Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
126	0.01383	0.3575	b1843	yobB	-8.48	0.503741	101 -- 118	168 -- 185	C-N hydrolase family protein	_____________100____________119\n_____________\|______________\|\n5'-CCU...AACUU____AG________UUUCU...CCA-3'\n______________AUAC__AGUUACAC\n______________\|\|\|\|__\|\|\|:\|\|\|\|\n______________UAUG__UCAGUGUG\n3'-UUU...GUGGU____AG________UACUA...UAG-5'\n_____________\|______________\|\n_____________186____________167\n	112 -- 118	168 -- 174	-13.9608 kcal/mol	3.09724 kcal/mol	0.286881 kcal/mol	100 119@LB@ \| \|@LB@5'-CCU...AACUU AG UUUCU...CCA-3'@LB@ AUAC AGUUACAC@LB@ \|\|\|\| \|\|\|:\|\|\|\|@LB@ UAUG UCAGUGUG@LB@3'-UUU...GUGGU AG UACUA...UAG-5'@LB@ \| \|@LB@ 186 167@LB@@LB@@LB@Energy -8.48 kcal/mol@LB@Hybridization Energy -13.9608 kcal/mol@LB@Unfolding Energy - mRNA 3.09724 kcal/mol@LB@Unfolding Energy - sRNA 0.286881 kcal/mol@LB@@LB@Position - mRNA 101 -- 118@LB@Position - sRNA 168 -- 185@LB@Position Seed - mRNA 112 -- 118@LB@Position Seed - sRNA 168 -- 174@LB@
82	0.008839	0.3575	b3680	yidL	-8.33	0.532337	91 -- 113	142 -- 164	AraC family putative transcriptional regulator	_____________90________________114\n_____________\|_________________\|\n5'-AAC...UGCGU________GCAG_____UUCUU...UGA-3'\n______________CGGGUCAG____UCAGA\n______________\|::\|\|\|\|:____\|\|\|\|\|\n______________GUUCAGUU____AGUCU\n3'-UUU...CGUCC________GAA______UAACG...UAG-5'\n_____________\|_________________\|\n_____________165_______________141\n	97 -- 103	151 -- 157	-14.3717 kcal/mol	4.36777 kcal/mol	4.37859 kcal/mol	90 114@LB@ \| \|@LB@5'-AAC...UGCGU GCAG UUCUU...UGA-3'@LB@ CGGGUCAG UCAGA@LB@ \|::\|\|\|\|: \|\|\|\|\|@LB@ GUUCAGUU AGUCU@LB@3'-UUU...CGUCC GAA UAACG...UAG-5'@LB@ \| \|@LB@ 165 141@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -14.3717 kcal/mol@LB@Unfolding Energy - mRNA 4.36777 kcal/mol@LB@Unfolding Energy - sRNA 4.37859 kcal/mol@LB@@LB@Position - mRNA 91 -- 113@LB@Position - sRNA 142 -- 164@LB@Position Seed - mRNA 97 -- 103@LB@Position Seed - sRNA 151 -- 157@LB@
160	0.01787	0.3749	b3935	priA	-8.27	0.542824	222 -- 250	110 -- 140	Primosome factor n' (replication factor Y)	_____________221_________________________251\n_____________\|___________________________\|\n5'-GAA...UAACC______AU___A_____G_________UAUGC...GCG-3'\n______________CACCGA__UUC_AGUCA_G_AUGAUGC\n______________\|\|\|\|:\|__:\|\|_\|\|\|\|\|_:_\|\|\|\|\|\|\|\n______________GUGGUU__GAG_UCAGU_U_UACUACG\n3'-UUU...AAAAU______AU_________G_G_______UCCGU...UAG-5'\n_____________\|___________________________\|\n_____________141_________________________109\n	193 -- 199	161 -- 167	-24.457 kcal/mol	4.47787 kcal/mol	7.72013 kcal/mol	221 251@LB@ \| \|@LB@5'-GAA...UAACC AU A G UAUGC...GCG-3'@LB@ CACCGA UUC AGUCA G AUGAUGC@LB@ \|\|\|\|:\| :\|\| \|\|\|\|\| : \|\|\|\|\|\|\|@LB@ GUGGUU GAG UCAGU U UACUACG@LB@3'-UUU...AAAAU AU G G UCCGU...UAG-5'@LB@ \| \|@LB@ 141 109@LB@@LB@@LB@Energy -8.27 kcal/mol@LB@Hybridization Energy -24.457 kcal/mol@LB@Unfolding Energy - mRNA 4.47787 kcal/mol@LB@Unfolding Energy - sRNA 7.72013 kcal/mol@LB@@LB@Position - mRNA 222 -- 250@LB@Position - sRNA 110 -- 140@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 161 -- 167@LB@
109	0.01201	0.3575	b1096	pabC	-8.08	0.578936	115 -- 139	144 -- 163	4-amino-4-deoxychorismate lyase component of para-aminobenzoate synthase multienzyme complex	_____________114____________140\n_____________\|______________\|\n5'-GUU...GUGUA_______CG_____GGUGG...ACG-3'\n______________ACUCCUU__GCUUC\n______________\|\|:\|\|:\|__\|\|\|\|\|\n______________UGGGGGA__CGAAG\n3'-UUU...CCCCG_______A______UAG-5'\n_____________\|______________\|\n_____________164____________143\n	29 -- 35	10 -- 16	-15.037 kcal/mol	0.971533 kcal/mol	6.96912 kcal/mol	114 140@LB@ \| \|@LB@5'-GUU...GUGUA CG GGUGG...ACG-3'@LB@ ACUCCUU GCUUC@LB@ \|\|:\|\|:\| \|\|\|\|\|@LB@ UGGGGGA CGAAG@LB@3'-UUU...CCCCG A UAG-5'@LB@ \| \|@LB@ 164 143@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -15.037 kcal/mol@LB@Unfolding Energy - mRNA 0.971533 kcal/mol@LB@Unfolding Energy - sRNA 6.96912 kcal/mol@LB@@LB@Position - mRNA 115 -- 139@LB@Position - sRNA 144 -- 163@LB@Position Seed - mRNA 29 -- 35@LB@Position Seed - sRNA 10 -- 16@LB@
199	0.02363	0.3833	b4141	yjeH	-8.04	0.585705	57 -- 67	64 -- 74	putative transporter	_____________56_____________68\n_____________\|______________\|\n5'-CAG...AAAUC___G_______C__AAAUU...CUG-3'\n______________UAC_CAGUUGC_CA\n______________\|\|\|_\|\|\|\|::\|_\|\|\n______________AUG_GUCAGUG_GU\n3'-UUU...UGGUU___A_______U__ACUAC...UAG-5'\n_____________\|______________\|\n_____________75_____________63\n	163 -- 169	170 -- 176	-11.2481 kcal/mol	2.09942 kcal/mol	0.433965 kcal/mol	56 68@LB@ \| \|@LB@5'-CAG...AAAUC G C AAAUU...CUG-3'@LB@ UAC CAGUUGC CA@LB@ \|\|\| \|\|\|\|::\| \|\|@LB@ AUG GUCAGUG GU@LB@3'-UUU...UGGUU A U ACUAC...UAG-5'@LB@ \| \|@LB@ 75 63@LB@@LB@@LB@Energy -8.04 kcal/mol@LB@Hybridization Energy -11.2481 kcal/mol@LB@Unfolding Energy - mRNA 2.09942 kcal/mol@LB@Unfolding Energy - sRNA 0.433965 kcal/mol@LB@@LB@Position - mRNA 57 -- 67@LB@Position - sRNA 64 -- 74@LB@Position Seed - mRNA 163 -- 169@LB@Position Seed - sRNA 170 -- 176@LB@
174	0.01972	0.3812	b0478	ybaL	-7.90	0.612018	5 -- 14	166 -- 176	inner membrane putative NAD(P)-binding transporter	_____________4___________15\n_____________\|___________\|\n_______5'-UUUA___________AAGCC...UGG-3'\n______________CAGUCGC_CAU\n______________\|\|\|\|\|:\|_\|\|\|\n______________GUCAGUG_GUA\n3'-UUU...UAUGA_______U___CUACG...UAG-5'\n_____________\|___________\|\n_____________177_________165\n	5 -- 11	170 -- 176	-11.743 kcal/mol	0.493889 kcal/mol	0.598087 kcal/mol	4 15@LB@ \| \|@LB@ 5'-UUUA AAGCC...UGG-3'@LB@ CAGUCGC CAU@LB@ \|\|\|\|\|:\| \|\|\|@LB@ GUCAGUG GUA@LB@3'-UUU...UAUGA U CUACG...UAG-5'@LB@ \| \|@LB@ 177 165@LB@@LB@@LB@Energy -7.90 kcal/mol@LB@Hybridization Energy -11.743 kcal/mol@LB@Unfolding Energy - mRNA 0.493889 kcal/mol@LB@Unfolding Energy - sRNA 0.598087 kcal/mol@LB@@LB@Position - mRNA 5 -- 14@LB@Position - sRNA 166 -- 176@LB@Position Seed - mRNA 5 -- 11@LB@Position Seed - sRNA 170 -- 176@LB@
195	0.02319	0.3833	b1233	ychJ	-7.86	0.620262	61 -- 80	1 -- 18	UPF0225 family protein	_____________60____________________________________81\n_____________\|_____________________________________\|\n5'-CUU...GCUAC_______________A___CUACU_____________ACGCC...UCA-3'\n______________UGCUCGGUUA_ACAU_GUG_____CAGGC_GGUUAAU\n______________\|:\|\|\|:\|\|:\|_\|\|\|\|_:\|\|_____\|\|\|\|\|_:\|\|:\|\|:\n______________AUGAGUCAGU_UGUA_UAC_____GUCCG_UCAGUUG\n3'-UUU...UGGUU__________G____C_____________U_______AAAGU...UAG-5'\n_____________\|_____________________________________\|\n_____________19____________________________________0\n	139 -- 145	171 -- 177	-29.0991 kcal/mol	9.80481 kcal/mol	8.18679 kcal/mol	60 81@LB@ \| \|@LB@5'-CUU...GCUAC A CUACU ACGCC...UCA-3'@LB@ UGCUCGGUUA ACAU GUG CAGGC GGUUAAU@LB@ \|:\|\|\|:\|\|:\| \|\|\|\| :\|\| \|\|\|\|\| :\|\|:\|\|:@LB@ AUGAGUCAGU UGUA UAC GUCCG UCAGUUG@LB@3'-UUU...UGGUU G C U AAAGU...UAG-5'@LB@ \| \|@LB@ 19 0@LB@@LB@@LB@Energy -7.86 kcal/mol@LB@Hybridization Energy -29.0991 kcal/mol@LB@Unfolding Energy - mRNA 9.80481 kcal/mol@LB@Unfolding Energy - sRNA 8.18679 kcal/mol@LB@@LB@Position - mRNA 61 -- 80@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 139 -- 145@LB@Position Seed - sRNA 171 -- 177@LB@
156	0.01739	0.3749	b4332	yjiJ	-7.83	0.625728	95 -- 115	80 -- 101	DUF1228 family putative inner membrane MFS superfamily transporter	_____________94_______116\n_____________\|________\|\n5'-AAC...GGUUU________ACAUC...UUU-3'\n______________GUCGCAUA\n______________\|\|\|:\|\|:\|\n______________CAGUGUGU\n3'-UUU...UGAGU________ACUAC...UAG-5'\n_____________\|________\|\n_____________102______79\n	23 -- 29	167 -- 173	-9.78459 kcal/mol	1.62979 kcal/mol	0.409692 kcal/mol	94 116@LB@ \| \|@LB@5'-AAC...GGUUU ACAUC...UUU-3'@LB@ GUCGCAUA@LB@ \|\|\|:\|\|:\|@LB@ CAGUGUGU@LB@3'-UUU...UGAGU ACUAC...UAG-5'@LB@ \| \|@LB@ 102 79@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -9.78459 kcal/mol@LB@Unfolding Energy - mRNA 1.62979 kcal/mol@LB@Unfolding Energy - sRNA 0.409692 kcal/mol@LB@@LB@Position - mRNA 95 -- 115@LB@Position - sRNA 80 -- 101@LB@Position Seed - mRNA 23 -- 29@LB@Position Seed - sRNA 167 -- 173@LB@
38	0.003319	0.2912	b3073	patA	-6.81	0.814367	213 -- 222	107 -- 116	putrescine:2-oxoglutaric acid aminotransferase PLP-dependent	_____________212________223\n_____________\|__________\|\n5'-CAU...GGUUA__________CAUCG...CAC-3'\n______________CCUUCGAGCG\n______________\|\|\|\|\|:\|\|\|:\n______________GGAAGUUCGU\n3'-UUU...AGUCA__________ACCAA...UAG-5'\n_____________\|__________\|\n_____________117________106\n	216 -- 222	107 -- 113	-14.0153 kcal/mol	3.04157 kcal/mol	5.58351 kcal/mol	212 223@LB@ \| \|@LB@5'-CAU...GGUUA CAUCG...CAC-3'@LB@ CCUUCGAGCG@LB@ \|\|\|\|\|:\|\|\|:@LB@ GGAAGUUCGU@LB@3'-UUU...AGUCA ACCAA...UAG-5'@LB@ \| \|@LB@ 117 106@LB@@LB@@LB@Energy -6.81 kcal/mol@LB@Hybridization Energy -14.0153 kcal/mol@LB@Unfolding Energy - mRNA 3.04157 kcal/mol@LB@Unfolding Energy - sRNA 5.58351 kcal/mol@LB@@LB@Position - mRNA 213 -- 222@LB@Position - sRNA 107 -- 116@LB@Position Seed - mRNA 216 -- 222@LB@Position Seed - sRNA 107 -- 113@LB@
171	0.01954	0.3812	b3687	ibpA	-6.40	0.875621	11 -- 20	10 -- 18	heat shock chaperone	_____________10____________21\n_____________\|_____________\|\n5'-AAC...GCCCC_______U_____AUAGA...GCU-3'\n______________CUCAGUC_AUGCA\n______________\|\|\|\|\|\|\|_\|::\|\|\n______________GAGUCAG_UGUGU\n3'-UUU...GUUAU_____________ACUAC...UAG-5'\n_____________\|_____________\|\n_____________19____________9\n	19 -- 25	172 -- 178	-14.2159 kcal/mol	5.36362 kcal/mol	0.433674 kcal/mol	10 21@LB@ \| \|@LB@5'-AAC...GCCCC U AUAGA...GCU-3'@LB@ CUCAGUC AUGCA@LB@ \|\|\|\|\|\|\| \|::\|\|@LB@ GAGUCAG UGUGU@LB@3'-UUU...GUUAU ACUAC...UAG-5'@LB@ \| \|@LB@ 19 9@LB@@LB@@LB@Energy -6.40 kcal/mol@LB@Hybridization Energy -14.2159 kcal/mol@LB@Unfolding Energy - mRNA 5.36362 kcal/mol@LB@Unfolding Energy - sRNA 0.433674 kcal/mol@LB@@LB@Position - mRNA 11 -- 20@LB@Position - sRNA 10 -- 18@LB@Position Seed - mRNA 19 -- 25@LB@Position Seed - sRNA 172 -- 178@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