Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
65	0.01282	0.5385	b0589	fepG	-12.08	0.045738	8 -- 17	74 -- 83	iron-enterobactin ABC transporter permease	_____________7__________18\n_____________\|__________\|\n____5'-CAUAUGG__________GGUGG...CGC-3'\n______________CGCGUUGGCU\n______________\|:\|\|\|\|\|\|\|\|\n______________GUGCAACCGA\n3'-CGC...UUCAA__________AAUCA...AAG-5'\n_____________\|__________\|\n_____________84_________73\n	11 -- 17	74 -- 80	-17.1529 kcal/mol	4.57841 kcal/mol	0.494551 kcal/mol	7 18@LB@ \| \|@LB@ 5'-CAUAUGG GGUGG...CGC-3'@LB@ CGCGUUGGCU@LB@ \|:\|\|\|\|\|\|\|\|@LB@ GUGCAACCGA@LB@3'-CGC...UUCAA AAUCA...AAG-5'@LB@ \| \|@LB@ 84 73@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -17.1529 kcal/mol@LB@Unfolding Energy - mRNA 4.57841 kcal/mol@LB@Unfolding Energy - sRNA 0.494551 kcal/mol@LB@@LB@Position - mRNA 8 -- 17@LB@Position - sRNA 74 -- 83@LB@Position Seed - mRNA 11 -- 17@LB@Position Seed - sRNA 74 -- 80@LB@
91	0.0156	0.5385	b0881	clpS	-13.09	0.030255	248 -- 265	74 -- 90	regulatory protein for ClpA substrate specificity	_____________247________________266\n_____________\|__________________\|\n5'-GCA...GAAGA___________AC_C___AAAAC...UCA-3'\n______________AAAAGUUCGCG__G_GCU\n______________\|\|\|\|\|\|\|\|:\|\|__\|_\|\|\|\n______________UUUUCAAGUGC__C_CGA\n3'-CGC...AGGCG___________AA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	252 -- 258	80 -- 86	-16.9257 kcal/mol	3.31752 kcal/mol	0.517587 kcal/mol	247 266@LB@ \| \|@LB@5'-GCA...GAAGA AC C AAAAC...UCA-3'@LB@ AAAAGUUCGCG G GCU@LB@ \|\|\|\|\|\|\|\|:\|\| \| \|\|\|@LB@ UUUUCAAGUGC C CGA@LB@3'-CGC...AGGCG AA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -13.09 kcal/mol@LB@Hybridization Energy -16.9257 kcal/mol@LB@Unfolding Energy - mRNA 3.31752 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 248 -- 265@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 252 -- 258@LB@Position Seed - sRNA 80 -- 86@LB@
96	0.0164	0.5385	b2670	alaE	-9.59	0.124335	245 -- 257	74 -- 86	alanine exporter alanine-inducible stress-responsive	_____________244___________258\n_____________\|_____________\|\n5'-CGG...GAUAC_______A_____GUUUA...UCU-3'\n______________GUUCGCG_UGGUU\n______________\|\|\|\|:\|\|_\|\|\|:\|\n______________CAAGUGC_ACCGA\n3'-CGC...GUUUU_______A_____AAUCA...AAG-5'\n_____________\|_____________\|\n_____________87____________73\n	245 -- 251	80 -- 86	-15.4589 kcal/mol	5.35611 kcal/mol	0.513318 kcal/mol	244 258@LB@ \| \|@LB@5'-CGG...GAUAC A GUUUA...UCU-3'@LB@ GUUCGCG UGGUU@LB@ \|\|\|\|:\|\| \|\|\|:\|@LB@ CAAGUGC ACCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -15.4589 kcal/mol@LB@Unfolding Energy - mRNA 5.35611 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 245 -- 257@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 80 -- 86@LB@
111	0.01894	0.5385	b2600	tyrA	-7.88	0.238290	191 -- 206	74 -- 89	fused chorismate mutase T/prephenate dehydrogenase	_____________190______________207\n_____________\|________________\|\n5'-UCG...CUUAA_________UA_____GCUGA...UGG-3'\n______________GAGGUUUAU__UGGUU\n______________:\|:\|\|\|:\|:__\|\|\|:\|\n______________UUUCAAGUG__ACCGA\n3'-CGC...GGCGU_________CA_____AAUCA...AAG-5'\n_____________\|________________\|\n_____________90_______________73\n	193 -- 199	81 -- 87	-12.4695 kcal/mol	4.06959 kcal/mol	0.517373 kcal/mol	190 207@LB@ \| \|@LB@5'-UCG...CUUAA UA GCUGA...UGG-3'@LB@ GAGGUUUAU UGGUU@LB@ :\|:\|\|\|:\|: \|\|\|:\|@LB@ UUUCAAGUG ACCGA@LB@3'-CGC...GGCGU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 90 73@LB@@LB@@LB@Energy -7.88 kcal/mol@LB@Hybridization Energy -12.4695 kcal/mol@LB@Unfolding Energy - mRNA 4.06959 kcal/mol@LB@Unfolding Energy - sRNA 0.517373 kcal/mol@LB@@LB@Position - mRNA 191 -- 206@LB@Position - sRNA 74 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 81 -- 87@LB@
136	0.02309	0.5385	b3223	nanE	-8.63	0.180292	34 -- 47	74 -- 86	putative N-acetylmannosamine-6-P epimerase	_____________33_____________48\n_____________\|______________\|\n5'-AUC...CUCGC_____G________GCGCC...AAA-3'\n______________GUUCA_CGUUGGUU\n______________\|\|\|\|\|_\|\|\|\|\|\|:\|\n______________CAAGU_GCAACCGA\n3'-CGC...GUUUU______________AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	41 -- 47	74 -- 80	-15.9355 kcal/mol	6.79344 kcal/mol	0.513318 kcal/mol	33 48@LB@ \| \|@LB@5'-AUC...CUCGC G GCGCC...AAA-3'@LB@ GUUCA CGUUGGUU@LB@ \|\|\|\|\| \|\|\|\|\|\|:\|@LB@ CAAGU GCAACCGA@LB@3'-CGC...GUUUU AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -8.63 kcal/mol@LB@Hybridization Energy -15.9355 kcal/mol@LB@Unfolding Energy - mRNA 6.79344 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 34 -- 47@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 74 -- 80@LB@
151	0.02561	0.5485	b4041	plsB	-9.39	0.134646	197 -- 210	74 -- 86	glycerol-3-phosphate O-acyltransferase	_____________196____________211\n_____________\|______________\|\n5'-UCG...ACAUC________CC____GGCCA...UGG-3'\n______________GUUUAUGU__GGCU\n______________\|\|\|:\|:\|\|__\|\|\|\|\n______________CAAGUGCA__CCGA\n3'-CGC...GUUUU________A_____AAUCA...AAG-5'\n_____________\|______________\|\n_____________87_____________73\n	198 -- 204	79 -- 85	-13.0466 kcal/mol	3.14742 kcal/mol	0.513318 kcal/mol	196 211@LB@ \| \|@LB@5'-UCG...ACAUC CC GGCCA...UGG-3'@LB@ GUUUAUGU GGCU@LB@ \|\|\|:\|:\|\| \|\|\|\|@LB@ CAAGUGCA CCGA@LB@3'-CGC...GUUUU A AAUCA...AAG-5'@LB@ \| \|@LB@ 87 73@LB@@LB@@LB@Energy -9.39 kcal/mol@LB@Hybridization Energy -13.0466 kcal/mol@LB@Unfolding Energy - mRNA 3.14742 kcal/mol@LB@Unfolding Energy - sRNA 0.513318 kcal/mol@LB@@LB@Position - mRNA 197 -- 210@LB@Position - sRNA 74 -- 86@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 79 -- 85@LB@
152	0.02564	0.5485	b0887	cydD	-10.22	0.096853	263 -- 271	74 -- 82	glutathione/cysteine ABC transporter export permease/ATPase	_____________262_______272\n_____________\|_________\|\n5'-AUU...UCCCA_________GAAUA...UGA-3'\n______________ACGUUGGCU\n______________\|\|\|\|\|\|\|\|\|\n______________UGCAACCGA\n3'-CGC...UCAAG_________AAUCA...AAG-5'\n_____________\|_________\|\n_____________83________73\n	265 -- 271	74 -- 80	-15.056 kcal/mol	4.4924 kcal/mol	0.342466 kcal/mol	262 272@LB@ \| \|@LB@5'-AUU...UCCCA GAAUA...UGA-3'@LB@ ACGUUGGCU@LB@ \|\|\|\|\|\|\|\|\|@LB@ UGCAACCGA@LB@3'-CGC...UCAAG AAUCA...AAG-5'@LB@ \| \|@LB@ 83 73@LB@@LB@@LB@Energy -10.22 kcal/mol@LB@Hybridization Energy -15.056 kcal/mol@LB@Unfolding Energy - mRNA 4.4924 kcal/mol@LB@Unfolding Energy - sRNA 0.342466 kcal/mol@LB@@LB@Position - mRNA 263 -- 271@LB@Position - sRNA 74 -- 82@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 74 -- 80@LB@
153	0.02565	0.5485	b2764	cysJ	-8.62	0.180864	16 -- 26	74 -- 84	sulfite reductase alpha subunit flavoprotein	_____________15__________27\n_____________\|___________\|\n5'-UUC...UUUCA___G_______AAUCU...UUG-3'\n______________UUA_GUUGGUU\n______________\|:\|_\|\|\|\|\|:\|\n______________AGU_CAACCGA\n3'-CGC...UUUCA___G_______AAUCA...AAG-5'\n_____________\|___________\|\n_____________85__________73\n	20 -- 26	74 -- 80	-11.948 kcal/mol	2.81948 kcal/mol	0.508159 kcal/mol	15 27@LB@ \| \|@LB@5'-UUC...UUUCA G AAUCU...UUG-3'@LB@ UUA GUUGGUU@LB@ \|:\| \|\|\|\|\|:\|@LB@ AGU CAACCGA@LB@3'-CGC...UUUCA G AAUCA...AAG-5'@LB@ \| \|@LB@ 85 73@LB@@LB@@LB@Energy -8.62 kcal/mol@LB@Hybridization Energy -11.948 kcal/mol@LB@Unfolding Energy - mRNA 2.81948 kcal/mol@LB@Unfolding Energy - sRNA 0.508159 kcal/mol@LB@@LB@Position - mRNA 16 -- 26@LB@Position - sRNA 74 -- 84@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 74 -- 80@LB@
180	0.03162	0.5559	b1941	fliI	-9.97	0.106944	57 -- 70	74 -- 88	flagellum-specific ATP synthase	_____________56______________71\n_____________\|_______________\|\n5'-CUG...ACCUU________A______GGCGC...GCG-3'\n______________AAGUUUGC__UGGCU\n______________\|\|\|\|\|::\|__\|\|\|\|\|\n______________UUCAAGUG__ACCGA\n3'-CGC...GCGUU________CA_____AAUCA...AAG-5'\n_____________\|_______________\|\n_____________89______________73\n	58 -- 64	81 -- 87	-13.0478 kcal/mol	2.55971 kcal/mol	0.516514 kcal/mol	56 71@LB@ \| \|@LB@5'-CUG...ACCUU A GGCGC...GCG-3'@LB@ AAGUUUGC UGGCU@LB@ \|\|\|\|\|::\| \|\|\|\|\|@LB@ UUCAAGUG ACCGA@LB@3'-CGC...GCGUU CA AAUCA...AAG-5'@LB@ \| \|@LB@ 89 73@LB@@LB@@LB@Energy -9.97 kcal/mol@LB@Hybridization Energy -13.0478 kcal/mol@LB@Unfolding Energy - mRNA 2.55971 kcal/mol@LB@Unfolding Energy - sRNA 0.516514 kcal/mol@LB@@LB@Position - mRNA 57 -- 70@LB@Position - sRNA 74 -- 88@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 81 -- 87@LB@
184	0.03259	0.5559	b0811	glnH	-9.61	0.123139	215 -- 230	74 -- 90	glutamine transporter subunit	_____________214________________231\n_____________\|__________________\|\n5'-AUC...GUAUU_______U__________GCACU...CCG-3'\n______________AAAAGUU_CAC__UGGCU\n______________\|\|\|\|\|\|\|_\|\|\|__\|\|\|\|\|\n______________UUUUCAA_GUG__ACCGA\n3'-CGC...AGGCG___________CA_____AAUCA...AAG-5'\n_____________\|__________________\|\n_____________91_________________73\n	215 -- 221	84 -- 90	-14.2101 kcal/mol	4.07847 kcal/mol	0.517587 kcal/mol	214 231@LB@ \| \|@LB@5'-AUC...GUAUU U GCACU...CCG-3'@LB@ AAAAGUU CAC UGGCU@LB@ \|\|\|\|\|\|\| \|\|\| \|\|\|\|\|@LB@ UUUUCAA GUG ACCGA@LB@3'-CGC...AGGCG CA AAUCA...AAG-5'@LB@ \| \|@LB@ 91 73@LB@@LB@@LB@Energy -9.61 kcal/mol@LB@Hybridization Energy -14.2101 kcal/mol@LB@Unfolding Energy - mRNA 4.07847 kcal/mol@LB@Unfolding Energy - sRNA 0.517587 kcal/mol@LB@@LB@Position - mRNA 215 -- 230@LB@Position - sRNA 74 -- 90@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 84 -- 90@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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