Input and runtime details for job 6793193 (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 6793193 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:27:03 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:32 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:26:02 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:26:10 CET 2018
	Job Completed		@ Fri Feb 16 21:26:45 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

Description of the job

RprA

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
53	0.001859	0.1218	b0529	folD	-11.41	0.136116	200 -- 226	61 -- 85	bifunctional 5 10-methylene-tetrahydrofolate dehydrogenase/ 5 10-methylene-tetrahydrofolate cyclohydrolase		_____________199_________________________227\n_____________\|___________________________\|\n5'-CAA...UCUCU_____CA___________UG_______AACGA...CAC-3'\n______________GAUGG__GCAAAGAUUAU__ACGGUAA\n______________\|\|\|\|\|__\|\|\|\|\|\|\|:\|\|:__\|\|:\|:\|\|\n______________CUACC__CGUUUCUGAUG__UGUCGUU\n3'-UUU...ACCCU__________________UG_______AAGCA...GCA-5'\n_____________\|___________________________\|\n_____________86__________________________60\n	220 -- 226	61 -- 67	-27.4215 kcal/mol	5.77154 kcal/mol	10.2439 kcal/mol	199 227@LB@ \| \|@LB@5'-CAA...UCUCU CA UG AACGA...CAC-3'@LB@ GAUGG GCAAAGAUUAU ACGGUAA@LB@ \|\|\|\|\| \|\|\|\|\|\|\|:\|\|: \|\|:\|:\|\|@LB@ CUACC CGUUUCUGAUG UGUCGUU@LB@3'-UUU...ACCCU UG AAGCA...GCA-5'@LB@ \| \|@LB@ 86 60@LB@@LB@@LB@Energy -11.41 kcal/mol@LB@Hybridization Energy -27.4215 kcal/mol@LB@Unfolding Energy - mRNA 5.77154 kcal/mol@LB@Unfolding Energy - sRNA 10.2439 kcal/mol@LB@@LB@Position - mRNA 200 -- 226@LB@Position - sRNA 61 -- 85@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 61 -- 67@LB@
113	0.004991	0.1545	b0888	trxB	-9.59	0.285839	209 -- 223	61 -- 75	thioredoxin reductase FAD/NAD(P)-binding		_____________208_____________224\n_____________\|_______________\|\n5'-AAC...GGCAC___CAA_________ACUGC...UGC-3'\n______________GAC___ACACAGUAA\n______________\|\|\|___\|\|\|\|\|\|:\|\|\n______________CUG___UGUGUCGUU\n3'-UUU...CGUUU___AUG_________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	217 -- 223	61 -- 67	-15.4977 kcal/mol	2.65453 kcal/mol	3.25399 kcal/mol	208 224@LB@ \| \|@LB@5'-AAC...GGCAC CAA ACUGC...UGC-3'@LB@ GAC ACACAGUAA@LB@ \|\|\| \|\|\|\|\|\|:\|\|@LB@ CUG UGUGUCGUU@LB@3'-UUU...CGUUU AUG AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4977 kcal/mol@LB@Unfolding Energy - mRNA 2.65453 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 209 -- 223@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 217 -- 223@LB@Position Seed - sRNA 61 -- 67@LB@
129	0.005822	0.1577	b0713	ybgL	-14.99	0.021088	226 -- 247	61 -- 83	UPF0271 family protein		_____________225_____________________248\n_____________\|_______________________\|\n5'-GCC...CGAUC_______________________CGCAG...AUG-3'\n______________UGGGCGAAGGCUGCGC_CAGCGA\n______________\|\|\|\|\|:\|\|\|:\|\|:\|:\|_\|\|\|\|:\|\n______________ACCCGUUUCUGAUGUG_GUCGUU\n3'-UUU...CCUCU________________U______AAGCA...GCA-5'\n_____________\|_______________________\|\n_____________84______________________60\n	234 -- 240	69 -- 75	-36.9571 kcal/mol	11.7384 kcal/mol	10.2322 kcal/mol	225 248@LB@ \| \|@LB@5'-GCC...CGAUC CGCAG...AUG-3'@LB@ UGGGCGAAGGCUGCGC CAGCGA@LB@ \|\|\|\|\|:\|\|\|:\|\|:\|:\| \|\|\|\|:\|@LB@ ACCCGUUUCUGAUGUG GUCGUU@LB@3'-UUU...CCUCU U AAGCA...GCA-5'@LB@ \| \|@LB@ 84 60@LB@@LB@@LB@Energy -14.99 kcal/mol@LB@Hybridization Energy -36.9571 kcal/mol@LB@Unfolding Energy - mRNA 11.7384 kcal/mol@LB@Unfolding Energy - sRNA 10.2322 kcal/mol@LB@@LB@Position - mRNA 226 -- 247@LB@Position - sRNA 61 -- 83@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 69 -- 75@LB@
136	0.006258	0.1605	b0219	yafV	-11.82	0.112632	212 -- 233	61 -- 78	putative NAD(P)-binding C-N hydrolase family amidase		_____________211____________________234\n_____________\|______________________\|\n5'-GUC...GGUUU___________UUUU_______CCACU...CCG-3'\n______________GAAGAUUACGC____GCAGCAA\n______________:\|\|\|\|:\|\|\|:\|____:\|\|\|\|\|\|\n______________UUUCUGAUGUG____UGUCGUU\n3'-UUU...ACCCG______________________AAGCA...GCA-5'\n_____________\|______________________\|\n_____________79_____________________60\n	227 -- 233	61 -- 67	-20.0989 kcal/mol	5.01896 kcal/mol	3.25783 kcal/mol	211 234@LB@ \| \|@LB@5'-GUC...GGUUU UUUU CCACU...CCG-3'@LB@ GAAGAUUACGC GCAGCAA@LB@ :\|\|\|\|:\|\|\|:\| :\|\|\|\|\|\|@LB@ UUUCUGAUGUG UGUCGUU@LB@3'-UUU...ACCCG AAGCA...GCA-5'@LB@ \| \|@LB@ 79 60@LB@@LB@@LB@Energy -11.82 kcal/mol@LB@Hybridization Energy -20.0989 kcal/mol@LB@Unfolding Energy - mRNA 5.01896 kcal/mol@LB@Unfolding Energy - sRNA 3.25783 kcal/mol@LB@@LB@Position - mRNA 212 -- 233@LB@Position - sRNA 61 -- 78@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 61 -- 67@LB@
138	0.006392	0.1605	b0345	lacI	-7.62	0.533808	7 -- 17	61 -- 71	lactose-inducible lac operon transcriptional repressor		_____________6___________18\n_____________\|___________\|\n_____5'-CAUUGA___G_______AAAAG...AAA-3'\n______________ACA_GCAGCGG\n______________\|\|\|_:\|\|\|\|::\n______________UGU_UGUCGUU\n3'-UUU...UCUGA___G_______AAGCA...GCA-5'\n_____________\|___________\|\n_____________72__________60\n	11 -- 17	61 -- 67	-13.1569 kcal/mol	2.35774 kcal/mol	3.17655 kcal/mol	6 18@LB@ \| \|@LB@ 5'-CAUUGA G AAAAG...AAA-3'@LB@ ACA GCAGCGG@LB@ \|\|\| :\|\|\|\|::@LB@ UGU UGUCGUU@LB@3'-UUU...UCUGA G AAGCA...GCA-5'@LB@ \| \|@LB@ 72 60@LB@@LB@@LB@Energy -7.62 kcal/mol@LB@Hybridization Energy -13.1569 kcal/mol@LB@Unfolding Energy - mRNA 2.35774 kcal/mol@LB@Unfolding Energy - sRNA 3.17655 kcal/mol@LB@@LB@Position - mRNA 7 -- 17@LB@Position - sRNA 61 -- 71@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 61 -- 67@LB@
145	0.006641	0.1605	b3316	rpsS	-10.41	0.208024	125 -- 141	61 -- 77	30S ribosomal subunit protein S19		_____________124_______________142\n_____________\|_________________\|\n5'-GCG...AAGGU____AG__C________CAAGC...CUU-3'\n______________AAGA__AC_CGCAGCAA\n______________\|\|\|\|__\|\|_\|:\|\|\|\|\|\|\n______________UUCU__UG_GUGUCGUU\n3'-UUU...CCCGU____GA__U________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________78________________60\n	135 -- 141	61 -- 67	-16.0034 kcal/mol	2.33428 kcal/mol	3.25748 kcal/mol	124 142@LB@ \| \|@LB@5'-GCG...AAGGU AG C CAAGC...CUU-3'@LB@ AAGA AC CGCAGCAA@LB@ \|\|\|\| \|\| \|:\|\|\|\|\|\|@LB@ UUCU UG GUGUCGUU@LB@3'-UUU...CCCGU GA U AAGCA...GCA-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -10.41 kcal/mol@LB@Hybridization Energy -16.0034 kcal/mol@LB@Unfolding Energy - mRNA 2.33428 kcal/mol@LB@Unfolding Energy - sRNA 3.25748 kcal/mol@LB@@LB@Position - mRNA 125 -- 141@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 61 -- 67@LB@
146	0.006661	0.1605	b4479	dgoR	-11.67	0.120911	94 -- 106	61 -- 74	D-galactonate catabolism operon transcriptional repressor		_____________93_____________107\n_____________\|______________\|\n5'-UUU...ACAUU______________ACGCG...AAC-3'\n______________AC_ACGCACGGCAA\n______________\|\|_\|\|:\|\|\|:\|\|\|\|\n______________UG_UGUGUGUCGUU\n3'-UUU...GUUUC__A___________AAGCA...GCA-5'\n_____________\|______________\|\n_____________75_____________60\n	100 -- 106	61 -- 67	-16.8512 kcal/mol	1.93692 kcal/mol	3.24589 kcal/mol	93 107@LB@ \| \|@LB@5'-UUU...ACAUU ACGCG...AAC-3'@LB@ AC ACGCACGGCAA@LB@ \|\| \|\|:\|\|\|:\|\|\|\|@LB@ UG UGUGUGUCGUU@LB@3'-UUU...GUUUC A AAGCA...GCA-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -11.67 kcal/mol@LB@Hybridization Energy -16.8512 kcal/mol@LB@Unfolding Energy - mRNA 1.93692 kcal/mol@LB@Unfolding Energy - sRNA 3.24589 kcal/mol@LB@@LB@Position - mRNA 94 -- 106@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 61 -- 67@LB@
158	0.007677	0.1668	b1267	yciO	-9.92	0.252655	228 -- 242	61 -- 75	putative RNA binding protein		_____________227_____________243\n_____________\|_______________\|\n5'-GCG...AUCCU___A__C________CGUCU...CAA-3'\n______________GAU_AC_CACAGCAA\n______________\|\|:_\|\|_\|\|\|\|\|\|\|\|\n______________CUG_UG_GUGUCGUU\n3'-UUU...CGUUU___A__U________AAGCA...GCA-5'\n_____________\|_______________\|\n_____________76______________60\n	236 -- 242	61 -- 67	-14.6343 kcal/mol	1.46218 kcal/mol	3.25399 kcal/mol	227 243@LB@ \| \|@LB@5'-GCG...AUCCU A C CGUCU...CAA-3'@LB@ GAU AC CACAGCAA@LB@ \|\|: \|\| \|\|\|\|\|\|\|\|@LB@ CUG UG GUGUCGUU@LB@3'-UUU...CGUUU A U AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -14.6343 kcal/mol@LB@Unfolding Energy - mRNA 1.46218 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 228 -- 242@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 236 -- 242@LB@Position Seed - sRNA 61 -- 67@LB@
169	0.008352	0.1723	b1222	narX	-15.18	0.018797	58 -- 74	61 -- 75	sensory histidine kinase in two-component regulatory system with NarL		_____________57________________75\n_____________\|_________________\|\n5'-AAA...AAAGC_____AC__________AUAAG...CUG-3'\n______________GACUA__CACACGGCAA\n______________\|\|\|\|\|__\|\|\|\|\|:\|\|\|\|\n______________CUGAU__GUGUGUCGUU\n3'-UUU...CGUUU_________________AAGCA...GCA-5'\n_____________\|_________________\|\n_____________76________________60\n	68 -- 74	61 -- 67	-20.5903 kcal/mol	2.1582 kcal/mol	3.25399 kcal/mol	57 75@LB@ \| \|@LB@5'-AAA...AAAGC AC AUAAG...CUG-3'@LB@ GACUA CACACGGCAA@LB@ \|\|\|\|\| \|\|\|\|\|:\|\|\|\|@LB@ CUGAU GUGUGUCGUU@LB@3'-UUU...CGUUU AAGCA...GCA-5'@LB@ \| \|@LB@ 76 60@LB@@LB@@LB@Energy -15.18 kcal/mol@LB@Hybridization Energy -20.5903 kcal/mol@LB@Unfolding Energy - mRNA 2.1582 kcal/mol@LB@Unfolding Energy - sRNA 3.25399 kcal/mol@LB@@LB@Position - mRNA 58 -- 74@LB@Position - sRNA 61 -- 75@LB@Position Seed - mRNA 68 -- 74@LB@Position Seed - sRNA 61 -- 67@LB@
35	0.0005607	0.05638	b1434	ydcN	-11.45	0.133710	242 -- 253	62 -- 74	putative DNA-binding transcriptional regulator	b1508 b1299	_____________241___________254\n_____________\|_____________\|\n5'-CGG...AAACA_____________GCGCG...CUA-3'\n______________ACUACGC_CAGCA\n______________\|\|\|\|\|:\|_\|\|\|\|\|\n______________UGAUGUG_GUCGU\n3'-UUU...GUUUC_______U_____UAAGC...GCA-5'\n_____________\|_____________\|\n_____________75____________61\n	242 -- 248	68 -- 74	-17.054 kcal/mol	2.36402 kcal/mol	3.24359 kcal/mol	241 254@LB@ \| \|@LB@5'-CGG...AAACA GCGCG...CUA-3'@LB@ ACUACGC CAGCA@LB@ \|\|\|\|\|:\| \|\|\|\|\|@LB@ UGAUGUG GUCGU@LB@3'-UUU...GUUUC U UAAGC...GCA-5'@LB@ \| \|@LB@ 75 61@LB@@LB@@LB@Energy -11.45 kcal/mol@LB@Hybridization Energy -17.054 kcal/mol@LB@Unfolding Energy - mRNA 2.36402 kcal/mol@LB@Unfolding Energy - sRNA 3.24359 kcal/mol@LB@@LB@Position - mRNA 242 -- 253@LB@Position - sRNA 62 -- 74@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 68 -- 74@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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