Input and runtime details for job 5344133 (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 5344133 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:28:43 CET 2018
	CopraRNA Started		@ Fri Feb 16 20:36:11 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:15:51 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:15:58 CET 2018
	Job Completed		@ Sat Feb 17 02:16:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5344133&toolName=CopraRNA ( 30 days expiry )

Description of the job

RybB

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
61	0.00311	0.1789	b0224	yafK	-14.83	0.030578	183 -- 204	1 -- 20	L D-transpeptidase-related protein		_____________182____________________205\n_____________\|______________________\|\n5'-UUA...CGUUU__________U_______AU__GUAAA...AAG-3'\n______________UAUCAAGGAA_AAGCAGU__GC\n______________:\|\|\|\|\|:\|\|\|_\|\|\|\|\|\|\|__\|\|\n______________GUAGUUUCUU_UUCGUCA__CG\n3'-UUU...CCCCU__________________C___-5'\n_____________\|_____________________\|\n_____________21____________________1\n	194 -- 200	4 -- 10	-21.3079 kcal/mol	5.02402 kcal/mol	1.45855 kcal/mol	182 205@LB@ \| \|@LB@5'-UUA...CGUUU U AU GUAAA...AAG-3'@LB@ UAUCAAGGAA AAGCAGU GC@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|\|\|\| \|\|@LB@ GUAGUUUCUU UUCGUCA CG@LB@3'-UUU...CCCCU C -5'@LB@ \| \|@LB@ 21 1@LB@@LB@@LB@Energy -14.83 kcal/mol@LB@Hybridization Energy -21.3079 kcal/mol@LB@Unfolding Energy - mRNA 5.02402 kcal/mol@LB@Unfolding Energy - sRNA 1.45855 kcal/mol@LB@@LB@Position - mRNA 183 -- 204@LB@Position - sRNA 1 -- 20@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 4 -- 10@LB@
62	0.003256	0.1843	b1243	oppA	-14.22	0.042360	208 -- 232	1 -- 21	oligopeptide ABC transporter periplasmic binding protein		_____________207_______________________233\n_____________\|_________________________\|\n5'-UGU...GACCA______CC_________UU___A__AGCUG...UCA-3'\n______________ACAUCA__AAGAGAAGU__AGU_GC\n______________\|\|\|\|\|\|__\|\|\|\|:\|\|\|:__\|\|\|_\|\|\n______________UGUAGU__UUCUUUUCG__UCA_CG\n3'-UUU...ACCCC______________________C__-5'\n_____________\|________________________\|\n_____________22_______________________1\n	218 -- 224	7 -- 13	-18.9529 kcal/mol	3.22094 kcal/mol	1.51103 kcal/mol	207 233@LB@ \| \|@LB@5'-UGU...GACCA CC UU A AGCUG...UCA-3'@LB@ ACAUCA AAGAGAAGU AGU GC@LB@ \|\|\|\|\|\| \|\|\|\|:\|\|\|: \|\|\| \|\|@LB@ UGUAGU UUCUUUUCG UCA CG@LB@3'-UUU...ACCCC C -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -14.22 kcal/mol@LB@Hybridization Energy -18.9529 kcal/mol@LB@Unfolding Energy - mRNA 3.22094 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 208 -- 232@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 218 -- 224@LB@Position Seed - sRNA 7 -- 13@LB@
63	0.003337	0.1851	b1453	ansP	-14.01	0.047364	263 -- 293	1 -- 34	L-asparagine transporter		_____________262_________________________________294\n_____________\|___________________________________\|\n5'-GUC...AAUGC________A__________C_________AUG___AAUCGCC-3'\n______________CCACGAAG_GGGG_UAUCA____AAAGCG___GGC\n______________\|\|\|\|:\|\|:_\|\|\|\|_:\|\|\|\|____\|\|\|\|\|:___\|\|\|\n______________GGUGUUUU_CCCC_GUAGU____UUUCGU___CCG\n3'-UUU...CCCGA________A____U_____UUCU______CA____-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	263 -- 269	28 -- 34	-31.7064 kcal/mol	13.4305 kcal/mol	4.26884 kcal/mol	262 294@LB@ \| \|@LB@5'-GUC...AAUGC A C AUG AAUCGCC-3'@LB@ CCACGAAG GGGG UAUCA AAAGCG GGC@LB@ \|\|\|\|:\|\|: \|\|\|\| :\|\|\|\| \|\|\|\|\|: \|\|\|@LB@ GGUGUUUU CCCC GUAGU UUUCGU CCG@LB@3'-UUU...CCCGA A U UUCU CA -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -14.01 kcal/mol@LB@Hybridization Energy -31.7064 kcal/mol@LB@Unfolding Energy - mRNA 13.4305 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 263 -- 293@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 263 -- 269@LB@Position Seed - sRNA 28 -- 34@LB@
64	0.003422	0.1851	b4238	nrdD	-18.31	0.003326	69 -- 106	1 -- 34	anaerobic ribonucleoside-triphosphate reductase		_____________68_____________________________________107\n_____________\|______________________________________\|\n5'-UAU...GCUCC________AA__U_C_______U___U______A____GAUUG...UCG-3'\n______________CCACGAAA__GG_G_GGCGUUG_GGA_AAGCGG_UGGC\n______________\|\|\|\|:\|\|\|__\|\|_\|_\|:\|:\|::_:\|\|_\|\|\|\|:\|_\|\|\|\|\n______________GGUGUUUU__CC_C_CUGUAGU_UCU_UUCGUC_ACCG\n3'-UUU...CCCGA________A_____________U___U___________-5'\n_____________\|_____________________________________\|\n_____________35____________________________________1\n	84 -- 90	16 -- 22	-34.2754 kcal/mol	11.6957 kcal/mol	4.26884 kcal/mol	68 107@LB@ \| \|@LB@5'-UAU...GCUCC AA U C U U A GAUUG...UCG-3'@LB@ CCACGAAA GG G GGCGUUG GGA AAGCGG UGGC@LB@ \|\|\|\|:\|\|\| \|\| \| \|:\|:\|:: :\|\| \|\|\|\|:\| \|\|\|\|@LB@ GGUGUUUU CC C CUGUAGU UCU UUCGUC ACCG@LB@3'-UUU...CCCGA A U U -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -18.31 kcal/mol@LB@Hybridization Energy -34.2754 kcal/mol@LB@Unfolding Energy - mRNA 11.6957 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 69 -- 106@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 16 -- 22@LB@
65	0.00343	0.1851	b4363	yjjB	-10.89	0.196296	181 -- 193	20 -- 32	DUF3815 family inner membrane protein		_____________180___________194\n_____________\|_____________\|\n5'-ACU...CACUG____UU_______UACGC...GGG-3'\n______________ACGA__UGGGGGC\n______________\|\|:\|__\|\|\|\|\|:\|\n______________UGUU__ACCCCUG\n3'-UUU...CGAGG____UU_______UAGUU...CCG-5'\n_____________\|_____________\|\n_____________33____________19\n	187 -- 193	20 -- 26	-17.0561 kcal/mol	4.01516 kcal/mol	2.14699 kcal/mol	180 194@LB@ \| \|@LB@5'-ACU...CACUG UU UACGC...GGG-3'@LB@ ACGA UGGGGGC@LB@ \|\|:\| \|\|\|\|\|:\|@LB@ UGUU ACCCCUG@LB@3'-UUU...CGAGG UU UAGUU...CCG-5'@LB@ \| \|@LB@ 33 19@LB@@LB@@LB@Energy -10.89 kcal/mol@LB@Hybridization Energy -17.0561 kcal/mol@LB@Unfolding Energy - mRNA 4.01516 kcal/mol@LB@Unfolding Energy - sRNA 2.14699 kcal/mol@LB@@LB@Position - mRNA 181 -- 193@LB@Position - sRNA 20 -- 32@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 20 -- 26@LB@
66	0.003537	0.1858	b0411	tsx	-15.28	0.023631	170 -- 194	1 -- 34	nucleoside channel receptor of phage T6 and colicin K		_____________169_________________________________195\n_____________\|___________________________________\|\n5'-AGG...CACUC_______________UU__________________AUACA...ACU-3'\n______________CCGCAA____GGGAU__UCAAA______CAGUGGC\n______________\|\|:\|\|\|____\|\|\|\|:__\|\|\|\|\|______\|\|\|\|\|\|\|\n______________GGUGUU____CCCUG__AGUUU______GUCACCG\n3'-UUU...CCCGA______UUAC_____U______CUUUUC_______-5'\n_____________\|__________________________________\|\n_____________35_________________________________1\n	188 -- 194	1 -- 7	-27.9509 kcal/mol	8.39787 kcal/mol	4.26884 kcal/mol	169 195@LB@ \| \|@LB@5'-AGG...CACUC UU AUACA...ACU-3'@LB@ CCGCAA GGGAU UCAAA CAGUGGC@LB@ \|\|:\|\|\| \|\|\|\|: \|\|\|\|\| \|\|\|\|\|\|\|@LB@ GGUGUU CCCUG AGUUU GUCACCG@LB@3'-UUU...CCCGA UUAC U CUUUUC -5'@LB@ \| \|@LB@ 35 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -27.9509 kcal/mol@LB@Unfolding Energy - mRNA 8.39787 kcal/mol@LB@Unfolding Energy - sRNA 4.26884 kcal/mol@LB@@LB@Position - mRNA 170 -- 194@LB@Position - sRNA 1 -- 34@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 1 -- 7@LB@
67	0.003548	0.1858	b4412	hokC	-18.22	0.003564	16 -- 36	7 -- 32	toxic membrane protein small	b1562 b0018	_____________15_________________________37\n_____________\|__________________________\|\n5'-AUU...AUAAA__________________________GAUAU...ACA-3'\n______________ACAAAAUGGG____UUAAAGAGA_GC\n______________\|\|\|\|\|\|\|\|\|\|____\|:\|\|\|\|\|:\|_\|\|\n______________UGUUUUACCC____AGUUUCUUU_CG\n3'-UUU...CGAGG__________CUGU_________U__UCACCG-5'\n_____________\|__________________________\|\n_____________33_________________________6\n	28 -- 34	10 -- 16	-22.2189 kcal/mol	1.46836 kcal/mol	2.53437 kcal/mol	15 37@LB@ \| \|@LB@5'-AUU...AUAAA GAUAU...ACA-3'@LB@ ACAAAAUGGG UUAAAGAGA GC@LB@ \|\|\|\|\|\|\|\|\|\| \|:\|\|\|\|\|:\| \|\|@LB@ UGUUUUACCC AGUUUCUUU CG@LB@3'-UUU...CGAGG CUGU U UCACCG-5'@LB@ \| \|@LB@ 33 6@LB@@LB@@LB@Energy -18.22 kcal/mol@LB@Hybridization Energy -22.2189 kcal/mol@LB@Unfolding Energy - mRNA 1.46836 kcal/mol@LB@Unfolding Energy - sRNA 2.53437 kcal/mol@LB@@LB@Position - mRNA 16 -- 36@LB@Position - sRNA 7 -- 32@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 10 -- 16@LB@
68	0.003723	0.191	b3131	agaR	-11.10	0.180958	280 -- 299	5 -- 22	transcriptional repressor of the aga regulon		_____________279__________________300\n_____________\|____________________\|\n5'-CAG...UCUGC____G________UGU____G-3'\n______________GACA_CAAGGGAG___GCAG\n______________\|\|\|\|_\|\|\|:\|:\|:___\|\|\|\|\n______________CUGU_GUUUCUUU___CGUC\n3'-UUU...UACCC____A________U______ACCG-5'\n_____________\|____________________\|\n_____________23___________________4\n	286 -- 292	10 -- 16	-17.5345 kcal/mol	4.90034 kcal/mol	1.53637 kcal/mol	279 300@LB@ \| \|@LB@5'-CAG...UCUGC G UGU G-3'@LB@ GACA CAAGGGAG GCAG@LB@ \|\|\|\| \|\|\|:\|:\|: \|\|\|\|@LB@ CUGU GUUUCUUU CGUC@LB@3'-UUU...UACCC A U ACCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -11.10 kcal/mol@LB@Hybridization Energy -17.5345 kcal/mol@LB@Unfolding Energy - mRNA 4.90034 kcal/mol@LB@Unfolding Energy - sRNA 1.53637 kcal/mol@LB@@LB@Position - mRNA 280 -- 299@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 286 -- 292@LB@Position Seed - sRNA 10 -- 16@LB@
69	0.003755	0.191	b0889	lrp	-14.02	0.046951	165 -- 212	1 -- 32	leucine-responsive global transcriptional regulator		_____________164______________________________________________213\n_____________\|________________________________________________\|\n5'-GUG...GUCAG______GUA____AGGAAUA________CAAUAAUAAU_____AUA__AAGAA...AGC-3'\n______________ACAGGA___GGGA_______CAGAGAGA__________GGUAG___GC\n______________\|\|\|::\|___\|\|\|\|_______\|\|:\|\|\|:\|__________:\|:\|\|___\|\|\n______________UGUUUU___CCCU_______GUUUCUUU__________UCGUC___CG\n3'-UUU...CGAGG______AC_____GUA___________________________AC___-5'\n_____________\|_______________________________________________\|\n_____________33______________________________________________1\n	186 -- 192	10 -- 16	-19.2298 kcal/mol	2.66644 kcal/mol	2.53929 kcal/mol	164 213@LB@ \| \|@LB@5'-GUG...GUCAG GUA AGGAAUA CAAUAAUAAU AUA AAGAA...AGC-3'@LB@ ACAGGA GGGA CAGAGAGA GGUAG GC@LB@ \|\|\|::\| \|\|\|\| \|\|:\|\|\|:\| :\|:\|\| \|\|@LB@ UGUUUU CCCU GUUUCUUU UCGUC CG@LB@3'-UUU...CGAGG AC GUA AC -5'@LB@ \| \|@LB@ 33 1@LB@@LB@@LB@Energy -14.02 kcal/mol@LB@Hybridization Energy -19.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.66644 kcal/mol@LB@Unfolding Energy - sRNA 2.53929 kcal/mol@LB@@LB@Position - mRNA 165 -- 212@LB@Position - sRNA 1 -- 32@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 10 -- 16@LB@
70	0.003861	0.1936	b3559	glyS	-15.28	0.023738	120 -- 130	1 -- 11	glycine tRNA synthetase beta subunit		_____________119_________131\n_____________\|___________\|\n5'-CGC...UGACC___________AGAAG...CGG-3'\n______________AAAGCAGUGGC\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________UUUCGUCACCG\n3'-UUU...UUUCU___________-5'\n_____________\|__________\|\n_____________12_________1\n	124 -- 130	1 -- 7	-20.0617 kcal/mol	3.50787 kcal/mol	1.27751 kcal/mol	119 131@LB@ \| \|@LB@5'-CGC...UGACC AGAAG...CGG-3'@LB@ AAAGCAGUGGC@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ UUUCGUCACCG@LB@3'-UUU...UUUCU -5'@LB@ \| \|@LB@ 12 1@LB@@LB@@LB@Energy -15.28 kcal/mol@LB@Hybridization Energy -20.0617 kcal/mol@LB@Unfolding Energy - mRNA 3.50787 kcal/mol@LB@Unfolding Energy - sRNA 1.27751 kcal/mol@LB@@LB@Position - mRNA 120 -- 130@LB@Position - sRNA 1 -- 11@LB@Position Seed - mRNA 124 -- 130@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