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
153	0.006198	0.1406	b3459	panM	-8.50	0.116540	144 -- 151	50 -- 57	PanD autocleavage accelerator panothenate synthesis	_____________143______152\n_____________\|________\|\n5'-AAA...AAGCC________AAUUA...UUG-3'\n______________UCCGAUUA\n______________\|\|\|\|\|\|\|\|\n______________AGGCUAAU\n3'-AUU...GGUUU________GCACU...AUG-5'\n_____________\|________\|\n_____________58_______49\n	145 -- 151	50 -- 56	-10.246 kcal/mol	1.44461 kcal/mol	0.317388 kcal/mol	143 152@LB@ \| \|@LB@5'-AAA...AAGCC AAUUA...UUG-3'@LB@ UCCGAUUA@LB@ \|\|\|\|\|\|\|\|@LB@ AGGCUAAU@LB@3'-AUU...GGUUU GCACU...AUG-5'@LB@ \| \|@LB@ 58 49@LB@@LB@@LB@Energy -8.50 kcal/mol@LB@Hybridization Energy -10.246 kcal/mol@LB@Unfolding Energy - mRNA 1.44461 kcal/mol@LB@Unfolding Energy - sRNA 0.317388 kcal/mol@LB@@LB@Position - mRNA 144 -- 151@LB@Position - sRNA 50 -- 57@LB@Position Seed - mRNA 145 -- 151@LB@Position Seed - sRNA 50 -- 56@LB@
12	3.867e-05	0.01134	b0728	sucC	-9.87	0.049323	145 -- 186	43 -- 73	succinyl-CoA synthetase beta subunit	_____________144_________________________________________187\n_____________\|___________________________________________\|\n5'-CGC...GAUAC_____________UACGGUUUAAA____AA_____________GAUGG...AAG-3'\n______________GAAAUAUUCGGUC___________AGAU__CGAUUAC_UGAAG\n______________:\|\|\|\|\|\|\|\|:\|:\|___________\|:\|\|__\|\|\|\|\|\|\|_\|\|\|\|\|\n______________UUUUAUAAGUCGG___________UUUA__GCUAAUG_ACUUC\n3'-AUU...GCCGA____________________________G________C_____AUUUU...AUG-5'\n_____________\|___________________________________________\|\n_____________74__________________________________________42\n	175 -- 181	49 -- 55	-26.5157 kcal/mol	7.48621 kcal/mol	9.17828 kcal/mol	144 187@LB@ \| \|@LB@5'-CGC...GAUAC UACGGUUUAAA AA GAUGG...AAG-3'@LB@ GAAAUAUUCGGUC AGAU CGAUUAC UGAAG@LB@ :\|\|\|\|\|\|\|\|:\|:\| \|:\|\| \|\|\|\|\|\|\| \|\|\|\|\|@LB@ UUUUAUAAGUCGG UUUA GCUAAUG ACUUC@LB@3'-AUU...GCCGA G C AUUUU...AUG-5'@LB@ \| \|@LB@ 74 42@LB@@LB@@LB@Energy -9.87 kcal/mol@LB@Hybridization Energy -26.5157 kcal/mol@LB@Unfolding Energy - mRNA 7.48621 kcal/mol@LB@Unfolding Energy - sRNA 9.17828 kcal/mol@LB@@LB@Position - mRNA 145 -- 186@LB@Position - sRNA 43 -- 73@LB@Position Seed - mRNA 175 -- 181@LB@Position Seed - sRNA 49 -- 55@LB@
200	0.009019	0.1567	b3343	tusB	-6.18	0.382258	145 -- 152	1 -- 8	mnm(5)-s(2)U34-tRNA synthesis 2-thiolation protein	_____________144______153\n_____________\|________\|\n5'-GCU...GCAGA________GCCGC...GCG-3'\n______________UGCCUUAC\n______________\|:\|\|:\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	146 -- 152	1 -- 7	-9.97017 kcal/mol	1.6972 kcal/mol	2.11603 kcal/mol	144 153@LB@ \| \|@LB@5'-GCU...GCAGA GCCGC...GCG-3'@LB@ UGCCUUAC@LB@ \|:\|\|:\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.18 kcal/mol@LB@Hybridization Energy -9.97017 kcal/mol@LB@Unfolding Energy - mRNA 1.6972 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 145 -- 152@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 146 -- 152@LB@Position Seed - sRNA 1 -- 7@LB@
20	9.41e-05	0.01655	b0721	sdhC	-12.56	0.006704	146 -- 157	4 -- 15	succinate dehydrogenase membrane subunit binds cytochrome b556	_____________145__________158\n_____________\|____________\|\n5'-UCC...AGUUA____________GUAGU...CCG-3'\n______________ACCUCUGUGCCC\n______________\|\|\|\|\|\|\|\|:\|\|\|\n______________UGGAGACAUGGG\n3'-AUU...UAGAA____________AUG-5'\n_____________\|____________\|\n_____________16___________3\n	151 -- 157	4 -- 10	-23.3451 kcal/mol	4.99288 kcal/mol	5.82084 kcal/mol	145 158@LB@ \| \|@LB@5'-UCC...AGUUA GUAGU...CCG-3'@LB@ ACCUCUGUGCCC@LB@ \|\|\|\|\|\|\|\|:\|\|\|@LB@ UGGAGACAUGGG@LB@3'-AUU...UAGAA AUG-5'@LB@ \| \|@LB@ 16 3@LB@@LB@@LB@Energy -12.56 kcal/mol@LB@Hybridization Energy -23.3451 kcal/mol@LB@Unfolding Energy - mRNA 4.99288 kcal/mol@LB@Unfolding Energy - sRNA 5.82084 kcal/mol@LB@@LB@Position - mRNA 146 -- 157@LB@Position - sRNA 4 -- 15@LB@Position Seed - mRNA 151 -- 157@LB@Position Seed - sRNA 4 -- 10@LB@
160	0.006479	0.1413	b0391	yaiE	-12.00	0.010520	148 -- 162	1 -- 15	UPF0345 family protein	_____________147_____________163\n_____________\|_______________\|\n5'-GAU...CCAGC_______GC______AGUGA...GCG-3'\n______________GCCUCUG__CCCUAU\n______________:\|\|\|\|\|\|__\|\|\|\|\|:\n______________UGGAGAC__GGGAUG\n3'-AUU...UAGAA_______AU______-5'\n_____________\|______________\|\n_____________16_____________1\n	148 -- 154	9 -- 15	-21.6181 kcal/mol	3.81195 kcal/mol	5.82808 kcal/mol	147 163@LB@ \| \|@LB@5'-GAU...CCAGC GC AGUGA...GCG-3'@LB@ GCCUCUG CCCUAU@LB@ :\|\|\|\|\|\| \|\|\|\|\|:@LB@ UGGAGAC GGGAUG@LB@3'-AUU...UAGAA AU -5'@LB@ \| \|@LB@ 16 1@LB@@LB@@LB@Energy -12.00 kcal/mol@LB@Hybridization Energy -21.6181 kcal/mol@LB@Unfolding Energy - mRNA 3.81195 kcal/mol@LB@Unfolding Energy - sRNA 5.82808 kcal/mol@LB@@LB@Position - mRNA 148 -- 162@LB@Position - sRNA 1 -- 15@LB@Position Seed - mRNA 148 -- 154@LB@Position Seed - sRNA 9 -- 15@LB@
33	0.0003369	0.03519	b0523	purE	-12.01	0.010423	150 -- 160	3 -- 13	N5-carboxyaminoimidazole ribonucleotide mutase	_____________149__________161\n_____________\|____________\|\n5'-UGG...GCUAU____________CUAAA...UGA-3'\n______________UCUCUGUGCCCU\n______________:\|\|\|\|\|\|:\|\|\|\|\n______________GGAGACAUGGGA\n3'-AUU...AGAAU____________UG-5'\n_____________\|____________\|\n_____________14___________2\n	154 -- 160	3 -- 9	-20.2448 kcal/mol	2.89849 kcal/mol	5.35591 kcal/mol	149 161@LB@ \| \|@LB@5'-UGG...GCUAU CUAAA...UGA-3'@LB@ UCUCUGUGCCCU@LB@ :\|\|\|\|\|\|:\|\|\|\|@LB@ GGAGACAUGGGA@LB@3'-AUU...AGAAU UG-5'@LB@ \| \|@LB@ 14 2@LB@@LB@@LB@Energy -12.01 kcal/mol@LB@Hybridization Energy -20.2448 kcal/mol@LB@Unfolding Energy - mRNA 2.89849 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 150 -- 160@LB@Position - sRNA 3 -- 13@LB@Position Seed - mRNA 154 -- 160@LB@Position Seed - sRNA 3 -- 9@LB@
199	0.008811	0.1558	b4515	cydX	-11.13	0.020449	151 -- 184	5 -- 31	cytochrome d (bd-I) ubiquinol oxidase subunit X	_____________150________________________________185\n_____________\|__________________________________\|\n5'-ACC...CCAAA_______UU______AAC___CACUC________AAGUA...GUC-3'\n______________GAAGAUA__GAACGU___ACC_____UCUGUACU\n______________:\|\|\|\|\|\|__\|\|\|\|:\|___\|\|\|_____\|\|\|\|\|\|\|:\n______________UUUCUAU__CUUGUA___UGG_____AGACAUGG\n3'-AUU...CAGAC_______________GAA________________GAUG-5'\n_____________\|__________________________________\|\n_____________32_________________________________4\n	178 -- 184	5 -- 11	-22.8813 kcal/mol	3.72257 kcal/mol	8.05162 kcal/mol	150 185@LB@ \| \|@LB@5'-ACC...CCAAA UU AAC CACUC AAGUA...GUC-3'@LB@ GAAGAUA GAACGU ACC UCUGUACU@LB@ :\|\|\|\|\|\| \|\|\|\|:\| \|\|\| \|\|\|\|\|\|\|:@LB@ UUUCUAU CUUGUA UGG AGACAUGG@LB@3'-AUU...CAGAC GAA GAUG-5'@LB@ \| \|@LB@ 32 4@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -22.8813 kcal/mol@LB@Unfolding Energy - mRNA 3.72257 kcal/mol@LB@Unfolding Energy - sRNA 8.05162 kcal/mol@LB@@LB@Position - mRNA 151 -- 184@LB@Position - sRNA 5 -- 31@LB@Position Seed - mRNA 178 -- 184@LB@Position Seed - sRNA 5 -- 11@LB@
58	0.000878	0.0531	b2150	mglB	-10.24	0.038484	153 -- 179	1 -- 24	methyl-galactoside transporter subunit	_____________152__________________________180\n_____________\|____________________________\|\n5'-GUA...CCGCC______________AAGCAC________AUAAG...AUA-3'\n______________GAGCAUU_UAUCUC______UACCCUGC\n______________\|\|:\|\|\|:_\|\|:\|\|\|______\|\|\|\|\|\|:\|\n______________CUUGUAG_AUGGAG______AUGGGAUG\n3'-AUU...UCUAU_______A______AC____________-5'\n_____________\|___________________________\|\n_____________25__________________________1\n	173 -- 179	1 -- 7	-24.5136 kcal/mol	6.27388 kcal/mol	8.02158 kcal/mol	152 180@LB@ \| \|@LB@5'-GUA...CCGCC AAGCAC AUAAG...AUA-3'@LB@ GAGCAUU UAUCUC UACCCUGC@LB@ \|\|:\|\|\|: \|\|:\|\|\| \|\|\|\|\|\|:\|@LB@ CUUGUAG AUGGAG AUGGGAUG@LB@3'-AUU...UCUAU A AC -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -10.24 kcal/mol@LB@Hybridization Energy -24.5136 kcal/mol@LB@Unfolding Energy - mRNA 6.27388 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 153 -- 179@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.003703	0.1147	b1728	ydjM	-2.69	0.937889	161 -- 167	1 -- 7	inner membrane protein regulated by LexA	_____________160_____168\n_____________\|_______\|\n5'-CGC...UAAAA_______ACUGU...AUA-3'\n______________AUCCUAU\n______________\|:\|\|\|\|:\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	161 -- 167	1 -- 7	-7.15055 kcal/mol	2.44298 kcal/mol	2.03949 kcal/mol	160 168@LB@ \| \|@LB@5'-CGC...UAAAA ACUGU...AUA-3'@LB@ AUCCUAU@LB@ \|:\|\|\|\|:@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -2.69 kcal/mol@LB@Hybridization Energy -7.15055 kcal/mol@LB@Unfolding Energy - mRNA 2.44298 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 161 -- 167@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 161 -- 167@LB@Position Seed - sRNA 1 -- 7@LB@
99	0.00311	0.1096	b2801	fucP	-13.12	0.004165	162 -- 172	46 -- 56	L-fucose transporter	_____________161_________173\n_____________\|___________\|\n5'-AUG...CAUAA___________CUUAA...CAC-3'\n______________CCGAUUACGUG\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCAC\n3'-AUU...GUUUA___________UUCAU...AUG-5'\n_____________\|___________\|\n_____________57__________45\n	166 -- 172	46 -- 52	-17.4041 kcal/mol	2.44124 kcal/mol	1.86194 kcal/mol	161 173@LB@ \| \|@LB@5'-AUG...CAUAA CUUAA...CAC-3'@LB@ CCGAUUACGUG@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCAC@LB@3'-AUU...GUUUA UUCAU...AUG-5'@LB@ \| \|@LB@ 57 45@LB@@LB@@LB@Energy -13.12 kcal/mol@LB@Hybridization Energy -17.4041 kcal/mol@LB@Unfolding Energy - mRNA 2.44124 kcal/mol@LB@Unfolding Energy - sRNA 1.86194 kcal/mol@LB@@LB@Position - mRNA 162 -- 172@LB@Position - sRNA 46 -- 56@LB@Position Seed - mRNA 166 -- 172@LB@Position Seed - sRNA 46 -- 52@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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