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
44	0.000471	0.03766	b3624	waaZ	-7.10	0.250129	289 -- 295	1 -- 7	lipopolysaccharide KdoIII transferase; lipopolysaccharide core biosynthesis protein	_____________288_____296\n_____________\|_______\|\n5'-AGA...UUCGG_______AUCGC-3'\n______________GCCCUAC\n______________:\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	289 -- 295	1 -- 7	-11.6335 kcal/mol	2.52016 kcal/mol	2.03949 kcal/mol	288 296@LB@ \| \|@LB@5'-AGA...UUCGG AUCGC-3'@LB@ GCCCUAC@LB@ :\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -7.10 kcal/mol@LB@Hybridization Energy -11.6335 kcal/mol@LB@Unfolding Energy - mRNA 2.52016 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 289 -- 295@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 289 -- 295@LB@Position Seed - sRNA 1 -- 7@LB@
21	0.0001601	0.02641	b2344	fadL	-13.31	0.003531	80 -- 135	1 -- 58	long-chain fatty acid outer membrane transporter	_____________79_________________________________________________________________136\n_____________\|__________________________________________________________________\|\n5'-UCC...AGCUG______CCUA___UCUCGCCACU________UUUCU____________________A_________ACUUC...UUU-3'\n______________GUCCGA____UAC___________GGUCUGA_____AAGAUG________UACCUC_G_ACCCUAC\n______________:\|\|\|\|\|____\|\|\|___________\|\|\|\|\|\|\|_____\|\|\|\|\|:________\|\|\|\|\|\|_\|_\|\|\|\|\|\|\|\n______________UAGGCU____AUG___________CCAGACU_____UUCUAU________AUGGAG_C_UGGGAUG\n3'-AUU...CGGUU______A______CACUUCAUUUU__________________CUUGUAGA______A_A_______-5'\n_____________\|_________________________________________________________________\|\n_____________59________________________________________________________________1\n	129 -- 135	1 -- 7	-38.7471 kcal/mol	12.7593 kcal/mol	12.7027 kcal/mol	79 136@LB@ \| \|@LB@5'-UCC...AGCUG CCUA UCUCGCCACU UUUCU A ACUUC...UUU-3'@LB@ GUCCGA UAC GGUCUGA AAGAUG UACCUC G ACCCUAC@LB@ :\|\|\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\|\|: \|\|\|\|\|\| \| \|\|\|\|\|\|\|@LB@ UAGGCU AUG CCAGACU UUCUAU AUGGAG C UGGGAUG@LB@3'-AUU...CGGUU A CACUUCAUUUU CUUGUAGA A A -5'@LB@ \| \|@LB@ 59 1@LB@@LB@@LB@Energy -13.31 kcal/mol@LB@Hybridization Energy -38.7471 kcal/mol@LB@Unfolding Energy - mRNA 12.7593 kcal/mol@LB@Unfolding Energy - sRNA 12.7027 kcal/mol@LB@@LB@Position - mRNA 80 -- 135@LB@Position - sRNA 1 -- 58@LB@Position Seed - mRNA 129 -- 135@LB@Position Seed - sRNA 1 -- 7@LB@
126	0.00422	0.1178	b1621	malX	-14.96	0.000732	43 -- 87	1 -- 56	maltose and glucose-specific PTS enzyme IIB component and IIC component	_____________42__________________________________________________________88\n_____________\|___________________________________________________________\|\n5'-AUG...ACUCC____________C___________________A______________UAUU________ACCCG...GCA-3'\n______________CUGAUUAUGUGA_______________AGAUA_AACGUUUUACCUUU____UAUCUUAU\n______________\|:\|\|\|\|\|:\|\|\|\|_______________\|\|\|\|\|_\|\|\|:\|:\|\|\|\|\|\|:\|____\|\|:\|:\|\|:\n______________GGCUAAUGCACU_______________UCUAU_UUGUAGAAUGGAGA____AUGGGAUG\n3'-AUU...GUUUA____________UCAUUUUCCAGACUU_____C______________C___________-5'\n_____________\|__________________________________________________________\|\n_____________57_________________________________________________________1\n	81 -- 87	1 -- 7	-37.7188 kcal/mol	10.08 kcal/mol	12.7022 kcal/mol	42 88@LB@ \| \|@LB@5'-AUG...ACUCC C A UAUU ACCCG...GCA-3'@LB@ CUGAUUAUGUGA AGAUA AACGUUUUACCUUU UAUCUUAU@LB@ \|:\|\|\|\|\|:\|\|\|\| \|\|\|\|\| \|\|\|:\|:\|\|\|\|\|\|:\| \|\|:\|:\|\|:@LB@ GGCUAAUGCACU UCUAU UUGUAGAAUGGAGA AUGGGAUG@LB@3'-AUU...GUUUA UCAUUUUCCAGACUU C C -5'@LB@ \| \|@LB@ 57 1@LB@@LB@@LB@Energy -14.96 kcal/mol@LB@Hybridization Energy -37.7188 kcal/mol@LB@Unfolding Energy - mRNA 10.08 kcal/mol@LB@Unfolding Energy - sRNA 12.7022 kcal/mol@LB@@LB@Position - mRNA 43 -- 87@LB@Position - sRNA 1 -- 56@LB@Position Seed - mRNA 81 -- 87@LB@Position Seed - sRNA 1 -- 7@LB@
92	0.002567	0.09816	b4120	melB	-8.04	0.151444	195 -- 202	1 -- 8	melibiose:sodium symporter	_____________194______203\n_____________\|________\|\n5'-AUA...CCCGA________GAGCA...ACA-3'\n______________UACCCUAU\n______________\|\|\|\|\|\|\|:\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	196 -- 202	1 -- 7	-10.9179 kcal/mol	0.779946 kcal/mol	2.11603 kcal/mol	194 203@LB@ \| \|@LB@5'-AUA...CCCGA GAGCA...ACA-3'@LB@ UACCCUAU@LB@ \|\|\|\|\|\|\|:@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -10.9179 kcal/mol@LB@Unfolding Energy - mRNA 0.779946 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 195 -- 202@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 196 -- 202@LB@Position Seed - sRNA 1 -- 7@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@
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@
134	0.004727	0.1241	b1655	mepH	-9.70	0.055155	231 -- 243	1 -- 13	murein DD-endopeptidase space-maker hydrolase	_____________230___________244\n_____________\|_____________\|\n5'-CGU...UCACG_____________UUUUU...AGA-3'\n______________CUCUGUGCUUUAC\n______________\|\|\|\|\|\|:\|::\|\|\|\n______________GAGACAUGGGAUG\n3'-AUU...GAAUG_____________-5'\n_____________\|____________\|\n_____________14___________1\n	237 -- 243	1 -- 7	-18.9465 kcal/mol	4.13106 kcal/mol	5.13393 kcal/mol	230 244@LB@ \| \|@LB@5'-CGU...UCACG UUUUU...AGA-3'@LB@ CUCUGUGCUUUAC@LB@ \|\|\|\|\|\|:\|::\|\|\|@LB@ GAGACAUGGGAUG@LB@3'-AUU...GAAUG -5'@LB@ \| \|@LB@ 14 1@LB@@LB@@LB@Energy -9.70 kcal/mol@LB@Hybridization Energy -18.9465 kcal/mol@LB@Unfolding Energy - mRNA 4.13106 kcal/mol@LB@Unfolding Energy - sRNA 5.13393 kcal/mol@LB@@LB@Position - mRNA 231 -- 243@LB@Position - sRNA 1 -- 13@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 1 -- 7@LB@
74	0.001232	0.05856	b3139	agaC	-9.25	0.073815	213 -- 219	1 -- 7	N-acetylgalactosamine-specific enzyme IIC component of PTS	_____________212_____220\n_____________\|_______\|\n5'-AAC...AAAUA_______UUCAG...CGA-3'\n______________ACCCUAC\n______________\|\|\|\|\|\|\|\n______________UGGGAUG\n3'-AUU...AGACA_______-5'\n_____________\|______\|\n_____________8______1\n	213 -- 219	1 -- 7	-11.8132 kcal/mol	0.545455 kcal/mol	2.03949 kcal/mol	212 220@LB@ \| \|@LB@5'-AAC...AAAUA UUCAG...CGA-3'@LB@ ACCCUAC@LB@ \|\|\|\|\|\|\|@LB@ UGGGAUG@LB@3'-AUU...AGACA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -9.25 kcal/mol@LB@Hybridization Energy -11.8132 kcal/mol@LB@Unfolding Energy - mRNA 0.545455 kcal/mol@LB@Unfolding Energy - sRNA 2.03949 kcal/mol@LB@@LB@Position - mRNA 213 -- 219@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 1 -- 7@LB@
69	0.001182	0.05856	b2962	yggX	-12.92	0.004967	226 -- 272	1 -- 57	oxidative damage protective factor for iron-sulfur proteins	_____________225________________________________________________________273\n_____________\|__________________________________________________________\|\n5'-UCA...UACUU___UGCA________C____________________G_______AG________CG__GAGCU...AGA-3'\n______________UCC____ACGUGAAG_AGAAGGUC__________AG_AUUUU_C__CUGUACCC__GC\n______________\|\|\|____\|\|\|\|\|\|\|\|_\|:\|\|\|\|\|\|__________\|:_\|\|:\|\|_\|__\|\|\|\|\|\|\|\|__:\|\n______________AGG____UGCACUUC_UUUUCCAG__________UU_UAGAA_G__GACAUGGG__UG\n3'-AUU...GGUUU___CUAA________A________ACUUUCUAUC__G_____U_GA________A___-5'\n_____________\|_________________________________________________________\|\n_____________58________________________________________________________1\n	262 -- 268	4 -- 10	-42.3698 kcal/mol	16.7751 kcal/mol	12.7026 kcal/mol	225 273@LB@ \| \|@LB@5'-UCA...UACUU UGCA C G AG CG GAGCU...AGA-3'@LB@ UCC ACGUGAAG AGAAGGUC AG AUUUU C CUGUACCC GC@LB@ \|\|\| \|\|\|\|\|\|\|\| \|:\|\|\|\|\|\| \|: \|\|:\|\| \| \|\|\|\|\|\|\|\| :\|@LB@ AGG UGCACUUC UUUUCCAG UU UAGAA G GACAUGGG UG@LB@3'-AUU...GGUUU CUAA A ACUUUCUAUC G U GA A -5'@LB@ \| \|@LB@ 58 1@LB@@LB@@LB@Energy -12.92 kcal/mol@LB@Hybridization Energy -42.3698 kcal/mol@LB@Unfolding Energy - mRNA 16.7751 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 226 -- 272@LB@Position - sRNA 1 -- 57@LB@Position Seed - mRNA 262 -- 268@LB@Position Seed - sRNA 4 -- 10@LB@
169	0.006985	0.1454	b0384	psiF	-5.27	0.543574	221 -- 228	1 -- 8	PsiF family protein	_____________220______229\n_____________\|________\|\n5'-CCC...CUGGU________UUUUC...UGA-3'\n______________UACCUUGC\n______________\|\|\|\|:\|:\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	222 -- 228	1 -- 7	-9.62499 kcal/mol	2.26355 kcal/mol	2.11603 kcal/mol	220 229@LB@ \| \|@LB@5'-CCC...CUGGU UUUUC...UGA-3'@LB@ UACCUUGC@LB@ \|\|\|\|:\|:\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -5.27 kcal/mol@LB@Hybridization Energy -9.62499 kcal/mol@LB@Unfolding Energy - mRNA 2.26355 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 221 -- 228@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 222 -- 228@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)

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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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