Input and runtime details for job 5172788 (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 5172788 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:22:50 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:35:14 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:35:22 CET 2018
	Job Completed		@ Fri Feb 16 20:35:53 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
125	0.005266	0.1416	b0957	ompA	-12.88	0.041122	280 -- 293	25 -- 39	outer membrane protein A (3a;II*;G;d)		_____________279_____________294\n_____________\|_______________\|\n5'-CUU...UAACA_______________GCUAAAC-3'\n______________CCUGGUACA_CUGGU\n______________\|\|\|\|\|\|\|\|\|_\|\|:\|:\n______________GGACCAUGU_GAUCG\n3'-UUU...ACCAA_________C_____UAAAA...UCG-5'\n_____________\|_______________\|\n_____________40______________24\n	282 -- 288	31 -- 37	-21.2564 kcal/mol	3.82713 kcal/mol	4.55153 kcal/mol	279 294@LB@ \| \|@LB@5'-CUU...UAACA GCUAAAC-3'@LB@ CCUGGUACA CUGGU@LB@ \|\|\|\|\|\|\|\|\| \|\|:\|:@LB@ GGACCAUGU GAUCG@LB@3'-UUU...ACCAA C UAAAA...UCG-5'@LB@ \| \|@LB@ 40 24@LB@@LB@@LB@Energy -12.88 kcal/mol@LB@Hybridization Energy -21.2564 kcal/mol@LB@Unfolding Energy - mRNA 3.82713 kcal/mol@LB@Unfolding Energy - sRNA 4.55153 kcal/mol@LB@@LB@Position - mRNA 280 -- 293@LB@Position - sRNA 25 -- 39@LB@Position Seed - mRNA 282 -- 288@LB@Position Seed - sRNA 31 -- 37@LB@
49	0.001147	0.07744	b3039	ygiD	-13.27	0.032900	280 -- 298	15 -- 33	4 5- DOPA-extradiol-dioxygenase		_____________279_________________299\n_____________\|___________________\|\n5'-ACG...UACCC__________GAAGU____GA-3'\n______________GCAGCUGGCA_____UGGG\n______________:\|\|\|\|\|:\|\|\|_____\|\|\|\|\n______________UGUCGAUCGU_____ACCC\n3'-UUU...GACCA__________AAAAU____AAUAC...UCG-5'\n_____________\|___________________\|\n_____________34__________________14\n	283 -- 289	24 -- 30	-23.43 kcal/mol	8.71058 kcal/mol	1.44754 kcal/mol	279 299@LB@ \| \|@LB@5'-ACG...UACCC GAAGU GA-3'@LB@ GCAGCUGGCA UGGG@LB@ :\|\|\|\|\|:\|\|\| \|\|\|\|@LB@ UGUCGAUCGU ACCC@LB@3'-UUU...GACCA AAAAU AAUAC...UCG-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -13.27 kcal/mol@LB@Hybridization Energy -23.43 kcal/mol@LB@Unfolding Energy - mRNA 8.71058 kcal/mol@LB@Unfolding Energy - sRNA 1.44754 kcal/mol@LB@@LB@Position - mRNA 280 -- 298@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 283 -- 289@LB@Position Seed - sRNA 24 -- 30@LB@
105	0.003867	0.1238	b0716	ybgO	-11.28	0.093728	281 -- 296	25 -- 40	putative fimbrial protein	b3048	_____________280______________297\n_____________\|________________\|\n5'-GCC...UGCUA__________U_____GGCG-3'\n______________UUUUGGUACA_CUGGU\n______________\|::\|\|\|\|\|\|\|_\|\|:\|:\n______________AGGACCAUGU_GAUCG\n3'-UUU...CACCA__________C_____UAAAA...UCG-5'\n_____________\|________________\|\n_____________41_______________24\n	284 -- 290	31 -- 37	-18.2853 kcal/mol	2.44789 kcal/mol	4.55365 kcal/mol	280 297@LB@ \| \|@LB@5'-GCC...UGCUA U GGCG-3'@LB@ UUUUGGUACA CUGGU@LB@ \|::\|\|\|\|\|\|\| \|\|:\|:@LB@ AGGACCAUGU GAUCG@LB@3'-UUU...CACCA C UAAAA...UCG-5'@LB@ \| \|@LB@ 41 24@LB@@LB@@LB@Energy -11.28 kcal/mol@LB@Hybridization Energy -18.2853 kcal/mol@LB@Unfolding Energy - mRNA 2.44789 kcal/mol@LB@Unfolding Energy - sRNA 4.55365 kcal/mol@LB@@LB@Position - mRNA 281 -- 296@LB@Position - sRNA 25 -- 40@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 31 -- 37@LB@
84	0.00278	0.1082	b1418	cybB	-11.15	0.099871	281 -- 297	37 -- 49	cytochrome b561		_____________280_______________298\n_____________\|_________________\|\n5'-AAC...GCAAU____UUUC_________UCC-3'\n______________GGAG____GUGGUUUCU\n______________\|\|\|\|____\|\|\|\|\|\|:\|\|\n______________CCUC____CACCAAGGA\n3'-UUU...CGAUU_________________CCAUG...UCG-5'\n_____________\|_________________\|\n_____________50________________36\n	291 -- 297	37 -- 43	-16.7846 kcal/mol	2.49998 kcal/mol	3.13428 kcal/mol	280 298@LB@ \| \|@LB@5'-AAC...GCAAU UUUC UCC-3'@LB@ GGAG GUGGUUUCU@LB@ \|\|\|\| \|\|\|\|\|\|:\|\|@LB@ CCUC CACCAAGGA@LB@3'-UUU...CGAUU CCAUG...UCG-5'@LB@ \| \|@LB@ 50 36@LB@@LB@@LB@Energy -11.15 kcal/mol@LB@Hybridization Energy -16.7846 kcal/mol@LB@Unfolding Energy - mRNA 2.49998 kcal/mol@LB@Unfolding Energy - sRNA 3.13428 kcal/mol@LB@@LB@Position - mRNA 281 -- 297@LB@Position - sRNA 37 -- 49@LB@Position Seed - mRNA 291 -- 297@LB@Position Seed - sRNA 37 -- 43@LB@
198	0.01161	0.1971	b2712	hypF	-10.23	0.151482	281 -- 290	24 -- 33	carbamoyl phosphate phosphatase and [NiFe] hydrogenase maturation protein		_____________280________291\n_____________\|__________\|\n5'-GAA...GUCUG__________CAGCA...UAA-3'\n______________GCAGCUGGCA\n______________:\|\|\|\|\|:\|\|\|\n______________UGUCGAUCGU\n3'-UUU...GACCA__________AAAAU...UCG-5'\n_____________\|__________\|\n_____________34_________23\n	284 -- 290	24 -- 30	-16.4359 kcal/mol	4.77953 kcal/mol	1.42716 kcal/mol	280 291@LB@ \| \|@LB@5'-GAA...GUCUG CAGCA...UAA-3'@LB@ GCAGCUGGCA@LB@ :\|\|\|\|\|:\|\|\|@LB@ UGUCGAUCGU@LB@3'-UUU...GACCA AAAAU...UCG-5'@LB@ \| \|@LB@ 34 23@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -16.4359 kcal/mol@LB@Unfolding Energy - mRNA 4.77953 kcal/mol@LB@Unfolding Energy - sRNA 1.42716 kcal/mol@LB@@LB@Position - mRNA 281 -- 290@LB@Position - sRNA 24 -- 33@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 24 -- 30@LB@
90	0.002979	0.1113	b3328	gspG	-12.13	0.061461	284 -- 293	37 -- 46	pseudopilin cryptic general secretion pathway		_____________283________294\n_____________\|__________\|\n5'-AAA...AGCCU__________AACCUAA-3'\n______________GGUGGUUCCU\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCACCAAGGA\n3'-UUU...UUCCU__________CCAUG...UCG-5'\n_____________\|__________\|\n_____________47_________36\n	287 -- 293	37 -- 43	-18.4741 kcal/mol	3.21142 kcal/mol	3.13317 kcal/mol	283 294@LB@ \| \|@LB@5'-AAA...AGCCU AACCUAA-3'@LB@ GGUGGUUCCU@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCACCAAGGA@LB@3'-UUU...UUCCU CCAUG...UCG-5'@LB@ \| \|@LB@ 47 36@LB@@LB@@LB@Energy -12.13 kcal/mol@LB@Hybridization Energy -18.4741 kcal/mol@LB@Unfolding Energy - mRNA 3.21142 kcal/mol@LB@Unfolding Energy - sRNA 3.13317 kcal/mol@LB@@LB@Position - mRNA 284 -- 293@LB@Position - sRNA 37 -- 46@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 37 -- 43@LB@
154	0.007726	0.1686	b4203	rplI	-9.34	0.218324	285 -- 297	29 -- 41	50S ribosomal subunit protein L9		_____________284___________298\n_____________\|_____________\|\n5'-AAA...GUAAC__________C__AGG-3'\n______________UUCCUGGUAC_GC\n______________\|\|\|\|\|\|\|\|\|\|_\|\|\n______________AAGGACCAUG_CG\n3'-UUU...CCACC__________U__AUCGU...UCG-5'\n_____________\|_____________\|\n_____________42____________28\n	288 -- 294	32 -- 38	-19.8737 kcal/mol	6.23655 kcal/mol	4.29727 kcal/mol	284 298@LB@ \| \|@LB@5'-AAA...GUAAC C AGG-3'@LB@ UUCCUGGUAC GC@LB@ \|\|\|\|\|\|\|\|\|\| \|\|@LB@ AAGGACCAUG CG@LB@3'-UUU...CCACC U AUCGU...UCG-5'@LB@ \| \|@LB@ 42 28@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -19.8737 kcal/mol@LB@Unfolding Energy - mRNA 6.23655 kcal/mol@LB@Unfolding Energy - sRNA 4.29727 kcal/mol@LB@@LB@Position - mRNA 285 -- 297@LB@Position - sRNA 29 -- 41@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 32 -- 38@LB@
83	0.002775	0.1082	b2049	cpsB	-6.85	0.497101	286 -- 298	17 -- 31	mannose-1-phosphate guanyltransferase		_____________285_____________299\n_____________\|_______________\|\n5'-ACA...UCCCA_______________CC-3'\n______________AGC_AGU_UUUUAUG\n______________\|\|\|_\|\|:_\|\|\|\|\|\|\|\n______________UCG_UCG_AAAAUAC\n3'-UUU...CCAUG___A___U_______CCAAU...UCG-5'\n_____________\|_______________\|\n_____________32______________16\n	292 -- 298	17 -- 23	-8.99018 kcal/mol	0.716641 kcal/mol	1.4259 kcal/mol	285 299@LB@ \| \|@LB@5'-ACA...UCCCA CC-3'@LB@ AGC AGU UUUUAUG@LB@ \|\|\| \|\|: \|\|\|\|\|\|\|@LB@ UCG UCG AAAAUAC@LB@3'-UUU...CCAUG A U CCAAU...UCG-5'@LB@ \| \|@LB@ 32 16@LB@@LB@@LB@Energy -6.85 kcal/mol@LB@Hybridization Energy -8.99018 kcal/mol@LB@Unfolding Energy - mRNA 0.716641 kcal/mol@LB@Unfolding Energy - sRNA 1.4259 kcal/mol@LB@@LB@Position - mRNA 286 -- 298@LB@Position - sRNA 17 -- 31@LB@Position Seed - mRNA 292 -- 298@LB@Position Seed - sRNA 17 -- 23@LB@
57	0.001403	0.08147	b0948	rlmL	-12.46	0.051711	286 -- 300	33 -- 47	23S rRNA m(2)G2445 and m(7)G2069 methyltransferases SAM-dependent		_____________285____________300\n_____________\|______________\|\n5'-GAC...AUGCC_________AG____-3'\n______________AGGUGGUUC__GGUG\n______________\|\|\|\|\|\|\|\|\|__\|\|\|:\n______________UCCACCAAG__CCAU\n3'-UUU...AUUCC_________GA____GUCGA...UCG-5'\n_____________\|_______________\|\n_____________48______________32\n	288 -- 294	39 -- 45	-21.3846 kcal/mol	5.67574 kcal/mol	3.25146 kcal/mol	285 300@LB@ \| \|@LB@5'-GAC...AUGCC AG -3'@LB@ AGGUGGUUC GGUG@LB@ \|\|\|\|\|\|\|\|\| \|\|\|:@LB@ UCCACCAAG CCAU@LB@3'-UUU...AUUCC GA GUCGA...UCG-5'@LB@ \| \|@LB@ 48 32@LB@@LB@@LB@Energy -12.46 kcal/mol@LB@Hybridization Energy -21.3846 kcal/mol@LB@Unfolding Energy - mRNA 5.67574 kcal/mol@LB@Unfolding Energy - sRNA 3.25146 kcal/mol@LB@@LB@Position - mRNA 286 -- 300@LB@Position - sRNA 33 -- 47@LB@Position Seed - mRNA 288 -- 294@LB@Position Seed - sRNA 39 -- 45@LB@
144	0.006813	0.158	b0111	ampE	-6.38	0.559697	294 -- 300	1 -- 7	ampicillin resistance inner membrane protein; putative signaling protein in beta-lactamase regulation		_____________293____300\n_____________\|______\|\n5'-CUU...CGUUC_______-3'\n______________UUUCGGC\n______________\|\|\|\|:\|\|\n______________AAAGUCG\n3'-UUU...UACAA_______-5'\n_____________\|______\|\n_____________8______1\n	294 -- 300	1 -- 7	-7.27697 kcal/mol	0.0992979 kcal/mol	0.796773 kcal/mol	293 300@LB@ \| \|@LB@5'-CUU...CGUUC -3'@LB@ UUUCGGC@LB@ \|\|\|\|:\|\|@LB@ AAAGUCG@LB@3'-UUU...UACAA -5'@LB@ \| \|@LB@ 8 1@LB@@LB@@LB@Energy -6.38 kcal/mol@LB@Hybridization Energy -7.27697 kcal/mol@LB@Unfolding Energy - mRNA 0.0992979 kcal/mol@LB@Unfolding Energy - sRNA 0.796773 kcal/mol@LB@@LB@Position - mRNA 294 -- 300@LB@Position - sRNA 1 -- 7@LB@Position Seed - mRNA 294 -- 300@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

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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

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