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	Additional homologs
52	0.004683	0.3024	b1130	phoP	-12.79	0.039529	186 -- 208	6 -- 31	response regulator in two-component regulatory system with PhoQ		_____________185________________________209\n_____________\|__________________________\|\n5'-GAG...UAAGA_________A________________ACUGG...CCA-3'\n______________CAGGGA_GA__AUAA_AAAUGCGCGU\n______________\|\|\|\|\|\|_\|\|__\|\|\|\|_\|\|\|\|\|\|\|\|\|\|\n______________GUCCCU_CU__UAUU_UUUACGCGCA\n3'-UUU...CUUAA______A__AC____G__________GAAAG-5'\n_____________\|__________________________\|\n_____________32_________________________5\n	202 -- 208	6 -- 12	-26.853 kcal/mol	6.30535 kcal/mol	7.75407 kcal/mol	185 209@LB@ \| \|@LB@5'-GAG...UAAGA A ACUGG...CCA-3'@LB@ CAGGGA GA AUAA AAAUGCGCGU@LB@ \|\|\|\|\|\| \|\| \|\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ GUCCCU CU UAUU UUUACGCGCA@LB@3'-UUU...CUUAA A AC G GAAAG-5'@LB@ \| \|@LB@ 32 5@LB@@LB@@LB@Energy -12.79 kcal/mol@LB@Hybridization Energy -26.853 kcal/mol@LB@Unfolding Energy - mRNA 6.30535 kcal/mol@LB@Unfolding Energy - sRNA 7.75407 kcal/mol@LB@@LB@Position - mRNA 186 -- 208@LB@Position - sRNA 6 -- 31@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 6 -- 12@LB@
144	0.01383	0.3104	b1135	rluE	-11.03	0.080673	174 -- 189	5 -- 20	23S rRNA pseudouridine(2457) synthase		_____________173______________190\n_____________\|________________\|\n5'-UGU...CCGUC____A___________AUUAG...AAC-3'\n______________AUGA_AGAUGCGCGUU\n______________\|\|:\|_\|:\|\|\|\|\|\|\|\|:\n______________UAUU_UUUACGCGCAG\n3'-UUU...ACUAC____G___________AAAG-5'\n_____________\|________________\|\n_____________21_______________4\n	183 -- 189	5 -- 11	-17.9797 kcal/mol	5.69694 kcal/mol	1.24804 kcal/mol	173 190@LB@ \| \|@LB@5'-UGU...CCGUC A AUUAG...AAC-3'@LB@ AUGA AGAUGCGCGUU@LB@ \|\|:\| \|:\|\|\|\|\|\|\|\|:@LB@ UAUU UUUACGCGCAG@LB@3'-UUU...ACUAC G AAAG-5'@LB@ \| \|@LB@ 21 4@LB@@LB@@LB@Energy -11.03 kcal/mol@LB@Hybridization Energy -17.9797 kcal/mol@LB@Unfolding Energy - mRNA 5.69694 kcal/mol@LB@Unfolding Energy - sRNA 1.24804 kcal/mol@LB@@LB@Position - mRNA 174 -- 189@LB@Position - sRNA 5 -- 20@LB@Position Seed - mRNA 183 -- 189@LB@Position Seed - sRNA 5 -- 11@LB@
68	0.006348	0.3087	b1202	ycgV	-6.40	0.429936	233 -- 244	4 -- 18	putative adhesin	b2647	_____________232_____________245\n_____________\|_______________\|\n5'-ACU...ACCAA_______________CGCUG...UUG-3'\n______________AGCAGAU___CGUCU\n______________\|:\|\|:\|\|___\|\|\|\|\|\n______________UUGUUUA___GCAGA\n3'-UUU...UACUA_______CGC_____AAG-5'\n_____________\|_______________\|\n_____________19______________3\n	233 -- 239	12 -- 18	-9.8712 kcal/mol	2.23703 kcal/mol	1.22995 kcal/mol	232 245@LB@ \| \|@LB@5'-ACU...ACCAA CGCUG...UUG-3'@LB@ AGCAGAU CGUCU@LB@ \|:\|\|:\|\| \|\|\|\|\|@LB@ UUGUUUA GCAGA@LB@3'-UUU...UACUA CGC AAG-5'@LB@ \| \|@LB@ 19 3@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -9.8712 kcal/mol@LB@Unfolding Energy - mRNA 2.23703 kcal/mol@LB@Unfolding Energy - sRNA 1.22995 kcal/mol@LB@@LB@Position - mRNA 233 -- 244@LB@Position - sRNA 4 -- 18@LB@Position Seed - mRNA 233 -- 239@LB@Position Seed - sRNA 12 -- 18@LB@
98	0.009835	0.3104	b1213	ychQ	-13.77	0.026325	164 -- 179	6 -- 23	SIRB family inner membrane protein		_____________163________________180\n_____________\|__________________\|\n5'-GAC...CUAUG__________________AACGC...AUC-3'\n______________GUGAUAACGA__GCGCGU\n______________:\|\|\|\|\|\|\|:\|__\|\|\|\|\|\|\n______________UACUAUUGUU__CGCGCA\n3'-UUU...CCUAC__________UA______GAAAG-5'\n_____________\|__________________\|\n_____________24_________________5\n	167 -- 173	14 -- 20	-20.3809 kcal/mol	4.08318 kcal/mol	2.52311 kcal/mol	163 180@LB@ \| \|@LB@5'-GAC...CUAUG AACGC...AUC-3'@LB@ GUGAUAACGA GCGCGU@LB@ :\|\|\|\|\|\|\|:\| \|\|\|\|\|\|@LB@ UACUAUUGUU CGCGCA@LB@3'-UUU...CCUAC UA GAAAG-5'@LB@ \| \|@LB@ 24 5@LB@@LB@@LB@Energy -13.77 kcal/mol@LB@Hybridization Energy -20.3809 kcal/mol@LB@Unfolding Energy - mRNA 4.08318 kcal/mol@LB@Unfolding Energy - sRNA 2.52311 kcal/mol@LB@@LB@Position - mRNA 164 -- 179@LB@Position - sRNA 6 -- 23@LB@Position Seed - mRNA 167 -- 173@LB@Position Seed - sRNA 14 -- 20@LB@
116	0.01184	0.3104	b1218	chaC	-12.45	0.045440	10 -- 29	8 -- 30	cation transport regulator		_____________9_______________________30\n_____________\|_______________________\|\n5'-AUA...GCCAA_______________________AUAAA...CGC-3'\n______________AGGG__GAUGAUGAUAAAUG_GC\n______________\|\|\|\|__\|\|\|\|\|\|:\|:\|\|\|\|\|_\|\|\n______________UCCC__CUACUAUUGUUUAC_CG\n3'-UUU...UUAAG____UA______________G__CAGAAAG-5'\n_____________\|_______________________\|\n_____________31______________________7\n	21 -- 27	11 -- 17	-25.0616 kcal/mol	5.19055 kcal/mol	7.41684 kcal/mol	9 30@LB@ \| \|@LB@5'-AUA...GCCAA AUAAA...CGC-3'@LB@ AGGG GAUGAUGAUAAAUG GC@LB@ \|\|\|\| \|\|\|\|\|\|:\|:\|\|\|\|\| \|\|@LB@ UCCC CUACUAUUGUUUAC CG@LB@3'-UUU...UUAAG UA G CAGAAAG-5'@LB@ \| \|@LB@ 31 7@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -25.0616 kcal/mol@LB@Unfolding Energy - mRNA 5.19055 kcal/mol@LB@Unfolding Energy - sRNA 7.41684 kcal/mol@LB@@LB@Position - mRNA 10 -- 29@LB@Position - sRNA 8 -- 30@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 11 -- 17@LB@
62	0.005646	0.3084	b1242	ychE	-13.92	0.024785	141 -- 151	1 -- 11	UPF0056 family inner membrane protein		_____________140_________152\n_____________\|___________\|\n5'-CAU...UGUCA___________CAACC...GCA-3'\n______________GCGCGUCUUUU\n______________\|\|\|\|\|\|\|\|\|\|:\n______________CGCGCAGAAAG\n3'-UUU...GUUUA___________-5'\n_____________\|__________\|\n_____________12_________1\n	145 -- 151	1 -- 7	-17.9236 kcal/mol	2.83374 kcal/mol	1.17076 kcal/mol	140 152@LB@ \| \|@LB@5'-CAU...UGUCA CAACC...GCA-3'@LB@ GCGCGUCUUUU@LB@ \|\|\|\|\|\|\|\|\|\|:@LB@ CGCGCAGAAAG@LB@3'-UUU...GUUUA -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -13.92 kcal/mol@LB@Hybridization Energy -17.9236 kcal/mol@LB@Unfolding Energy - mRNA 2.83374 kcal/mol@LB@Unfolding Energy - sRNA 1.17076 kcal/mol@LB@@LB@Position - mRNA 141 -- 151@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 1 -- 7@LB@
139	0.01337	0.3104	b1255	yciC	-11.25	0.074167	287 -- 299	1 -- 13	UPF0259 family inner membrane protein		_____________286___________300\n_____________\|_____________\|\n5'-AAU...UUGCU__________A__A-3'\n______________AUGUGCGUUU_UC\n______________\|\|\|:\|\|\|\|:\|_\|\|\n______________UACGCGCAGA_AG\n3'-UUU...UUGUU__________A__-5'\n_____________\|____________\|\n_____________14___________1\n	290 -- 296	4 -- 10	-15.0519 kcal/mol	2.63141 kcal/mol	1.17519 kcal/mol	286 300@LB@ \| \|@LB@5'-AAU...UUGCU A A-3'@LB@ AUGUGCGUUU UC@LB@ \|\|\|:\|\|\|\|:\| \|\|@LB@ UACGCGCAGA AG@LB@3'-UUU...UUGUU A -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -15.0519 kcal/mol@LB@Unfolding Energy - mRNA 2.63141 kcal/mol@LB@Unfolding Energy - sRNA 1.17519 kcal/mol@LB@@LB@Position - mRNA 287 -- 299@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 290 -- 296@LB@Position Seed - sRNA 4 -- 10@LB@
113	0.01159	0.3104	b1279	yciS	-9.20	0.164515	90 -- 101	6 -- 18	DUF1049 family inner membrane protein function unknown		_____________89____________102\n_____________\|_____________\|\n5'-ACC...UCAUC_____________GGAUG...UGU-3'\n______________AAC_AAUGCGUGU\n______________\|\|\|_\|\|\|\|\|\|:\|\|\n______________UUG_UUACGCGCA\n3'-UUU...UACUA___U_________GAAAG-5'\n_____________\|_____________\|\n_____________19____________5\n	95 -- 101	6 -- 12	-13.4585 kcal/mol	3.04139 kcal/mol	1.21878 kcal/mol	89 102@LB@ \| \|@LB@5'-ACC...UCAUC GGAUG...UGU-3'@LB@ AAC AAUGCGUGU@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ UUG UUACGCGCA@LB@3'-UUU...UACUA U GAAAG-5'@LB@ \| \|@LB@ 19 5@LB@@LB@@LB@Energy -9.20 kcal/mol@LB@Hybridization Energy -13.4585 kcal/mol@LB@Unfolding Energy - mRNA 3.04139 kcal/mol@LB@Unfolding Energy - sRNA 1.21878 kcal/mol@LB@@LB@Position - mRNA 90 -- 101@LB@Position - sRNA 6 -- 18@LB@Position Seed - mRNA 95 -- 101@LB@Position Seed - sRNA 6 -- 12@LB@
97	0.009805	0.3104	b1306	pspC	-10.74	0.090670	128 -- 139	7 -- 18	psp operon transcription co-activator		_____________127__________140\n_____________\|____________\|\n5'-CCG...AGCAA____________AACGU...CGG-3'\n______________AACGGAUGCGCG\n______________\|\|\|::\|\|\|\|\|\|\|\n______________UUGUUUACGCGC\n3'-UUU...UACUA____________AGAAAG-5'\n_____________\|____________\|\n_____________19___________6\n	133 -- 139	7 -- 13	-18.5075 kcal/mol	6.55818 kcal/mol	1.20891 kcal/mol	127 140@LB@ \| \|@LB@5'-CCG...AGCAA AACGU...CGG-3'@LB@ AACGGAUGCGCG@LB@ \|\|\|::\|\|\|\|\|\|\|@LB@ UUGUUUACGCGC@LB@3'-UUU...UACUA AGAAAG-5'@LB@ \| \|@LB@ 19 6@LB@@LB@@LB@Energy -10.74 kcal/mol@LB@Hybridization Energy -18.5075 kcal/mol@LB@Unfolding Energy - mRNA 6.55818 kcal/mol@LB@Unfolding Energy - sRNA 1.20891 kcal/mol@LB@@LB@Position - mRNA 128 -- 139@LB@Position - sRNA 7 -- 18@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 7 -- 13@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@

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)

Job resubmission

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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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