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
148	0.00596	0.1406	b3426	glpD	-7.81	0.172743	213 -- 222	50 -- 59	sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding		_____________212________223\n_____________\|__________\|\n5'-AAC...CCAAA__________UGAUA...AGG-3'\n______________GAUCUGAUUG\n______________:\|\|\|:\|\|\|\|:\n______________UUAGGCUAAU\n3'-AUU...UCGGU__________GCACU...AUG-5'\n_____________\|__________\|\n_____________60_________49\n	216 -- 222	50 -- 56	-9.79708 kcal/mol	1.6903 kcal/mol	0.31771 kcal/mol	212 223@LB@ \| \|@LB@5'-AAC...CCAAA UGAUA...AGG-3'@LB@ GAUCUGAUUG@LB@ :\|\|\|:\|\|\|\|:@LB@ UUAGGCUAAU@LB@3'-AUU...UCGGU GCACU...AUG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -9.79708 kcal/mol@LB@Unfolding Energy - mRNA 1.6903 kcal/mol@LB@Unfolding Energy - sRNA 0.31771 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 50 -- 56@LB@
46	0.0005017	0.03778	b1713	pheT	-7.80	0.173677	95 -- 107	17 -- 29	phenylalanine tRNA synthetase beta subunit		_____________94____________108\n_____________\|_____________\|\n5'-CUG...GAUGG_____________GACUA...ACG-3'\n______________GGAUGGAGCGUCU\n______________:\|\|\|:\|\|:\|:\|\|\|\n______________UCUAUCUUGUAGA\n3'-AUU...GACUU_____________AUGGA...AUG-5'\n_____________\|_____________\|\n_____________30____________16\n	100 -- 106	18 -- 24	-17.5948 kcal/mol	5.55471 kcal/mol	4.26164 kcal/mol	94 108@LB@ \| \|@LB@5'-CUG...GAUGG GACUA...ACG-3'@LB@ GGAUGGAGCGUCU@LB@ :\|\|\|:\|\|:\|:\|\|\|@LB@ UCUAUCUUGUAGA@LB@3'-AUU...GACUU AUGGA...AUG-5'@LB@ \| \|@LB@ 30 16@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -17.5948 kcal/mol@LB@Unfolding Energy - mRNA 5.55471 kcal/mol@LB@Unfolding Energy - sRNA 4.26164 kcal/mol@LB@@LB@Position - mRNA 95 -- 107@LB@Position - sRNA 17 -- 29@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 18 -- 24@LB@
147	0.005606	0.1342	b3085	ygjP	-7.80	0.173342	13 -- 33	55 -- 72	putative metal dependent hydrolase		_____________12____________________34\n_____________\|_____________________\|\n5'-AAC...GCAGC_________UCC____CU___CACGC...AAC-3'\n______________AAAUAUUCA___GCCG__UCC\n______________\|\|\|\|\|\|\|\|\|___\|\|\|:__\|\|\|\n______________UUUAUAAGU___CGGU__AGG\n3'-AUU...CCGAU________________UU___CUAAU...AUG-5'\n_____________\|_____________________\|\n_____________73____________________54\n	14 -- 20	65 -- 71	-15.2572 kcal/mol	1.39359 kcal/mol	6.08601 kcal/mol	12 34@LB@ \| \|@LB@5'-AAC...GCAGC UCC CU CACGC...AAC-3'@LB@ AAAUAUUCA GCCG UCC@LB@ \|\|\|\|\|\|\|\|\| \|\|\|: \|\|\|@LB@ UUUAUAAGU CGGU AGG@LB@3'-AUU...CCGAU UU CUAAU...AUG-5'@LB@ \| \|@LB@ 73 54@LB@@LB@@LB@Energy -7.80 kcal/mol@LB@Hybridization Energy -15.2572 kcal/mol@LB@Unfolding Energy - mRNA 1.39359 kcal/mol@LB@Unfolding Energy - sRNA 6.08601 kcal/mol@LB@@LB@Position - mRNA 13 -- 33@LB@Position - sRNA 55 -- 72@LB@Position Seed - mRNA 14 -- 20@LB@Position Seed - sRNA 65 -- 71@LB@
60	0.0009057	0.0531	b2740	ygbN	-7.72	0.181404	16 -- 72	3 -- 58	putative transporter		_____________15__________________________________________________________73\n_____________\|___________________________________________________________\|\n5'-GUG...CGCCU_______G_G_____A__UC___G_____UC___UGU______AA__________G___CACCG...UCC-3'\n______________GUUCGAU_A_GUGGG_UA__AGG_CUGGA__GGU___GAAUAU___ACCUC_GUG_CCU\n______________:\|:\|\|\|\|_\|_\|\|\|::_\|\|__\|\|\|_\|\|\|:\|__\|:\|___\|\|\|:\|\|___\|\|\|\|\|_\|\|:_\|\|\|\n______________UAGGCUA_U_CACUU_AU__UCC_GACUU__CUA___CUUGUA___UGGAG_CAU_GGA\n3'-AUU...CGGUU_______A_G_____C__UU___A_____U____U________GAA_____A___G___UG-5'\n_____________\|___________________________________________________________\|\n_____________59__________________________________________________________2\n	16 -- 22	52 -- 58	-40.891 kcal/mol	20.495 kcal/mol	12.7026 kcal/mol	15 73@LB@ \| \|@LB@5'-GUG...CGCCU G G A UC G UC UGU AA G CACCG...UCC-3'@LB@ GUUCGAU A GUGGG UA AGG CUGGA GGU GAAUAU ACCUC GUG CCU@LB@ :\|:\|\|\|\| \| \|\|\|:: \|\| \|\|\| \|\|\|:\| \|:\| \|\|\|:\|\| \|\|\|\|\| \|\|: \|\|\|@LB@ UAGGCUA U CACUU AU UCC GACUU CUA CUUGUA UGGAG CAU GGA@LB@3'-AUU...CGGUU A G C UU A U U GAA A G UG-5'@LB@ \| \|@LB@ 59 2@LB@@LB@@LB@Energy -7.72 kcal/mol@LB@Hybridization Energy -40.891 kcal/mol@LB@Unfolding Energy - mRNA 20.495 kcal/mol@LB@Unfolding Energy - sRNA 12.7026 kcal/mol@LB@@LB@Position - mRNA 16 -- 72@LB@Position - sRNA 3 -- 58@LB@Position Seed - mRNA 16 -- 22@LB@Position Seed - sRNA 52 -- 58@LB@
97	0.002764	0.1002	b3935	priA	-7.71	0.181779	237 -- 247	3 -- 14	Primosome factor n' (replication factor Y)		_____________236__________248\n_____________\|____________\|\n5'-GAA...CGCUU____________UGACU...GCG-3'\n______________CCUC_GUACCUU\n______________\|\|\|\|_\|\|\|\|\|:\|\n______________GGAG_CAUGGGA\n3'-AUU...AGAAU____A_______UG-5'\n_____________\|____________\|\n_____________15___________2\n	241 -- 247	3 -- 9	-14.2439 kcal/mol	1.19768 kcal/mol	5.35591 kcal/mol	236 248@LB@ \| \|@LB@5'-GAA...CGCUU UGACU...GCG-3'@LB@ CCUC GUACCUU@LB@ \|\|\|\| \|\|\|\|\|:\|@LB@ GGAG CAUGGGA@LB@3'-AUU...AGAAU A UG-5'@LB@ \| \|@LB@ 15 2@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -14.2439 kcal/mol@LB@Unfolding Energy - mRNA 1.19768 kcal/mol@LB@Unfolding Energy - sRNA 5.35591 kcal/mol@LB@@LB@Position - mRNA 237 -- 247@LB@Position - sRNA 3 -- 14@LB@Position Seed - mRNA 241 -- 247@LB@Position Seed - sRNA 3 -- 9@LB@
163	0.006545	0.1413	b0532	sfmD	-7.71	0.181786	104 -- 132	48 -- 76	putative outer membrane export usher protein	b3144 b4317 b0940	_____________103____________________________133\n_____________\|______________________________\|\n5'-UCA...GGAAA______________A___UUAA________GUUCA...GCU-3'\n______________GCUGAAAU_UUCAG_CCG____UGAUUAUG\n______________\|\|\|:\|\|\|\|_\|\|\|\|\|_\|\|:____:\|\|\|\|\|:\|\n______________CGAUUUUA_AAGUC_GGU____GCUAAUGC\n3'-AUU...CCCGC________U_________UUAG________ACUUC...AUG-5'\n_____________\|______________________________\|\n_____________77_____________________________47\n	126 -- 132	48 -- 54	-23.9612 kcal/mol	8.59534 kcal/mol	7.67378 kcal/mol	103 133@LB@ \| \|@LB@5'-UCA...GGAAA A UUAA GUUCA...GCU-3'@LB@ GCUGAAAU UUCAG CCG UGAUUAUG@LB@ \|\|\|:\|\|\|\| \|\|\|\|\| \|\|: :\|\|\|\|\|:\|@LB@ CGAUUUUA AAGUC GGU GCUAAUGC@LB@3'-AUU...CCCGC U UUAG ACUUC...AUG-5'@LB@ \| \|@LB@ 77 47@LB@@LB@@LB@Energy -7.71 kcal/mol@LB@Hybridization Energy -23.9612 kcal/mol@LB@Unfolding Energy - mRNA 8.59534 kcal/mol@LB@Unfolding Energy - sRNA 7.67378 kcal/mol@LB@@LB@Position - mRNA 104 -- 132@LB@Position - sRNA 48 -- 76@LB@Position Seed - mRNA 126 -- 132@LB@Position Seed - sRNA 48 -- 54@LB@
140	0.005114	0.1284	b3993	thiE	-7.64	0.188958	243 -- 250	4 -- 11	thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)		_____________242______251\n_____________\|________\|\n5'-CAC...CAGGA________GGUGG...UAC-3'\n______________CUGUACCC\n______________\|\|\|\|\|\|\|\|\n______________GACAUGGG\n3'-AUU...AUGGA________AUG-5'\n_____________\|________\|\n_____________12_______3\n	244 -- 250	4 -- 10	-13.9053 kcal/mol	2.83489 kcal/mol	3.45361 kcal/mol	242 251@LB@ \| \|@LB@5'-CAC...CAGGA GGUGG...UAC-3'@LB@ CUGUACCC@LB@ \|\|\|\|\|\|\|\|@LB@ GACAUGGG@LB@3'-AUU...AUGGA AUG-5'@LB@ \| \|@LB@ 12 3@LB@@LB@@LB@Energy -7.64 kcal/mol@LB@Hybridization Energy -13.9053 kcal/mol@LB@Unfolding Energy - mRNA 2.83489 kcal/mol@LB@Unfolding Energy - sRNA 3.45361 kcal/mol@LB@@LB@Position - mRNA 243 -- 250@LB@Position - sRNA 4 -- 11@LB@Position Seed - mRNA 244 -- 250@LB@Position Seed - sRNA 4 -- 10@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@
195	0.008707	0.1558	b3318	rplW	-7.58	0.194751	202 -- 213	43 -- 55	50S ribosomal subunit protein L23		_____________201___________214\n_____________\|_____________\|\n5'-GCA...UGGCA_____________AACGU...AAG-3'\n______________UGAUU_CGUGAAG\n______________:\|\|\|\|_\|\|\|\|\|\|\|\n______________GCUAA_GCACUUC\n3'-AUU...UUUAG_____U_______AUUUU...AUG-5'\n_____________\|_____________\|\n_____________56____________42\n	207 -- 213	43 -- 49	-13.4464 kcal/mol	2.60751 kcal/mol	3.2693 kcal/mol	201 214@LB@ \| \|@LB@5'-GCA...UGGCA AACGU...AAG-3'@LB@ UGAUU CGUGAAG@LB@ :\|\|\|\| \|\|\|\|\|\|\|@LB@ GCUAA GCACUUC@LB@3'-AUU...UUUAG U AUUUU...AUG-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.58 kcal/mol@LB@Hybridization Energy -13.4464 kcal/mol@LB@Unfolding Energy - mRNA 2.60751 kcal/mol@LB@Unfolding Energy - sRNA 3.2693 kcal/mol@LB@@LB@Position - mRNA 202 -- 213@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 207 -- 213@LB@Position Seed - sRNA 43 -- 49@LB@
166	0.006804	0.1439	b0475	hemH	-7.56	0.197603	220 -- 228	1 -- 9	ferrochelatase		_____________219_______229\n_____________\|_________\|\n5'-CGG...AACCG_________UGGCA...GCG-3'\n______________GUAUCCUGC\n______________\|\|\|:\|\|\|:\|\n______________CAUGGGAUG\n3'-AUU...GGAGA_________-5'\n_____________\|________\|\n_____________10_______1\n	222 -- 228	1 -- 7	-12.5413 kcal/mol	2.87943 kcal/mol	2.12872 kcal/mol	219 229@LB@ \| \|@LB@5'-CGG...AACCG UGGCA...GCG-3'@LB@ GUAUCCUGC@LB@ \|\|\|:\|\|\|:\|@LB@ CAUGGGAUG@LB@3'-AUU...GGAGA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -7.56 kcal/mol@LB@Hybridization Energy -12.5413 kcal/mol@LB@Unfolding Energy - mRNA 2.87943 kcal/mol@LB@Unfolding Energy - sRNA 2.12872 kcal/mol@LB@@LB@Position - mRNA 220 -- 228@LB@Position - sRNA 1 -- 9@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)

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