Input and runtime details for job 6756176 (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 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

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
175	0.01993	0.3669	b0183	rnhB	-5.94	0.199165	195 -- 215	23 -- 41	ribonuclease HII degrades RNA of DNA-RNA hybrids	_____________194___________________216\n_____________\|_____________________\|\n5'-AAU...GAGUU_____AA___UC_________UAUCC...UCC-3'\n______________AGCAC__UGA__GAAUUUGUU\n______________\|\|\|\|\|__\|:\|__:\|\|\|\|:\|\|\|\n______________UCGUG__AUU__UUUAAGCAA\n3'-UUU...GUUCU_____A____U__________UGUGG...CAA-5'\n_____________\|_____________________\|\n_____________42____________________22\n	209 -- 215	23 -- 29	-11.3649 kcal/mol	3.77136 kcal/mol	1.64896 kcal/mol	194 216@LB@ \| \|@LB@5'-AAU...GAGUU AA UC UAUCC...UCC-3'@LB@ AGCAC UGA GAAUUUGUU@LB@ \|\|\|\|\| \|:\| :\|\|\|\|:\|\|\|@LB@ UCGUG AUU UUUAAGCAA@LB@3'-UUU...GUUCU A U UGUGG...CAA-5'@LB@ \| \|@LB@ 42 22@LB@@LB@@LB@Energy -5.94 kcal/mol@LB@Hybridization Energy -11.3649 kcal/mol@LB@Unfolding Energy - mRNA 3.77136 kcal/mol@LB@Unfolding Energy - sRNA 1.64896 kcal/mol@LB@@LB@Position - mRNA 195 -- 215@LB@Position - sRNA 23 -- 41@LB@Position Seed - mRNA 209 -- 215@LB@Position Seed - sRNA 23 -- 29@LB@
124	0.01089	0.2829	b0186	ldcC	-10.51	0.011388	34 -- 66	24 -- 58	lysine decarboxylase 2 constitutive	_____________33___________________________________67\n_____________\|____________________________________\|\n5'-AAA...AUCUC___G__________CU____________________CGUUA...UUA-3'\n______________GAC_UG_UUAAGCA__GAAG_AUUUAAAAAA_UCGU\n______________:\|\|_\|\|_\|\|\|\|\|\|\|__\|\|\|\|_\|:\|\|\|\|\|\|\|\|_\|\|\|\|\n______________UUG_AC_AAUUCGU__CUUC_UGAAUUUUUU_AGCA\n3'-UUU...CUACU___A__G_______U_____G__________A____AUGUG...CAA-5'\n_____________\|____________________________________\|\n_____________59___________________________________23\n	53 -- 59	32 -- 38	-24.2219 kcal/mol	7.43557 kcal/mol	6.27608 kcal/mol	33 67@LB@ \| \|@LB@5'-AAA...AUCUC G CU CGUUA...UUA-3'@LB@ GAC UG UUAAGCA GAAG AUUUAAAAAA UCGU@LB@ :\|\| \|\| \|\|\|\|\|\|\| \|\|\|\| \|:\|\|\|\|\|\|\|\| \|\|\|\|@LB@ UUG AC AAUUCGU CUUC UGAAUUUUUU AGCA@LB@3'-UUU...CUACU A G U G A AUGUG...CAA-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.51 kcal/mol@LB@Hybridization Energy -24.2219 kcal/mol@LB@Unfolding Energy - mRNA 7.43557 kcal/mol@LB@Unfolding Energy - sRNA 6.27608 kcal/mol@LB@@LB@Position - mRNA 34 -- 66@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 32 -- 38@LB@
54	0.002706	0.1597	b0200	gmhB	-8.11	0.056337	123 -- 141	35 -- 53	D D-heptose 1 7-bisphosphate phosphatase	_____________122_________________142\n_____________\|___________________\|\n5'-AAA...AUCAG_____U____A________UCUUG...ACG-3'\n______________GUUUA_GCGA_GAGCACUU\n______________\|:\|\|\|_\|\|:\|_:\|\|\|\|\|\|\|\n______________CGAAU_CGUU_UUCGUGAA\n3'-UUU...UUGAA_____U____C________UUUUU...CAA-5'\n_____________\|___________________\|\n_____________54__________________34\n	135 -- 141	35 -- 41	-19.8402 kcal/mol	5.62708 kcal/mol	6.10399 kcal/mol	122 142@LB@ \| \|@LB@5'-AAA...AUCAG U A UCUUG...ACG-3'@LB@ GUUUA GCGA GAGCACUU@LB@ \|:\|\|\| \|\|:\| :\|\|\|\|\|\|\|@LB@ CGAAU CGUU UUCGUGAA@LB@3'-UUU...UUGAA U C UUUUU...CAA-5'@LB@ \| \|@LB@ 54 34@LB@@LB@@LB@Energy -8.11 kcal/mol@LB@Hybridization Energy -19.8402 kcal/mol@LB@Unfolding Energy - mRNA 5.62708 kcal/mol@LB@Unfolding Energy - sRNA 6.10399 kcal/mol@LB@@LB@Position - mRNA 123 -- 141@LB@Position - sRNA 35 -- 53@LB@Position Seed - mRNA 135 -- 141@LB@Position Seed - sRNA 35 -- 41@LB@
83	0.005546	0.2146	b0221	fadE	-11.24	0.006780	20 -- 32	37 -- 49	acyl coenzyme A dehydrogenase	_____________19____________33\n_____________\|_____________\|\n5'-GUG...GCCAA_____________GGGCA...GGA-3'\n______________AAGCGAGAAGUAC\n______________\|\|\|\|:\|\|\|\|\|:\|\|\n______________UUCGUUCUUCGUG\n3'-UUU...ACGAA_____________AAUUU...CAA-5'\n_____________\|_____________\|\n_____________50____________36\n	26 -- 32	37 -- 43	-19.9972 kcal/mol	2.7283 kcal/mol	6.03369 kcal/mol	19 33@LB@ \| \|@LB@5'-GUG...GCCAA GGGCA...GGA-3'@LB@ AAGCGAGAAGUAC@LB@ \|\|\|\|:\|\|\|\|\|:\|\|@LB@ UUCGUUCUUCGUG@LB@3'-UUU...ACGAA AAUUU...CAA-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.24 kcal/mol@LB@Hybridization Energy -19.9972 kcal/mol@LB@Unfolding Energy - mRNA 2.7283 kcal/mol@LB@Unfolding Energy - sRNA 6.03369 kcal/mol@LB@@LB@Position - mRNA 20 -- 32@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 26 -- 32@LB@Position Seed - sRNA 37 -- 43@LB@
55	0.002761	0.1597	b0238	gpt	-5.76	0.219641	15 -- 42	30 -- 59	xanthine phosphoribosyltransferase; xanthine-guanine phosphoribosyltransferase	_____________14_____________________________43\n_____________\|______________________________\|\n5'-AUG...ACACA____AG____________UAUG________UACCA...UUG-3'\n______________AGAC__GCUU__GCGAGA____UUUGAGAA\n______________\|:\|\|__\|\|\|\|__\|\|:\|\|\|____:\|\|:\|:\|\|\n______________UUUG__CGAA__CGUUCU____GAAUUUUU\n3'-UUU...CCUAC____AA____UU______UCGU________UAAGC...CAA-5'\n_____________\|______________________________\|\n_____________60_____________________________29\n	36 -- 42	30 -- 36	-17.3334 kcal/mol	5.3037 kcal/mol	6.27042 kcal/mol	14 43@LB@ \| \|@LB@5'-AUG...ACACA AG UAUG UACCA...UUG-3'@LB@ AGAC GCUU GCGAGA UUUGAGAA@LB@ \|:\|\| \|\|\|\| \|\|:\|\|\| :\|\|:\|:\|\|@LB@ UUUG CGAA CGUUCU GAAUUUUU@LB@3'-UUU...CCUAC AA UU UCGU UAAGC...CAA-5'@LB@ \| \|@LB@ 60 29@LB@@LB@@LB@Energy -5.76 kcal/mol@LB@Hybridization Energy -17.3334 kcal/mol@LB@Unfolding Energy - mRNA 5.3037 kcal/mol@LB@Unfolding Energy - sRNA 6.27042 kcal/mol@LB@@LB@Position - mRNA 15 -- 42@LB@Position - sRNA 30 -- 59@LB@Position Seed - mRNA 36 -- 42@LB@Position Seed - sRNA 30 -- 36@LB@
172	0.01959	0.3668	b0336	codB	-6.02	0.190787	88 -- 108	28 -- 40	cytosine transporter	_____________87____________________109\n_____________\|_____________________\|\n5'-CCA...UUUUU_____CAUUCAUA________AUAUU...UUU-3'\n______________GCACU________UAAAAAAU\n______________\|\|\|\|\|________\|\|\|\|\|\|\|\|\n______________CGUGA________AUUUUUUA\n3'-UUU...UUCUU_____________________AGCAA...CAA-5'\n_____________\|_____________________\|\n_____________41____________________27\n	102 -- 108	28 -- 34	-8.50412 kcal/mol	0.843154 kcal/mol	1.63611 kcal/mol	87 109@LB@ \| \|@LB@5'-CCA...UUUUU CAUUCAUA AUAUU...UUU-3'@LB@ GCACU UAAAAAAU@LB@ \|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ CGUGA AUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -6.02 kcal/mol@LB@Hybridization Energy -8.50412 kcal/mol@LB@Unfolding Energy - mRNA 0.843154 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 88 -- 108@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 102 -- 108@LB@Position Seed - sRNA 28 -- 34@LB@
163	0.0182	0.3566	b0397	sbcC	-8.10	0.056577	196 -- 210	26 -- 43	exonuclease dsDNA ATP-dependent	_____________195________________211\n_____________\|__________________\|\n5'-GAA...AACAC__________________UCAGC...UUG-3'\n______________GAAGCAU___GAAAAUUC\n______________\|\|\|\|\|\|:___:\|\|\|\|\|\|\|\n______________CUUCGUG___UUUUUAAG\n3'-UUU...UCGUU_______AAU________CAAUG...CAA-5'\n_____________\|__________________\|\n_____________44_________________25\n	204 -- 210	26 -- 32	-13.6528 kcal/mol	1.79109 kcal/mol	3.75931 kcal/mol	195 211@LB@ \| \|@LB@5'-GAA...AACAC UCAGC...UUG-3'@LB@ GAAGCAU GAAAAUUC@LB@ \|\|\|\|\|\|: :\|\|\|\|\|\|\|@LB@ CUUCGUG UUUUUAAG@LB@3'-UUU...UCGUU AAU CAAUG...CAA-5'@LB@ \| \|@LB@ 44 25@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -13.6528 kcal/mol@LB@Unfolding Energy - mRNA 1.79109 kcal/mol@LB@Unfolding Energy - sRNA 3.75931 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 26 -- 43@LB@Position Seed - mRNA 204 -- 210@LB@Position Seed - sRNA 26 -- 32@LB@
35	0.001338	0.121	b0405	queA	-9.92	0.017135	73 -- 106	26 -- 60	S-adenosylmethionine:tRNA ribosyltransferase-isomerase	_____________72____________________________________107\n_____________\|_____________________________________\|\n5'-GGG...UCCGC_____GG___A__U_____U_________________AUCGA...GGC-3'\n______________GAGAU__GCU_AA_GCAGG_GAGC___UAAAAAAUUC\n______________\|\|:\|:__\|\|\|_\|\|_\|\|\|:\|_:\|\|\|___\|\|\|\|\|\|\|\|\|\|\n______________CUUUG__CGA_UU_CGUUC_UUCG___AUUUUUUAAG\n3'-UUU...CCCUA_____AA___A_____________UGA__________CAAUG...CAA-5'\n_____________\|_____________________________________\|\n_____________61____________________________________25\n	100 -- 106	26 -- 32	-25.4572 kcal/mol	9.25896 kcal/mol	6.27609 kcal/mol	72 107@LB@ \| \|@LB@5'-GGG...UCCGC GG A U U AUCGA...GGC-3'@LB@ GAGAU GCU AA GCAGG GAGC UAAAAAAUUC@LB@ \|\|:\|: \|\|\| \|\| \|\|\|:\| :\|\|\| \|\|\|\|\|\|\|\|\|\|@LB@ CUUUG CGA UU CGUUC UUCG AUUUUUUAAG@LB@3'-UUU...CCCUA AA A UGA CAAUG...CAA-5'@LB@ \| \|@LB@ 61 25@LB@@LB@@LB@Energy -9.92 kcal/mol@LB@Hybridization Energy -25.4572 kcal/mol@LB@Unfolding Energy - mRNA 9.25896 kcal/mol@LB@Unfolding Energy - sRNA 6.27609 kcal/mol@LB@@LB@Position - mRNA 73 -- 106@LB@Position - sRNA 26 -- 60@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 26 -- 32@LB@
77	0.004637	0.1935	b0407	yajC	-7.39	0.087827	147 -- 158	37 -- 48	SecYEG protein translocase auxillary subunit	_____________146__________159\n_____________\|____________\|\n5'-UCU...UCAGG____________CACCU...UUU-3'\n______________GGCGAGAAGUAC\n______________:\|\|:\|\|\|\|\|:\|\|\n______________UCGUUCUUCGUG\n3'-UUU...CGAAU____________AAUUU...CAA-5'\n_____________\|____________\|\n_____________49___________36\n	152 -- 158	37 -- 43	-17.5904 kcal/mol	4.37033 kcal/mol	5.83483 kcal/mol	146 159@LB@ \| \|@LB@5'-UCU...UCAGG CACCU...UUU-3'@LB@ GGCGAGAAGUAC@LB@ :\|\|:\|\|\|\|\|:\|\|@LB@ UCGUUCUUCGUG@LB@3'-UUU...CGAAU AAUUU...CAA-5'@LB@ \| \|@LB@ 49 36@LB@@LB@@LB@Energy -7.39 kcal/mol@LB@Hybridization Energy -17.5904 kcal/mol@LB@Unfolding Energy - mRNA 4.37033 kcal/mol@LB@Unfolding Energy - sRNA 5.83483 kcal/mol@LB@@LB@Position - mRNA 147 -- 158@LB@Position - sRNA 37 -- 48@LB@Position Seed - mRNA 152 -- 158@LB@Position Seed - sRNA 37 -- 43@LB@
67	0.003475	0.1645	b0416	nusB	-6.41	0.154688	140 -- 154	27 -- 40	transcription antitermination protein	_____________139_____________155\n_____________\|_______________\|\n5'-AAG...UGACC__________U____AAUGU...AGU-3'\n______________GCGCUUGAAA_GAUU\n______________\|\|:\|\|\|:\|\|\|_:\|\|\|\n______________CGUGAAUUUU_UUAA\n3'-UUU...UUCUU_______________GCAAU...CAA-5'\n_____________\|_______________\|\n_____________41______________26\n	142 -- 148	32 -- 38	-12.213 kcal/mol	4.16264 kcal/mol	1.6425 kcal/mol	139 155@LB@ \| \|@LB@5'-AAG...UGACC U AAUGU...AGU-3'@LB@ GCGCUUGAAA GAUU@LB@ \|\|:\|\|\|:\|\|\| :\|\|\|@LB@ CGUGAAUUUU UUAA@LB@3'-UUU...UUCUU GCAAU...CAA-5'@LB@ \| \|@LB@ 41 26@LB@@LB@@LB@Energy -6.41 kcal/mol@LB@Hybridization Energy -12.213 kcal/mol@LB@Unfolding Energy - mRNA 4.16264 kcal/mol@LB@Unfolding Energy - sRNA 1.6425 kcal/mol@LB@@LB@Position - mRNA 140 -- 154@LB@Position - sRNA 27 -- 40@LB@Position Seed - mRNA 142 -- 148@LB@Position Seed - sRNA 32 -- 38@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