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
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@
103	0.003241	0.1101	b0837	yliI	-8.40	0.123505	223 -- 230	4 -- 11	soluble aldose sugar dehydrogenase	_____________222______231\n_____________\|________\|\n5'-GUC...UUUCC________CUUAU...AAC-3'\n______________UUGUGCCC\n______________:\|\|\|:\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	224 -- 230	4 -- 10	-12.324 kcal/mol	0.491988 kcal/mol	3.45361 kcal/mol	222 231@LB@ \| \|@LB@5'-GUC...UUUCC CUUAU...AAC-3'@LB@ UUGUGCCC@LB@ :\|\|\|:\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -8.40 kcal/mol@LB@Hybridization Energy -12.324 kcal/mol@LB@Unfolding Energy - mRNA 0.491988 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 223 -- 230@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 4 -- 10@LB@
139	0.005017	0.127	b2603	yfiR	-11.92	0.011246	223 -- 243	1 -- 19	putative periplasmic inhibitor of YfiN activity	_____________222___________________244\n_____________\|_____________________\|\n5'-GUA...ACUGU___________AUUC______UGACG...GUA-3'\n______________UCUUACUUCUG____UCCUGC\n______________\|\|\|\|\|\|:\|\|\|\|____:\|\|\|:\|\n______________AGAAUGGAGAC____GGGAUG\n3'-AUU...CUUGU___________AU________-5'\n_____________\|____________________\|\n_____________20___________________1\n	227 -- 233	9 -- 15	-21.8705 kcal/mol	2.00959 kcal/mol	7.96751 kcal/mol	222 244@LB@ \| \|@LB@5'-GUA...ACUGU AUUC UGACG...GUA-3'@LB@ UCUUACUUCUG UCCUGC@LB@ \|\|\|\|\|\|:\|\|\|\| :\|\|\|:\|@LB@ AGAAUGGAGAC GGGAUG@LB@3'-AUU...CUUGU AU -5'@LB@ \| \|@LB@ 20 1@LB@@LB@@LB@Energy -11.92 kcal/mol@LB@Hybridization Energy -21.8705 kcal/mol@LB@Unfolding Energy - mRNA 2.00959 kcal/mol@LB@Unfolding Energy - sRNA 7.96751 kcal/mol@LB@@LB@Position - mRNA 223 -- 243@LB@Position - sRNA 1 -- 19@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 9 -- 15@LB@
9	1.988e-05	0.007771	b1985	yeeO	-11.51	0.015356	224 -- 255	1 -- 39	putative multdrug exporter MATE family	_____________223_____________________________________256\n_____________\|_______________________________________\|\n5'-GAU...CAAUU______GGCUUU___________________________GCCAG...GCU-3'\n______________AAGGUC_________GAAUAUCU__CCUCUG__CUUUAC\n______________\|\|\|\|\|\|_________\|\|\|:\|\|\|\|__\|\|\|\|\|\|__\|::\|\|\|\n______________UUCCAG_________CUUGUAGA__GGAGAC__GGGAUG\n3'-AUU...UCAUU______ACUUUCUAU________AU______AU______-5'\n_____________\|______________________________________\|\n_____________40_____________________________________1\n	237 -- 243	17 -- 23	-28.0657 kcal/mol	5.21805 kcal/mol	11.3576 kcal/mol	223 256@LB@ \| \|@LB@5'-GAU...CAAUU GGCUUU GCCAG...GCU-3'@LB@ AAGGUC GAAUAUCU CCUCUG CUUUAC@LB@ \|\|\|\|\|\| \|\|\|:\|\|\|\| \|\|\|\|\|\| \|::\|\|\|@LB@ UUCCAG CUUGUAGA GGAGAC GGGAUG@LB@3'-AUU...UCAUU ACUUUCUAU AU AU -5'@LB@ \| \|@LB@ 40 1@LB@@LB@@LB@Energy -11.51 kcal/mol@LB@Hybridization Energy -28.0657 kcal/mol@LB@Unfolding Energy - mRNA 5.21805 kcal/mol@LB@Unfolding Energy - sRNA 11.3576 kcal/mol@LB@@LB@Position - mRNA 224 -- 255@LB@Position - sRNA 1 -- 39@LB@Position Seed - mRNA 237 -- 243@LB@Position Seed - sRNA 17 -- 23@LB@
57	0.0008523	0.0526	b3281	aroE	-7.63	0.189523	225 -- 232	52 -- 59	dehydroshikimate reductase NAD(P)-binding	_____________224______233\n_____________\|________\|\n5'-UUU...UUGGU________AGCCC...AUG-3'\n______________AAUCCGAU\n______________\|\|\|\|\|\|\|\|\n______________UUAGGCUA\n3'-AUU...UCGGU________AUGCA...AUG-5'\n_____________\|________\|\n_____________60_______51\n	226 -- 232	52 -- 58	-9.52512 kcal/mol	1.61129 kcal/mol	0.296943 kcal/mol	224 233@LB@ \| \|@LB@5'-UUU...UUGGU AGCCC...AUG-3'@LB@ AAUCCGAU@LB@ \|\|\|\|\|\|\|\|@LB@ UUAGGCUA@LB@3'-AUU...UCGGU AUGCA...AUG-5'@LB@ \| \|@LB@ 60 51@LB@@LB@@LB@Energy -7.63 kcal/mol@LB@Hybridization Energy -9.52512 kcal/mol@LB@Unfolding Energy - mRNA 1.61129 kcal/mol@LB@Unfolding Energy - sRNA 0.296943 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 52 -- 59@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 52 -- 58@LB@
179	0.007709	0.1511	b4111	proP	-8.76	0.100034	225 -- 232	49 -- 56	proline/glycine betaine transporter	_____________224______233\n_____________\|________\|\n5'-CAC...UAAAA________CCUUC...GUA-3'\n______________CCGAUUAC\n______________\|\|\|\|\|\|\|\|\n______________GGCUAAUG\n3'-AUU...GUUUA________CACUU...AUG-5'\n_____________\|________\|\n_____________57_______48\n	226 -- 232	49 -- 55	-10.6643 kcal/mol	1.60159 kcal/mol	0.317884 kcal/mol	224 233@LB@ \| \|@LB@5'-CAC...UAAAA CCUUC...GUA-3'@LB@ CCGAUUAC@LB@ \|\|\|\|\|\|\|\|@LB@ GGCUAAUG@LB@3'-AUU...GUUUA CACUU...AUG-5'@LB@ \| \|@LB@ 57 48@LB@@LB@@LB@Energy -8.76 kcal/mol@LB@Hybridization Energy -10.6643 kcal/mol@LB@Unfolding Energy - mRNA 1.60159 kcal/mol@LB@Unfolding Energy - sRNA 0.317884 kcal/mol@LB@@LB@Position - mRNA 225 -- 232@LB@Position - sRNA 49 -- 56@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 49 -- 55@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@
42	0.0004615	0.03766	b3341	rpsG	-11.13	0.020425	227 -- 249	53 -- 76	30S ribosomal subunit protein S7	_____________226______________________250\n_____________\|________________________\|\n5'-CGG...GGUCA__GU________U___________AGUUC...AUG-3'\n______________GC__AAA_AUUC_GCCGGAUCCGA\n______________\|\|__\|\|\|_\|\|\|\|_\|\|\|::\|\|\|\|\|\|\n______________CG__UUU_UAAG_CGGUUUAGGCU\n3'-AUU...CCCGC__AU___A____U___________AAUGC...AUG-5'\n_____________\|________________________\|\n_____________77_______________________52\n	243 -- 249	53 -- 59	-23.8099 kcal/mol	6.33566 kcal/mol	6.36489 kcal/mol	226 250@LB@ \| \|@LB@5'-CGG...GGUCA GU U AGUUC...AUG-3'@LB@ GC AAA AUUC GCCGGAUCCGA@LB@ \|\| \|\|\| \|\|\|\| \|\|\|::\|\|\|\|\|\|@LB@ CG UUU UAAG CGGUUUAGGCU@LB@3'-AUU...CCCGC AU A U AAUGC...AUG-5'@LB@ \| \|@LB@ 77 52@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -23.8099 kcal/mol@LB@Unfolding Energy - mRNA 6.33566 kcal/mol@LB@Unfolding Energy - sRNA 6.36489 kcal/mol@LB@@LB@Position - mRNA 227 -- 249@LB@Position - sRNA 53 -- 76@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 53 -- 59@LB@
76	0.001511	0.06993	b3465	rsmD	-10.43	0.033857	227 -- 244	49 -- 65	16S rRNA m(2)G966 methyltransferase SAM-dependent	_____________226________________245\n_____________\|__________________\|\n5'-UUG...GGCAG____________C_____UGGCG...GCC-3'\n______________CGGCCAAAUCCG_AUUAU\n______________\|:\|\|\|\|\|\|\|\|\|\|_\|\|\|\|:\n______________GUCGGUUUAGGC_UAAUG\n3'-AUU...UAUAA__________________CACUU...AUG-5'\n_____________\|__________________\|\n_____________66_________________48\n	232 -- 238	54 -- 60	-22.129 kcal/mol	5.5281 kcal/mol	6.19707 kcal/mol	226 245@LB@ \| \|@LB@5'-UUG...GGCAG C UGGCG...GCC-3'@LB@ CGGCCAAAUCCG AUUAU@LB@ \|:\|\|\|\|\|\|\|\|\|\| \|\|\|\|:@LB@ GUCGGUUUAGGC UAAUG@LB@3'-AUU...UAUAA CACUU...AUG-5'@LB@ \| \|@LB@ 66 48@LB@@LB@@LB@Energy -10.43 kcal/mol@LB@Hybridization Energy -22.129 kcal/mol@LB@Unfolding Energy - mRNA 5.5281 kcal/mol@LB@Unfolding Energy - sRNA 6.19707 kcal/mol@LB@@LB@Position - mRNA 227 -- 244@LB@Position - sRNA 49 -- 65@LB@Position Seed - mRNA 232 -- 238@LB@Position Seed - sRNA 54 -- 60@LB@
70	0.001199	0.05856	b0954	fabA	-10.37	0.035200	228 -- 254	4 -- 31	beta-hydroxydecanoyl thioester dehydrase	_____________227__________________________255\n_____________\|____________________________\|\n5'-GUG...AUACA_________C_U___________GU_G_GGUGA...ACA-3'\n______________AAAGA_AGA_C_UCUUGCCUCUG__C_C\n______________\|\|\|\|\|_\|\|\|_\|_\|\|\|\|:\|\|\|\|\|\|__\|_\|\n______________UUUCU_UCU_G_AGAAUGGAGAC__G_G\n3'-AUU...CAGAC_____A___U_U___________AU_G_AUG-5'\n_____________\|____________________________\|\n_____________32___________________________3\n	243 -- 249	9 -- 15	-26.2676 kcal/mol	7.86183 kcal/mol	8.05676 kcal/mol	227 255@LB@ \| \|@LB@5'-GUG...AUACA C U GU G GGUGA...ACA-3'@LB@ AAAGA AGA C UCUUGCCUCUG C C@LB@ \|\|\|\|\| \|\|\| \| \|\|\|\|:\|\|\|\|\|\| \| \|@LB@ UUUCU UCU G AGAAUGGAGAC G G@LB@3'-AUU...CAGAC A U U AU G AUG-5'@LB@ \| \|@LB@ 32 3@LB@@LB@@LB@Energy -10.37 kcal/mol@LB@Hybridization Energy -26.2676 kcal/mol@LB@Unfolding Energy - mRNA 7.86183 kcal/mol@LB@Unfolding Energy - sRNA 8.05676 kcal/mol@LB@@LB@Position - mRNA 228 -- 254@LB@Position - sRNA 4 -- 31@LB@Position Seed - mRNA 243 -- 249@LB@Position Seed - sRNA 9 -- 15@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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