Input and runtime details for job 3429477 (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 3429477 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:26:36 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:27:01 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:15:20 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:15:27 CET 2018
	Job Completed		@ Fri Feb 16 20:15:52 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3429477&toolName=CopraRNA ( 30 days expiry )

Description of the job

OxyS

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
13	0.002299	0.5385	b3663	yicN	-11.49	0.058154	241 -- 256	60 -- 78	DUF1198 family protein	_____________240_________________257\n_____________\|___________________\|\n5'-CUU...GUUUG___________________GCUGA...AUC-3'\n______________UGGU__UGGUU_UUCGGGU\n______________\|\|\|:__\|:\|\|\|_\|\|\|\|:\|\|\n______________ACCG__AUCAA_AAGCUCA\n3'-CGC...GUGCA____AA_____U_______ACUCU...AAG-5'\n_____________\|___________________\|\n_____________79__________________59\n	250 -- 256	60 -- 66	-15.2298 kcal/mol	2.94333 kcal/mol	0.797083 kcal/mol	240 257@LB@ \| \|@LB@5'-CUU...GUUUG GCUGA...AUC-3'@LB@ UGGU UGGUU UUCGGGU@LB@ \|\|\|: \|:\|\|\| \|\|\|\|:\|\|@LB@ ACCG AUCAA AAGCUCA@LB@3'-CGC...GUGCA AA U ACUCU...AAG-5'@LB@ \| \|@LB@ 79 59@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -15.2298 kcal/mol@LB@Unfolding Energy - mRNA 2.94333 kcal/mol@LB@Unfolding Energy - sRNA 0.797083 kcal/mol@LB@@LB@Position - mRNA 241 -- 256@LB@Position - sRNA 60 -- 78@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 60 -- 66@LB@
86	0.01521	0.5385	b0605	ahpC	-11.47	0.058587	74 -- 93	73 -- 89	alkyl hydroperoxide reductase C22 subunit	_____________73___________________94\n_____________\|____________________\|\n5'-ACC...GGUGC_________AAA____U___ACGAA...GGA-3'\n______________AAAGUUCAC___GUUG_CUU\n______________\|\|\|\|\|\|\|\|\|___\|\|\|\|_\|\|\|\n______________UUUCAAGUG___CAAC_GAA\n3'-CGC...GGCGU________________C___AUCAA...AAG-5'\n_____________\|____________________\|\n_____________90___________________72\n	76 -- 82	81 -- 87	-14.6327 kcal/mol	2.64398 kcal/mol	0.517627 kcal/mol	73 94@LB@ \| \|@LB@5'-ACC...GGUGC AAA U ACGAA...GGA-3'@LB@ AAAGUUCAC GUUG CUU@LB@ \|\|\|\|\|\|\|\|\| \|\|\|\| \|\|\|@LB@ UUUCAAGUG CAAC GAA@LB@3'-CGC...GGCGU C AUCAA...AAG-5'@LB@ \| \|@LB@ 90 72@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -14.6327 kcal/mol@LB@Unfolding Energy - mRNA 2.64398 kcal/mol@LB@Unfolding Energy - sRNA 0.517627 kcal/mol@LB@@LB@Position - mRNA 74 -- 93@LB@Position - sRNA 73 -- 89@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 81 -- 87@LB@
15	0.002894	0.5385	b2780	pyrG	-11.46	0.058961	111 -- 140	60 -- 90	CTP synthetase	_____________110_______________________________141\n_____________\|_________________________________\|\n5'-UGU...AUAAU________________ACA___CA_________AUACU...GCC-3'\n______________GAAAGUUUG___UGGC___GGU__UGUUCGGGU\n______________:\|\|\|\|\|\|::___\|\|\|\|___:\|\|__\|:\|\|\|\|:\|\|\n______________UUUUCAAGU___ACCG___UCA__AUAAGCUCA\n3'-CGC...AGGCG_________GCA____AAA______________ACUCU...AAG-5'\n_____________\|_________________________________\|\n_____________91________________________________59\n	134 -- 140	60 -- 66	-21.5125 kcal/mol	8.34782 kcal/mol	1.70935 kcal/mol	110 141@LB@ \| \|@LB@5'-UGU...AUAAU ACA CA AUACU...GCC-3'@LB@ GAAAGUUUG UGGC GGU UGUUCGGGU@LB@ :\|\|\|\|\|\|:: \|\|\|\| :\|\| \|:\|\|\|\|:\|\|@LB@ UUUUCAAGU ACCG UCA AUAAGCUCA@LB@3'-CGC...AGGCG GCA AAA ACUCU...AAG-5'@LB@ \| \|@LB@ 91 59@LB@@LB@@LB@Energy -11.46 kcal/mol@LB@Hybridization Energy -21.5125 kcal/mol@LB@Unfolding Energy - mRNA 8.34782 kcal/mol@LB@Unfolding Energy - sRNA 1.70935 kcal/mol@LB@@LB@Position - mRNA 111 -- 140@LB@Position - sRNA 60 -- 90@LB@Position Seed - mRNA 134 -- 140@LB@Position Seed - sRNA 60 -- 66@LB@
27	0.005053	0.5385	b2058	wcaB	-11.44	0.059229	168 -- 190	61 -- 82	putative acyl transferase	_____________167______________________191\n_____________\|________________________\|\n5'-ACC...GGCAA____C_____GA____________GGCGC...AGA-3'\n______________ACGU_UGGCU__UGG_UAUUCGGG\n______________\|\|\|\|_\|\|\|\|\|__\|:\|_\|\|\|\|\|\|:\|\n______________UGCA_ACCGA__AUC_AUAAGCUC\n3'-CGC...UCAAG__________A____A________AACUC...AAG-5'\n_____________\|________________________\|\n_____________83_______________________60\n	184 -- 190	61 -- 67	-21.3941 kcal/mol	8.91056 kcal/mol	1.03929 kcal/mol	167 191@LB@ \| \|@LB@5'-ACC...GGCAA C GA GGCGC...AGA-3'@LB@ ACGU UGGCU UGG UAUUCGGG@LB@ \|\|\|\| \|\|\|\|\| \|:\| \|\|\|\|\|\|:\|@LB@ UGCA ACCGA AUC AUAAGCUC@LB@3'-CGC...UCAAG A A AACUC...AAG-5'@LB@ \| \|@LB@ 83 60@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -21.3941 kcal/mol@LB@Unfolding Energy - mRNA 8.91056 kcal/mol@LB@Unfolding Energy - sRNA 1.03929 kcal/mol@LB@@LB@Position - mRNA 168 -- 190@LB@Position - sRNA 61 -- 82@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 61 -- 67@LB@
149	0.0249	0.5467	b0737	tolQ	-11.44	0.059241	123 -- 143	57 -- 77	membrane spanning protein in TolA-TolQ-TolR complex	_____________122___________________144\n_____________\|_____________________\|\n5'-GCA...GCAGA____C__________C_____CCCAC...CCA-3'\n______________GGUU_UGGUUGUUUG_GUUGA\n______________\|\|:\|_\|:\|\|\|:\|\|:\|_\|\|\|\|\|\n______________CCGA_AUCAAUAAGC_CAACU\n3'-CGC...UGCAA____A__________U_____CUUUG...AAG-5'\n_____________\|_____________________\|\n_____________78____________________56\n	130 -- 136	64 -- 70	-20.7122 kcal/mol	8.05008 kcal/mol	1.21841 kcal/mol	122 144@LB@ \| \|@LB@5'-GCA...GCAGA C C CCCAC...CCA-3'@LB@ GGUU UGGUUGUUUG GUUGA@LB@ \|\|:\| \|:\|\|\|:\|\|:\| \|\|\|\|\|@LB@ CCGA AUCAAUAAGC CAACU@LB@3'-CGC...UGCAA A U CUUUG...AAG-5'@LB@ \| \|@LB@ 78 56@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -20.7122 kcal/mol@LB@Unfolding Energy - mRNA 8.05008 kcal/mol@LB@Unfolding Energy - sRNA 1.21841 kcal/mol@LB@@LB@Position - mRNA 123 -- 143@LB@Position - sRNA 57 -- 77@LB@Position Seed - mRNA 130 -- 136@LB@Position Seed - sRNA 64 -- 70@LB@
89	0.01549	0.5385	b3147	lpoA	-11.44	0.059349	235 -- 255	64 -- 83	OM lipoprotein stimulator of MrcA transpeptidase	_____________234___________________256\n_____________\|_____________________\|\n5'-UAU...AGCCG_______U__GCCU_______UGGCA...AUC-3'\n______________CGCGUUG_CU____GUUGUUC\n______________\|:\|\|\|\|\|_\|\|____\|\|\|:\|\|\|\n______________GUGCAAC_GA____CAAUAAG\n3'-CGC...UUCAA_______C__AAU________CUCAA...AAG-5'\n_____________\|_____________________\|\n_____________84____________________63\n	249 -- 255	64 -- 70	-16.9353 kcal/mol	4.93537 kcal/mol	0.560651 kcal/mol	234 256@LB@ \| \|@LB@5'-UAU...AGCCG U GCCU UGGCA...AUC-3'@LB@ CGCGUUG CU GUUGUUC@LB@ \|:\|\|\|\|\| \|\| \|\|\|:\|\|\|@LB@ GUGCAAC GA CAAUAAG@LB@3'-CGC...UUCAA C AAU CUCAA...AAG-5'@LB@ \| \|@LB@ 84 63@LB@@LB@@LB@Energy -11.44 kcal/mol@LB@Hybridization Energy -16.9353 kcal/mol@LB@Unfolding Energy - mRNA 4.93537 kcal/mol@LB@Unfolding Energy - sRNA 0.560651 kcal/mol@LB@@LB@Position - mRNA 235 -- 255@LB@Position - sRNA 64 -- 83@LB@Position Seed - mRNA 249 -- 255@LB@Position Seed - sRNA 64 -- 70@LB@
11	0.002269	0.5385	b1205	ychH	-11.36	0.061344	181 -- 195	75 -- 90	DUF2583 family putative inner membrane protein	_____________180______________196\n_____________\|________________\|\n5'-CAA...ACCCA___________GA___GACAU...UAC-3'\n______________GAAAGUUC_CG__GGU\n______________:\|\|\|\|\|\|\|_\|\|__\|\|:\n______________UUUUCAAG_GC__CCG\n3'-CGC...AGGCG________U__AA___AAAUC...AAG-5'\n_____________\|________________\|\n_____________91_______________74\n	182 -- 188	83 -- 89	-14.0006 kcal/mol	2.12575 kcal/mol	0.517251 kcal/mol	180 196@LB@ \| \|@LB@5'-CAA...ACCCA GA GACAU...UAC-3'@LB@ GAAAGUUC CG GGU@LB@ :\|\|\|\|\|\|\| \|\| \|\|:@LB@ UUUUCAAG GC CCG@LB@3'-CGC...AGGCG U AA AAAUC...AAG-5'@LB@ \| \|@LB@ 91 74@LB@@LB@@LB@Energy -11.36 kcal/mol@LB@Hybridization Energy -14.0006 kcal/mol@LB@Unfolding Energy - mRNA 2.12575 kcal/mol@LB@Unfolding Energy - sRNA 0.517251 kcal/mol@LB@@LB@Position - mRNA 181 -- 195@LB@Position - sRNA 75 -- 90@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 83 -- 89@LB@
69	0.01301	0.5385	b0174	ispU	-11.35	0.061456	97 -- 106	71 -- 80	undecaprenyl pyrophosphate synthase	_____________96_________107\n_____________\|__________\|\n5'-CGU...AAGUA__________UAAGG...AAA-3'\n______________GUUGGCUUUA\n______________\|\|\|\|\|\|\|\|\|\|\n______________CAACCGAAAU\n3'-CGC...AAGUG__________CAAUA...AAG-5'\n_____________\|__________\|\n_____________81_________70\n	100 -- 106	71 -- 77	-14.3232 kcal/mol	2.73321 kcal/mol	0.236872 kcal/mol	96 107@LB@ \| \|@LB@5'-CGU...AAGUA UAAGG...AAA-3'@LB@ GUUGGCUUUA@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CAACCGAAAU@LB@3'-CGC...AAGUG CAAUA...AAG-5'@LB@ \| \|@LB@ 81 70@LB@@LB@@LB@Energy -11.35 kcal/mol@LB@Hybridization Energy -14.3232 kcal/mol@LB@Unfolding Energy - mRNA 2.73321 kcal/mol@LB@Unfolding Energy - sRNA 0.236872 kcal/mol@LB@@LB@Position - mRNA 97 -- 106@LB@Position - sRNA 71 -- 80@LB@Position Seed - mRNA 100 -- 106@LB@Position Seed - sRNA 71 -- 77@LB@
92	0.01569	0.5385	b1246	oppD	-11.32	0.062179	266 -- 290	69 -- 90	oligopeptide ABC transporter ATPase	_____________265_______________________291\n_____________\|_________________________\|\n5'-AGC...AACGU_____A_______GUCAC_______ACCCC...ACG-3'\n______________GAAAG_UUUGCGU_____CUUUAGU\n______________:\|\|\|\|_\|\|::\|\|\|_____\|\|\|\|\|\|\|\n______________UUUUC_AAGUGCA_____GAAAUCA\n3'-CGC...AGGCG_____________ACC_________AUAAG...AAG-5'\n_____________\|_________________________\|\n_____________91________________________68\n	284 -- 290	69 -- 75	-14.6652 kcal/mol	2.76867 kcal/mol	0.572281 kcal/mol	265 291@LB@ \| \|@LB@5'-AGC...AACGU A GUCAC ACCCC...ACG-3'@LB@ GAAAG UUUGCGU CUUUAGU@LB@ :\|\|\|\| \|\|::\|\|\| \|\|\|\|\|\|\|@LB@ UUUUC AAGUGCA GAAAUCA@LB@3'-CGC...AGGCG ACC AUAAG...AAG-5'@LB@ \| \|@LB@ 91 68@LB@@LB@@LB@Energy -11.32 kcal/mol@LB@Hybridization Energy -14.6652 kcal/mol@LB@Unfolding Energy - mRNA 2.76867 kcal/mol@LB@Unfolding Energy - sRNA 0.572281 kcal/mol@LB@@LB@Position - mRNA 266 -- 290@LB@Position - sRNA 69 -- 90@LB@Position Seed - mRNA 284 -- 290@LB@Position Seed - sRNA 69 -- 75@LB@
29	0.005218	0.5385	b3433	asd	-11.22	0.064904	208 -- 219	71 -- 82	aspartate-semialdehyde dehydrogenase NAD(P)-binding	_____________207__________220\n_____________\|____________\|\n5'-UCA...GAAAA____________UCGGC...UCU-3'\n______________AUGUUGGUUUUA\n______________\|:\|\|\|\|\|:\|\|\|\|\n______________UGCAACCGAAAU\n3'-CGC...UCAAG____________CAAUA...AAG-5'\n_____________\|____________\|\n_____________83___________70\n	213 -- 219	71 -- 77	-13.9075 kcal/mol	2.30708 kcal/mol	0.38228 kcal/mol	207 220@LB@ \| \|@LB@5'-UCA...GAAAA UCGGC...UCU-3'@LB@ AUGUUGGUUUUA@LB@ \|:\|\|\|\|\|:\|\|\|\|@LB@ UGCAACCGAAAU@LB@3'-CGC...UCAAG CAAUA...AAG-5'@LB@ \| \|@LB@ 83 70@LB@@LB@@LB@Energy -11.22 kcal/mol@LB@Hybridization Energy -13.9075 kcal/mol@LB@Unfolding Energy - mRNA 2.30708 kcal/mol@LB@Unfolding Energy - sRNA 0.38228 kcal/mol@LB@@LB@Position - mRNA 208 -- 219@LB@Position - sRNA 71 -- 82@LB@Position Seed - mRNA 213 -- 219@LB@Position Seed - sRNA 71 -- 77@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)

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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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