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@
197	0.04129	0.6177	b1205	ychH	-8.72	0.074776	153 -- 162	43 -- 52	DUF2583 family putative inner membrane protein	_____________152________163\n_____________\|__________\|\n5'-CAA...AUAAG__________AUUCC...UAC-3'\n______________GAAGAGGGGU\n______________:\|\|\|\|\|\|::\|\n______________UUUCUCCUUA\n3'-UUU...GGCAG__________AAGUA...ACA-5'\n_____________\|__________\|\n_____________53_________42\n	156 -- 162	43 -- 49	-11.7568 kcal/mol	2.17132 kcal/mol	0.865937 kcal/mol	152 163@LB@ \| \|@LB@5'-CAA...AUAAG AUUCC...UAC-3'@LB@ GAAGAGGGGU@LB@ :\|\|\|\|\|\|::\|@LB@ UUUCUCCUUA@LB@3'-UUU...GGCAG AAGUA...ACA-5'@LB@ \| \|@LB@ 53 42@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -11.7568 kcal/mol@LB@Unfolding Energy - mRNA 2.17132 kcal/mol@LB@Unfolding Energy - sRNA 0.865937 kcal/mol@LB@@LB@Position - mRNA 153 -- 162@LB@Position - sRNA 43 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 43 -- 49@LB@
13	0.003065	0.593	b4529	ydbJ	-10.82	0.027981	161 -- 194	44 -- 78	DUF333 family putative lipoprotein	_____________160___________________________________195\n_____________\|_____________________________________\|\n5'-GCA...UAUUU________________________AA__UC_______GAAAA...GUU-3'\n______________AUGG_CGGUGUCGU__UUGGCUUG__GA__AGAGGAA\n______________\|\|\|\|_\|::\|:\|\|\|:__\|\|\|\|\|::\|__:\|__\|\|\|\|\|\|\|\n______________UACC_GUUAUAGCG__AACCGGGC__UU__UCUCCUU\n_____3'-UUUUUU____G_________AU________AG___________AAAGU...ACA-5'\n_____________\|_____________________________________\|\n_____________79____________________________________43\n	188 -- 194	44 -- 50	-34.9495 kcal/mol	10.5981 kcal/mol	13.5333 kcal/mol	160 195@LB@ \| \|@LB@5'-GCA...UAUUU AA UC GAAAA...GUU-3'@LB@ AUGG CGGUGUCGU UUGGCUUG GA AGAGGAA@LB@ \|\|\|\| \|::\|:\|\|\|: \|\|\|\|\|::\| :\| \|\|\|\|\|\|\|@LB@ UACC GUUAUAGCG AACCGGGC UU UCUCCUU@LB@ 3'-UUUUUU G AU AG AAAGU...ACA-5'@LB@ \| \|@LB@ 79 43@LB@@LB@@LB@Energy -10.82 kcal/mol@LB@Hybridization Energy -34.9495 kcal/mol@LB@Unfolding Energy - mRNA 10.5981 kcal/mol@LB@Unfolding Energy - sRNA 13.5333 kcal/mol@LB@@LB@Position - mRNA 161 -- 194@LB@Position - sRNA 44 -- 78@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
156	0.03128	0.6177	b4512	ybdD	-7.87	0.110479	26 -- 38	43 -- 55	DUF466 family protein	_____________25____________39\n_____________\|_____________\|\n5'-GCA...UCAGA__G__________GUUGG...GGG-3'\n______________GU_AGGGGGGGAU\n______________\|\|_\|::\|:\|\|:\|\|\n______________CA_UUUCUCCUUA\n3'-UUU...CCGGG__G__________AAGUA...ACA-5'\n_____________\|_____________\|\n_____________56____________42\n	32 -- 38	43 -- 49	-14.3671 kcal/mol	5.55181 kcal/mol	0.946481 kcal/mol	25 39@LB@ \| \|@LB@5'-GCA...UCAGA G GUUGG...GGG-3'@LB@ GU AGGGGGGGAU@LB@ \|\| \|::\|:\|\|:\|\|@LB@ CA UUUCUCCUUA@LB@3'-UUU...CCGGG G AAGUA...ACA-5'@LB@ \| \|@LB@ 56 42@LB@@LB@@LB@Energy -7.87 kcal/mol@LB@Hybridization Energy -14.3671 kcal/mol@LB@Unfolding Energy - mRNA 5.55181 kcal/mol@LB@Unfolding Energy - sRNA 0.946481 kcal/mol@LB@@LB@Position - mRNA 26 -- 38@LB@Position - sRNA 43 -- 55@LB@Position Seed - mRNA 32 -- 38@LB@Position Seed - sRNA 43 -- 49@LB@
57	0.01201	0.6177	b2959	yggL	-9.33	0.056423	82 -- 92	47 -- 57	DUF469 family protein	_____________81__________93\n_____________\|___________\|\n5'-GUA...AAAAC___________CAAUG...CAU-3'\n______________CUGUCAGAGAG\n______________\|:\|\|\|\|:\|\|\|\|\n______________GGCAGUUUCUC\n3'-UUU...AACCG___________CUUAA...ACA-5'\n_____________\|___________\|\n_____________58__________46\n	86 -- 92	47 -- 53	-15.1623 kcal/mol	3.10124 kcal/mol	2.73556 kcal/mol	81 93@LB@ \| \|@LB@5'-GUA...AAAAC CAAUG...CAU-3'@LB@ CUGUCAGAGAG@LB@ \|:\|\|\|\|:\|\|\|\|@LB@ GGCAGUUUCUC@LB@3'-UUU...AACCG CUUAA...ACA-5'@LB@ \| \|@LB@ 58 46@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -15.1623 kcal/mol@LB@Unfolding Energy - mRNA 3.10124 kcal/mol@LB@Unfolding Energy - sRNA 2.73556 kcal/mol@LB@@LB@Position - mRNA 82 -- 92@LB@Position - sRNA 47 -- 57@LB@Position Seed - mRNA 86 -- 92@LB@Position Seed - sRNA 47 -- 53@LB@
83	0.0176	0.6177	b2457	eutM	-9.48	0.052376	185 -- 194	44 -- 53	ethanolamine utilization protein putative carboxysome structural protein	_____________184________195\n_____________\|__________\|\n5'-UAU...CCUGA__________AGCAC...UUA-3'\n______________UAAAGAGGAA\n______________:\|\|\|\|\|\|\|\|\|\n______________GUUUCUCCUU\n3'-UUU...GGGCA__________AAAGU...ACA-5'\n_____________\|__________\|\n_____________54_________43\n	188 -- 194	44 -- 50	-11.8586 kcal/mol	1.44575 kcal/mol	0.927997 kcal/mol	184 195@LB@ \| \|@LB@5'-UAU...CCUGA AGCAC...UUA-3'@LB@ UAAAGAGGAA@LB@ :\|\|\|\|\|\|\|\|\|@LB@ GUUUCUCCUU@LB@3'-UUU...GGGCA AAAGU...ACA-5'@LB@ \| \|@LB@ 54 43@LB@@LB@@LB@Energy -9.48 kcal/mol@LB@Hybridization Energy -11.8586 kcal/mol@LB@Unfolding Energy - mRNA 1.44575 kcal/mol@LB@Unfolding Energy - sRNA 0.927997 kcal/mol@LB@@LB@Position - mRNA 185 -- 194@LB@Position - sRNA 44 -- 53@LB@Position Seed - mRNA 188 -- 194@LB@Position Seed - sRNA 44 -- 50@LB@
174	0.03548	0.6177	b2437	eutR	-7.66	0.121193	279 -- 299	38 -- 55	eut operon transcriptional activator AraC family	_____________278___________________300\n_____________\|_____________________\|\n5'-CGC...CGAAG_______U___UAAUG_____C-3'\n______________GUCGAAG_GGA_____UUCAU\n______________\|\|\|:\|\|\|_\|\|\|_____\|\|\|\|\|\n______________CAGUUUC_CCU_____AAGUA\n3'-UUU...CCGGG_______U___UA________AAAAA...ACA-5'\n_____________\|_____________________\|\n_____________56____________________37\n	279 -- 285	49 -- 55	-15.2982 kcal/mol	6.46344 kcal/mol	1.17036 kcal/mol	278 300@LB@ \| \|@LB@5'-CGC...CGAAG U UAAUG C-3'@LB@ GUCGAAG GGA UUCAU@LB@ \|\|\|:\|\|\| \|\|\| \|\|\|\|\|@LB@ CAGUUUC CCU AAGUA@LB@3'-UUU...CCGGG U UA AAAAA...ACA-5'@LB@ \| \|@LB@ 56 37@LB@@LB@@LB@Energy -7.66 kcal/mol@LB@Hybridization Energy -15.2982 kcal/mol@LB@Unfolding Energy - mRNA 6.46344 kcal/mol@LB@Unfolding Energy - sRNA 1.17036 kcal/mol@LB@@LB@Position - mRNA 279 -- 299@LB@Position - sRNA 38 -- 55@LB@Position Seed - mRNA 279 -- 285@LB@Position Seed - sRNA 49 -- 55@LB@
182	0.03771	0.6177	b0397	sbcC	-11.00	0.025718	84 -- 100	39 -- 56	exonuclease dsDNA ATP-dependent	_____________83_________________101\n_____________\|__________________\|\n5'-GAA...CUCAG___________UG_____AUCGC...UUG-3'\n______________CGUCGAAGAGG___UUCA\n______________\|\|\|\|:\|\|\|\|\|\|___\|\|\|\|\n______________GCAGUUUCUCC___AAGU\n3'-UUU...ACCGG___________UUA____AAAAA...ACA-5'\n_____________\|__________________\|\n_____________57_________________38\n	88 -- 94	46 -- 52	-19.0672 kcal/mol	6.9127 kcal/mol	1.15786 kcal/mol	83 101@LB@ \| \|@LB@5'-GAA...CUCAG UG AUCGC...UUG-3'@LB@ CGUCGAAGAGG UUCA@LB@ \|\|\|\|:\|\|\|\|\|\| \|\|\|\|@LB@ GCAGUUUCUCC AAGU@LB@3'-UUU...ACCGG UUA AAAAA...ACA-5'@LB@ \| \|@LB@ 57 38@LB@@LB@@LB@Energy -11.00 kcal/mol@LB@Hybridization Energy -19.0672 kcal/mol@LB@Unfolding Energy - mRNA 6.9127 kcal/mol@LB@Unfolding Energy - sRNA 1.15786 kcal/mol@LB@@LB@Position - mRNA 84 -- 100@LB@Position - sRNA 39 -- 56@LB@Position Seed - mRNA 88 -- 94@LB@Position Seed - sRNA 46 -- 52@LB@
192	0.04008	0.6177	b2822	recC	-5.02	0.370915	179 -- 195	44 -- 57	exonuclease V (RecBCD complex) gamma chain	_____________178_______________196\n_____________\|_________________\|\n5'-AGU...CCGAA_______U__UC_____CCGCU...AGA-3'\n______________UCGUCAG_AG__AGGAG\n______________:\|\|\|\|\|:_\|\|__\|\|\|\|:\n______________GGCAGUU_UC__UCCUU\n3'-UUU...AACCG_________________AAAGU...ACA-5'\n_____________\|_________________\|\n_____________58________________43\n	179 -- 185	51 -- 57	-11.1502 kcal/mol	3.39036 kcal/mol	2.73756 kcal/mol	178 196@LB@ \| \|@LB@5'-AGU...CCGAA U UC CCGCU...AGA-3'@LB@ UCGUCAG AG AGGAG@LB@ :\|\|\|\|\|: \|\| \|\|\|\|:@LB@ GGCAGUU UC UCCUU@LB@3'-UUU...AACCG AAAGU...ACA-5'@LB@ \| \|@LB@ 58 43@LB@@LB@@LB@Energy -5.02 kcal/mol@LB@Hybridization Energy -11.1502 kcal/mol@LB@Unfolding Energy - mRNA 3.39036 kcal/mol@LB@Unfolding Energy - sRNA 2.73756 kcal/mol@LB@@LB@Position - mRNA 179 -- 195@LB@Position - sRNA 44 -- 57@LB@Position Seed - mRNA 179 -- 185@LB@Position Seed - sRNA 51 -- 57@LB@
82	0.01753	0.6177	b2204	napH	-9.88	0.043521	152 -- 162	42 -- 52	ferredoxin-type protein	_____________151_________163\n_____________\|___________\|\n5'-CAC...UGGCG___________AGGUC...UCU-3'\n______________AAAGGGGAGUU\n______________\|\|\|\|:\|\|\|:\|\|\n______________UUUCUCCUUAA\n3'-UUU...GGCAG___________AGUAA...ACA-5'\n_____________\|___________\|\n_____________53__________41\n	156 -- 162	42 -- 48	-12.4472 kcal/mol	1.70007 kcal/mol	0.866923 kcal/mol	151 163@LB@ \| \|@LB@5'-CAC...UGGCG AGGUC...UCU-3'@LB@ AAAGGGGAGUU@LB@ \|\|\|\|:\|\|\|:\|\|@LB@ UUUCUCCUUAA@LB@3'-UUU...GGCAG AGUAA...ACA-5'@LB@ \| \|@LB@ 53 41@LB@@LB@@LB@Energy -9.88 kcal/mol@LB@Hybridization Energy -12.4472 kcal/mol@LB@Unfolding Energy - mRNA 1.70007 kcal/mol@LB@Unfolding Energy - sRNA 0.866923 kcal/mol@LB@@LB@Position - mRNA 152 -- 162@LB@Position - sRNA 42 -- 52@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 42 -- 48@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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