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
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@
151	0.01442	0.3104	b1395	paaH	-15.43	0.013105	189 -- 216	8 -- 31	3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent	_____________188__________________________217\n_____________\|____________________________\|\n5'-GGC...GUUCA______AAUA_C________________AAACU...UGU-3'\n______________CGGGGA____G_AUGAUGAUAAAUGUGC\n______________\|:\|\|\|\|____\|_\|\|\|\|\|:\|:\|\|\|\|\|:\|\|\n______________GUCCCU____C_UACUAUUGUUUACGCG\n3'-UUU...CUUAA______A_____________________CAGAAAG-5'\n_____________\|____________________________\|\n_____________32___________________________7\n	210 -- 216	8 -- 14	-28.6523 kcal/mol	5.47369 kcal/mol	7.74551 kcal/mol	188 217@LB@ \| \|@LB@5'-GGC...GUUCA AAUA C AAACU...UGU-3'@LB@ CGGGGA G AUGAUGAUAAAUGUGC@LB@ \|:\|\|\|\| \| \|\|\|\|\|:\|:\|\|\|\|\|:\|\|@LB@ GUCCCU C UACUAUUGUUUACGCG@LB@3'-UUU...CUUAA A CAGAAAG-5'@LB@ \| \|@LB@ 32 7@LB@@LB@@LB@Energy -15.43 kcal/mol@LB@Hybridization Energy -28.6523 kcal/mol@LB@Unfolding Energy - mRNA 5.47369 kcal/mol@LB@Unfolding Energy - sRNA 7.74551 kcal/mol@LB@@LB@Position - mRNA 189 -- 216@LB@Position - sRNA 8 -- 31@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 8 -- 14@LB@
123	0.01235	0.3104	b0097	secM	-7.65	0.286972	189 -- 203	7 -- 21	regulator of secA translation	_____________188_____________204\n_____________\|_______________\|\n5'-UGG...AUCGG________UAA____AGUGG...CGC-3'\n______________GAUGGCAA___CGUG\n______________\|\|\|::\|\|\|___\|\|:\|\n______________CUAUUGUU___GCGC\n3'-UUU...UACUA________UAC____AGAAAG-5'\n_____________\|_______________\|\n_____________22______________6\n	190 -- 196	14 -- 20	-12.5088 kcal/mol	3.61266 kcal/mol	1.24179 kcal/mol	188 204@LB@ \| \|@LB@5'-UGG...AUCGG UAA AGUGG...CGC-3'@LB@ GAUGGCAA CGUG@LB@ \|\|\|::\|\|\| \|\|:\|@LB@ CUAUUGUU GCGC@LB@3'-UUU...UACUA UAC AGAAAG-5'@LB@ \| \|@LB@ 22 6@LB@@LB@@LB@Energy -7.65 kcal/mol@LB@Hybridization Energy -12.5088 kcal/mol@LB@Unfolding Energy - mRNA 3.61266 kcal/mol@LB@Unfolding Energy - sRNA 1.24179 kcal/mol@LB@@LB@Position - mRNA 189 -- 203@LB@Position - sRNA 7 -- 21@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 14 -- 20@LB@
75	0.006972	0.3087	b4348	hsdS	-13.63	0.027959	190 -- 211	7 -- 29	specificity determinant for hsdM and hsdR	_____________189_____________________212\n_____________\|_______________________\|\n5'-CUG...UUGGU_______A_____________G_GAAAU...UAA-3'\n______________GGGGUGA_GG_AAUGAGUGCG_G\n______________\|\|\|:\|\|\|_\|:_\|\|::\|:\|\|\|\|_\|\n______________CCCUACU_CU_UUGUUUACGC_C\n3'-UUU...UAAGU_______A__A__________G_AGAAAG-5'\n_____________\|_______________________\|\n_____________30______________________6\n	203 -- 209	9 -- 15	-24.9713 kcal/mol	3.9222 kcal/mol	7.41901 kcal/mol	189 212@LB@ \| \|@LB@5'-CUG...UUGGU A G GAAAU...UAA-3'@LB@ GGGGUGA GG AAUGAGUGCG G@LB@ \|\|\|:\|\|\| \|: \|\|::\|:\|\|\|\| \|@LB@ CCCUACU CU UUGUUUACGC C@LB@3'-UUU...UAAGU A A G AGAAAG-5'@LB@ \| \|@LB@ 30 6@LB@@LB@@LB@Energy -13.63 kcal/mol@LB@Hybridization Energy -24.9713 kcal/mol@LB@Unfolding Energy - mRNA 3.9222 kcal/mol@LB@Unfolding Energy - sRNA 7.41901 kcal/mol@LB@@LB@Position - mRNA 190 -- 211@LB@Position - sRNA 7 -- 29@LB@Position Seed - mRNA 203 -- 209@LB@Position Seed - sRNA 9 -- 15@LB@
72	0.006739	0.3087	b2520	yfhM	-8.19	0.237735	190 -- 217	6 -- 30	bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein	_____________189__________________________218\n_____________\|____________________________\|\n5'-CUC...GUGGC________AAA____AA____UA_____AGCCG...CUU-3'\n______________AGGGAUGA___AUGA__AAGU__CGCGU\n______________\|\|\|\|\|\|\|\|___\|\|:\|__\|\|:\|__\|\|\|\|\|\n______________UCCCUACU___UAUU__UUUA__GCGCA\n3'-UUU...UUAAG________AC_____G_____C______GAAAG-5'\n_____________\|____________________________\|\n_____________31___________________________5\n	191 -- 197	23 -- 29	-19.496 kcal/mol	3.87755 kcal/mol	7.4255 kcal/mol	189 218@LB@ \| \|@LB@5'-CUC...GUGGC AAA AA UA AGCCG...CUU-3'@LB@ AGGGAUGA AUGA AAGU CGCGU@LB@ \|\|\|\|\|\|\|\| \|\|:\| \|\|:\| \|\|\|\|\|@LB@ UCCCUACU UAUU UUUA GCGCA@LB@3'-UUU...UUAAG AC G C GAAAG-5'@LB@ \| \|@LB@ 31 5@LB@@LB@@LB@Energy -8.19 kcal/mol@LB@Hybridization Energy -19.496 kcal/mol@LB@Unfolding Energy - mRNA 3.87755 kcal/mol@LB@Unfolding Energy - sRNA 7.4255 kcal/mol@LB@@LB@Position - mRNA 190 -- 217@LB@Position - sRNA 6 -- 30@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 23 -- 29@LB@
125	0.01241	0.3104	b0002	thrA	-8.21	0.235915	191 -- 205	9 -- 21	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________190_____________206\n_____________\|_______________\|\n5'-CCA...AACGA________CC_____AGUGU...UGG-3'\n______________GGUAACAA__AUGCG\n______________\|:\|\|\|\|\|\|__\|\|\|\|\|\n______________CUAUUGUU__UACGC\n3'-UUU...UACUA_______________GCAGAAAG-5'\n_____________\|_______________\|\n_____________22______________8\n	192 -- 198	14 -- 20	-12.9357 kcal/mol	3.48482 kcal/mol	1.23627 kcal/mol	190 206@LB@ \| \|@LB@5'-CCA...AACGA CC AGUGU...UGG-3'@LB@ GGUAACAA AUGCG@LB@ \|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUAUUGUU UACGC@LB@3'-UUU...UACUA GCAGAAAG-5'@LB@ \| \|@LB@ 22 8@LB@@LB@@LB@Energy -8.21 kcal/mol@LB@Hybridization Energy -12.9357 kcal/mol@LB@Unfolding Energy - mRNA 3.48482 kcal/mol@LB@Unfolding Energy - sRNA 1.23627 kcal/mol@LB@@LB@Position - mRNA 191 -- 205@LB@Position - sRNA 9 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 14 -- 20@LB@
24	0.001508	0.1943	b0150	fhuA	-11.07	0.079438	192 -- 210	5 -- 21	ferrichrome outer membrane transporter	_____________191_________________211\n_____________\|___________________\|\n5'-GGA...UCAGA____UAC___UG_______CCAAA...CAG-3'\n______________GAUA___CAA__GCGCGUU\n______________\|\|\|\|___\|\|\|__\|\|\|\|\|\|:\n______________CUAU___GUU__CGCGCAG\n3'-UUU...UACUA____U_____UA_______AAAG-5'\n_____________\|___________________\|\n_____________22__________________4\n	204 -- 210	5 -- 11	-17.2518 kcal/mol	4.92886 kcal/mol	1.24955 kcal/mol	191 211@LB@ \| \|@LB@5'-GGA...UCAGA UAC UG CCAAA...CAG-3'@LB@ GAUA CAA GCGCGUU@LB@ \|\|\|\| \|\|\| \|\|\|\|\|\|:@LB@ CUAU GUU CGCGCAG@LB@3'-UUU...UACUA U UA AAAG-5'@LB@ \| \|@LB@ 22 4@LB@@LB@@LB@Energy -11.07 kcal/mol@LB@Hybridization Energy -17.2518 kcal/mol@LB@Unfolding Energy - mRNA 4.92886 kcal/mol@LB@Unfolding Energy - sRNA 1.24955 kcal/mol@LB@@LB@Position - mRNA 192 -- 210@LB@Position - sRNA 5 -- 21@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 5 -- 11@LB@
38	0.002512	0.2224	b0436	tig	-7.88	0.265562	192 -- 204	10 -- 21	peptidyl-prolyl cis/trans isomerase (trigger factor)	_____________191___________205\n_____________\|_____________\|\n5'-UAC...UUUGA_______A_____AAGUU...UCA-3'\n______________GGUAACA_GAUGC\n______________\|:\|\|\|\|\|_:\|\|\|\|\n______________CUAUUGU_UUACG\n3'-UUU...UACUA_____________CGCAG...AAG-5'\n_____________\|_____________\|\n_____________22____________9\n	192 -- 198	15 -- 21	-12.2618 kcal/mol	3.15229 kcal/mol	1.23076 kcal/mol	191 205@LB@ \| \|@LB@5'-UAC...UUUGA A AAGUU...UCA-3'@LB@ GGUAACA GAUGC@LB@ \|:\|\|\|\|\| :\|\|\|\|@LB@ CUAUUGU UUACG@LB@3'-UUU...UACUA CGCAG...AAG-5'@LB@ \| \|@LB@ 22 9@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.2618 kcal/mol@LB@Unfolding Energy - mRNA 3.15229 kcal/mol@LB@Unfolding Energy - sRNA 1.23076 kcal/mol@LB@@LB@Position - mRNA 192 -- 204@LB@Position - sRNA 10 -- 21@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 15 -- 21@LB@
167	0.01599	0.3104	b4220	tamA	-9.57	0.142740	193 -- 207	4 -- 21	translocation and assembly module for autotransporter export outer membrane subunit	_____________192________________208\n_____________\|__________________\|\n5'-CGC...UUCAG__GA______________AUAUC...GAC-3'\n______________GA____AAAUGUGCG_CU\n______________\|\|____\|\|\|\|\|:\|\|\|_\|\|\n______________CU____UUUACGCGC_GA\n3'-UUU...UACUA__AUUG_________A__AAG-5'\n_____________\|__________________\|\n_____________22_________________3\n	199 -- 205	7 -- 13	-13.0971 kcal/mol	2.26836 kcal/mol	1.2552 kcal/mol	192 208@LB@ \| \|@LB@5'-CGC...UUCAG GA AUAUC...GAC-3'@LB@ GA AAAUGUGCG CU@LB@ \|\| \|\|\|\|\|:\|\|\| \|\|@LB@ CU UUUACGCGC GA@LB@3'-UUU...UACUA AUUG A AAG-5'@LB@ \| \|@LB@ 22 3@LB@@LB@@LB@Energy -9.57 kcal/mol@LB@Hybridization Energy -13.0971 kcal/mol@LB@Unfolding Energy - mRNA 2.26836 kcal/mol@LB@Unfolding Energy - sRNA 1.2552 kcal/mol@LB@@LB@Position - mRNA 193 -- 207@LB@Position - sRNA 4 -- 21@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 7 -- 13@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@

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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