Input and runtime details for job 5882223 (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 5882223 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:39:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 03:02:39 CET 2018
	Post-Processing Finished		@ Sat Feb 17 03:02:47 CET 2018
	Job Completed		@ Sat Feb 17 03:03:15 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
190	0.008456	0.1558	b0036	caiD	-8.40	0.123663	110 -- 117	1 -- 8	carnitinyl-CoA dehydratase	_____________109______118\n_____________\|________\|\n5'-UGG...GGAAC________CAGCU...AAA-3'\n______________UACCCUGC\n______________\|\|\|\|\|\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	111 -- 117	1 -- 7	-12.4513 kcal/mol	1.95818 kcal/mol	2.11603 kcal/mol	109 118@LB@ \| \|@LB@5'-UGG...GGAAC CAGCU...AAA-3'@LB@ UACCCUGC@LB@ \|\|\|\|\|\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.4513 kcal/mol@LB@Unfolding Energy - mRNA 1.95818 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 110 -- 117@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 111 -- 117@LB@Position Seed - sRNA 1 -- 7@LB@
129	0.004413	0.1199	b0062	araA	-8.60	0.109835	267 -- 273	1 -- 7	L-arabinose isomerase	_____________266_____274\n_____________\|_______\|\n5'-CGC...CGGAA_______GUCAG...ACG-3'\n______________ACCCUGC\n______________\|\|\|\|\|:\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	267 -- 273	1 -- 7	-12.3746 kcal/mol	1.75625 kcal/mol	2.03949 kcal/mol	266 274@LB@ \| \|@LB@5'-CGC...CGGAA GUCAG...ACG-3'@LB@ ACCCUGC@LB@ \|\|\|\|\|:\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -8.60 kcal/mol@LB@Hybridization Energy -12.3746 kcal/mol@LB@Unfolding Energy - mRNA 1.75625 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 267 -- 273@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 267 -- 273@LB@Position Seed - sRNA 1 -- 7@LB@
137	0.004974	0.127	b0092	ddlB	-6.99	0.263821	283 -- 297	43 -- 56	D-alanine:D-alanine ligase	_____________282_____________298\n_____________\|_______________\|\n5'-UUC...GUUAG____AC_________GCG-3'\n______________CCGG__UGCGUGAAG\n______________\|\|\|:__\|:\|\|\|\|\|\|\|\n______________GGCU__AUGCACUUC\n3'-AUU...GUUUA____A__________AUUUU...AUG-5'\n_____________\|_______________\|\n_____________57______________42\n	291 -- 297	43 -- 49	-17.3937 kcal/mol	7.14584 kcal/mol	3.27327 kcal/mol	282 298@LB@ \| \|@LB@5'-UUC...GUUAG AC GCG-3'@LB@ CCGG UGCGUGAAG@LB@ \|\|\|: \|:\|\|\|\|\|\|\|@LB@ GGCU AUGCACUUC@LB@3'-AUU...GUUUA A AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -6.99 kcal/mol@LB@Hybridization Energy -17.3937 kcal/mol@LB@Unfolding Energy - mRNA 7.14584 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 283 -- 297@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 43 -- 49@LB@
16	5.617e-05	0.01183	b0116	lpd	-12.59	0.006546	264 -- 293	29 -- 63	dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase	_____________263__________________________________294\n_____________\|____________________________________\|\n5'-CCG...CCGCU___U____________C___UUU_____________ACCGUAA-3'\n______________GCC___UCCG_UUGCG_UGA______AGGUCUGGAA\n______________\|\|\|___\|\|\|\|_\|\|:\|\|_\|\|\|______\|\|\|\|\|\|\|:\|\|\n______________CGG___AGGC_AAUGC_ACU______UCCAGACUUU\n3'-AUU...UAAGU___UUU____U_________UCAUUU__________CUAUC...AUG-5'\n_____________\|____________________________________\|\n_____________64___________________________________28\n	286 -- 292	30 -- 36	-30.8342 kcal/mol	7.36676 kcal/mol	10.8887 kcal/mol	263 294@LB@ \| \|@LB@5'-CCG...CCGCU U C UUU ACCGUAA-3'@LB@ GCC UCCG UUGCG UGA AGGUCUGGAA@LB@ \|\|\| \|\|\|\| \|\|:\|\| \|\|\| \|\|\|\|\|\|\|:\|\|@LB@ CGG AGGC AAUGC ACU UCCAGACUUU@LB@3'-AUU...UAAGU UUU U UCAUUU CUAUC...AUG-5'@LB@ \| \|@LB@ 64 28@LB@@LB@@LB@Energy -12.59 kcal/mol@LB@Hybridization Energy -30.8342 kcal/mol@LB@Unfolding Energy - mRNA 7.36676 kcal/mol@LB@Unfolding Energy - sRNA 10.8887 kcal/mol@LB@@LB@Position - mRNA 264 -- 293@LB@Position - sRNA 29 -- 63@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 30 -- 36@LB@
85	0.002234	0.09158	b0118	acnB	-9.43	0.065848	121 -- 128	1 -- 8	aconitate hydratase 2; aconitase B; 2-methyl-cis-aconitate hydratase	_____________120______129\n_____________\|________\|\n5'-GAG...GCAUU________AAACU...UGC-3'\n______________UACCCUAC\n______________\|\|\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	122 -- 128	1 -- 7	-13.4001 kcal/mol	1.87598 kcal/mol	2.11603 kcal/mol	120 129@LB@ \| \|@LB@5'-GAG...GCAUU AAACU...UGC-3'@LB@ UACCCUAC@LB@ \|\|\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.4001 kcal/mol@LB@Unfolding Energy - mRNA 1.87598 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 121 -- 128@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 122 -- 128@LB@Position Seed - sRNA 1 -- 7@LB@
124	0.004173	0.1178	b0131	panD	-9.38	0.067843	182 -- 197	22 -- 38	aspartate 1-decarboxylase	_____________181_______________198\n_____________\|_________________\|\n5'-AUU...CGACA____A____________GUUAU...UUG-3'\n______________GGGU__GAAAGGUAGAA\n______________:\|\|\|__\|\|\|\|\|:\|\|\|\|\|\n______________UCCA__CUUUCUAUCUU\n3'-AUU...CAUUU____GA___________GUAGA...AUG-5'\n_____________\|_________________\|\n_____________39________________21\n	191 -- 197	22 -- 28	-16.986 kcal/mol	1.71047 kcal/mol	5.81616 kcal/mol	181 198@LB@ \| \|@LB@5'-AUU...CGACA A GUUAU...UUG-3'@LB@ GGGU GAAAGGUAGAA@LB@ :\|\|\| \|\|\|\|\|:\|\|\|\|\|@LB@ UCCA CUUUCUAUCUU@LB@3'-AUU...CAUUU GA GUAGA...AUG-5'@LB@ \| \|@LB@ 39 21@LB@@LB@@LB@Energy -9.38 kcal/mol@LB@Hybridization Energy -16.986 kcal/mol@LB@Unfolding Energy - mRNA 1.71047 kcal/mol@LB@Unfolding Energy - sRNA 5.81616 kcal/mol@LB@@LB@Position - mRNA 182 -- 197@LB@Position - sRNA 22 -- 38@LB@Position Seed - mRNA 191 -- 197@LB@Position Seed - sRNA 22 -- 28@LB@
194	0.008663	0.1558	b0213	yafS	-5.39	0.521143	17 -- 34	51 -- 73	putative S-adenosyl-L-methionine-dependent methyltransferase	_____________16______________________35\n_____________\|_______________________\|\n5'-UGG...GGUGA_______________________GCCAG...UCA-3'\n______________GAAAUAU__GGCC___UCCGGUU\n______________:\|\|\|\|\|\|__:\|\|\|___\|\|\|\|:\|\|\n______________UUUUAUA__UCGG___AGGCUAA\n3'-AUU...GCCGA_______AG____UUU_______UGCAC...AUG-5'\n_____________\|_______________________\|\n_____________74______________________50\n	28 -- 34	51 -- 57	-15.2768 kcal/mol	3.69768 kcal/mol	6.213 kcal/mol	16 35@LB@ \| \|@LB@5'-UGG...GGUGA GCCAG...UCA-3'@LB@ GAAAUAU GGCC UCCGGUU@LB@ :\|\|\|\|\|\| :\|\|\| \|\|\|\|:\|\|@LB@ UUUUAUA UCGG AGGCUAA@LB@3'-AUU...GCCGA AG UUU UGCAC...AUG-5'@LB@ \| \|@LB@ 74 50@LB@@LB@@LB@Energy -5.39 kcal/mol@LB@Hybridization Energy -15.2768 kcal/mol@LB@Unfolding Energy - mRNA 3.69768 kcal/mol@LB@Unfolding Energy - sRNA 6.213 kcal/mol@LB@@LB@Position - mRNA 17 -- 34@LB@Position - sRNA 51 -- 73@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
157	0.006279	0.1407	b0312	betB	-8.02	0.153308	1 -- 12	52 -- 63	betaine aldehyde dehydrogenase NAD-dependent	______________1___________13\n______________\|___________\|\n___________5'-____________GAGCG...ACG-3'\n______________GUCGAAUCUGGU\n______________\|:\|:\|\|\|\|:\|:\|\n______________CGGUUUAGGCUA\n3'-AUU...UAAGU____________AUGCA...AUG-5'\n_____________\|____________\|\n_____________64___________51\n	6 -- 12	52 -- 58	-15.0997 kcal/mol	0.969406 kcal/mol	6.13017 kcal/mol	1 13@LB@ \| \|@LB@ 5'- GAGCG...ACG-3'@LB@ GUCGAAUCUGGU@LB@ \|:\|:\|\|\|\|:\|:\|@LB@ CGGUUUAGGCUA@LB@3'-AUU...UAAGU AUGCA...AUG-5'@LB@ \| \|@LB@ 64 51@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -15.0997 kcal/mol@LB@Unfolding Energy - mRNA 0.969406 kcal/mol@LB@Unfolding Energy - sRNA 6.13017 kcal/mol@LB@@LB@Position - mRNA 1 -- 12@LB@Position - sRNA 52 -- 63@LB@Position Seed - mRNA 6 -- 12@LB@Position Seed - sRNA 52 -- 58@LB@
54	0.0007615	0.04961	b0313	betI	-7.44	0.209816	47 -- 68	32 -- 57	choline-inducible betIBA-betT divergent operon transcriptional repressor	_____________46_________________________69\n_____________\|__________________________\|\n5'-CAG...CCUUU___C________U_____________UCAUC...CGC-3'\n______________UCC___UGC_UG__GUGAAAGGUCUG\n______________\|\|\|___\|:\|_\|\|__\|\|:\|\|\|\|\|\|\|\|\|\n______________AGG___AUG_AC__CAUUUUCCAGAC\n3'-AUU...GGUUU___CUA___C__UU____________UUUCU...AUG-5'\n_____________\|__________________________\|\n_____________58_________________________31\n	62 -- 68	32 -- 38	-22.1015 kcal/mol	6.64828 kcal/mol	7.92091 kcal/mol	46 69@LB@ \| \|@LB@5'-CAG...CCUUU C U UCAUC...CGC-3'@LB@ UCC UGC UG GUGAAAGGUCUG@LB@ \|\|\| \|:\| \|\| \|\|:\|\|\|\|\|\|\|\|\|@LB@ AGG AUG AC CAUUUUCCAGAC@LB@3'-AUU...GGUUU CUA C UU UUUCU...AUG-5'@LB@ \| \|@LB@ 58 31@LB@@LB@@LB@Energy -7.44 kcal/mol@LB@Hybridization Energy -22.1015 kcal/mol@LB@Unfolding Energy - mRNA 6.64828 kcal/mol@LB@Unfolding Energy - sRNA 7.92091 kcal/mol@LB@@LB@Position - mRNA 47 -- 68@LB@Position - sRNA 32 -- 57@LB@Position Seed - mRNA 62 -- 68@LB@Position Seed - sRNA 32 -- 38@LB@
34	0.0003499	0.03519	b0333	prpC	-9.01	0.085770	169 -- 175	1 -- 7	2-methylcitrate synthase	_____________168_____176\n_____________\|_______\|\n5'-ACU...UCUCG_______AAAUG...GCA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	169 -- 175	1 -- 7	-11.7504 kcal/mol	0.722985 kcal/mol	2.03949 kcal/mol	168 176@LB@ \| \|@LB@5'-ACU...UCUCG AAAUG...GCA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.01 kcal/mol@LB@Hybridization Energy -11.7504 kcal/mol@LB@Unfolding Energy - mRNA 0.722985 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 169 -- 175@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 169 -- 175@LB@Position Seed - sRNA 1 -- 7@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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service.

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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