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@
31	0.005384	0.5385	b0159	mtn	-14.65	0.015942	9 -- 52	71 -- 108	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase	_____________8____________________________________________53\n_____________\|____________________________________________\|\n___5'-GAUACGCC__C____G__CUC_A____________UC_______C_______ACGCC...UCU-3'\n______________CG_GAUC_CU___G_AGAUCCGCAGGA__UCAUGUU_GGUUUUA\n______________\|\|_\|\|\|\|_\|\|___\|_\|\|\|\|\|\|\|\|\|::\|__\|\|\|:\|\|\|_\|\|:\|\|\|\|\n______________GC_CUAG_GA___C_UCUAGGCGUUUU__AGUGCAA_CCGAAAU\n__________3'-C__________C________________CA_______________CAAUA...AAG-5'\n_____________\|____________________________________________\|\n_____________109__________________________________________70\n	46 -- 52	71 -- 77	-39.2779 kcal/mol	12.7007 kcal/mol	11.9275 kcal/mol	8 53@LB@ \| \|@LB@ 5'-GAUACGCC C G CUC A UC C ACGCC...UCU-3'@LB@ CG GAUC CU G AGAUCCGCAGGA UCAUGUU GGUUUUA@LB@ \|\| \|\|\|\| \|\| \| \|\|\|\|\|\|\|\|\|::\| \|\|\|:\|\|\| \|\|:\|\|\|\|@LB@ GC CUAG GA C UCUAGGCGUUUU AGUGCAA CCGAAAU@LB@ 3'-C C CA CAAUA...AAG-5'@LB@ \| \|@LB@ 109 70@LB@@LB@@LB@Energy -14.65 kcal/mol@LB@Hybridization Energy -39.2779 kcal/mol@LB@Unfolding Energy - mRNA 12.7007 kcal/mol@LB@Unfolding Energy - sRNA 11.9275 kcal/mol@LB@@LB@Position - mRNA 9 -- 52@LB@Position - sRNA 71 -- 108@LB@Position Seed - mRNA 46 -- 52@LB@Position Seed - sRNA 71 -- 77@LB@
194	0.03409	0.5559	b1836	yebV	-7.98	0.229830	12 -- 23	77 -- 87	uncharacterized protein	_____________11___________24\n_____________\|____________\|\n5'-CCA...GGAUU________A___AAAAA...CUG-3'\n______________GGUUCGCG_UUG\n______________:\|\|\|\|:\|\|_\|\|\|\n______________UCAAGUGC_AAC\n3'-CGC...CGUUU____________CGAAA...AAG-5'\n_____________\|____________\|\n_____________88___________76\n	13 -- 19	80 -- 86	-12.5297 kcal/mol	4.04369 kcal/mol	0.505155 kcal/mol	11 24@LB@ \| \|@LB@5'-CCA...GGAUU A AAAAA...CUG-3'@LB@ GGUUCGCG UUG@LB@ :\|\|\|\|:\|\| \|\|\|@LB@ UCAAGUGC AAC@LB@3'-CGC...CGUUU CGAAA...AAG-5'@LB@ \| \|@LB@ 88 76@LB@@LB@@LB@Energy -7.98 kcal/mol@LB@Hybridization Energy -12.5297 kcal/mol@LB@Unfolding Energy - mRNA 4.04369 kcal/mol@LB@Unfolding Energy - sRNA 0.505155 kcal/mol@LB@@LB@Position - mRNA 12 -- 23@LB@Position - sRNA 77 -- 87@LB@Position Seed - mRNA 13 -- 19@LB@Position Seed - sRNA 80 -- 86@LB@
12	0.002293	0.5385	b1823	cspC	-13.69	0.023618	13 -- 32	14 -- 35	stress protein member of the CspA-family	_____________12_____________________33\n_____________\|______________________\|\n5'-UAU...UAACA________________C_____ACAGU...UCU-3'\n______________GAUUUC__GGGUUAAA_GAGGU\n______________\|\|:\|\|\|__\|\|\|\|\|\|\|\|_\|\|\|\|\|\n______________CUGAAG__CCCAAUUU_CUCCA\n3'-CGC...CGUCA______UU________U_____CGGCG...AAG-5'\n_____________\|______________________\|\n_____________36_____________________13\n	20 -- 26	20 -- 26	-23.8593 kcal/mol	6.83349 kcal/mol	3.33183 kcal/mol	12 33@LB@ \| \|@LB@5'-UAU...UAACA C ACAGU...UCU-3'@LB@ GAUUUC GGGUUAAA GAGGU@LB@ \|\|:\|\|\| \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGAAG CCCAAUUU CUCCA@LB@3'-CGC...CGUCA UU U CGGCG...AAG-5'@LB@ \| \|@LB@ 36 13@LB@@LB@@LB@Energy -13.69 kcal/mol@LB@Hybridization Energy -23.8593 kcal/mol@LB@Unfolding Energy - mRNA 6.83349 kcal/mol@LB@Unfolding Energy - sRNA 3.33183 kcal/mol@LB@@LB@Position - mRNA 13 -- 32@LB@Position - sRNA 14 -- 35@LB@Position Seed - mRNA 20 -- 26@LB@Position Seed - sRNA 20 -- 26@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@
58	0.01138	0.5385	b2595	bamD	-7.85	0.240744	21 -- 29	72 -- 80	BamABCDE complex OM biogenesis lipoprotein	_____________20________30\n_____________\|_________\|\n5'-CUG...ACCGA_________CGGAC...AUG-3'\n______________GUUGGUUUU\n______________\|\|\|\|\|:\|\|\|\n______________CAACCGAAA\n3'-CGC...AAGUG_________UCAAU...AAG-5'\n_____________\|_________\|\n_____________81________71\n	23 -- 29	72 -- 78	-10.2023 kcal/mol	2.1418 kcal/mol	0.205868 kcal/mol	20 30@LB@ \| \|@LB@5'-CUG...ACCGA CGGAC...AUG-3'@LB@ GUUGGUUUU@LB@ \|\|\|\|\|:\|\|\|@LB@ CAACCGAAA@LB@3'-CGC...AAGUG UCAAU...AAG-5'@LB@ \| \|@LB@ 81 71@LB@@LB@@LB@Energy -7.85 kcal/mol@LB@Hybridization Energy -10.2023 kcal/mol@LB@Unfolding Energy - mRNA 2.1418 kcal/mol@LB@Unfolding Energy - sRNA 0.205868 kcal/mol@LB@@LB@Position - mRNA 21 -- 29@LB@Position - sRNA 72 -- 80@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 72 -- 78@LB@
156	0.02672	0.5559	b0957	ompA	-9.60	0.124024	22 -- 30	81 -- 89	outer membrane protein A (3a;II*;G;d)	_____________21________31\n_____________\|_________\|\n5'-CUU...CUGAC_________ACUUG...AAC-3'\n______________GGAGUUCAC\n______________::\|\|\|\|\|\|\|\n______________UUUCAAGUG\n3'-CGC...GGCGU_________CAACC...AAG-5'\n_____________\|_________\|\n_____________90________80\n	24 -- 30	81 -- 87	-11.1644 kcal/mol	1.067 kcal/mol	0.501582 kcal/mol	21 31@LB@ \| \|@LB@5'-CUU...CUGAC ACUUG...AAC-3'@LB@ GGAGUUCAC@LB@ ::\|\|\|\|\|\|\|@LB@ UUUCAAGUG@LB@3'-CGC...GGCGU CAACC...AAG-5'@LB@ \| \|@LB@ 90 80@LB@@LB@@LB@Energy -9.60 kcal/mol@LB@Hybridization Energy -11.1644 kcal/mol@LB@Unfolding Energy - mRNA 1.067 kcal/mol@LB@Unfolding Energy - sRNA 0.501582 kcal/mol@LB@@LB@Position - mRNA 22 -- 30@LB@Position - sRNA 81 -- 89@LB@Position Seed - mRNA 24 -- 30@LB@Position Seed - sRNA 81 -- 87@LB@
192	0.03364	0.5559	b2333	yfcP	-8.48	0.190877	22 -- 36	61 -- 77	putative fimbrial-like adhesin protein	_____________21________________37\n_____________\|_________________\|\n5'-GCA...UACCC_________A_______CUUCA...AUU-3'\n______________GGUUUUGGU___UCGAG\n______________\|\|:\|\|\|:\|\|___\|\|\|\|\|\n______________CCGAAAUCA___AGCUC\n3'-CGC...UGCAA_________AUA_____AACUC...AAG-5'\n_____________\|_________________\|\n_____________78________________60\n	23 -- 29	70 -- 76	-16.4218 kcal/mol	7.14733 kcal/mol	0.796269 kcal/mol	21 37@LB@ \| \|@LB@5'-GCA...UACCC A CUUCA...AUU-3'@LB@ GGUUUUGGU UCGAG@LB@ \|\|:\|\|\|:\|\| \|\|\|\|\|@LB@ CCGAAAUCA AGCUC@LB@3'-CGC...UGCAA AUA AACUC...AAG-5'@LB@ \| \|@LB@ 78 60@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -16.4218 kcal/mol@LB@Unfolding Energy - mRNA 7.14733 kcal/mol@LB@Unfolding Energy - sRNA 0.796269 kcal/mol@LB@@LB@Position - mRNA 22 -- 36@LB@Position - sRNA 61 -- 77@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 70 -- 76@LB@
67	0.01284	0.5385	b1294	sapA	-9.42	0.132690	25 -- 48	61 -- 86	antimicrobial peptide transport ABC transporter periplasmic binding protein	_____________24_________________________49\n_____________\|__________________________\|\n5'-UAC...AAGUU________GA___A_______A____AAAUC...ACA-3'\n______________GUUC_UGU__GUU_UAGUUAU__GAG\n______________\|\|\|\|_:\|\|__\|:\|_\|\|\|\|\|\|\|__\|\|\|\n______________CAAG_GCA__CGA_AUCAAUA__CUC\n3'-CGC...GUUUU____U___AC___A_______AG___AACUC...AAG-5'\n_____________\|__________________________\|\n_____________87_________________________60\n	38 -- 44	66 -- 72	-17.3513 kcal/mol	6.21881 kcal/mol	1.70915 kcal/mol	24 49@LB@ \| \|@LB@5'-UAC...AAGUU GA A A AAAUC...ACA-3'@LB@ GUUC UGU GUU UAGUUAU GAG@LB@ \|\|\|\| :\|\| \|:\| \|\|\|\|\|\|\| \|\|\|@LB@ CAAG GCA CGA AUCAAUA CUC@LB@3'-CGC...GUUUU U AC A AG AACUC...AAG-5'@LB@ \| \|@LB@ 87 60@LB@@LB@@LB@Energy -9.42 kcal/mol@LB@Hybridization Energy -17.3513 kcal/mol@LB@Unfolding Energy - mRNA 6.21881 kcal/mol@LB@Unfolding Energy - sRNA 1.70915 kcal/mol@LB@@LB@Position - mRNA 25 -- 48@LB@Position - sRNA 61 -- 86@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 66 -- 72@LB@
117	0.01966	0.5385	b1203	ychF	-10.24	0.095997	26 -- 41	73 -- 87	catalase inhibitor protein; ATPase K+-dependent ribosome-associated	_____________25_______________42\n_____________\|________________\|\n5'-GAA...AAUGU_______A_A______GACCA...CAU-3'\n______________GGUUUAC_G_UGGCUU\n______________:\|\|\|:\|\|_\|_\|\|\|\|\|\|\n______________UCAAGUG_C_ACCGAA\n3'-CGC...CGUUU_________A______AUCAA...AAG-5'\n_____________\|________________\|\n_____________88_______________72\n	26 -- 32	81 -- 87	-15.1856 kcal/mol	4.42747 kcal/mol	0.51474 kcal/mol	25 42@LB@ \| \|@LB@5'-GAA...AAUGU A A GACCA...CAU-3'@LB@ GGUUUAC G UGGCUU@LB@ :\|\|\|:\|\| \| \|\|\|\|\|\|@LB@ UCAAGUG C ACCGAA@LB@3'-CGC...CGUUU A AUCAA...AAG-5'@LB@ \| \|@LB@ 88 72@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -15.1856 kcal/mol@LB@Unfolding Energy - mRNA 4.42747 kcal/mol@LB@Unfolding Energy - sRNA 0.51474 kcal/mol@LB@@LB@Position - mRNA 26 -- 41@LB@Position - sRNA 73 -- 87@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 81 -- 87@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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