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
139	0.0229	0.526	b3958	argC	-10.25	0.086580	11 -- 36	23 -- 56	N-acetyl-gamma-glutamylphosphate reductase NAD(P)-binding	_____________10___________________________________37\n_____________\|____________________________________\|\n5'-AUC...AGCGC_______CUC__________________________UUGUU...CUG-3'\n______________GGUAAAU___GAUA__________AAUGGCGGUAAU\n______________\|\|\|\|\|\|:___\|\|:\|__________\|\|\|\|:\|\|\|\|\|\|\|\n______________CCAUUUG___CUGU__________UUACUGCCAUUA\n3'-UUU...UAUCC_______U______AAGUCUUUAC____________UUUAU...UCG-5'\n_____________\|____________________________________\|\n_____________57___________________________________22\n	30 -- 36	23 -- 29	-21.8632 kcal/mol	5.30467 kcal/mol	6.31216 kcal/mol	10 37@LB@ \| \|@LB@5'-AUC...AGCGC CUC UUGUU...CUG-3'@LB@ GGUAAAU GAUA AAUGGCGGUAAU@LB@ \|\|\|\|\|\|: \|\|:\| \|\|\|\|:\|\|\|\|\|\|\|@LB@ CCAUUUG CUGU UUACUGCCAUUA@LB@3'-UUU...UAUCC U AAGUCUUUAC UUUAU...UCG-5'@LB@ \| \|@LB@ 57 22@LB@@LB@@LB@Energy -10.25 kcal/mol@LB@Hybridization Energy -21.8632 kcal/mol@LB@Unfolding Energy - mRNA 5.30467 kcal/mol@LB@Unfolding Energy - sRNA 6.31216 kcal/mol@LB@@LB@Position - mRNA 11 -- 36@LB@Position - sRNA 23 -- 56@LB@Position Seed - mRNA 30 -- 36@LB@Position Seed - sRNA 23 -- 29@LB@
167	0.02708	0.531	b3705	yidC	-10.20	0.088356	85 -- 115	24 -- 58	membrane protein insertase	_____________84____________________________________116\n_____________\|_____________________________________\|\n5'-CGC...GGUUU__A____UAAA_____GU_________U_________AACGC...CCC-3'\n______________GG_GUGA____AGGCA________UGG_UGACGGUGA\n______________\|\|_\|\|:\|____\|\|:\|\|________\|\|:_\|\|\|\|\|\|\|:\|\n______________CC_CAUU____UCUGU________ACU_ACUGCCAUU\n3'-UUU...UUUAU__C____UG_______AAGUCUUU___U_________AUUUA...UCG-5'\n_____________\|_____________________________________\|\n_____________59____________________________________23\n	109 -- 115	24 -- 30	-23.9536 kcal/mol	7.45063 kcal/mol	6.30019 kcal/mol	84 116@LB@ \| \|@LB@5'-CGC...GGUUU A UAAA GU U AACGC...CCC-3'@LB@ GG GUGA AGGCA UGG UGACGGUGA@LB@ \|\| \|\|:\| \|\|:\|\| \|\|: \|\|\|\|\|\|\|:\|@LB@ CC CAUU UCUGU ACU ACUGCCAUU@LB@3'-UUU...UUUAU C UG AAGUCUUU U AUUUA...UCG-5'@LB@ \| \|@LB@ 59 23@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -23.9536 kcal/mol@LB@Unfolding Energy - mRNA 7.45063 kcal/mol@LB@Unfolding Energy - sRNA 6.30019 kcal/mol@LB@@LB@Position - mRNA 85 -- 115@LB@Position - sRNA 24 -- 58@LB@Position Seed - mRNA 109 -- 115@LB@Position Seed - sRNA 24 -- 30@LB@
119	0.019	0.5155	b0904	focA	-10.20	0.088413	192 -- 208	1 -- 18	formate channel	_____________191________________209\n_____________\|__________________\|\n5'-GAG...AAGAG______________A___UGACA...AGA-3'\n______________AGAGUUAGUG_UGA_AGC\n______________\|:\|\|\|\|\|:\|\|_\|\|\|_\|\|\|\n______________UUUCAAUUAC_ACU_UCG\n3'-UUU...AUUUA__________U___A___-5'\n_____________\|_________________\|\n_____________19________________1\n	195 -- 201	9 -- 15	-16.1977 kcal/mol	5.93514 kcal/mol	0.0611543 kcal/mol	191 209@LB@ \| \|@LB@5'-GAG...AAGAG A UGACA...AGA-3'@LB@ AGAGUUAGUG UGA AGC@LB@ \|:\|\|\|\|\|:\|\| \|\|\| \|\|\|@LB@ UUUCAAUUAC ACU UCG@LB@3'-UUU...AUUUA U A -5'@LB@ \| \|@LB@ 19 1@LB@@LB@@LB@Energy -10.20 kcal/mol@LB@Hybridization Energy -16.1977 kcal/mol@LB@Unfolding Energy - mRNA 5.93514 kcal/mol@LB@Unfolding Energy - sRNA 0.0611543 kcal/mol@LB@@LB@Position - mRNA 192 -- 208@LB@Position - sRNA 1 -- 18@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 9 -- 15@LB@
133	0.02154	0.526	b1105	lpoB	-10.17	0.089721	187 -- 196	50 -- 59	OM lipoprotein stimulator of MrcB transpeptidase	_____________186________197\n_____________\|__________\|\n5'-UUA...UUGUA__________CUUGA...AAC-3'\n______________AGGGGUGAAU\n______________\|\|\|\|\|\|:\|\|:\n______________UCCCCAUUUG\n3'-UUU...CUUUA__________UCUGU...UCG-5'\n_____________\|__________\|\n_____________60_________49\n	190 -- 196	50 -- 56	-15.1396 kcal/mol	4.24097 kcal/mol	0.728772 kcal/mol	186 197@LB@ \| \|@LB@5'-UUA...UUGUA CUUGA...AAC-3'@LB@ AGGGGUGAAU@LB@ \|\|\|\|\|\|:\|\|:@LB@ UCCCCAUUUG@LB@3'-UUU...CUUUA UCUGU...UCG-5'@LB@ \| \|@LB@ 60 49@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -15.1396 kcal/mol@LB@Unfolding Energy - mRNA 4.24097 kcal/mol@LB@Unfolding Energy - sRNA 0.728772 kcal/mol@LB@@LB@Position - mRNA 187 -- 196@LB@Position - sRNA 50 -- 59@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 50 -- 56@LB@
56	0.007094	0.4159	b1242	ychE	-10.14	0.091024	67 -- 90	1 -- 23	UPF0056 family inner membrane protein	_____________66_______________________91\n_____________\|________________________\|\n5'-CAU...ACAAC_______CAA___C_A________AAUUU...GCA-3'\n______________UAGAUAA___UAA_G_AUGAUAGC\n______________\|\|:\|\|\|\|___\|\|\|_\|_\|\|\|\|\|\|\|\|\n______________AUUUAUU___AUU_C_UACUAUCG\n3'-UUU...CCAUU_______UCA___A__________-5'\n_____________\|_______________________\|\n_____________24______________________1\n	84 -- 90	1 -- 7	-13.9916 kcal/mol	3.74778 kcal/mol	0.105066 kcal/mol	66 91@LB@ \| \|@LB@5'-CAU...ACAAC CAA C A AAUUU...GCA-3'@LB@ UAGAUAA UAA G AUGAUAGC@LB@ \|\|:\|\|\|\| \|\|\| \| \|\|\|\|\|\|\|\|@LB@ AUUUAUU AUU C UACUAUCG@LB@3'-UUU...CCAUU UCA A -5'@LB@ \| \|@LB@ 24 1@LB@@LB@@LB@Energy -10.14 kcal/mol@LB@Hybridization Energy -13.9916 kcal/mol@LB@Unfolding Energy - mRNA 3.74778 kcal/mol@LB@Unfolding Energy - sRNA 0.105066 kcal/mol@LB@@LB@Position - mRNA 67 -- 90@LB@Position - sRNA 1 -- 23@LB@Position Seed - mRNA 84 -- 90@LB@Position Seed - sRNA 1 -- 7@LB@
95	0.01574	0.5059	b2714	ascG	-10.13	0.091468	184 -- 220	14 -- 55	asc operon transcriptional repressor; prpBC operon repressor	_____________183________________________________________221\n_____________\|__________________________________________\|\n5'-AAA...UGCGU_____G_____________AU_______AC____CUG_____GGCGA...AAG-3'\n______________GUAAA_GGAU_____GAAA__GAUGACG__GAUG___GAAGU\n______________\|\|\|\|\|_:\|\|:_____\|\|\|\|__:\|\|\|\|\|\|__:\|\|:___:\|\|\|\|\n______________CAUUU_UCUG_____CUUU__UUACUGC__UUAU___UUUCA\n3'-UUU...AUCCC_____G____UAAGU____AC_______CA____UUA_____AUUAC...UCG-5'\n_____________\|__________________________________________\|\n_____________56_________________________________________13\n	200 -- 206	28 -- 34	-22.7561 kcal/mol	6.30192 kcal/mol	6.32604 kcal/mol	183 221@LB@ \| \|@LB@5'-AAA...UGCGU G AU AC CUG GGCGA...AAG-3'@LB@ GUAAA GGAU GAAA GAUGACG GAUG GAAGU@LB@ \|\|\|\|\| :\|\|: \|\|\|\| :\|\|\|\|\|\| :\|\|: :\|\|\|\|@LB@ CAUUU UCUG CUUU UUACUGC UUAU UUUCA@LB@3'-UUU...AUCCC G UAAGU AC CA UUA AUUAC...UCG-5'@LB@ \| \|@LB@ 56 13@LB@@LB@@LB@Energy -10.13 kcal/mol@LB@Hybridization Energy -22.7561 kcal/mol@LB@Unfolding Energy - mRNA 6.30192 kcal/mol@LB@Unfolding Energy - sRNA 6.32604 kcal/mol@LB@@LB@Position - mRNA 184 -- 220@LB@Position - sRNA 14 -- 55@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 28 -- 34@LB@
109	0.01701	0.5123	b2075	mdtB	-10.10	0.092694	6 -- 26	38 -- 56	multidrug efflux system subunit B	_____________5_____________________27\n_____________\|_____________________\|\n______5'-CAUCU_____CGC_____________CAGUC...CCG-3'\n______________GGUGA___CGGGCAUUCAGGA\n______________\|\|\|:\|___\|:\|:\|\|\|\|\|\|\|:\|\n______________CCAUU___GUCUGUAAGUCUU\n3'-UUU...UAUCC_____U_______________UACUU...UCG-5'\n_____________\|_____________________\|\n_____________57____________________37\n	18 -- 24	40 -- 46	-22.2525 kcal/mol	5.90254 kcal/mol	6.25055 kcal/mol	5 27@LB@ \| \|@LB@ 5'-CAUCU CGC CAGUC...CCG-3'@LB@ GGUGA CGGGCAUUCAGGA@LB@ \|\|\|:\| \|:\|:\|\|\|\|\|\|\|:\|@LB@ CCAUU GUCUGUAAGUCUU@LB@3'-UUU...UAUCC U UACUU...UCG-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -22.2525 kcal/mol@LB@Unfolding Energy - mRNA 5.90254 kcal/mol@LB@Unfolding Energy - sRNA 6.25055 kcal/mol@LB@@LB@Position - mRNA 6 -- 26@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 18 -- 24@LB@Position Seed - sRNA 40 -- 46@LB@
123	0.01951	0.5155	b0032	carA	-10.10	0.092857	258 -- 264	55 -- 61	carbamoyl phosphate synthetase small subunit glutamine amidotransferase	_____________257_____265\n_____________\|_______\|\n5'-UUG...GGGCC_______CAACA...AUA-3'\n______________AUAGGGG\n______________\|\|\|\|\|\|\|\n______________UAUCCCC\n3'-UUU...AACUU_______AUUUG...UCG-5'\n_____________\|_______\|\n_____________62______54\n	258 -- 264	55 -- 61	-10.8319 kcal/mol	0.710423 kcal/mol	0.0258473 kcal/mol	257 265@LB@ \| \|@LB@5'-UUG...GGGCC CAACA...AUA-3'@LB@ AUAGGGG@LB@ \|\|\|\|\|\|\|@LB@ UAUCCCC@LB@3'-UUU...AACUU AUUUG...UCG-5'@LB@ \| \|@LB@ 62 54@LB@@LB@@LB@Energy -10.10 kcal/mol@LB@Hybridization Energy -10.8319 kcal/mol@LB@Unfolding Energy - mRNA 0.710423 kcal/mol@LB@Unfolding Energy - sRNA 0.0258473 kcal/mol@LB@@LB@Position - mRNA 258 -- 264@LB@Position - sRNA 55 -- 61@LB@Position Seed - mRNA 258 -- 264@LB@Position Seed - sRNA 55 -- 61@LB@
112	0.01793	0.5155	b1418	cybB	-10.08	0.093429	125 -- 145	33 -- 57	cytochrome b561	_____________124_______________________146\n_____________\|_________________________\|\n5'-AAC...AAAAC_________________________AUUUU...UCC-3'\n______________GGGUGAACA_AUAUUU___AAUGAA\n______________\|\|\|\|:\|\|\|\|_\|:\|\|\|:___\|\|\|\|\|\|\n______________CCCAUUUGU_UGUAAG___UUACUU\n3'-UUU...UUAUC_________C______UCU______ACUGC...UCG-5'\n_____________\|_________________________\|\n_____________58________________________32\n	127 -- 133	49 -- 55	-19.5073 kcal/mol	3.1607 kcal/mol	6.2643 kcal/mol	124 146@LB@ \| \|@LB@5'-AAC...AAAAC AUUUU...UCC-3'@LB@ GGGUGAACA AUAUUU AAUGAA@LB@ \|\|\|\|:\|\|\|\| \|:\|\|\|: \|\|\|\|\|\|@LB@ CCCAUUUGU UGUAAG UUACUU@LB@3'-UUU...UUAUC C UCU ACUGC...UCG-5'@LB@ \| \|@LB@ 58 32@LB@@LB@@LB@Energy -10.08 kcal/mol@LB@Hybridization Energy -19.5073 kcal/mol@LB@Unfolding Energy - mRNA 3.1607 kcal/mol@LB@Unfolding Energy - sRNA 6.2643 kcal/mol@LB@@LB@Position - mRNA 125 -- 145@LB@Position - sRNA 33 -- 57@LB@Position Seed - mRNA 127 -- 133@LB@Position Seed - sRNA 49 -- 55@LB@
102	0.01618	0.5059	b3306	rpsH	-10.04	0.095208	179 -- 210	1 -- 36	30S ribosomal subunit protein S8	_____________178____________________________________211\n_____________\|______________________________________\|\n5'-AGC...CCAAU_____C________________ACA_______GCAU__AAGAU...AAG-3'\n______________UGAAU_ACGG____GAGUAAAG_____GAUGA____GC\n______________\|\|\|\|\|_\|\|\|\|____:\|:\|\|\|\|\|_____\|\|\|\|\|____\|\|\n______________ACUUA_UGCC____UUUAUUUC_____CUACU____CG\n3'-UUU...UCUUU_____C____AUUA________AAUUA_____AU____-5'\n_____________\|_____________________________________\|\n_____________37____________________________________1\n	190 -- 196	15 -- 21	-20.3749 kcal/mol	4.57112 kcal/mol	5.76239 kcal/mol	178 211@LB@ \| \|@LB@5'-AGC...CCAAU C ACA GCAU AAGAU...AAG-3'@LB@ UGAAU ACGG GAGUAAAG GAUGA GC@LB@ \|\|\|\|\| \|\|\|\| :\|:\|\|\|\|\| \|\|\|\|\| \|\|@LB@ ACUUA UGCC UUUAUUUC CUACU CG@LB@3'-UUU...UCUUU C AUUA AAUUA AU -5'@LB@ \| \|@LB@ 37 1@LB@@LB@@LB@Energy -10.04 kcal/mol@LB@Hybridization Energy -20.3749 kcal/mol@LB@Unfolding Energy - mRNA 4.57112 kcal/mol@LB@Unfolding Energy - sRNA 5.76239 kcal/mol@LB@@LB@Position - mRNA 179 -- 210@LB@Position - sRNA 1 -- 36@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 15 -- 21@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