Input and runtime details for job 1654565 (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 1654565 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:23:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:05 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:25:53 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:26:01 CET 2018
	Job Completed		@ Fri Feb 16 22:26:34 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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	Additional homologs
146	0.005657	0.1365	b4322	uxuA	-7.47	0.371307	180 -- 195	52 -- 75	mannonate hydrolase		_____________179______________________196\n_____________\|________________________\|\n5'-CAU...ACCCA________________________AAAUC...AUA-3'\n______________CUAUGU________GAAAGAGGAA\n______________\|\|\|\|\|:________:\|\|\|:\|\|\|\|\|\n______________GAUACG________UUUUUUCCUU\n3'-UUU...AACAC______UCAUUAAG__________CAUUC...ACG-5'\n_____________\|________________________\|\n_____________76_______________________51\n	189 -- 195	52 -- 58	-13.8583 kcal/mol	2.68591 kcal/mol	3.70263 kcal/mol	179 196@LB@ \| \|@LB@5'-CAU...ACCCA AAAUC...AUA-3'@LB@ CUAUGU GAAAGAGGAA@LB@ \|\|\|\|\|: :\|\|\|:\|\|\|\|\|@LB@ GAUACG UUUUUUCCUU@LB@3'-UUU...AACAC UCAUUAAG CAUUC...ACG-5'@LB@ \| \|@LB@ 76 51@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -13.8583 kcal/mol@LB@Unfolding Energy - mRNA 2.68591 kcal/mol@LB@Unfolding Energy - sRNA 3.70263 kcal/mol@LB@@LB@Position - mRNA 180 -- 195@LB@Position - sRNA 52 -- 75@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 52 -- 58@LB@
153	0.00596	0.1368	b3892	fdoI	-11.89	0.036676	181 -- 200	31 -- 53	formate dehydrogenase-O cytochrome b556 subunit		_____________180_____________________201\n_____________\|_______________________\|\n5'-CCA...ACGAA___A___________________AUGAA...UGG-3'\n______________GAG_AAGACGA___GGAGCGCAA\n______________:\|\|_\|\|\|\|\|:\|___\|\|\|\|\|\|\|\|\|\n______________UUC_UUCUGUU___CCUCGCGUU\n3'-UUU...UUUCC___A_______AUA_________GCGGG...ACG-5'\n_____________\|_______________________\|\n_____________54______________________30\n	194 -- 200	31 -- 37	-24.6235 kcal/mol	2.95491 kcal/mol	9.77014 kcal/mol	180 201@LB@ \| \|@LB@5'-CCA...ACGAA A AUGAA...UGG-3'@LB@ GAG AAGACGA GGAGCGCAA@LB@ :\|\| \|\|\|\|\|:\| \|\|\|\|\|\|\|\|\|@LB@ UUC UUCUGUU CCUCGCGUU@LB@3'-UUU...UUUCC A AUA GCGGG...ACG-5'@LB@ \| \|@LB@ 54 30@LB@@LB@@LB@Energy -11.89 kcal/mol@LB@Hybridization Energy -24.6235 kcal/mol@LB@Unfolding Energy - mRNA 2.95491 kcal/mol@LB@Unfolding Energy - sRNA 9.77014 kcal/mol@LB@@LB@Position - mRNA 181 -- 200@LB@Position - sRNA 31 -- 53@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 31 -- 37@LB@
38	0.0003163	0.02889	b4315	fimI	-9.52	0.141947	182 -- 216	45 -- 80	fimbrial protein involved in type 1 pilus biosynthesis		_____________181___________________________________217\n_____________\|_____________________________________\|\n5'-UGC...CACCC______GAUAAAAAUAACGAU________________UAUUU...AAU-3'\n______________UUGUGC_______________GAAAAGGAAG__AGAU\n______________\|\|\|\|\|\|_______________:\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________AACACG_______________UUUUUCCUUC__UCUG\n3'-UUU...UAGUU______AUACGUCAUUAAGU___________AU____UUAUA...ACG-5'\n_____________\|_____________________________________\|\n_____________81____________________________________44\n	206 -- 212	51 -- 57	-20.4045 kcal/mol	5.26447 kcal/mol	5.61905 kcal/mol	181 217@LB@ \| \|@LB@5'-UGC...CACCC GAUAAAAAUAACGAU UAUUU...AAU-3'@LB@ UUGUGC GAAAAGGAAG AGAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ AACACG UUUUUCCUUC UCUG@LB@3'-UUU...UAGUU AUACGUCAUUAAGU AU UUAUA...ACG-5'@LB@ \| \|@LB@ 81 44@LB@@LB@@LB@Energy -9.52 kcal/mol@LB@Hybridization Energy -20.4045 kcal/mol@LB@Unfolding Energy - mRNA 5.26447 kcal/mol@LB@Unfolding Energy - sRNA 5.61905 kcal/mol@LB@@LB@Position - mRNA 182 -- 216@LB@Position - sRNA 45 -- 80@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 51 -- 57@LB@
7	8.167e-06	0.003921	b1531	marA	-12.70	0.022098	183 -- 204	40 -- 62	multiple antibiotic resistance transcriptional regulator		_____________182_____________________205\n_____________\|_______________________\|\n5'-AAG...GUAAA______________U________CCAGA...AGC-3'\n______________CAAAAAA_GAGGUA_GACGAUGU\n______________\|\|\|\|\|\|\|_\|\|:\|\|\|_\|\|\|:\|\|:\|\n______________GUUUUUU_CUUCAU_CUGUUAUA\n3'-UUU...AUUAA_______C______U________CCUCG...ACG-5'\n_____________\|_______________________\|\n_____________63______________________39\n	198 -- 204	40 -- 46	-19.9636 kcal/mol	3.18051 kcal/mol	4.08673 kcal/mol	182 205@LB@ \| \|@LB@5'-AAG...GUAAA U CCAGA...AGC-3'@LB@ CAAAAAA GAGGUA GACGAUGU@LB@ \|\|\|\|\|\|\| \|\|:\|\|\| \|\|\|:\|\|:\|@LB@ GUUUUUU CUUCAU CUGUUAUA@LB@3'-UUU...AUUAA C U CCUCG...ACG-5'@LB@ \| \|@LB@ 63 39@LB@@LB@@LB@Energy -12.70 kcal/mol@LB@Hybridization Energy -19.9636 kcal/mol@LB@Unfolding Energy - mRNA 3.18051 kcal/mol@LB@Unfolding Energy - sRNA 4.08673 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 40 -- 62@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 40 -- 46@LB@
57	0.0009345	0.05776	b3755	yieP	-11.62	0.043293	183 -- 203	41 -- 61	putative transcriptional regulator		_____________182____________________204\n_____________\|______________________\|\n5'-UUC...AAAAA___________A__________CCUUU...CCG-3'\n______________GAAAAAGGAAG_UAAG_UAAUG\n______________:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|_:\|\|\|:\n______________UUUUUUCCUUC_AUUC_GUUAU\n3'-UUU...UUAAG________________U_____ACCUC...ACG-5'\n_____________\|______________________\|\n_____________62_____________________40\n	187 -- 193	51 -- 57	-16.3745 kcal/mol	2.38082 kcal/mol	2.36907 kcal/mol	182 204@LB@ \| \|@LB@5'-UUC...AAAAA A CCUUU...CCG-3'@LB@ GAAAAAGGAAG UAAG UAAUG@LB@ :\|\|\|\|\|\|\|\|\|\| \|\|\|\| :\|\|\|:@LB@ UUUUUUCCUUC AUUC GUUAU@LB@3'-UUU...UUAAG U ACCUC...ACG-5'@LB@ \| \|@LB@ 62 40@LB@@LB@@LB@Energy -11.62 kcal/mol@LB@Hybridization Energy -16.3745 kcal/mol@LB@Unfolding Energy - mRNA 2.38082 kcal/mol@LB@Unfolding Energy - sRNA 2.36907 kcal/mol@LB@@LB@Position - mRNA 183 -- 203@LB@Position - sRNA 41 -- 61@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
69	0.001222	0.06239	b0699	ybfA	-13.19	0.016050	183 -- 205	37 -- 62	DUF2517 family protein		_____________182________________________206\n_____________\|__________________________\|\n5'-AUG...AGAUA____________AAA___________ACUCU...GGA-3'\n______________CAAAAGGGGGAG______AGUAUGGA\n______________\|\|\|\|\|::\|\|:\|\|______\|:\|\|\|\|\|\|\n______________GUUUUUUCCUUC______UUAUACCU\n3'-UUU...AUUAA____________AUUCUG________CGCGU...ACG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	199 -- 205	37 -- 43	-21.7 kcal/mol	3.27833 kcal/mol	5.2343 kcal/mol	182 206@LB@ \| \|@LB@5'-AUG...AGAUA AAA ACUCU...GGA-3'@LB@ CAAAAGGGGGAG AGUAUGGA@LB@ \|\|\|\|\|::\|\|:\|\| \|:\|\|\|\|\|\|@LB@ GUUUUUUCCUUC UUAUACCU@LB@3'-UUU...AUUAA AUUCUG CGCGU...ACG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -21.7 kcal/mol@LB@Unfolding Energy - mRNA 3.27833 kcal/mol@LB@Unfolding Energy - sRNA 5.2343 kcal/mol@LB@@LB@Position - mRNA 183 -- 205@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 37 -- 43@LB@
84	0.001972	0.08273	b0968	yccX	-8.34	0.253881	183 -- 226	2 -- 49	weak acylphosphatase		_____________182_________________________________________________227\n_____________\|___________________________________________________\|\n5'-GGC...CAUUA_______GGA_____A________G_AA__C___________AA_______GGUUU...CCG-3'\n______________AGGAUAA____GAGC_GCAAUGUC_A__GU_______UGCAU__UUGCCUG\n______________\|:\|\|:\|\|____\|\|\|\|_\|\|\|\|:\|:\|_\|__\|:_______\|\|\|\|\|__\|::\|\|\|\|\n______________UUCUGUU____CUCG_CGUUGCGG_U__CG_______ACGUA__AGUGGAC\n3'-UUU...CUUCA_______AUAC_____________G_AG__AACUGCA______________G-5'\n_____________\|___________________________________________________\|\n_____________50__________________________________________________1\n	220 -- 226	2 -- 8	-35.2137 kcal/mol	10.0937 kcal/mol	16.7804 kcal/mol	182 227@LB@ \| \|@LB@5'-GGC...CAUUA GGA A G AA C AA GGUUU...CCG-3'@LB@ AGGAUAA GAGC GCAAUGUC A GU UGCAU UUGCCUG@LB@ \|:\|\|:\|\| \|\|\|\| \|\|\|\|:\|:\| \| \|: \|\|\|\|\| \|::\|\|\|\|@LB@ UUCUGUU CUCG CGUUGCGG U CG ACGUA AGUGGAC@LB@3'-UUU...CUUCA AUAC G AG AACUGCA G-5'@LB@ \| \|@LB@ 50 1@LB@@LB@@LB@Energy -8.34 kcal/mol@LB@Hybridization Energy -35.2137 kcal/mol@LB@Unfolding Energy - mRNA 10.0937 kcal/mol@LB@Unfolding Energy - sRNA 16.7804 kcal/mol@LB@@LB@Position - mRNA 183 -- 226@LB@Position - sRNA 2 -- 49@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 2 -- 8@LB@
150	0.005897	0.1368	b0887	cydD	-10.72	0.073556	183 -- 190	1 -- 8	glutathione/cysteine ABC transporter export permease/ATPase		_____________182______191\n_____________\|________\|\n5'-AUU...AUAAC________UAAGC...UGA-3'\n______________UCACCUGC\n______________\|\|\|\|\|\|\|\|\n______________AGUGGACG\n3'-UUU...ACGUA________-5'\n_____________\|_______\|\n_____________9_______1\n	184 -- 190	1 -- 7	-15.001 kcal/mol	1.91816 kcal/mol	2.36381 kcal/mol	182 191@LB@ \| \|@LB@5'-AUU...AUAAC UAAGC...UGA-3'@LB@ UCACCUGC@LB@ \|\|\|\|\|\|\|\|@LB@ AGUGGACG@LB@3'-UUU...ACGUA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -10.72 kcal/mol@LB@Hybridization Energy -15.001 kcal/mol@LB@Unfolding Energy - mRNA 1.91816 kcal/mol@LB@Unfolding Energy - sRNA 2.36381 kcal/mol@LB@@LB@Position - mRNA 183 -- 190@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.0001471	0.01851	b0997	torA	-9.78	0.123932	184 -- 203	41 -- 60	trimethylamine N-oxide (TMAO) reductase I catalytic subunit	b3551 b1872	_____________183__________________204\n_____________\|____________________\|\n5'-UAC...GCGAU__________A__A______AACAA...CGC-3'\n______________AAGAAGGAAG_AA_AUAAUG\n______________\|\|:\|\|\|\|\|\|\|_\|\|_\|:\|\|\|:\n______________UUUUUCCUUC_UU_UGUUAU\n3'-UUU...UAAGU__________A__C______ACCUC...ACG-5'\n_____________\|____________________\|\n_____________61___________________40\n	187 -- 193	51 -- 57	-13.1224 kcal/mol	1.37417 kcal/mol	1.96633 kcal/mol	183 204@LB@ \| \|@LB@5'-UAC...GCGAU A A AACAA...CGC-3'@LB@ AAGAAGGAAG AA AUAAUG@LB@ \|\|:\|\|\|\|\|\|\| \|\| \|:\|\|\|:@LB@ UUUUUCCUUC UU UGUUAU@LB@3'-UUU...UAAGU A C ACCUC...ACG-5'@LB@ \| \|@LB@ 61 40@LB@@LB@@LB@Energy -9.78 kcal/mol@LB@Hybridization Energy -13.1224 kcal/mol@LB@Unfolding Energy - mRNA 1.37417 kcal/mol@LB@Unfolding Energy - sRNA 1.96633 kcal/mol@LB@@LB@Position - mRNA 184 -- 203@LB@Position - sRNA 41 -- 60@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 51 -- 57@LB@
98	0.003129	0.1114	b0357	frmR	-9.19	0.168108	184 -- 207	25 -- 48	regulator protein that represses frmRAB operon		_____________183______________________208\n_____________\|________________________\|\n5'-CUG...CAUGC________A__U___AA_______GUACU...CCG-3'\n______________AGAUGAUG_GG_GCG__AUGCCCA\n______________\|\|\|::\|\|:_\|\|_\|\|\|__\|:\|\|\|\|\|\n______________UCUGUUAU_CC_CGC__UGCGGGU\n3'-UUU...UUCAU________A__U___GU_______AGCGA...ACG-5'\n_____________\|________________________\|\n_____________49_______________________24\n	201 -- 207	25 -- 31	-27.7971 kcal/mol	6.33291 kcal/mol	12.271 kcal/mol	183 208@LB@ \| \|@LB@5'-CUG...CAUGC A U AA GUACU...CCG-3'@LB@ AGAUGAUG GG GCG AUGCCCA@LB@ \|\|\|::\|\|: \|\| \|\|\| \|:\|\|\|\|\|@LB@ UCUGUUAU CC CGC UGCGGGU@LB@3'-UUU...UUCAU A U GU AGCGA...ACG-5'@LB@ \| \|@LB@ 49 24@LB@@LB@@LB@Energy -9.19 kcal/mol@LB@Hybridization Energy -27.7971 kcal/mol@LB@Unfolding Energy - mRNA 6.33291 kcal/mol@LB@Unfolding Energy - sRNA 12.271 kcal/mol@LB@@LB@Position - mRNA 184 -- 207@LB@Position - sRNA 25 -- 48@LB@Position Seed - mRNA 201 -- 207@LB@Position Seed - sRNA 25 -- 31@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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