Input and runtime details for job 1229462 (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 1229462 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:25:41 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:25:59 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:22:57 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:23:04 CET 2018
	Job Completed		@ Fri Feb 16 20:23:29 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
82	0.0113	0.4523	b3747	kup	-9.05	0.148352	64 -- 70	53 -- 59	potassium transporter		_____________63______71\n_____________\|_______\|\n5'-AAA...AAAGG_______UUUUU...GUG-3'\n______________GGGGGUA\n______________:\|\|\|\|\|\|\n______________UCCCCAU\n3'-UUU...CUUUA_______UUGUC...UCG-5'\n_____________\|_______\|\n_____________60______52\n	64 -- 70	53 -- 59	-11.6233 kcal/mol	2.51972 kcal/mol	0.0564539 kcal/mol	63 71@LB@ \| \|@LB@5'-AAA...AAAGG UUUUU...GUG-3'@LB@ GGGGGUA@LB@ :\|\|\|\|\|\|@LB@ UCCCCAU@LB@3'-UUU...CUUUA UUGUC...UCG-5'@LB@ \| \|@LB@ 60 52@LB@@LB@@LB@Energy -9.05 kcal/mol@LB@Hybridization Energy -11.6233 kcal/mol@LB@Unfolding Energy - mRNA 2.51972 kcal/mol@LB@Unfolding Energy - sRNA 0.0564539 kcal/mol@LB@@LB@Position - mRNA 64 -- 70@LB@Position - sRNA 53 -- 59@LB@Position Seed - mRNA 64 -- 70@LB@Position Seed - sRNA 53 -- 59@LB@
28	0.00198	0.2275	b2821	ptrA	-8.02	0.226801	174 -- 191	5 -- 22	protease III		_____________173________________192\n_____________\|__________________\|\n5'-GCU...ACAGA____U________U____GGUCC...CCA-3'\n______________AAAU_AAGUUGAU_AUGA\n______________\|\|\|\|_\|\|\|\|\|:\|\|_\|\|\|\|\n______________UUUA_UUCAAUUA_UACU\n3'-UUU...CAUUA____U________C____AUCG-5'\n_____________\|__________________\|\n_____________23_________________4\n	180 -- 186	10 -- 16	-10.4485 kcal/mol	2.32937 kcal/mol	0.0977783 kcal/mol	173 192@LB@ \| \|@LB@5'-GCU...ACAGA U U GGUCC...CCA-3'@LB@ AAAU AAGUUGAU AUGA@LB@ \|\|\|\| \|\|\|\|\|:\|\| \|\|\|\|@LB@ UUUA UUCAAUUA UACU@LB@3'-UUU...CAUUA U C AUCG-5'@LB@ \| \|@LB@ 23 4@LB@@LB@@LB@Energy -8.02 kcal/mol@LB@Hybridization Energy -10.4485 kcal/mol@LB@Unfolding Energy - mRNA 2.32937 kcal/mol@LB@Unfolding Energy - sRNA 0.0977783 kcal/mol@LB@@LB@Position - mRNA 174 -- 191@LB@Position - sRNA 5 -- 22@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 10 -- 16@LB@
187	0.03165	0.5492	b2717	hycI	-9.48	0.123006	243 -- 251	1 -- 9	protease involved in processing C-terminal end of HycE		_____________242_______252\n_____________\|_________\|\n5'-AGC...UGGGC_________GCAGG...ACU-3'\n______________GAUGAUGGC\n______________\|\|\|\|\|\|:\|\|\n______________CUACUAUCG\n3'-UUU...AAUUA_________-5'\n_____________\|________\|\n_____________10_______1\n	245 -- 251	1 -- 7	-13.2104 kcal/mol	3.71514 kcal/mol	0.0200155 kcal/mol	242 252@LB@ \| \|@LB@5'-AGC...UGGGC GCAGG...ACU-3'@LB@ GAUGAUGGC@LB@ \|\|\|\|\|\|:\|\|@LB@ CUACUAUCG@LB@3'-UUU...AAUUA -5'@LB@ \| \|@LB@ 10 1@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -13.2104 kcal/mol@LB@Unfolding Energy - mRNA 3.71514 kcal/mol@LB@Unfolding Energy - sRNA 0.0200155 kcal/mol@LB@@LB@Position - mRNA 243 -- 251@LB@Position - sRNA 1 -- 9@LB@Position Seed - mRNA 245 -- 251@LB@Position Seed - sRNA 1 -- 7@LB@
191	0.03238	0.5507	b0445	ybaE	-8.08	0.221556	124 -- 136	4 -- 16	putative ABC transporter periplasmic binding protein		_____________123___________137\n_____________\|_____________\|\n5'-CGU...GACAC_____________UGAGU...GUU-3'\n______________GGUUAAUGGUGAU\n______________:\|\|\|\|\|\|\|:\|\|\|\|\n______________UCAAUUACUACUA\n3'-UUU...UUAUU_____________UCG-5'\n_____________\|_____________\|\n_____________17____________3\n	130 -- 136	4 -- 10	-14.6304 kcal/mol	6.50117 kcal/mol	0.0488422 kcal/mol	123 137@LB@ \| \|@LB@5'-CGU...GACAC UGAGU...GUU-3'@LB@ GGUUAAUGGUGAU@LB@ :\|\|\|\|\|\|\|:\|\|\|\|@LB@ UCAAUUACUACUA@LB@3'-UUU...UUAUU UCG-5'@LB@ \| \|@LB@ 17 3@LB@@LB@@LB@Energy -8.08 kcal/mol@LB@Hybridization Energy -14.6304 kcal/mol@LB@Unfolding Energy - mRNA 6.50117 kcal/mol@LB@Unfolding Energy - sRNA 0.0488422 kcal/mol@LB@@LB@Position - mRNA 124 -- 136@LB@Position - sRNA 4 -- 16@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 4 -- 10@LB@
196	0.0332	0.554	b0128	yadH	-11.13	0.056665	104 -- 121	39 -- 55	putative ABC transporter permease		_____________103________________122\n_____________\|__________________\|\n5'-UUA...GUUAA_______G__________UAUUA...UCA-3'\n______________GUGAGCA_GGCAUUCAGG\n______________\|\|:\|:\|\|_\|:\|\|\|\|\|\|\|:\n______________CAUUUGU_CUGUAAGUCU\n3'-UUU...AUCCC__________________UUACU...UCG-5'\n_____________\|__________________\|\n_____________56_________________38\n	114 -- 120	40 -- 46	-20.6932 kcal/mol	3.311 kcal/mol	6.24918 kcal/mol	103 122@LB@ \| \|@LB@5'-UUA...GUUAA G UAUUA...UCA-3'@LB@ GUGAGCA GGCAUUCAGG@LB@ \|\|:\|:\|\| \|:\|\|\|\|\|\|\|:@LB@ CAUUUGU CUGUAAGUCU@LB@3'-UUU...AUCCC UUACU...UCG-5'@LB@ \| \|@LB@ 56 38@LB@@LB@@LB@Energy -11.13 kcal/mol@LB@Hybridization Energy -20.6932 kcal/mol@LB@Unfolding Energy - mRNA 3.311 kcal/mol@LB@Unfolding Energy - sRNA 6.24918 kcal/mol@LB@@LB@Position - mRNA 104 -- 121@LB@Position - sRNA 39 -- 55@LB@Position Seed - mRNA 114 -- 120@LB@Position Seed - sRNA 40 -- 46@LB@
79	0.01117	0.4523	b1593	ynfK	-13.04	0.021217	188 -- 210	1 -- 21	putative dethiobiotin synthetase		_____________187_____________________211\n_____________\|_______________________\|\n5'-CAC...AUAAC________________CUGA___GUUUC...CGG-3'\n______________GGUGGAGUUAGUGAUG____AGC\n______________::\|::\|\|\|\|\|:\|\|\|\|\|____\|\|\|\n______________UUAUUUCAAUUACUAC____UCG\n3'-UUU...AUUAU________________UA_____-5'\n_____________\|______________________\|\n_____________22_____________________1\n	197 -- 203	6 -- 12	-19.4081 kcal/mol	6.29658 kcal/mol	0.0669945 kcal/mol	187 211@LB@ \| \|@LB@5'-CAC...AUAAC CUGA GUUUC...CGG-3'@LB@ GGUGGAGUUAGUGAUG AGC@LB@ ::\|::\|\|\|\|\|:\|\|\|\|\| \|\|\|@LB@ UUAUUUCAAUUACUAC UCG@LB@3'-UUU...AUUAU UA -5'@LB@ \| \|@LB@ 22 1@LB@@LB@@LB@Energy -13.04 kcal/mol@LB@Hybridization Energy -19.4081 kcal/mol@LB@Unfolding Energy - mRNA 6.29658 kcal/mol@LB@Unfolding Energy - sRNA 0.0669945 kcal/mol@LB@@LB@Position - mRNA 188 -- 210@LB@Position - sRNA 1 -- 21@LB@Position Seed - mRNA 197 -- 203@LB@Position Seed - sRNA 6 -- 12@LB@
12	0.000426	0.1165	b2331	smrB	-16.71	0.002472	163 -- 205	16 -- 57	putative DNA endonuclease		_____________162____________________________________________206\n_____________\|______________________________________________\|\n5'-UCA...GAGUC________UGUA___AAA________A______A____________AAAGA...GAC-3'\n______________GGGUAAAC____GGA___UUAGAAAU_GA_GAC___GAUAAAUGAA\n______________\|\|\|\|\|\|\|\|____:\|\|___\|:\|\|\|\|\|\|_:\|_\|\|\|___:\|\|\|\|\|\|:\|\|\n______________CCCAUUUG____UCU___AGUCUUUA_UU_CUG___UUAUUUAUUU\n3'-UUU...UUAUC_______________GUA________C__A___CCA__________CAAUU...UCG-5'\n_____________\|______________________________________________\|\n_____________58_____________________________________________15\n	199 -- 205	16 -- 22	-27.8577 kcal/mol	4.82255 kcal/mol	6.32306 kcal/mol	162 206@LB@ \| \|@LB@5'-UCA...GAGUC UGUA AAA A A AAAGA...GAC-3'@LB@ GGGUAAAC GGA UUAGAAAU GA GAC GAUAAAUGAA@LB@ \|\|\|\|\|\|\|\| :\|\| \|:\|\|\|\|\|\| :\| \|\|\| :\|\|\|\|\|\|:\|\|@LB@ CCCAUUUG UCU AGUCUUUA UU CUG UUAUUUAUUU@LB@3'-UUU...UUAUC GUA C A CCA CAAUU...UCG-5'@LB@ \| \|@LB@ 58 15@LB@@LB@@LB@Energy -16.71 kcal/mol@LB@Hybridization Energy -27.8577 kcal/mol@LB@Unfolding Energy - mRNA 4.82255 kcal/mol@LB@Unfolding Energy - sRNA 6.32306 kcal/mol@LB@@LB@Position - mRNA 163 -- 205@LB@Position - sRNA 16 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@LB@
200	0.03384	0.5555	b0316	yahB	-11.86	0.039401	41 -- 57	47 -- 61	putative DNA-bindng transcriptional regulator	b0504	_____________40________________58\n_____________\|_________________\|\n5'-CUG...ACUGC__________UUU____AUAUG...CUU-3'\n______________GUGGGGGUAA___CAGA\n______________:\|:\|\|\|\|\|\|\|___\|\|\|\|\n______________UAUCCCCAUU___GUCU\n3'-UUU...AACUU__________U______GUAAG...UCG-5'\n_____________\|_________________\|\n_____________62________________46\n	44 -- 50	52 -- 58	-17.391 kcal/mol	3.44789 kcal/mol	2.08204 kcal/mol	40 58@LB@ \| \|@LB@5'-CUG...ACUGC UUU AUAUG...CUU-3'@LB@ GUGGGGGUAA CAGA@LB@ :\|:\|\|\|\|\|\|\| \|\|\|\|@LB@ UAUCCCCAUU GUCU@LB@3'-UUU...AACUU U GUAAG...UCG-5'@LB@ \| \|@LB@ 62 46@LB@@LB@@LB@Energy -11.86 kcal/mol@LB@Hybridization Energy -17.391 kcal/mol@LB@Unfolding Energy - mRNA 3.44789 kcal/mol@LB@Unfolding Energy - sRNA 2.08204 kcal/mol@LB@@LB@Position - mRNA 41 -- 57@LB@Position - sRNA 47 -- 61@LB@Position Seed - mRNA 44 -- 50@LB@Position Seed - sRNA 52 -- 58@LB@
149	0.02481	0.526	b2108	yehA	-13.80	0.014025	228 -- 241	1 -- 14	putative fimbrial-like adhesin protein		_____________227____________242\n_____________\|______________\|\n5'-GUU...UUAUA______________UAUGC...UUG-3'\n______________UUAAUGAUGAUGGU\n______________\|\|\|\|\|\|\|\|\|\|\|:\|:\n______________AAUUACUACUAUCG\n3'-UUU...AUUUC______________-5'\n_____________\|_____________\|\n_____________15____________1\n	235 -- 241	1 -- 7	-16.5389 kcal/mol	2.69058 kcal/mol	0.0473494 kcal/mol	227 242@LB@ \| \|@LB@5'-GUU...UUAUA UAUGC...UUG-3'@LB@ UUAAUGAUGAUGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|:\|:@LB@ AAUUACUACUAUCG@LB@3'-UUU...AUUUC -5'@LB@ \| \|@LB@ 15 1@LB@@LB@@LB@Energy -13.80 kcal/mol@LB@Hybridization Energy -16.5389 kcal/mol@LB@Unfolding Energy - mRNA 2.69058 kcal/mol@LB@Unfolding Energy - sRNA 0.0473494 kcal/mol@LB@@LB@Position - mRNA 228 -- 241@LB@Position - sRNA 1 -- 14@LB@Position Seed - mRNA 235 -- 241@LB@Position Seed - sRNA 1 -- 7@LB@
157	0.02559	0.526	b2057	wcaC	-8.75	0.168472	165 -- 205	16 -- 58	putative glycosyl transferase		_____________164___________________________________________206\n_____________\|_____________________________________________\|\n5'-GUC...GCGCU__U__________AAA____CGC_______A_____U________UAUUU...CAC-3'\n______________GG_GGUGGG_AGA_____AG____GAGUGA_GGUAA_UAAAUGAA\n______________\|\|_\|\|\|:::_\|\|\|_____\|\|____\|\|:\|\|\|_\|\|\|\|\|_\|\|\|\|\|:\|\|\n______________CC_CCAUUU_UCU_____UC____CUUACU_CCAUU_AUUUAUUU\n3'-UUU...UUUAU_________G___GUAAG__UUUA______G______________CAAUU...UCG-5'\n_____________\|_____________________________________________\|\n_____________59____________________________________________15\n	199 -- 205	16 -- 22	-25.2337 kcal/mol	10.162 kcal/mol	6.32308 kcal/mol	164 206@LB@ \| \|@LB@5'-GUC...GCGCU U AAA CGC A U UAUUU...CAC-3'@LB@ GG GGUGGG AGA AG GAGUGA GGUAA UAAAUGAA@LB@ \|\| \|\|\|::: \|\|\| \|\| \|\|:\|\|\| \|\|\|\|\| \|\|\|\|\|:\|\|@LB@ CC CCAUUU UCU UC CUUACU CCAUU AUUUAUUU@LB@3'-UUU...UUUAU G GUAAG UUUA G CAAUU...UCG-5'@LB@ \| \|@LB@ 59 15@LB@@LB@@LB@Energy -8.75 kcal/mol@LB@Hybridization Energy -25.2337 kcal/mol@LB@Unfolding Energy - mRNA 10.162 kcal/mol@LB@Unfolding Energy - sRNA 6.32308 kcal/mol@LB@@LB@Position - mRNA 165 -- 205@LB@Position - sRNA 16 -- 58@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 16 -- 22@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