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	Additional homologs
151	0.006118	0.1406	b1103	hinT	-6.52	0.328434	216 -- 241	45 -- 70	purine nucleoside phosphoramidase dadA activator protein		_____________215________________________242\n_____________\|__________________________\|\n5'-CAA...AAACU_________A_____AUUCGU_____GAUCC...CGC-3'\n______________AUAUUCAGC_AAAUU______CGUGA\n______________\|\|\|\|\|\|\|\|\|_\|\|\|\|:______\|\|\|\|\|\n______________UAUAAGUCG_UUUAG______GCACU\n3'-AUU...GAUUU_________G_____GCUAAU_____UCAUU...AUG-5'\n_____________\|__________________________\|\n_____________71_________________________44\n	218 -- 224	62 -- 68	-20.3535 kcal/mol	5.67357 kcal/mol	8.1779 kcal/mol	215 242@LB@ \| \|@LB@5'-CAA...AAACU A AUUCGU GAUCC...CGC-3'@LB@ AUAUUCAGC AAAUU CGUGA@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\|: \|\|\|\|\|@LB@ UAUAAGUCG UUUAG GCACU@LB@3'-AUU...GAUUU G GCUAAU UCAUU...AUG-5'@LB@ \| \|@LB@ 71 44@LB@@LB@@LB@Energy -6.52 kcal/mol@LB@Hybridization Energy -20.3535 kcal/mol@LB@Unfolding Energy - mRNA 5.67357 kcal/mol@LB@Unfolding Energy - sRNA 8.1779 kcal/mol@LB@@LB@Position - mRNA 216 -- 241@LB@Position - sRNA 45 -- 70@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 62 -- 68@LB@
36	0.0003681	0.03584	b1136	icd	-11.32	0.017792	275 -- 286	49 -- 60	isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase		_____________274__________287\n_____________\|____________\|\n5'-GUA...CCUGA____________CCCUU...AAG-3'\n______________AAAUCCGAUUAU\n______________\|\|\|\|\|\|\|\|\|\|\|:\n______________UUUAGGCUAAUG\n3'-AUU...GUCGG____________CACUU...AUG-5'\n_____________\|____________\|\n_____________61___________48\n	280 -- 286	49 -- 55	-13.1162 kcal/mol	1.49253 kcal/mol	0.319946 kcal/mol	274 287@LB@ \| \|@LB@5'-GUA...CCUGA CCCUU...AAG-3'@LB@ AAAUCCGAUUAU@LB@ \|\|\|\|\|\|\|\|\|\|\|:@LB@ UUUAGGCUAAUG@LB@3'-AUU...GUCGG CACUU...AUG-5'@LB@ \| \|@LB@ 61 48@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -13.1162 kcal/mol@LB@Unfolding Energy - mRNA 1.49253 kcal/mol@LB@Unfolding Energy - sRNA 0.319946 kcal/mol@LB@@LB@Position - mRNA 275 -- 286@LB@Position - sRNA 49 -- 60@LB@Position Seed - mRNA 280 -- 286@LB@Position Seed - sRNA 49 -- 55@LB@
132	0.004657	0.1239	b1200	dhaK	-7.52	0.201505	172 -- 179	1 -- 8	dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit		_____________171______180\n_____________\|________\|\n5'-UUC...AUCCA________CGUAA...UGU-3'\n______________UGCCCUAC\n______________\|:\|\|\|\|\|\|\n______________AUGGGAUG\n3'-AUU...GAGAC________-5'\n_____________\|_______\|\n_____________9_______1\n	173 -- 179	1 -- 7	-12.1513 kcal/mol	2.5392 kcal/mol	2.11603 kcal/mol	171 180@LB@ \| \|@LB@5'-UUC...AUCCA CGUAA...UGU-3'@LB@ UGCCCUAC@LB@ \|:\|\|\|\|\|\|@LB@ AUGGGAUG@LB@3'-AUU...GAGAC -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -7.52 kcal/mol@LB@Hybridization Energy -12.1513 kcal/mol@LB@Unfolding Energy - mRNA 2.5392 kcal/mol@LB@Unfolding Energy - sRNA 2.11603 kcal/mol@LB@@LB@Position - mRNA 172 -- 179@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 173 -- 179@LB@Position Seed - sRNA 1 -- 7@LB@
37	0.0003769	0.03584	b1212	prmC	-14.52	0.001141	215 -- 228	43 -- 56	RF-1 and RF-2 N5-glutamine methyltransferase		_____________214____________229\n_____________\|______________\|\n5'-CGU...CAACA______________CAAUA...GCA-3'\n______________CUGGUUACGUGAAG\n______________\|:\|:\|\|\|\|\|\|\|\|\|\|\n______________GGCUAAUGCACUUC\n3'-AUU...GUUUA______________AUUUU...AUG-5'\n_____________\|______________\|\n_____________57_____________42\n	222 -- 228	43 -- 49	-20.863 kcal/mol	3.08488 kcal/mol	3.27327 kcal/mol	214 229@LB@ \| \|@LB@5'-CGU...CAACA CAAUA...GCA-3'@LB@ CUGGUUACGUGAAG@LB@ \|:\|:\|\|\|\|\|\|\|\|\|\|@LB@ GGCUAAUGCACUUC@LB@3'-AUU...GUUUA AUUUU...AUG-5'@LB@ \| \|@LB@ 57 42@LB@@LB@@LB@Energy -14.52 kcal/mol@LB@Hybridization Energy -20.863 kcal/mol@LB@Unfolding Energy - mRNA 3.08488 kcal/mol@LB@Unfolding Energy - sRNA 3.27327 kcal/mol@LB@@LB@Position - mRNA 215 -- 228@LB@Position - sRNA 43 -- 56@LB@Position Seed - mRNA 222 -- 228@LB@Position Seed - sRNA 43 -- 49@LB@
68	0.001174	0.05856	b1253	yciA	-8.30	0.130708	128 -- 145	3 -- 21	acyl-CoA esterase		_____________127__________________146\n_____________\|____________________\|\n5'-UUU...CGCUG______________UC____CAGGA...GGU-3'\n______________UAUCU__CCUCUGU__UCCU\n______________:\|\|\|\|__\|\|\|\|\|\|\|__:\|\|\|\n______________GUAGA__GGAGACA__GGGA\n3'-AUU...AUCUU_____AU_______U_____UG-5'\n_____________\|____________________\|\n_____________22___________________2\n	133 -- 139	8 -- 14	-17.321 kcal/mol	1.04882 kcal/mol	7.99052 kcal/mol	127 146@LB@ \| \|@LB@5'-UUU...CGCUG UC CAGGA...GGU-3'@LB@ UAUCU CCUCUGU UCCU@LB@ :\|\|\|\| \|\|\|\|\|\|\| :\|\|\|@LB@ GUAGA GGAGACA GGGA@LB@3'-AUU...AUCUU AU U UG-5'@LB@ \| \|@LB@ 22 2@LB@@LB@@LB@Energy -8.30 kcal/mol@LB@Hybridization Energy -17.321 kcal/mol@LB@Unfolding Energy - mRNA 1.04882 kcal/mol@LB@Unfolding Energy - sRNA 7.99052 kcal/mol@LB@@LB@Position - mRNA 128 -- 145@LB@Position - sRNA 3 -- 21@LB@Position Seed - mRNA 133 -- 139@LB@Position Seed - sRNA 8 -- 14@LB@
5	1.055e-05	0.007422	b1287	yciW	-9.98	0.045809	266 -- 289	4 -- 27	putative oxidoreductase		_____________265______________________290\n_____________\|________________________\|\n5'-GUC...ACGGA___U______C________GU___GGAAG...CAA-3'\n______________GUA_GACGUU_UGCCUCUG__CCC\n______________:\|\|_:\|\|:\|:_\|:\|\|\|\|\|\|__\|\|\|\n______________UAU_UUGUAG_AUGGAGAC__GGG\n3'-AUU...CUUUC___C______A________AU___AUG-5'\n_____________\|________________________\|\n_____________28_______________________3\n	278 -- 284	9 -- 15	-26.8114 kcal/mol	8.80708 kcal/mol	8.0435 kcal/mol	265 290@LB@ \| \|@LB@5'-GUC...ACGGA U C GU GGAAG...CAA-3'@LB@ GUA GACGUU UGCCUCUG CCC@LB@ :\|\| :\|\|:\|: \|:\|\|\|\|\|\| \|\|\|@LB@ UAU UUGUAG AUGGAGAC GGG@LB@3'-AUU...CUUUC C A AU AUG-5'@LB@ \| \|@LB@ 28 3@LB@@LB@@LB@Energy -9.98 kcal/mol@LB@Hybridization Energy -26.8114 kcal/mol@LB@Unfolding Energy - mRNA 8.80708 kcal/mol@LB@Unfolding Energy - sRNA 8.0435 kcal/mol@LB@@LB@Position - mRNA 266 -- 289@LB@Position - sRNA 4 -- 27@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 9 -- 15@LB@
53	0.0007581	0.04961	b1302	puuE	-16.93	0.000076	166 -- 207	20 -- 57	4-aminobutyrate aminotransferase PLP-dependent	b2662	_____________165_________________________________________208\n_____________\|___________________________________________\|\n5'-AGC...UAAUU________AC_______AGUC_______G_____C________ACAAU...CGC-3'\n______________UCCGAUUA__CGUGAAG____AAAAGGU_UGAAA_AU_GAGCA\n______________\|\|\|\|\|\|\|\|__\|\|\|\|\|\|\|____\|\|\|\|\|\|\|_\|\|\|\|\|_\|\|_\|\|:\|\|\n______________AGGCUAAU__GCACUUC____UUUUCCA_ACUUU_UA_CUUGU\n3'-AUU...GGUUU_________________A__________G_____C__U_____AGAAU...AUG-5'\n_____________\|___________________________________________\|\n_____________58__________________________________________19\n	176 -- 182	43 -- 49	-36.956 kcal/mol	7.85943 kcal/mol	12.1551 kcal/mol	165 208@LB@ \| \|@LB@5'-AGC...UAAUU AC AGUC G C ACAAU...CGC-3'@LB@ UCCGAUUA CGUGAAG AAAAGGU UGAAA AU GAGCA@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\|\|\| \|\| \|\|:\|\|@LB@ AGGCUAAU GCACUUC UUUUCCA ACUUU UA CUUGU@LB@3'-AUU...GGUUU A G C U AGAAU...AUG-5'@LB@ \| \|@LB@ 58 19@LB@@LB@@LB@Energy -16.93 kcal/mol@LB@Hybridization Energy -36.956 kcal/mol@LB@Unfolding Energy - mRNA 7.85943 kcal/mol@LB@Unfolding Energy - sRNA 12.1551 kcal/mol@LB@@LB@Position - mRNA 166 -- 207@LB@Position - sRNA 20 -- 57@LB@Position Seed - mRNA 176 -- 182@LB@Position Seed - sRNA 43 -- 49@LB@
59	0.0008996	0.0531	b1310	ycjN	-10.87	0.024752	113 -- 129	42 -- 59	putative ABC sugar transporter periplasmic binding protein		_____________112________________130\n_____________\|__________________\|\n5'-UUC...GUCGG__________________UGAUA...UUA-3'\n______________GAUCUGAUUA_GUGAAGU\n______________:\|\|\|:\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UUAGGCUAAU_CACUUCA\n3'-AUU...UCGGU__________G_______UUUUC...AUG-5'\n_____________\|__________________\|\n_____________60_________________41\n	123 -- 129	42 -- 48	-20.0101 kcal/mol	5.87569 kcal/mol	3.27976 kcal/mol	112 130@LB@ \| \|@LB@5'-UUC...GUCGG UGAUA...UUA-3'@LB@ GAUCUGAUUA GUGAAGU@LB@ :\|\|\|:\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UUAGGCUAAU CACUUCA@LB@3'-AUU...UCGGU G UUUUC...AUG-5'@LB@ \| \|@LB@ 60 41@LB@@LB@@LB@Energy -10.87 kcal/mol@LB@Hybridization Energy -20.0101 kcal/mol@LB@Unfolding Energy - mRNA 5.87569 kcal/mol@LB@Unfolding Energy - sRNA 3.27976 kcal/mol@LB@@LB@Position - mRNA 113 -- 129@LB@Position - sRNA 42 -- 59@LB@Position Seed - mRNA 123 -- 129@LB@Position Seed - sRNA 42 -- 48@LB@
80	0.001713	0.07533	b1343	dbpA	-13.62	0.002663	221 -- 243	1 -- 24	ATP-dependent RNA helicase specific for 23S rRNA		_____________220______________________244\n_____________\|________________________\|\n5'-ACG...ACCCU______________CC_____A__UCACG...CGC-3'\n______________GAAUGUUUUGCCUC___GCCC_AC\n______________\|\|\|::\|:\|\|:\|\|\|\|___:\|\|\|_\|\|\n______________CUUGUAGAAUGGAG___UGGG_UG\n3'-AUU...UCUAU______________ACA____A__-5'\n_____________\|_______________________\|\n_____________25______________________1\n	228 -- 234	11 -- 17	-24.5457 kcal/mol	2.92371 kcal/mol	8.02158 kcal/mol	220 244@LB@ \| \|@LB@5'-ACG...ACCCU CC A UCACG...CGC-3'@LB@ GAAUGUUUUGCCUC GCCC AC@LB@ \|\|\|::\|:\|\|:\|\|\|\| :\|\|\| \|\|@LB@ CUUGUAGAAUGGAG UGGG UG@LB@3'-AUU...UCUAU ACA A -5'@LB@ \| \|@LB@ 25 1@LB@@LB@@LB@Energy -13.62 kcal/mol@LB@Hybridization Energy -24.5457 kcal/mol@LB@Unfolding Energy - mRNA 2.92371 kcal/mol@LB@Unfolding Energy - sRNA 8.02158 kcal/mol@LB@@LB@Position - mRNA 221 -- 243@LB@Position - sRNA 1 -- 24@LB@Position Seed - mRNA 228 -- 234@LB@Position Seed - sRNA 11 -- 17@LB@
24	0.0002009	0.02687	b1487	ddpA	-9.43	0.065911	261 -- 269	48 -- 56	D D-dipeptide ABC transporter periplasmic binding protein		_____________260_______270\n_____________\|_________\|\n5'-UCA...AUUUC_________CACGC...UGA-3'\n______________CCGGUUGCG\n______________\|\|\|:\|\|:\|\|\n______________GGCUAAUGC\n3'-AUU...GUUUA_________ACUUC...AUG-5'\n_____________\|_________\|\n_____________57________47\n	263 -- 269	48 -- 54	-13.2683 kcal/mol	2.26031 kcal/mol	1.55919 kcal/mol	260 270@LB@ \| \|@LB@5'-UCA...AUUUC CACGC...UGA-3'@LB@ CCGGUUGCG@LB@ \|\|\|:\|\|:\|\|@LB@ GGCUAAUGC@LB@3'-AUU...GUUUA ACUUC...AUG-5'@LB@ \| \|@LB@ 57 47@LB@@LB@@LB@Energy -9.43 kcal/mol@LB@Hybridization Energy -13.2683 kcal/mol@LB@Unfolding Energy - mRNA 2.26031 kcal/mol@LB@Unfolding Energy - sRNA 1.55919 kcal/mol@LB@@LB@Position - mRNA 261 -- 269@LB@Position - sRNA 48 -- 56@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 48 -- 54@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

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

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

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching