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
171	0.00925	0.1803	b3832	rmuC	-14.29	0.017807	191 -- 257	1 -- 50	DNA recombination protein	_____________190___________________________________________________________________258\n_____________\|_____________________________________________________________________\|\n5'-AAA...GCGUC______CGUUG___A____UCAAUCA____UUAC_______UU_____G___________GCAA_____UGGCU...AGC-3'\n______________AGGAGG_____UGG_UUUC_______UGGU____GCAGUUA__GCGUU__GUGGG_UGUG____UUGGC\n______________\|\|\|\|\|\|_____\|\|\|_\|\|:\|_______\|\|\|\|____:\|\|\|:\|\|__\|\|:\|\|__:\|\|\|\|_\|:\|\|____\|::\|\|\n______________UCCUCC_____ACC_AAGG_______ACCA____UGUCGAU__CGUAA__UACCC_AUAC____AGUCG\n3'-UUU...CCGAU________________________________________________AA_____A____AAAA_____-5'\n_____________\|____________________________________________________________________\|\n_____________51___________________________________________________________________1\n	225 -- 231	27 -- 33	-40.6833 kcal/mol	21.7322 kcal/mol	4.6634 kcal/mol	190 258@LB@ \| \|@LB@5'-AAA...GCGUC CGUUG A UCAAUCA UUAC UU G GCAA UGGCU...AGC-3'@LB@ AGGAGG UGG UUUC UGGU GCAGUUA GCGUU GUGGG UGUG UUGGC@LB@ \|\|\|\|\|\| \|\|\| \|\|:\| \|\|\|\| :\|\|\|:\|\| \|\|:\|\| :\|\|\|\| \|:\|\| \|::\|\|@LB@ UCCUCC ACC AAGG ACCA UGUCGAU CGUAA UACCC AUAC AGUCG@LB@3'-UUU...CCGAU AA A AAAA -5'@LB@ \| \|@LB@ 51 1@LB@@LB@@LB@Energy -14.29 kcal/mol@LB@Hybridization Energy -40.6833 kcal/mol@LB@Unfolding Energy - mRNA 21.7322 kcal/mol@LB@Unfolding Energy - sRNA 4.6634 kcal/mol@LB@@LB@Position - mRNA 191 -- 257@LB@Position - sRNA 1 -- 50@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 27 -- 33@LB@
12	4.171e-05	0.01168	b0814	ompX	-14.35	0.017131	192 -- 226	1 -- 48	outer membrane protein X	_____________191______________________________________________227\n_____________\|________________________________________________\|\n5'-CUG...CAUUU_________A___AAAAAAAUU__________________C_______ACUGG...CAC-3'\n______________GAGGUGGUU__UG_________GCA____________UGU_UUUCAGC\n______________\|\|\|\|\|\|\|\|\|__\|\|_________\|\|\|____________\|\|\|_\|\|\|\|\|\|\|\n______________CUCCACCAA__AC_________CGU____________ACA_AAAGUCG\n3'-UUU...GAUUC_________GG__CAUGUCGAU___AAAAUACCCAAU___A_______-5'\n_____________\|_______________________________________________\|\n_____________49______________________________________________1\n	220 -- 226	1 -- 7	-27.166 kcal/mol	8.20777 kcal/mol	4.60955 kcal/mol	191 227@LB@ \| \|@LB@5'-CUG...CAUUU A AAAAAAAUU C ACUGG...CAC-3'@LB@ GAGGUGGUU UG GCA UGU UUUCAGC@LB@ \|\|\|\|\|\|\|\|\| \|\| \|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CUCCACCAA AC CGU ACA AAAGUCG@LB@3'-UUU...GAUUC GG CAUGUCGAU AAAAUACCCAAU A -5'@LB@ \| \|@LB@ 49 1@LB@@LB@@LB@Energy -14.35 kcal/mol@LB@Hybridization Energy -27.166 kcal/mol@LB@Unfolding Energy - mRNA 8.20777 kcal/mol@LB@Unfolding Energy - sRNA 4.60955 kcal/mol@LB@@LB@Position - mRNA 192 -- 226@LB@Position - sRNA 1 -- 48@LB@Position Seed - mRNA 220 -- 226@LB@Position Seed - sRNA 1 -- 7@LB@
28	0.000409	0.0491	b1688	ydiK	-9.69	0.189548	195 -- 219	1 -- 33	UPF0118 family inner membrane protein	_____________194_______________________________220\n_____________\|_________________________________\|\n5'-AUG...GAAAA__________________UAA_____CG_____CCAGG...CCU-3'\n______________GUAGUUA________UGG___AUGUU__UCAGC\n______________::\|\|:\|\|________\|\|\|___\|\|\|\|\|__\|\|\|\|\|\n______________UGUCGAU________ACC___UACAA__AGUCG\n3'-UUU...GACCA_______CGUAAAAU___CAA_____AA_____-5'\n_____________\|________________________________\|\n_____________34_______________________________1\n	195 -- 201	27 -- 33	-14.5165 kcal/mol	3.32905 kcal/mol	1.49313 kcal/mol	194 220@LB@ \| \|@LB@5'-AUG...GAAAA UAA CG CCAGG...CCU-3'@LB@ GUAGUUA UGG AUGUU UCAGC@LB@ ::\|\|:\|\| \|\|\| \|\|\|\|\| \|\|\|\|\|@LB@ UGUCGAU ACC UACAA AGUCG@LB@3'-UUU...GACCA CGUAAAAU CAA AA -5'@LB@ \| \|@LB@ 34 1@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -14.5165 kcal/mol@LB@Unfolding Energy - mRNA 3.32905 kcal/mol@LB@Unfolding Energy - sRNA 1.49313 kcal/mol@LB@@LB@Position - mRNA 195 -- 219@LB@Position - sRNA 1 -- 33@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 27 -- 33@LB@
50	0.001175	0.07744	b3543	dppB	-14.13	0.019609	196 -- 210	1 -- 17	dipeptide/heme ABC transporter permease	_____________195_______________211\n_____________\|_________________\|\n5'-CGG...AAUCC__________G______UUAUU...AUC-3'\n______________GGGUUAUGUU___CAGU\n______________\|\|\|\|\|\|\|\|\|\|___\|\|\|:\n______________CCCAAUACAA___GUCG\n3'-UUU...AAAUA__________AAA____-5'\n_____________\|________________\|\n_____________18_______________1\n	199 -- 205	8 -- 14	-17.9134 kcal/mol	2.84721 kcal/mol	0.931609 kcal/mol	195 211@LB@ \| \|@LB@5'-CGG...AAUCC G UUAUU...AUC-3'@LB@ GGGUUAUGUU CAGU@LB@ \|\|\|\|\|\|\|\|\|\| \|\|\|:@LB@ CCCAAUACAA GUCG@LB@3'-UUU...AAAUA AAA -5'@LB@ \| \|@LB@ 18 1@LB@@LB@@LB@Energy -14.13 kcal/mol@LB@Hybridization Energy -17.9134 kcal/mol@LB@Unfolding Energy - mRNA 2.84721 kcal/mol@LB@Unfolding Energy - sRNA 0.931609 kcal/mol@LB@@LB@Position - mRNA 196 -- 210@LB@Position - sRNA 1 -- 17@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 8 -- 14@LB@
119	0.005024	0.1407	b2342	fadI	-9.59	0.197573	199 -- 214	6 -- 21	beta-ketoacyl-CoA thiolase anaerobic subunit	_____________198______________215\n_____________\|________________\|\n5'-UCC...GAGUG________CAG_____ACCGC...AUG-3'\n______________UUAUGGGU___GUUUU\n______________\|\|\|\|\|\|\|\|___\|\|\|\|\|\n______________AAUACCCA___CAAAA\n3'-UUU...CGUAA________AUA_____AGUCG-5'\n_____________\|________________\|\n_____________22_______________5\n	200 -- 206	14 -- 20	-13.0434 kcal/mol	3.24348 kcal/mol	0.208077 kcal/mol	198 215@LB@ \| \|@LB@5'-UCC...GAGUG CAG ACCGC...AUG-3'@LB@ UUAUGGGU GUUUU@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|@LB@ AAUACCCA CAAAA@LB@3'-UUU...CGUAA AUA AGUCG-5'@LB@ \| \|@LB@ 22 5@LB@@LB@@LB@Energy -9.59 kcal/mol@LB@Hybridization Energy -13.0434 kcal/mol@LB@Unfolding Energy - mRNA 3.24348 kcal/mol@LB@Unfolding Energy - sRNA 0.208077 kcal/mol@LB@@LB@Position - mRNA 199 -- 214@LB@Position - sRNA 6 -- 21@LB@Position Seed - mRNA 200 -- 206@LB@Position Seed - sRNA 14 -- 20@LB@
36	0.0006761	0.06313	b0759	galE	-8.98	0.250354	205 -- 236	22 -- 48	UDP-galactose-4-epimerase	_____________204_______________________________237\n_____________\|_________________________________\|\n5'-GCA...UAUGA___UUC_____A__GG____A____________GGAAG...UCU-3'\n______________GAG___UGGUU_CC__UGGU_GCGGUUA_CAUU\n______________\|\|\|___\|\|\|\|\|_\|\|__\|\|\|\|_:\|:\|:\|\|_\|\|\|\|\n______________CUC___ACCAA_GG__ACCA_UGUCGAU_GUAA\n3'-UUU...GAUUC___C________________________C____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________49________________________________21\n	226 -- 232	27 -- 33	-23.3933 kcal/mol	9.85191 kcal/mol	4.55969 kcal/mol	204 237@LB@ \| \|@LB@5'-GCA...UAUGA UUC A GG A GGAAG...UCU-3'@LB@ GAG UGGUU CC UGGU GCGGUUA CAUU@LB@ \|\|\| \|\|\|\|\| \|\| \|\|\|\| :\|:\|:\|\| \|\|\|\|@LB@ CUC ACCAA GG ACCA UGUCGAU GUAA@LB@3'-UUU...GAUUC C C AAUAC...UCG-5'@LB@ \| \|@LB@ 49 21@LB@@LB@@LB@Energy -8.98 kcal/mol@LB@Hybridization Energy -23.3933 kcal/mol@LB@Unfolding Energy - mRNA 9.85191 kcal/mol@LB@Unfolding Energy - sRNA 4.55969 kcal/mol@LB@@LB@Position - mRNA 205 -- 236@LB@Position - sRNA 22 -- 48@LB@Position Seed - mRNA 226 -- 232@LB@Position Seed - sRNA 27 -- 33@LB@
97	0.003376	0.117	b2145	yeiS	-12.83	0.042234	207 -- 237	4 -- 35	DUF2542 family protein	_____________206_______________________________238\n_____________\|_________________________________\|\n5'-AUG...UGGAU___________U______C_____CC_______UCCUU...AUA-3'\n______________GUACAGC_AGU_UUUUGU__GUUG__GUUUUUU\n______________\|\|\|\|\|\|\|_\|\|:_\|\|\|\|:\|__\|\|\|:__\|\|\|\|\|\|:\n______________CAUGUCG_UCG_AAAAUA__CAAU__CAAAAAG\n3'-UUU...AGGAC_______A___U______CC____A________UCG-5'\n_____________\|_________________________________\|\n_____________36________________________________3\n	231 -- 237	4 -- 10	-21.2811 kcal/mol	6.9566 kcal/mol	1.49488 kcal/mol	206 238@LB@ \| \|@LB@5'-AUG...UGGAU U C CC UCCUU...AUA-3'@LB@ GUACAGC AGU UUUUGU GUUG GUUUUUU@LB@ \|\|\|\|\|\|\| \|\|: \|\|\|\|:\| \|\|\|: \|\|\|\|\|\|:@LB@ CAUGUCG UCG AAAAUA CAAU CAAAAAG@LB@3'-UUU...AGGAC A U CC A UCG-5'@LB@ \| \|@LB@ 36 3@LB@@LB@@LB@Energy -12.83 kcal/mol@LB@Hybridization Energy -21.2811 kcal/mol@LB@Unfolding Energy - mRNA 6.9566 kcal/mol@LB@Unfolding Energy - sRNA 1.49488 kcal/mol@LB@@LB@Position - mRNA 207 -- 237@LB@Position - sRNA 4 -- 35@LB@Position Seed - mRNA 231 -- 237@LB@Position Seed - sRNA 4 -- 10@LB@
109	0.004204	0.1296	b1384	feaR	-11.47	0.085662	210 -- 231	1 -- 26	transcriptional activator for tynA and feaB	_____________209________________________232\n_____________\|__________________________\|\n5'-UGU...ACCCC___________AUA___AG_______AAUGG...CGG-3'\n______________GCA____GUGG___AUG__UUUCAGC\n______________\|\|\|____:\|\|\|___\|\|\|__\|\|\|\|\|\|\|\n______________CGU____UACC___UAC__AAAGUCG\n3'-UUU...UCGAU___AAAA____CAA___AA_______-5'\n_____________\|_________________________\|\n_____________27________________________1\n	225 -- 231	1 -- 7	-17.3605 kcal/mol	4.42522 kcal/mol	1.46544 kcal/mol	209 232@LB@ \| \|@LB@5'-UGU...ACCCC AUA AG AAUGG...CGG-3'@LB@ GCA GUGG AUG UUUCAGC@LB@ \|\|\| :\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CGU UACC UAC AAAGUCG@LB@3'-UUU...UCGAU AAAA CAA AA -5'@LB@ \| \|@LB@ 27 1@LB@@LB@@LB@Energy -11.47 kcal/mol@LB@Hybridization Energy -17.3605 kcal/mol@LB@Unfolding Energy - mRNA 4.42522 kcal/mol@LB@Unfolding Energy - sRNA 1.46544 kcal/mol@LB@@LB@Position - mRNA 210 -- 231@LB@Position - sRNA 1 -- 26@LB@Position Seed - mRNA 225 -- 231@LB@Position Seed - sRNA 1 -- 7@LB@
113	0.004738	0.1404	b3197	kdsD	-14.34	0.017174	210 -- 240	1 -- 35	D-arabinose 5-phosphate isomerase	_____________209_________________________________241\n_____________\|___________________________________\|\n5'-AGG...CGCAC___G________ACC________U__AC_______AAGCA...ACA-3'\n______________GUA_AGUUA_CA______GGGUU_UG__UUUCAGC\n______________\|\|\|_\|\|:\|\|_\|\|______\|\|\|\|\|_\|\|__\|\|\|\|\|\|\|\n______________CAU_UCGAU_GU______CCCAA_AC__AAAGUCG\n3'-UUU...AGGAC___G_____C__AAAAUA_____U__AA_______-5'\n_____________\|__________________________________\|\n_____________36_________________________________1\n	234 -- 240	1 -- 7	-24.924 kcal/mol	9.08416 kcal/mol	1.49508 kcal/mol	209 241@LB@ \| \|@LB@5'-AGG...CGCAC G ACC U AC AAGCA...ACA-3'@LB@ GUA AGUUA CA GGGUU UG UUUCAGC@LB@ \|\|\| \|\|:\|\| \|\| \|\|\|\|\| \|\| \|\|\|\|\|\|\|@LB@ CAU UCGAU GU CCCAA AC AAAGUCG@LB@3'-UUU...AGGAC G C AAAAUA U AA -5'@LB@ \| \|@LB@ 36 1@LB@@LB@@LB@Energy -14.34 kcal/mol@LB@Hybridization Energy -24.924 kcal/mol@LB@Unfolding Energy - mRNA 9.08416 kcal/mol@LB@Unfolding Energy - sRNA 1.49508 kcal/mol@LB@@LB@Position - mRNA 210 -- 240@LB@Position - sRNA 1 -- 35@LB@Position Seed - mRNA 234 -- 240@LB@Position Seed - sRNA 1 -- 7@LB@
101	0.003756	0.123	b2972	pppA	-13.47	0.029286	211 -- 222	1 -- 12	bifunctional prepilin leader peptidase/ methylase	_____________210__________223\n_____________\|____________\|\n5'-UAA...UUUUG____________AAUAC...GGC-3'\n______________AUGUUUUUCAGC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________UACAAAAAGUCG\n3'-UUU...CCCAA____________-5'\n_____________\|___________\|\n_____________13__________1\n	216 -- 222	1 -- 7	-17.018 kcal/mol	2.64154 kcal/mol	0.904394 kcal/mol	210 223@LB@ \| \|@LB@5'-UAA...UUUUG AAUAC...GGC-3'@LB@ AUGUUUUUCAGC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ UACAAAAAGUCG@LB@3'-UUU...CCCAA -5'@LB@ \| \|@LB@ 13 1@LB@@LB@@LB@Energy -13.47 kcal/mol@LB@Hybridization Energy -17.018 kcal/mol@LB@Unfolding Energy - mRNA 2.64154 kcal/mol@LB@Unfolding Energy - sRNA 0.904394 kcal/mol@LB@@LB@Position - mRNA 211 -- 222@LB@Position - sRNA 1 -- 12@LB@Position Seed - mRNA 216 -- 222@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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