Input and runtime details for job 1765463 (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 1765463 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:41:59 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:42:13 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 19:57:45 CET 2018
	Post-Processing Finished		@ Fri Feb 16 19:57:53 CET 2018
	Job Completed		@ Fri Feb 16 19:58:19 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
103	0.02062	0.6177	b1332	ynaJ	-7.81	0.113347	36 -- 54	40 -- 55	DUF2534 family putative inner membrane protein	_____________35__________________55\n_____________\|___________________\|\n5'-AAA...ACUGA____GCC____A_______CCCGC...CCA-3'\n______________GUCA___GAGA_GAAUUUC\n______________\|\|\|\|___:\|\|\|_\|\|\|\|\|\|\|\n______________CAGU___UUCU_CUUAAAG\n3'-UUU...CCGGG___________C_______UAAAA...ACA-5'\n_____________\|___________________\|\n_____________56__________________39\n	48 -- 54	40 -- 46	-13.2524 kcal/mol	4.4222 kcal/mol	1.01784 kcal/mol	35 55@LB@ \| \|@LB@5'-AAA...ACUGA GCC A CCCGC...CCA-3'@LB@ GUCA GAGA GAAUUUC@LB@ \|\|\|\| :\|\|\| \|\|\|\|\|\|\|@LB@ CAGU UUCU CUUAAAG@LB@3'-UUU...CCGGG C UAAAA...ACA-5'@LB@ \| \|@LB@ 56 39@LB@@LB@@LB@Energy -7.81 kcal/mol@LB@Hybridization Energy -13.2524 kcal/mol@LB@Unfolding Energy - mRNA 4.4222 kcal/mol@LB@Unfolding Energy - sRNA 1.01784 kcal/mol@LB@@LB@Position - mRNA 36 -- 54@LB@Position - sRNA 40 -- 55@LB@Position Seed - mRNA 48 -- 54@LB@Position Seed - sRNA 40 -- 46@LB@
116	0.02318	0.6177	b1726	yniB	-7.96	0.105879	188 -- 195	47 -- 54	putative inner membrane protein	_____________187______196\n_____________\|________\|\n5'-AAG...CUUAA________AACUC...UGA-3'\n______________UCAAGGAG\n______________\|\|\|\|:\|\|\|\n______________AGUUUCUC\n3'-UUU...CGGGC________CUUAA...ACA-5'\n_____________\|________\|\n_____________55_______46\n	189 -- 195	47 -- 53	-9.99546 kcal/mol	1.13532 kcal/mol	0.897871 kcal/mol	187 196@LB@ \| \|@LB@5'-AAG...CUUAA AACUC...UGA-3'@LB@ UCAAGGAG@LB@ \|\|\|\|:\|\|\|@LB@ AGUUUCUC@LB@3'-UUU...CGGGC CUUAA...ACA-5'@LB@ \| \|@LB@ 55 46@LB@@LB@@LB@Energy -7.96 kcal/mol@LB@Hybridization Energy -9.99546 kcal/mol@LB@Unfolding Energy - mRNA 1.13532 kcal/mol@LB@Unfolding Energy - sRNA 0.897871 kcal/mol@LB@@LB@Position - mRNA 188 -- 195@LB@Position - sRNA 47 -- 54@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 47 -- 53@LB@
26	0.004859	0.5992	b1753	ynjA	-8.90	0.068656	186 -- 195	43 -- 52	carboxymuconolactone decarboxylase family protein	_____________185________196\n_____________\|__________\|\n5'-ACU...CGCCA__________GCCUG...GGU-3'\n______________GAAGAGGAAU\n______________:\|\|\|\|\|\|\|\|\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	189 -- 195	43 -- 49	-11.6028 kcal/mol	1.83308 kcal/mol	0.865937 kcal/mol	185 196@LB@ \| \|@LB@5'-ACU...CGCCA GCCUG...GGU-3'@LB@ GAAGAGGAAU@LB@ :\|\|\|\|\|\|\|\|\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.90 kcal/mol@LB@Hybridization Energy -11.6028 kcal/mol@LB@Unfolding Energy - mRNA 1.83308 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 186 -- 195@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 43 -- 49@LB@
99	0.01953	0.6177	b2473	ypfH	-12.09	0.015349	8 -- 40	44 -- 76	palmitoyl-CoA esterase activity uncertain physiological substrate	_____________7__________________________________41\n_____________\|__________________________________\|\n____5'-ACUUUCA_____CAAGA_____C___________C______GAGGC...GGG-3'\n______________GGCCG_____UGUUA_UGGUCCGUCAG_G_GGAA\n______________\|\|\|\|:_____:\|:\|\|_\|\|\|:\|\|\|\|\|\|:_\|_\|\|\|\|\n______________CCGGU_____GCGAU_ACCGGGCAGUU_C_CCUU\n___3'-UUUUUUUA_____UAUA______A___________U_U____AAAGU...ACA-5'\n_____________\|__________________________________\|\n_____________77_________________________________43\n	28 -- 34	51 -- 57	-34.8713 kcal/mol	9.35151 kcal/mol	13.433 kcal/mol	7 41@LB@ \| \|@LB@ 5'-ACUUUCA CAAGA C C GAGGC...GGG-3'@LB@ GGCCG UGUUA UGGUCCGUCAG G GGAA@LB@ \|\|\|\|: :\|:\|\| \|\|\|:\|\|\|\|\|\|: \| \|\|\|\|@LB@ CCGGU GCGAU ACCGGGCAGUU C CCUU@LB@ 3'-UUUUUUUA UAUA A U U AAAGU...ACA-5'@LB@ \| \|@LB@ 77 43@LB@@LB@@LB@Energy -12.09 kcal/mol@LB@Hybridization Energy -34.8713 kcal/mol@LB@Unfolding Energy - mRNA 9.35151 kcal/mol@LB@Unfolding Energy - sRNA 13.433 kcal/mol@LB@@LB@Position - mRNA 8 -- 40@LB@Position - sRNA 44 -- 76@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 51 -- 57@LB@
188	0.03926	0.6177	b4547	ypfN	-8.44	0.084930	187 -- 194	44 -- 51	putative membrane protein UPF0370 family	_____________186______195\n_____________\|________\|\n5'-UGA...UCUGC________AUAAG...AGA-3'\n______________AAGAGGAA\n______________\|\|\|\|\|\|\|\|\n______________UUCUCCUU\n3'-UUU...GCAGU________AAAGU...ACA-5'\n_____________\|________\|\n_____________52_______43\n	188 -- 194	44 -- 50	-10.245 kcal/mol	0.953219 kcal/mol	0.848077 kcal/mol	186 195@LB@ \| \|@LB@5'-UGA...UCUGC AUAAG...AGA-3'@LB@ AAGAGGAA@LB@ \|\|\|\|\|\|\|\|@LB@ UUCUCCUU@LB@3'-UUU...GCAGU AAAGU...ACA-5'@LB@ \| \|@LB@ 52 43@LB@@LB@@LB@Energy -8.44 kcal/mol@LB@Hybridization Energy -10.245 kcal/mol@LB@Unfolding Energy - mRNA 0.953219 kcal/mol@LB@Unfolding Energy - sRNA 0.848077 kcal/mol@LB@@LB@Position - mRNA 187 -- 194@LB@Position - sRNA 44 -- 51@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
48	0.00943	0.6129	b3033	yqiB	-8.72	0.074798	113 -- 121	44 -- 52	DUF1249 protein YqiB	_____________112_______122\n_____________\|_________\|\n5'-UGG...GUAGA_________AAUCG...GCG-3'\n______________AGAGGGGAA\n______________\|:\|\|:\|\|\|\|\n______________UUUCUCCUU\n3'-UUU...GGCAG_________AAAGU...ACA-5'\n_____________\|_________\|\n_____________53________43\n	115 -- 121	44 -- 50	-10.7393 kcal/mol	1.15971 kcal/mol	0.860683 kcal/mol	112 122@LB@ \| \|@LB@5'-UGG...GUAGA AAUCG...GCG-3'@LB@ AGAGGGGAA@LB@ \|:\|\|:\|\|\|\|@LB@ UUUCUCCUU@LB@3'-UUU...GGCAG AAAGU...ACA-5'@LB@ \| \|@LB@ 53 43@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -10.7393 kcal/mol@LB@Unfolding Energy - mRNA 1.15971 kcal/mol@LB@Unfolding Energy - sRNA 0.860683 kcal/mol@LB@@LB@Position - mRNA 113 -- 121@LB@Position - sRNA 44 -- 52@LB@Position Seed - mRNA 115 -- 121@LB@Position Seed - sRNA 44 -- 50@LB@
97	0.01904	0.6177	b3102	yqjG	-9.04	0.064335	159 -- 168	44 -- 53	putative S-transferase	_____________158________169\n_____________\|__________\|\n5'-GCA...AAAAA__________GCUCC...GGC-3'\n______________CGAGGAGGAA\n______________\|:\|:\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	162 -- 168	44 -- 50	-13.5343 kcal/mol	3.56251 kcal/mol	0.927997 kcal/mol	158 169@LB@ \| \|@LB@5'-GCA...AAAAA GCUCC...GGC-3'@LB@ CGAGGAGGAA@LB@ \|:\|:\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.04 kcal/mol@LB@Hybridization Energy -13.5343 kcal/mol@LB@Unfolding Energy - mRNA 3.56251 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 159 -- 168@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 162 -- 168@LB@Position Seed - sRNA 44 -- 50@LB@
123	0.02427	0.6177	b4485	ytfR	-5.89	0.261942	32 -- 42	44 -- 54	putative sugar ABC transporter ATPase	_____________31__________43\n_____________\|___________\|\n5'-CCU...AAGAA_______A___GAAAA...GCC-3'\n______________UUAGAGA_GAA\n______________\|:\|:\|\|\|_\|\|\|\n______________AGUUUCU_CUU\n3'-UUU...CGGGC_______C___AAAGU...ACA-5'\n_____________\|___________\|\n_____________55__________43\n	32 -- 38	48 -- 54	-7.06152 kcal/mol	0.22708 kcal/mol	0.939671 kcal/mol	31 43@LB@ \| \|@LB@5'-CCU...AAGAA A GAAAA...GCC-3'@LB@ UUAGAGA GAA@LB@ \|:\|:\|\|\| \|\|\|@LB@ AGUUUCU CUU@LB@3'-UUU...CGGGC C AAAGU...ACA-5'@LB@ \| \|@LB@ 55 43@LB@@LB@@LB@Energy -5.89 kcal/mol@LB@Hybridization Energy -7.06152 kcal/mol@LB@Unfolding Energy - mRNA 0.22708 kcal/mol@LB@Unfolding Energy - sRNA 0.939671 kcal/mol@LB@@LB@Position - mRNA 32 -- 42@LB@Position - sRNA 44 -- 54@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 48 -- 54@LB@
10	0.001925	0.593	b2910	zapA	-12.97	0.010115	44 -- 65	38 -- 56	FtsZ stabilizer	_____________43_____________________66\n_____________\|______________________\|\n5'-GUU...UUCGU______AG________A_____GAUAU...AUC-3'\n______________CGUCAA__GGAGGAAU_UUCAU\n______________\|\|\|\|\|\|__:\|\|\|\|\|\|\|_\|\|\|\|\|\n______________GCAGUU__UCUCCUUA_AAGUA\n3'-UUU...ACCGG______________________AAAAA...ACA-5'\n_____________\|______________________\|\n_____________57_____________________37\n	53 -- 59	43 -- 49	-19.9082 kcal/mol	5.76295 kcal/mol	1.17918 kcal/mol	43 66@LB@ \| \|@LB@5'-GUU...UUCGU AG A GAUAU...AUC-3'@LB@ CGUCAA GGAGGAAU UUCAU@LB@ \|\|\|\|\|\| :\|\|\|\|\|\|\| \|\|\|\|\|@LB@ GCAGUU UCUCCUUA AAGUA@LB@3'-UUU...ACCGG AAAAA...ACA-5'@LB@ \| \|@LB@ 57 37@LB@@LB@@LB@Energy -12.97 kcal/mol@LB@Hybridization Energy -19.9082 kcal/mol@LB@Unfolding Energy - mRNA 5.76295 kcal/mol@LB@Unfolding Energy - sRNA 1.17918 kcal/mol@LB@@LB@Position - mRNA 44 -- 65@LB@Position - sRNA 38 -- 56@LB@Position Seed - mRNA 53 -- 59@LB@Position Seed - sRNA 43 -- 49@LB@
6	0.0006545	0.351	b1857	znuA	-11.78	0.017745	58 -- 67	45 -- 54	zinc ABC transporter periplasmic binding protein	_____________57_________68\n_____________\|__________\|\n5'-GCG...ACACA__________CGCGG...AAC-3'\n______________UCAGAGAGGA\n______________\|\|\|:\|\|\|\|\|\|\n______________AGUUUCUCCU\n3'-UUU...CGGGC__________UAAAG...ACA-5'\n_____________\|__________\|\n_____________55_________44\n	61 -- 67	45 -- 51	-14.7441 kcal/mol	2.03423 kcal/mol	0.929144 kcal/mol	57 68@LB@ \| \|@LB@5'-GCG...ACACA CGCGG...AAC-3'@LB@ UCAGAGAGGA@LB@ \|\|\|:\|\|\|\|\|\|@LB@ AGUUUCUCCU@LB@3'-UUU...CGGGC UAAAG...ACA-5'@LB@ \| \|@LB@ 55 44@LB@@LB@@LB@Energy -11.78 kcal/mol@LB@Hybridization Energy -14.7441 kcal/mol@LB@Unfolding Energy - mRNA 2.03423 kcal/mol@LB@Unfolding Energy - sRNA 0.929144 kcal/mol@LB@@LB@Position - mRNA 58 -- 67@LB@Position - sRNA 45 -- 54@LB@Position Seed - mRNA 61 -- 67@LB@Position Seed - sRNA 45 -- 51@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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