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
148	0.0249	0.5467	b2131	osmF	-10.26	0.095288	236 -- 244	75 -- 83	putative ABC transporter periplasmic binding protein	_____________235_______245\n_____________\|_________\|\n5'-AGG...CUGGU_________AGCCG...UCG-3'\n______________UAUGUUGGC\n______________:\|:\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	238 -- 244	75 -- 81	-12.6611 kcal/mol	1.90691 kcal/mol	0.492259 kcal/mol	235 245@LB@ \| \|@LB@5'-AGG...CUGGU AGCCG...UCG-3'@LB@ UAUGUUGGC@LB@ :\|:\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.26 kcal/mol@LB@Hybridization Energy -12.6611 kcal/mol@LB@Unfolding Energy - mRNA 1.90691 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 236 -- 244@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 238 -- 244@LB@Position Seed - sRNA 75 -- 81@LB@
139	0.02326	0.5385	b1651	gloA	-10.25	0.095619	225 -- 233	75 -- 83	glyoxalase I Ni-dependent	_____________224_______234\n_____________\|_________\|\n5'-UGG...UGCUG_________GAUUU...AAA-3'\n______________CGCGUUGGC\n______________\|:\|\|\|\|\|\|\|\n______________GUGCAACCG\n3'-CGC...UUCAA_________AAAUC...AAG-5'\n_____________\|_________\|\n_____________84________74\n	227 -- 233	75 -- 81	-16.4206 kcal/mol	5.67498 kcal/mol	0.492259 kcal/mol	224 234@LB@ \| \|@LB@5'-UGG...UGCUG GAUUU...AAA-3'@LB@ CGCGUUGGC@LB@ \|:\|\|\|\|\|\|\|@LB@ GUGCAACCG@LB@3'-CGC...UUCAA AAAUC...AAG-5'@LB@ \| \|@LB@ 84 74@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -16.4206 kcal/mol@LB@Unfolding Energy - mRNA 5.67498 kcal/mol@LB@Unfolding Energy - sRNA 0.492259 kcal/mol@LB@@LB@Position - mRNA 225 -- 233@LB@Position - sRNA 75 -- 83@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 75 -- 81@LB@
32	0.005403	0.5385	b0951	pqiB	-10.24	0.095947	95 -- 108	69 -- 82	paraquat-inducible SoxRS-regulated MCE domain protein	_____________94_____________109\n_____________\|______________\|\n5'-CUG...CAUUA_____U________CGUCA...UUC-3'\n______________AUGUU_GCUUUAGU\n______________\|:\|\|\|_\|\|\|\|\|\|\|\|\n______________UGCAA_CGAAAUCA\n3'-CGC...UCAAG_____C________AUAAG...AAG-5'\n_____________\|______________\|\n_____________83_____________68\n	102 -- 108	69 -- 75	-13.4891 kcal/mol	2.8545 kcal/mol	0.389912 kcal/mol	94 109@LB@ \| \|@LB@5'-CUG...CAUUA U CGUCA...UUC-3'@LB@ AUGUU GCUUUAGU@LB@ \|:\|\|\| \|\|\|\|\|\|\|\|@LB@ UGCAA CGAAAUCA@LB@3'-CGC...UCAAG C AUAAG...AAG-5'@LB@ \| \|@LB@ 83 68@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -13.4891 kcal/mol@LB@Unfolding Energy - mRNA 2.8545 kcal/mol@LB@Unfolding Energy - sRNA 0.389912 kcal/mol@LB@@LB@Position - mRNA 95 -- 108@LB@Position - sRNA 69 -- 82@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 69 -- 75@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@
71	0.01305	0.5385	b3843	ubiD	-10.23	0.096580	123 -- 132	80 -- 89	3-octaprenyl-4-hydroxybenzoate decarboxylase	_____________122________133\n_____________\|__________\|\n5'-CGC...CCGUC__________CUAAU...UGG-3'\n______________AGAGUUCACG\n______________\|:\|\|\|\|\|\|\|\|\n______________UUUCAAGUGC\n3'-CGC...GGCGU__________AACCG...AAG-5'\n_____________\|__________\|\n_____________90_________79\n	126 -- 132	80 -- 86	-13.04 kcal/mol	2.30553 kcal/mol	0.506316 kcal/mol	122 133@LB@ \| \|@LB@5'-CGC...CCGUC CUAAU...UGG-3'@LB@ AGAGUUCACG@LB@ \|:\|\|\|\|\|\|\|\|@LB@ UUUCAAGUGC@LB@3'-CGC...GGCGU AACCG...AAG-5'@LB@ \| \|@LB@ 90 79@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -13.04 kcal/mol@LB@Unfolding Energy - mRNA 2.30553 kcal/mol@LB@Unfolding Energy - sRNA 0.506316 kcal/mol@LB@@LB@Position - mRNA 123 -- 132@LB@Position - sRNA 80 -- 89@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 80 -- 86@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@
193	0.03391	0.5559	b3642	pyrE	-10.20	0.097546	70 -- 90	57 -- 80	orotate phosphoribosyltransferase	_____________69_______________________91\n_____________\|________________________\|\n5'-CGG...AUCUU_______C___CC_______GG__AUCGA...AUU-3'\n______________GUUGGCU_UGG_____CGAG__GA\n______________\|\|\|\|\|\|\|_\|:\|_____\|\|\|\|__\|\|\n______________CAACCGA_AUC_____GCUC__CU\n3'-CGC...AAGUG_______A___AAUAA____AA__CUUUG...AAG-5'\n_____________\|________________________\|\n_____________81_______________________56\n	70 -- 76	74 -- 80	-18.9167 kcal/mol	7.49492 kcal/mol	1.21861 kcal/mol	69 91@LB@ \| \|@LB@5'-CGG...AUCUU C CC GG AUCGA...AUU-3'@LB@ GUUGGCU UGG CGAG GA@LB@ \|\|\|\|\|\|\| \|:\| \|\|\|\| \|\|@LB@ CAACCGA AUC GCUC CU@LB@3'-CGC...AAGUG A AAUAA AA CUUUG...AAG-5'@LB@ \| \|@LB@ 81 56@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -18.9167 kcal/mol@LB@Unfolding Energy - mRNA 7.49492 kcal/mol@LB@Unfolding Energy - sRNA 1.21861 kcal/mol@LB@@LB@Position - mRNA 70 -- 90@LB@Position - sRNA 57 -- 80@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 74 -- 80@LB@
143	0.02402	0.5467	b4029	yjbH	-10.20	0.097639	107 -- 117	75 -- 85	DUF940 family extracellular polysaccharide protein	_____________106_________118\n_____________\|___________\|\n5'-GCG...CAUUA___________CUCGC...AUU-3'\n______________UUUAUGUUGGC\n______________\|\|:\|:\|\|\|\|\|\|\n______________AAGUGCAACCG\n3'-CGC...UUUUC___________AAAUC...AAG-5'\n_____________\|___________\|\n_____________86__________74\n	111 -- 117	75 -- 81	-14.6823 kcal/mol	3.97178 kcal/mol	0.509769 kcal/mol	106 118@LB@ \| \|@LB@5'-GCG...CAUUA CUCGC...AUU-3'@LB@ UUUAUGUUGGC@LB@ \|\|:\|:\|\|\|\|\|\|@LB@ AAGUGCAACCG@LB@3'-CGC...UUUUC AAAUC...AAG-5'@LB@ \| \|@LB@ 86 74@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -14.6823 kcal/mol@LB@Unfolding Energy - mRNA 3.97178 kcal/mol@LB@Unfolding Energy - sRNA 0.509769 kcal/mol@LB@@LB@Position - mRNA 107 -- 117@LB@Position - sRNA 75 -- 85@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 75 -- 81@LB@
81	0.01462	0.5385	b3296	rpsD	-10.19	0.098165	202 -- 218	60 -- 78	30S ribosomal subunit protein S4	_____________201_________________219\n_____________\|___________________\|\n5'-AAG...GAAAA____A____A_________CCUAA...AAA-3'\n______________UGGC___AG_UAUUUGGGU\n______________\|\|\|\|___\|\|_\|\|\|\|:\|:\|\|\n______________ACCG___UC_AUAAGCUCA\n3'-CGC...GUGCA____AAA__A_________ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	212 -- 218	60 -- 66	-14.6837 kcal/mol	3.69927 kcal/mol	0.797083 kcal/mol	201 219@LB@ \| \|@LB@5'-AAG...GAAAA A A CCUAA...AAA-3'@LB@ UGGC AG UAUUUGGGU@LB@ \|\|\|\| \|\| \|\|\|\|:\|:\|\|@LB@ ACCG UC AUAAGCUCA@LB@3'-CGC...GUGCA AAA A ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -10.19 kcal/mol@LB@Hybridization Energy -14.6837 kcal/mol@LB@Unfolding Energy - mRNA 3.69927 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 202 -- 218@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 212 -- 218@LB@Position Seed - sRNA 60 -- 66@LB@
118	0.01985	0.5385	b2318	truA	-10.16	0.099312	131 -- 143	70 -- 82	tRNA pseudouridine(38-40) synthase	_____________130___________144\n_____________\|_____________\|\n5'-GUG...CGAUA_____C_______CGGCG...GCA-3'\n______________ACGUU_GCUUUGG\n______________\|\|\|\|\|_\|\|\|\|\|:\|\n______________UGCAA_CGAAAUC\n3'-CGC...UCAAG_____C_______AAUAA...AAG-5'\n_____________\|_____________\|\n_____________83____________69\n	137 -- 143	70 -- 76	-13.1761 kcal/mol	2.62838 kcal/mol	0.389672 kcal/mol	130 144@LB@ \| \|@LB@5'-GUG...CGAUA C CGGCG...GCA-3'@LB@ ACGUU GCUUUGG@LB@ \|\|\|\|\| \|\|\|\|\|:\|@LB@ UGCAA CGAAAUC@LB@3'-CGC...UCAAG C AAUAA...AAG-5'@LB@ \| \|@LB@ 83 69@LB@@LB@@LB@Energy -10.16 kcal/mol@LB@Hybridization Energy -13.1761 kcal/mol@LB@Unfolding Energy - mRNA 2.62838 kcal/mol@LB@Unfolding Energy - sRNA 0.389672 kcal/mol@LB@@LB@Position - mRNA 131 -- 143@LB@Position - sRNA 70 -- 82@LB@Position Seed - mRNA 137 -- 143@LB@Position Seed - sRNA 70 -- 76@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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