Input and runtime details for job 7819033 (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 7819033 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:17 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:46 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 21:05:24 CET 2018
	Post-Processing Finished		@ Fri Feb 16 21:05:32 CET 2018
	Job Completed		@ Fri Feb 16 21:05:57 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
198	0.02539	0.4256	b1624	ydgJ	-9.27	0.170491	217 -- 246	45 -- 70	putative oxidoreductase	_____________216____________________________247\n_____________\|______________________________\|\n5'-GUA...CAUCC________UU______GUA____U______GCAAA...CGG-3'\n______________GUGUUGGG__GAUUGG___UGGU_AUGCGA\n______________:\|\|\|\|\|\|:__:\|\|::\|___\|\|\|:_\|\|\|\|:\|\n______________UACAACCU__UUAGUC___ACCG_UACGUU\n3'-UUU...AAAUA________U______________U______ACCGG...UUG-5'\n_____________\|______________________________\|\n_____________71_____________________________44\n	218 -- 224	63 -- 69	-23.4852 kcal/mol	9.77058 kcal/mol	4.44589 kcal/mol	216 247@LB@ \| \|@LB@5'-GUA...CAUCC UU GUA U GCAAA...CGG-3'@LB@ GUGUUGGG GAUUGG UGGU AUGCGA@LB@ :\|\|\|\|\|\|: :\|\|::\| \|\|\|: \|\|\|\|:\|@LB@ UACAACCU UUAGUC ACCG UACGUU@LB@3'-UUU...AAAUA U U ACCGG...UUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -9.27 kcal/mol@LB@Hybridization Energy -23.4852 kcal/mol@LB@Unfolding Energy - mRNA 9.77058 kcal/mol@LB@Unfolding Energy - sRNA 4.44589 kcal/mol@LB@@LB@Position - mRNA 217 -- 246@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 63 -- 69@LB@
14	0.0005336	0.1268	b0178	skp	-14.43	0.011083	94 -- 112	46 -- 65	periplasmic chaperone	_____________93___________________113\n_____________\|____________________\|\n5'-CUC...ACAAA____UG______________GCGAU...UCC-3'\n______________GGAA___UAGUGGUAGUGUA\n______________\|\|\|\|___:\|\|\|\|\|:\|:\|\|:\|\n______________CCUU___GUCACCGUUACGU\n3'-UUU...UACAA____UUA_____________UACCG...UUG-5'\n_____________\|____________________\|\n_____________66___________________45\n	105 -- 111	47 -- 53	-21.6303 kcal/mol	3.11688 kcal/mol	4.07994 kcal/mol	93 113@LB@ \| \|@LB@5'-CUC...ACAAA UG GCGAU...UCC-3'@LB@ GGAA UAGUGGUAGUGUA@LB@ \|\|\|\| :\|\|\|\|\|:\|:\|\|:\|@LB@ CCUU GUCACCGUUACGU@LB@3'-UUU...UACAA UUA UACCG...UUG-5'@LB@ \| \|@LB@ 66 45@LB@@LB@@LB@Energy -14.43 kcal/mol@LB@Hybridization Energy -21.6303 kcal/mol@LB@Unfolding Energy - mRNA 3.11688 kcal/mol@LB@Unfolding Energy - sRNA 4.07994 kcal/mol@LB@@LB@Position - mRNA 94 -- 112@LB@Position - sRNA 46 -- 65@LB@Position Seed - mRNA 105 -- 111@LB@Position Seed - sRNA 47 -- 53@LB@
48	0.003417	0.237	b0002	thrA	-15.68	0.005086	222 -- 242	46 -- 65	Bifunctional aspartokinase/homoserine dehydrogenase 1	_____________221___________________243\n_____________\|_____________________\|\n5'-CCA...UCGGC__UAC___________A____GAACG...UGG-3'\n______________GG___AUCAGUGGCAA_UGCA\n______________\|\|___\|\|\|\|\|\|\|\|\|\|\|_\|\|\|\|\n______________CC___UAGUCACCGUU_ACGU\n3'-UUU...UACAA__UUU________________UACCG...UUG-5'\n_____________\|_____________________\|\n_____________66____________________45\n	231 -- 237	50 -- 56	-24.9116 kcal/mol	5.14883 kcal/mol	4.07994 kcal/mol	221 243@LB@ \| \|@LB@5'-CCA...UCGGC UAC A GAACG...UGG-3'@LB@ GG AUCAGUGGCAA UGCA@LB@ \|\| \|\|\|\|\|\|\|\|\|\|\| \|\|\|\|@LB@ CC UAGUCACCGUU ACGU@LB@3'-UUU...UACAA UUU UACCG...UUG-5'@LB@ \| \|@LB@ 66 45@LB@@LB@@LB@Energy -15.68 kcal/mol@LB@Hybridization Energy -24.9116 kcal/mol@LB@Unfolding Energy - mRNA 5.14883 kcal/mol@LB@Unfolding Energy - sRNA 4.07994 kcal/mol@LB@@LB@Position - mRNA 222 -- 242@LB@Position - sRNA 46 -- 65@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 50 -- 56@LB@
125	0.01291	0.3474	b3006	exbB	-11.08	0.071576	189 -- 220	46 -- 66	membrane spanning protein in TonB-ExbB-ExbD complex	_____________188______________________________221\n_____________\|________________________________\|\n5'-CGC...CGUCC______UACA______GUAAUAAUU_______GACGG...CCU-3'\n______________UGGAGA____CAGUGG_________UAAUGCA\n______________\|\|\|\|:\|____\|\|\|\|\|\|_________:\|\|\|\|\|\|\n______________ACCUUU____GUCACC_________GUUACGU\n3'-UUU...AUACA______UA________________________UACCG...UUG-5'\n_____________\|________________________________\|\n_____________67_______________________________45\n	214 -- 220	46 -- 52	-19.4381 kcal/mol	4.26886 kcal/mol	4.08842 kcal/mol	188 221@LB@ \| \|@LB@5'-CGC...CGUCC UACA GUAAUAAUU GACGG...CCU-3'@LB@ UGGAGA CAGUGG UAAUGCA@LB@ \|\|\|\|:\| \|\|\|\|\|\| :\|\|\|\|\|\|@LB@ ACCUUU GUCACC GUUACGU@LB@3'-UUU...AUACA UA UACCG...UUG-5'@LB@ \| \|@LB@ 67 45@LB@@LB@@LB@Energy -11.08 kcal/mol@LB@Hybridization Energy -19.4381 kcal/mol@LB@Unfolding Energy - mRNA 4.26886 kcal/mol@LB@Unfolding Energy - sRNA 4.08842 kcal/mol@LB@@LB@Position - mRNA 189 -- 220@LB@Position - sRNA 46 -- 66@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 46 -- 52@LB@
157	0.01802	0.3828	b3693	dgoK	-7.47	0.356536	125 -- 141	46 -- 60	2-oxo-3-deoxygalactonate kinase	_____________124_______________142\n_____________\|_________________\|\n5'-CAG...ACGAC_____GAC_________GCAGA...CAG-3'\n______________AUCAG___GGCGAUGCG\n______________\|\|\|\|\|___\|\|\|:\|\|\|\|:\n______________UAGUC___CCGUUACGU\n3'-UUU...CCUUU_____A___________UACCG...UUG-5'\n_____________\|_________________\|\n_____________61________________45\n	134 -- 140	47 -- 53	-18.5317 kcal/mol	7.63037 kcal/mol	3.43341 kcal/mol	124 142@LB@ \| \|@LB@5'-CAG...ACGAC GAC GCAGA...CAG-3'@LB@ AUCAG GGCGAUGCG@LB@ \|\|\|\|\| \|\|\|:\|\|\|\|:@LB@ UAGUC CCGUUACGU@LB@3'-UUU...CCUUU A UACCG...UUG-5'@LB@ \| \|@LB@ 61 45@LB@@LB@@LB@Energy -7.47 kcal/mol@LB@Hybridization Energy -18.5317 kcal/mol@LB@Unfolding Energy - mRNA 7.63037 kcal/mol@LB@Unfolding Energy - sRNA 3.43341 kcal/mol@LB@@LB@Position - mRNA 125 -- 141@LB@Position - sRNA 46 -- 60@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 47 -- 53@LB@
44	0.002732	0.2088	b3450	ugpC	-10.48	0.096645	106 -- 116	47 -- 57	sn-glycerol-3-phosphate ABC transporter ATPase	_____________105_________117\n_____________\|___________\|\n5'-GUG...GUGAU___________UGUUA...UCG-3'\n______________GGUGGCGAUGU\n______________:\|\|\|\|\|:\|\|\|:\n______________UCACCGUUACG\n3'-UUU...UUUAG___________UUACC...UUG-5'\n_____________\|___________\|\n_____________58__________46\n	110 -- 116	47 -- 53	-17.083 kcal/mol	3.56469 kcal/mol	3.03952 kcal/mol	105 117@LB@ \| \|@LB@5'-GUG...GUGAU UGUUA...UCG-3'@LB@ GGUGGCGAUGU@LB@ :\|\|\|\|\|:\|\|\|:@LB@ UCACCGUUACG@LB@3'-UUU...UUUAG UUACC...UUG-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -10.48 kcal/mol@LB@Hybridization Energy -17.083 kcal/mol@LB@Unfolding Energy - mRNA 3.56469 kcal/mol@LB@Unfolding Energy - sRNA 3.03952 kcal/mol@LB@@LB@Position - mRNA 106 -- 116@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 110 -- 116@LB@Position Seed - sRNA 47 -- 53@LB@
55	0.003921	0.237	b1781	yeaE	-12.93	0.026626	223 -- 235	47 -- 59	aldo-keto reductase methylglyoxal to acetol NADPH-dependent	_____________222___________236\n_____________\|_____________\|\n5'-GUU...UCAAU_____________CUCAC...CAG-3'\n______________UUAGUGGCGAUGU\n______________\|:\|\|\|\|\|\|:\|\|\|:\n______________AGUCACCGUUACG\n3'-UUU...CUUUU_____________UUACC...UUG-5'\n_____________\|_____________\|\n_____________60____________46\n	229 -- 235	47 -- 53	-19.9127 kcal/mol	3.5603 kcal/mol	3.42309 kcal/mol	222 236@LB@ \| \|@LB@5'-GUU...UCAAU CUCAC...CAG-3'@LB@ UUAGUGGCGAUGU@LB@ \|:\|\|\|\|\|\|:\|\|\|:@LB@ AGUCACCGUUACG@LB@3'-UUU...CUUUU UUACC...UUG-5'@LB@ \| \|@LB@ 60 46@LB@@LB@@LB@Energy -12.93 kcal/mol@LB@Hybridization Energy -19.9127 kcal/mol@LB@Unfolding Energy - mRNA 3.5603 kcal/mol@LB@Unfolding Energy - sRNA 3.42309 kcal/mol@LB@@LB@Position - mRNA 223 -- 235@LB@Position - sRNA 47 -- 59@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 47 -- 53@LB@
75	0.006388	0.2822	b2813	mltA	-10.80	0.082551	232 -- 252	47 -- 66	membrane-bound lytic murein transglycosylase A	_____________231____________________253\n_____________\|______________________\|\n5'-UGC...UCUUA____CAC_______________UUGCC...AAG-3'\n______________UGGG___GGUU_GUGGCAAUGC\n______________\|\|\|:___::\|:_\|\|\|\|\|\|\|\|\|\|\n______________ACCU___UUAG_CACCGUUACG\n3'-UUU...AUACA____U______U__________UUACC...UUG-5'\n_____________\|______________________\|\n_____________67_____________________46\n	246 -- 252	47 -- 53	-21.5988 kcal/mol	6.72365 kcal/mol	4.0775 kcal/mol	231 253@LB@ \| \|@LB@5'-UGC...UCUUA CAC UUGCC...AAG-3'@LB@ UGGG GGUU GUGGCAAUGC@LB@ \|\|\|: ::\|: \|\|\|\|\|\|\|\|\|\|@LB@ ACCU UUAG CACCGUUACG@LB@3'-UUU...AUACA U U UUACC...UUG-5'@LB@ \| \|@LB@ 67 46@LB@@LB@@LB@Energy -10.80 kcal/mol@LB@Hybridization Energy -21.5988 kcal/mol@LB@Unfolding Energy - mRNA 6.72365 kcal/mol@LB@Unfolding Energy - sRNA 4.0775 kcal/mol@LB@@LB@Position - mRNA 232 -- 252@LB@Position - sRNA 47 -- 66@LB@Position Seed - mRNA 246 -- 252@LB@Position Seed - sRNA 47 -- 53@LB@
95	0.008588	0.304	b4551	yheV	-11.20	0.067476	257 -- 273	47 -- 65	DUF2387 family putative metal-binding protein	_____________256_________________274\n_____________\|___________________\|\n5'-AUC...GCGCA___U_____A_________GGCGC...UUG-3'\n______________GGA___UCA_UGGCGAUGU\n______________\|\|\|___\|\|\|_\|\|\|\|:\|\|\|:\n______________CCU___AGU_ACCGUUACG\n3'-UUU...UACAA___UUU___C_________UUACC...UUG-5'\n_____________\|___________________\|\n_____________66__________________46\n	267 -- 273	47 -- 53	-19.3348 kcal/mol	4.06987 kcal/mol	4.06844 kcal/mol	256 274@LB@ \| \|@LB@5'-AUC...GCGCA U A GGCGC...UUG-3'@LB@ GGA UCA UGGCGAUGU@LB@ \|\|\| \|\|\| \|\|\|\|:\|\|\|:@LB@ CCU AGU ACCGUUACG@LB@3'-UUU...UACAA UUU C UUACC...UUG-5'@LB@ \| \|@LB@ 66 46@LB@@LB@@LB@Energy -11.20 kcal/mol@LB@Hybridization Energy -19.3348 kcal/mol@LB@Unfolding Energy - mRNA 4.06987 kcal/mol@LB@Unfolding Energy - sRNA 4.06844 kcal/mol@LB@@LB@Position - mRNA 257 -- 273@LB@Position - sRNA 47 -- 65@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 47 -- 53@LB@
171	0.02062	0.4033	b3192	mlaC	-11.25	0.065504	113 -- 124	47 -- 58	ABC transporter maintaining OM lipid asymmetry periplasmic binding protein	_____________112__________125\n_____________\|____________\|\n5'-GGA...AAGAA____________GCCAG...AGG-3'\n______________UAGUGGCGAUGC\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GUCACCGUUACG\n3'-UUU...UUUUA____________UUACC...UUG-5'\n_____________\|____________\|\n_____________59___________46\n	118 -- 124	47 -- 53	-20.0531 kcal/mol	5.42731 kcal/mol	3.37136 kcal/mol	112 125@LB@ \| \|@LB@5'-GGA...AAGAA GCCAG...AGG-3'@LB@ UAGUGGCGAUGC@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GUCACCGUUACG@LB@3'-UUU...UUUUA UUACC...UUG-5'@LB@ \| \|@LB@ 59 46@LB@@LB@@LB@Energy -11.25 kcal/mol@LB@Hybridization Energy -20.0531 kcal/mol@LB@Unfolding Energy - mRNA 5.42731 kcal/mol@LB@Unfolding Energy - sRNA 3.37136 kcal/mol@LB@@LB@Position - mRNA 113 -- 124@LB@Position - sRNA 47 -- 58@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 47 -- 53@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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