'-UUU A CACUCA A A UA U A AGAAAG-5'@LB@ \| \|@LB@ 70 6@LB@@LB@@LB@Energy -14.51 kcal/mol@LB@Hybridization Energy -52.4461 kcal/mol@LB@Unfolding Energy - mRNA 16.168 kcal/mol@LB@Unfolding Energy - sRNA 21.7638 kcal/mol@LB@@LB@Position - mRNA 147 -- 213@LB@Position - sRNA 7 -- 69@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 48 -- 54@LB@
14	0.0004057	0.09812	b0886	cydC	-15.95	0.010534	194 -- 211	2 -- 21	glutathione/cysteine ABC transporter export permease/ATPase	_____________193__________________212\n_____________\|____________________\|\n5'-GCG...GAGGA___U________________GCUAC...UCG-3'\n______________GAU__UAAAUGCGCG_CUUU\n______________\|\|\|__:\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CUA__GUUUACGCGC_GAAA\n3'-UUU...UACUA___UU__________A____G-5'\n_____________\|____________________\|\n_____________22___________________1\n	201 -- 207	7 -- 13	-19.6155 kcal/mol	2.41081 kcal/mol	1.25756 kcal/mol	193 212@LB@ \| \|@LB@5'-GCG...GAGGA U GCUAC...UCG-3'@LB@ GAU UAAAUGCGCG CUUU@LB@ \|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CUA GUUUACGCGC GAAA@LB@3'-UUU...UACUA UU A G-5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -15.95 kcal/mol@LB@Hybridization Energy -19.6155 kcal/mol@LB@Unfolding Energy - mRNA 2.41081 kcal/mol@LB@Unfolding Energy - sRNA 1.25756 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 2 -- 21@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 7 -- 13@LB@
15	0.000461	0.102	b2140	dusC	-12.07	0.053129	194 -- 211	3 -- 22	tRNA-dihydrouridine synthase C	_____________193__________________212\n_____________\|____________________\|\n5'-AAU...GCGGG_________________G__ACUGG...UUG-3'\n______________UGAUGAU__AUGCGUGU_UU\n______________\|\|\|\|:\|:__\|\|\|\|\|:\|\|_\|\|\n______________ACUAUUG__UACGCGCA_AA\n3'-UUU...CUACU_______UU________G__AG-5'\n_____________\|____________________\|\n_____________23___________________2\n	202 -- 208	6 -- 12	-18.0697 kcal/mol	4.73944 kcal/mol	1.259 kcal/mol	193 212@LB@ \| \|@LB@5'-AAU...GCGGG G ACUGG...UUG-3'@LB@ UGAUGAU AUGCGUGU UU@LB@ \|\|\|\|:\|: \|\|\|\|\|:\|\| \|\|@LB@ ACUAUUG UACGCGCA AA@LB@3'-UUU...CUACU UU G AG-5'@LB@ \| \|@LB@ 23 2@LB@@LB@@LB@Energy -12.07 kcal/mol@LB@Hybridization Energy -18.0697 kcal/mol@LB@Unfolding Energy - mRNA 4.73944 kcal/mol@LB@Unfolding Energy - sRNA 1.259 kcal/mol@LB@@LB@Position - mRNA 194 -- 211@LB@Position - sRNA 3 -- 22@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
16	0.0004819	0.102	b0957	ompA	-13.00	0.036257	182 -- 195	8 -- 22	outer membrane protein A (3a;II*;G;d)	_____________181_____________196\n_____________\|_______________\|\n5'-CUU...UUGGA_______________AAAAA...AAC-3'\n______________UGAUAACGAG_GCGC\n______________\|\|\|\|\|\|\|:\|:_\|\|\|\|\n______________ACUAUUGUUU_CGCG\n3'-UUU...CUACU__________A____CAGAAAG-5'\n_____________\|_______________\|\n_____________23______________7\n	185 -- 191	13 -- 19	-17.7455 kcal/mol	3.5039 kcal/mol	1.23838 kcal/mol	181 196@LB@ \| \|@LB@5'-CUU...UUGGA AAAAA...AAC-3'@LB@ UGAUAACGAG GCGC@LB@ \|\|\|\|\|\|\|:\|: \|\|\|\|@LB@ ACUAUUGUUU CGCG@LB@3'-UUU...CUACU A CAGAAAG-5'@LB@ \| \|@LB@ 23 7@LB@@LB@@LB@Energy -13.00 kcal/mol@LB@Hybridization Energy -17.7455 kcal/mol@LB@Unfolding Energy - mRNA 3.5039 kcal/mol@LB@Unfolding Energy - sRNA 1.23838 kcal/mol@LB@@LB@Position - mRNA 182 -- 195@LB@Position - sRNA 8 -- 22@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 13 -- 19@LB@
17	0.0005644	0.1124	b0949	uup	-13.14	0.034258	282 -- 297	4 -- 21	replication regulatory ABC-F family DNA-binding ATPase	_____________281________________298\n_____________\|__________________\|\n5'-GAU...UCGAA__________________GUC-3'\n______________GAUAACGAA__CGUGUUU\n______________\|\|\|\|\|\|:\|\|__\|\|:\|\|:\|\n______________CUAUUGUUU__GCGCAGA\n3'-UUU...UACUA_________AC_______AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	291 -- 297	4 -- 10	-16.3224 kcal/mol	1.92683 kcal/mol	1.2552 kcal/mol	281 298@LB@ \| \|@LB@5'-GAU...UCGAA GUC-3'@LB@ GAUAACGAA CGUGUUU@LB@ \|\|\|\|\|\|:\|\| \|\|:\|\|:\|@LB@ CUAUUGUUU GCGCAGA@LB@3'-UUU...UACUA AC AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.3224 kcal/mol@LB@Unfolding Energy - mRNA 1.92683 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 282 -- 297@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 4 -- 10@LB@
18	0.00061	0.1147	b2126	yehU	-11.17	0.076396	235 -- 252	1 -- 18	inner membrane putative sensory kinase in two-component system with YehT	_____________234________________253\n_____________\|__________________\|\n5'-GUC...GCUUC__________________UAGUC...UAA-3'\n______________AGCAGAUGUGCGUUUUUU\n______________\|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:\n______________UUGUUUACGCGCAGAAAG\n3'-UUU...UACUA__________________-5'\n_____________\|_________________\|\n_____________19________________1\n	246 -- 252	1 -- 7	-22.3117 kcal/mol	9.89973 kcal/mol	1.24077 kcal/mol	234 253@LB@ \| \|@LB@5'-GUC...GCUUC UAGUC...UAA-3'@LB@ AGCAGAUGUGCGUUUUUU@LB@ \|:\|\|:\|\|\|:\|\|\|\|:\|\|\|:@LB@ UUGUUUACGCGCAGAAAG@LB@3'-UUU...UACUA -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -11.17 kcal/mol@LB@Hybridization Energy -22.3117 kcal/mol@LB@Unfolding Energy - mRNA 9.89973 kcal/mol@LB@Unfolding Energy - sRNA 1.24077 kcal/mol@LB@@LB@Position - mRNA 235 -- 252@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 1 -- 7@LB@
19	0.0006629	0.1181	b2909	ygfB	-11.13	0.077732	186 -- 206	4 -- 22	UPF0149 family protein	_____________185___________________207\n_____________\|_____________________\|\n5'-AAA...CCCUU___C_________UUA_____AUACA...UCA-3'\n______________UGA_GACGAAUGC___UGUCU\n______________\|\|\|_:\|\|:\|\|\|\|\|___:\|\|\|\|\n______________ACU_UUGUUUACG___GCAGA\n3'-UUU...CUACU___A_________C_______AAG-5'\n_____________\|_____________________\|\n_____________23____________________3\n	192 -- 198	10 -- 16	-17.2827 kcal/mol	4.89762 kcal/mol	1.2572 kcal/mol	185 207@LB@ \| \|@LB@5'-AAA...CCCUU C UUA AUACA...UCA-3'@LB@ UGA GACGAAUGC UGUCU@LB@ \|\|\| :\|\|:\|\|\|\|\| :\|\|\|\|@LB@ ACU UUGUUUACG GCAGA@LB@3'-UUU...CUACU A C AAG-5'@LB@ \| \|@LB@ 23 3@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -17.2827 kcal/mol@LB@Unfolding Energy - mRNA 4.89762 kcal/mol@LB@Unfolding Energy - sRNA 1.2572 kcal/mol@LB@@LB@Position - mRNA 186 -- 206@LB@Position - sRNA 4 -- 22@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 10 -- 16@LB@
20	0.0008552	0.1448	b4137	cutA	-9.23	0.162618	220 -- 236	1 -- 16	divalent-cation tolerance protein copper sensitivity	_____________219_______________237\n_____________\|_________________\|\n5'-CAA...AAGUU_____AC_______G__GUGGU...CGG-3'\n______________CGAAU__CGCGUCU_UC\n______________\|:\|\|\|__\|\|\|\|\|\|\|_\|\|\n______________GUUUA__GCGCAGA_AG\n3'-UUU...CUAUU_____C________A__-5'\n_____________\|________________\|\n_____________17_______________1\n	227 -- 233	4 -- 10	-14.9299 kcal/mol	4.46216 kcal/mol	1.23857 kcal/mol	219 237@LB@ \| \|@LB@5'-CAA...AAGUU AC G GUGGU...CGG-3'@LB@ CGAAU CGCGUCU UC@LB@ \|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUUUA GCGCAGA AG@LB@3'-UUU...CUAUU C A -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -9.23 kcal/mol@LB@Hybridization Energy -14.9299 kcal/mol@LB@Unfolding Energy - mRNA 4.46216 kcal/mol@LB@Unfolding Energy - sRNA 1.23857 kcal/mol@LB@@LB@Position - mRNA 220 -- 236@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@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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