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
176	0.01279	0.2504	b3980	tufB	-13.59	0.058494	200 -- 216	7 -- 22	translation elongation factor EF-Tu 2	b3339	_____________199_______________217\n_____________\|_________________\|\n5'-UCC...CAAUC______U__________UUGAA...CUA-3'\n______________GAUGUC_AAAGAAAAGU\n______________\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________CUGUAG_UUUCUUUUCG\n3'-UUU...UACCC_________________UCACCG-5'\n_____________\|_________________\|\n_____________23________________6\n	210 -- 216	7 -- 13	-16.0105 kcal/mol	1.82662 kcal/mol	0.590875 kcal/mol	199 217@LB@ \| \|@LB@5'-UCC...CAAUC U UUGAA...CUA-3'@LB@ GAUGUC AAAGAAAAGU@LB@ \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ CUGUAG UUUCUUUUCG@LB@3'-UUU...UACCC UCACCG-5'@LB@ \| \|@LB@ 23 6@LB@@LB@@LB@Energy -13.59 kcal/mol@LB@Hybridization Energy -16.0105 kcal/mol@LB@Unfolding Energy - mRNA 1.82662 kcal/mol@LB@Unfolding Energy - sRNA 0.590875 kcal/mol@LB@@LB@Position - mRNA 200 -- 216@LB@Position - sRNA 7 -- 22@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 7 -- 13@LB@
96	0.005909	0.216	b0511	ybbW	-13.57	0.059054	201 -- 236	1 -- 27	putative allantoin transporter		_____________200___________________________________237\n_____________\|_____________________________________\|\n5'-UGG...GAUUU____A_____________ACUAUUCC____AC_C___UAUAG...UUA-3'\n______________AUGG__ACAUCAGAGAAA________AGCA__G_GGC\n______________\|\|\|\|__\|\|\|\|\|\|:\|\|\|\|\|________\|\|\|\|__\|_\|\|\|\n______________UACC__UGUAGUUUCUUU________UCGU__C_CCG\n3'-UUU...UGUUU____CC___________________________A___-5'\n_____________\|____________________________________\|\n_____________28___________________________________1\n	211 -- 217	10 -- 16	-23.7564 kcal/mol	7.66376 kcal/mol	2.51867 kcal/mol	200 237@LB@ \| \|@LB@5'-UGG...GAUUU A ACUAUUCC AC C UAUAG...UUA-3'@LB@ AUGG ACAUCAGAGAAA AGCA G GGC@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|\|\|\| \|\|\|\| \| \|\|\|@LB@ UACC UGUAGUUUCUUU UCGU C CCG@LB@3'-UUU...UGUUU CC A -5'@LB@ \| \|@LB@ 28 1@LB@@LB@@LB@Energy -13.57 kcal/mol@LB@Hybridization Energy -23.7564 kcal/mol@LB@Unfolding Energy - mRNA 7.66376 kcal/mol@LB@Unfolding Energy - sRNA 2.51867 kcal/mol@LB@@LB@Position - mRNA 201 -- 236@LB@Position - sRNA 1 -- 27@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 10 -- 16@LB@
163	0.01202	0.2504	b1482	osmC	-10.53	0.225653	203 -- 226	1 -- 22	lipoyl-dependent Cys-based peroxidase hydroperoxide resistance; salt-shock inducible membrane protein; peroxiredoxin		_____________202_______________________227\n_____________\|_________________________\|\n5'-UAG...ACAAU___A___CAU_________CA____ACACU...CGU-3'\n______________GAC_AUC___AAGAAAGGU___GGC\n______________\|\|\|_\|\|\|___\|\|\|\|\|\|:\|:___\|\|\|\n______________CUG_UAG___UUCUUUUCG___CCG\n3'-UUU...UACCC_______U___________UCA___-5'\n_____________\|________________________\|\n_____________23_______________________1\n	215 -- 221	7 -- 13	-17.1921 kcal/mol	5.11752 kcal/mol	1.54023 kcal/mol	202 227@LB@ \| \|@LB@5'-UAG...ACAAU A CAU CA ACACU...CGU-3'@LB@ GAC AUC AAGAAAGGU GGC@LB@ \|\|\| \|\|\| \|\|\|\|\|\|:\|: \|\|\|@LB@ CUG UAG UUCUUUUCG CCG@LB@3'-UUU...UACCC U UCA -5'@LB@ \| \|@LB@ 23 1@LB@@LB@@LB@Energy -10.53 kcal/mol@LB@Hybridization Energy -17.1921 kcal/mol@LB@Unfolding Energy - mRNA 5.11752 kcal/mol@LB@Unfolding Energy - sRNA 1.54023 kcal/mol@LB@@LB@Position - mRNA 203 -- 226@LB@Position - sRNA 1 -- 22@LB@Position Seed - mRNA 215 -- 221@LB@Position Seed - sRNA 7 -- 13@LB@
184	0.0132	0.2504	b2897	sdhE	-10.91	0.194803	203 -- 220	7 -- 23	flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair		_____________202________________221\n_____________\|__________________\|\n5'-GUA...AAGAU_________CAAC_____CCGCA...ACA-3'\n______________GGACAUUAA____AAAGC\n______________\|\|\|\|\|\|:\|\|____\|\|\|\|\|\n______________CCUGUAGUU____UUUCG\n3'-UUU...UUACC_________UCU______UCACCG-5'\n_____________\|__________________\|\n_____________24_________________6\n	205 -- 211	15 -- 21	-14.6885 kcal/mol	3.17611 kcal/mol	0.599063 kcal/mol	202 221@LB@ \| \|@LB@5'-GUA...AAGAU CAAC CCGCA...ACA-3'@LB@ GGACAUUAA AAAGC@LB@ \|\|\|\|\|\|:\|\| \|\|\|\|\|@LB@ CCUGUAGUU UUUCG@LB@3'-UUU...UUACC UCU UCACCG-5'@LB@ \| \|@LB@ 24 6@LB@@LB@@LB@Energy -10.91 kcal/mol@LB@Hybridization Energy -14.6885 kcal/mol@LB@Unfolding Energy - mRNA 3.17611 kcal/mol@LB@Unfolding Energy - sRNA 0.599063 kcal/mol@LB@@LB@Position - mRNA 203 -- 220@LB@Position - sRNA 7 -- 23@LB@Position Seed - mRNA 205 -- 211@LB@Position Seed - sRNA 15 -- 21@LB@
57	0.003017	0.1789	b2950	yggR	-13.19	0.071427	205 -- 223	1 -- 21	putative PilT family AAA+ ATPase		_____________204___________________224\n_____________\|_____________________\|\n5'-UUC...UAUGA____G_______UU_______CCUUA...GAA-3'\n______________AUAU_GAAGAAA____GUGGC\n______________\|:\|\|_:\|\|\|\|\|\|____\|\|\|\|\|\n______________UGUA_UUUCUUU____CACCG\n3'-UUU...ACCCC____G_______UCGU_____-5'\n_____________\|____________________\|\n_____________22___________________1\n	210 -- 216	10 -- 16	-17.7325 kcal/mol	3.03326 kcal/mol	1.51103 kcal/mol	204 224@LB@ \| \|@LB@5'-UUC...UAUGA G UU CCUUA...GAA-3'@LB@ AUAU GAAGAAA GUGGC@LB@ \|:\|\| :\|\|\|\|\|\| \|\|\|\|\|@LB@ UGUA UUUCUUU CACCG@LB@3'-UUU...ACCCC G UCGU -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.19 kcal/mol@LB@Hybridization Energy -17.7325 kcal/mol@LB@Unfolding Energy - mRNA 3.03326 kcal/mol@LB@Unfolding Energy - sRNA 1.51103 kcal/mol@LB@@LB@Position - mRNA 205 -- 223@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 10 -- 16@LB@
191	0.01405	0.2529	b3532	bcsB	-12.45	0.101006	205 -- 235	1 -- 16	regulator of cellulose synthase cyclic di-GMP binding		_____________204_____________________________236\n_____________\|_______________________________\|\n5'-AAG...GAUGA________CUAUUCUGGAUUUGU________UAUGG...UCA-3'\n______________AAAGAAAA_______________GCAGUGGC\n______________\|\|\|\|\|\|\|\|_______________\|\|\|\|\|\|\|\|\n______________UUUCUUUU_______________CGUCACCG\n3'-UUU...UGUAG_______________________________-5'\n_____________\|______________________________\|\n_____________17_____________________________1\n	229 -- 235	1 -- 7	-19.2133 kcal/mol	5.41496 kcal/mol	1.34555 kcal/mol	204 236@LB@ \| \|@LB@5'-AAG...GAUGA CUAUUCUGGAUUUGU UAUGG...UCA-3'@LB@ AAAGAAAA GCAGUGGC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\|\|@LB@ UUUCUUUU CGUCACCG@LB@3'-UUU...UGUAG -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -12.45 kcal/mol@LB@Hybridization Energy -19.2133 kcal/mol@LB@Unfolding Energy - mRNA 5.41496 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 205 -- 235@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 229 -- 235@LB@Position Seed - sRNA 1 -- 7@LB@
93	0.00579	0.2147	b1256	ompW	-13.14	0.073154	206 -- 220	1 -- 16	outer membrane protein W		_____________205______________221\n_____________\|________________\|\n5'-GAC...AUGAA____UU__________GGCUU...CUG-3'\n______________AAAG__AA_CAGUGGC\n______________\|\|\|\|__\|\|_\|\|\|\|\|\|\|\n______________UUUC__UU_GUCACCG\n3'-UUU...UGUAG____UU__C_______-5'\n_____________\|_______________\|\n_____________17______________1\n	214 -- 220	1 -- 7	-16.0357 kcal/mol	1.55126 kcal/mol	1.34555 kcal/mol	205 221@LB@ \| \|@LB@5'-GAC...AUGAA UU GGCUU...CUG-3'@LB@ AAAG AA CAGUGGC@LB@ \|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ UUUC UU GUCACCG@LB@3'-UUU...UGUAG UU C -5'@LB@ \| \|@LB@ 17 1@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -16.0357 kcal/mol@LB@Unfolding Energy - mRNA 1.55126 kcal/mol@LB@Unfolding Energy - sRNA 1.34555 kcal/mol@LB@@LB@Position - mRNA 206 -- 220@LB@Position - sRNA 1 -- 16@LB@Position Seed - mRNA 214 -- 220@LB@Position Seed - sRNA 1 -- 7@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@
32	0.001499	0.1635	b0661	miaB	-12.88	0.082685	213 -- 250	6 -- 36	tRNA-i(6)A37 methylthiotransferase		_____________212____________________________________251\n_____________\|______________________________________\|\n5'-CGC...AAAAA_______UU_AAACC_____C_______U___C_____CGAUU...AAC-3'\n______________CUCCAUA__A_____UGGGG_UGUCAGA_GAA_GAGUA\n______________\|\|\|\|\|:\|__\|_____\|\|\|\|\|_::\|\|\|:\|_\|\|\|_:\|\|:\|\n______________GAGGUGU__U_____ACCCC_GUAGUUU_CUU_UUCGU\n3'-UUU...UACCC_______UU___________U_________________CACCG-5'\n_____________\|______________________________________\|\n_____________37_____________________________________5\n	234 -- 240	14 -- 20	-26.1374 kcal/mol	6.57825 kcal/mol	6.67617 kcal/mol	212 251@LB@ \| \|@LB@5'-CGC...AAAAA UU AAACC C U C CGAUU...AAC-3'@LB@ CUCCAUA A UGGGG UGUCAGA GAA GAGUA@LB@ \|\|\|\|\|:\| \| \|\|\|\|\| ::\|\|\|:\| \|\|\| :\|\|:\|@LB@ GAGGUGU U ACCCC GUAGUUU CUU UUCGU@LB@3'-UUU...UACCC UU U CACCG-5'@LB@ \| \|@LB@ 37 5@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -26.1374 kcal/mol@LB@Unfolding Energy - mRNA 6.57825 kcal/mol@LB@Unfolding Energy - sRNA 6.67617 kcal/mol@LB@@LB@Position - mRNA 213 -- 250@LB@Position - sRNA 6 -- 36@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 14 -- 20@LB@
158	0.01161	0.2504	b3907	rhaT	-15.90	0.016445	218 -- 234	1 -- 28	L-rhamnose:proton symporter		_____________217__________________________235\n_____________\|____________________________\|\n5'-AUG...AUUAC____________U_______________AUUUG...CAU-3'\n______________GAUGGGGAUAUU____________UGGC\n______________:\|\|\|\|\|\|\|:\|\|:____________\|\|\|\|\n______________UUACCCCUGUAG____________ACCG\n3'-UUU...GUGUU____________UUUCUUUUCGUC____-5'\n_____________\|___________________________\|\n_____________29__________________________1\n	223 -- 229	17 -- 23	-20.3321 kcal/mol	1.91011 kcal/mol	2.519 kcal/mol	217 235@LB@ \| \|@LB@5'-AUG...AUUAC U AUUUG...CAU-3'@LB@ GAUGGGGAUAUU UGGC@LB@ :\|\|\|\|\|\|\|:\|\|: \|\|\|\|@LB@ UUACCCCUGUAG ACCG@LB@3'-UUU...GUGUU UUUCUUUUCGUC -5'@LB@ \| \|@LB@ 29 1@LB@@LB@@LB@Energy -15.90 kcal/mol@LB@Hybridization Energy -20.3321 kcal/mol@LB@Unfolding Energy - mRNA 1.91011 kcal/mol@LB@Unfolding Energy - sRNA 2.519 kcal/mol@LB@@LB@Position - mRNA 218 -- 234@LB@Position - sRNA 1 -- 28@LB@Position Seed - mRNA 223 -- 229@LB@Position Seed - sRNA 17 -- 23@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