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
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@
115	0.004814	0.1404	b2743	pcm	-10.63	0.126788	157 -- 183	29 -- 48	L-isoaspartate protein carboxylmethyltransferase type II		_____________156_________________________184\n_____________\|___________________________\|\n5'-AUC...CGCAA__U_______CAGA_____UAA_____GUGGG...AAA-3'\n______________GA_GUGGUUU____CUGGU___ACAGC\n______________\|\|_\|\|\|\|\|\|:____\|\|\|\|\|___\|\|\|\|\|\n______________CU_CACCAAG____GACCA___UGUCG\n3'-UUU...GAUUC__C________________________AUCGU...UCG-5'\n_____________\|___________________________\|\n_____________49__________________________28\n	160 -- 166	39 -- 45	-22.1612 kcal/mol	7.2267 kcal/mol	4.30129 kcal/mol	156 184@LB@ \| \|@LB@5'-AUC...CGCAA U CAGA UAA GUGGG...AAA-3'@LB@ GA GUGGUUU CUGGU ACAGC@LB@ \|\| \|\|\|\|\|\|: \|\|\|\|\| \|\|\|\|\|@LB@ CU CACCAAG GACCA UGUCG@LB@3'-UUU...GAUUC C AUCGU...UCG-5'@LB@ \| \|@LB@ 49 28@LB@@LB@@LB@Energy -10.63 kcal/mol@LB@Hybridization Energy -22.1612 kcal/mol@LB@Unfolding Energy - mRNA 7.2267 kcal/mol@LB@Unfolding Energy - sRNA 4.30129 kcal/mol@LB@@LB@Position - mRNA 157 -- 183@LB@Position - sRNA 29 -- 48@LB@Position Seed - mRNA 160 -- 166@LB@Position Seed - sRNA 39 -- 45@LB@
120	0.005024	0.1407	b2564	pdxJ	-10.23	0.151404	275 -- 296	21 -- 43	pyridoxine 5'-phosphate synthase		_____________274_____________________297\n_____________\|_______________________\|\n5'-AAA...UACCC__A___________GCC______AUUG-3'\n______________GG_UCC_GGUGCAG___GCGUUU\n______________\|\|_\|\|\|_\|\|\|:\|\|\|___\|\|:\|\|\|\n______________CC_AGG_CCAUGUC___CGUAAA\n3'-UUU...CUCCA__A___A_______GAU______AUACC...UCG-5'\n_____________\|_______________________\|\n_____________44______________________20\n	281 -- 287	30 -- 36	-24.4803 kcal/mol	9.69131 kcal/mol	4.55861 kcal/mol	274 297@LB@ \| \|@LB@5'-AAA...UACCC A GCC AUUG-3'@LB@ GG UCC GGUGCAG GCGUUU@LB@ \|\| \|\|\| \|\|\|:\|\|\| \|\|:\|\|\|@LB@ CC AGG CCAUGUC CGUAAA@LB@3'-UUU...CUCCA A A GAU AUACC...UCG-5'@LB@ \| \|@LB@ 44 20@LB@@LB@@LB@Energy -10.23 kcal/mol@LB@Hybridization Energy -24.4803 kcal/mol@LB@Unfolding Energy - mRNA 9.69131 kcal/mol@LB@Unfolding Energy - sRNA 4.55861 kcal/mol@LB@@LB@Position - mRNA 275 -- 296@LB@Position - sRNA 21 -- 43@LB@Position Seed - mRNA 281 -- 287@LB@Position Seed - sRNA 30 -- 36@LB@
143	0.00681	0.158	b2418	pdxK	-15.34	0.008827	271 -- 292	15 -- 47	pyridoxal-pyridoxamine kinase/hydroxymethylpyrimidine kinase		_____________270_______________________________293\n_____________\|_________________________________\|\n5'-CAU...GUCGC_________________________________CAACAGCA-3'\n______________AGGUGGUUU_____ACGGC_AGC_____GUGGG\n______________\|\|\|\|\|\|\|\|:_____\|\|:\|\|_\|\|\|_____:\|\|\|\|\n______________UCCACCAAG_____UGUCG_UCG_____UACCC\n3'-UUU...AUUCC_________GACCA_____A___UAAAA_____AAUAC...UCG-5'\n_____________\|_________________________________\|\n_____________48________________________________14\n	273 -- 279	39 -- 45	-26.4553 kcal/mol	6.54205 kcal/mol	4.57348 kcal/mol	270 293@LB@ \| \|@LB@5'-CAU...GUCGC CAACAGCA-3'@LB@ AGGUGGUUU ACGGC AGC GUGGG@LB@ \|\|\|\|\|\|\|\|: \|\|:\|\| \|\|\| :\|\|\|\|@LB@ UCCACCAAG UGUCG UCG UACCC@LB@3'-UUU...AUUCC GACCA A UAAAA AAUAC...UCG-5'@LB@ \| \|@LB@ 48 14@LB@@LB@@LB@Energy -15.34 kcal/mol@LB@Hybridization Energy -26.4553 kcal/mol@LB@Unfolding Energy - mRNA 6.54205 kcal/mol@LB@Unfolding Energy - sRNA 4.57348 kcal/mol@LB@@LB@Position - mRNA 271 -- 292@LB@Position - sRNA 15 -- 47@LB@Position Seed - mRNA 273 -- 279@LB@Position Seed - sRNA 39 -- 45@LB@
7	1.492e-05	0.007162	b0903	pflB	-20.16	0.000088	81 -- 115	14 -- 49	formate C-acetyltransferase 1 anaerobic; pyruvate formate-lyase 1		_____________80____________________________________116\n_____________\|_____________________________________\|\n5'-CAC...UUAUC__U________GU____UG_____A___AC_______CAUUU...ACU-3'\n______________GG_GGUGGUUU__UGGU__GGUUG_CAU____UGGGU\n______________\|\|_\|\|\|\|\|\|\|:__\|\|\|\|__:\|:\|:_\|\|\|____\|\|\|\|\|\n______________CC_CCACCAAG__ACCA__UCGAU_GUA____ACCCA\n3'-UUU...CGAUU__U________G_____UG_____C___AAAU_____AUACA...UCG-5'\n_____________\|_____________________________________\|\n_____________50____________________________________13\n	85 -- 91	39 -- 45	-33.3931 kcal/mol	8.66349 kcal/mol	4.57395 kcal/mol	80 116@LB@ \| \|@LB@5'-CAC...UUAUC U GU UG A AC CAUUU...ACU-3'@LB@ GG GGUGGUUU UGGU GGUUG CAU UGGGU@LB@ \|\| \|\|\|\|\|\|\|: \|\|\|\| :\|:\|: \|\|\| \|\|\|\|\|@LB@ CC CCACCAAG ACCA UCGAU GUA ACCCA@LB@3'-UUU...CGAUU U G UG C AAAU AUACA...UCG-5'@LB@ \| \|@LB@ 50 13@LB@@LB@@LB@Energy -20.16 kcal/mol@LB@Hybridization Energy -33.3931 kcal/mol@LB@Unfolding Energy - mRNA 8.66349 kcal/mol@LB@Unfolding Energy - sRNA 4.57395 kcal/mol@LB@@LB@Position - mRNA 81 -- 115@LB@Position - sRNA 14 -- 49@LB@Position Seed - mRNA 85 -- 91@LB@Position Seed - sRNA 39 -- 45@LB@
137	0.006165	0.1512	b1024	pgaA	-6.60	0.530802	267 -- 274	1 -- 8	biofilm adhesin polysaccharide PGA secretin; OM porin; poly-beta-1 6-N-acetyl-D-glucosamine export protein		_____________266______275\n_____________\|________\|\n5'-CUC...CCGCA________AGCGA...CUG-3'\n______________UUUUUAGC\n______________\|\|\|\|:\|\|\|\n______________AAAAGUCG\n3'-UUU...AUACA________-5'\n_____________\|_______\|\n_____________9_______1\n	268 -- 274	1 -- 7	-8.19691 kcal/mol	0.802454 kcal/mol	0.799201 kcal/mol	266 275@LB@ \| \|@LB@5'-CUC...CCGCA AGCGA...CUG-3'@LB@ UUUUUAGC@LB@ \|\|\|\|:\|\|\|@LB@ AAAAGUCG@LB@3'-UUU...AUACA -5'@LB@ \| \|@LB@ 9 1@LB@@LB@@LB@Energy -6.60 kcal/mol@LB@Hybridization Energy -8.19691 kcal/mol@LB@Unfolding Energy - mRNA 0.802454 kcal/mol@LB@Unfolding Energy - sRNA 0.799201 kcal/mol@LB@@LB@Position - mRNA 267 -- 274@LB@Position - sRNA 1 -- 8@LB@Position Seed - mRNA 268 -- 274@LB@Position Seed - sRNA 1 -- 7@LB@
156	0.007969	0.1694	b4025	pgi	-9.69	0.190093	4 -- 41	3 -- 36	glucosephosphate isomerase		_____________3_______________________________________42\n_____________\|_______________________________________\|\n________5'-AGC__G_______U__ACG______GUC___CGGA_______UCCAC...AAG-3'\n______________GG_GCGGUUG_CA____AUGGG___AUG____UUUUUCA\n______________\|\|_:\|:\|:\|:_\|\|____\|\|\|\|\|___\|\|\|____\|\|\|\|\|\|\|\n______________CC_UGUCGAU_GU____UACCC___UAC____AAAAAGU\n3'-UUU...AAGGA__A_______C__AAAA_____AA_______________CG-5'\n_____________\|_______________________________________\|\n_____________37______________________________________2\n	35 -- 41	3 -- 9	-21.0745 kcal/mol	9.8922 kcal/mol	1.49503 kcal/mol	3 42@LB@ \| \|@LB@ 5'-AGC G U ACG GUC CGGA UCCAC...AAG-3'@LB@ GG GCGGUUG CA AUGGG AUG UUUUUCA@LB@ \|\| :\|:\|:\|: \|\| \|\|\|\|\| \|\|\| \|\|\|\|\|\|\|@LB@ CC UGUCGAU GU UACCC UAC AAAAAGU@LB@3'-UUU...AAGGA A C AAAA AA CG-5'@LB@ \| \|@LB@ 37 2@LB@@LB@@LB@Energy -9.69 kcal/mol@LB@Hybridization Energy -21.0745 kcal/mol@LB@Unfolding Energy - mRNA 9.8922 kcal/mol@LB@Unfolding Energy - sRNA 1.49503 kcal/mol@LB@@LB@Position - mRNA 4 -- 41@LB@Position - sRNA 3 -- 36@LB@Position Seed - mRNA 35 -- 41@LB@Position Seed - sRNA 3 -- 9@LB@
178	0.009929	0.1875	b1278	pgpB	-11.49	0.084643	145 -- 171	10 -- 41	phosphatidylglycerophosphatase B		_____________144______________________________172\n_____________\|________________________________\|\n5'-GUU...AAUUU_______AA_____________CA________AUUGU...AAC-3'\n______________UUCCUGG_____CUGGCGUUUU____GUUAUG\n______________\|\|\|\|\|\|\|_____\|\|:\|\|:\|\|\|\|____\|\|\|\|\|\|\n______________AAGGACC_____GAUCGUAAAA____CAAUAC\n3'-UUU...CCACC_______AUGUC__________UACC______AAAAA...UCG-5'\n_____________\|________________________________\|\n_____________42_______________________________9\n	157 -- 163	20 -- 26	-25.137 kcal/mol	9.03979 kcal/mol	4.60294 kcal/mol	144 172@LB@ \| \|@LB@5'-GUU...AAUUU AA CA AUUGU...AAC-3'@LB@ UUCCUGG CUGGCGUUUU GUUAUG@LB@ \|\|\|\|\|\|\| \|\|:\|\|:\|\|\|\| \|\|\|\|\|\|@LB@ AAGGACC GAUCGUAAAA CAAUAC@LB@3'-UUU...CCACC AUGUC UACC AAAAA...UCG-5'@LB@ \| \|@LB@ 42 9@LB@@LB@@LB@Energy -11.49 kcal/mol@LB@Hybridization Energy -25.137 kcal/mol@LB@Unfolding Energy - mRNA 9.03979 kcal/mol@LB@Unfolding Energy - sRNA 4.60294 kcal/mol@LB@@LB@Position - mRNA 145 -- 171@LB@Position - sRNA 10 -- 41@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 20 -- 26@LB@
117	0.004938	0.1407	b2560	pgpC	-11.09	0.102961	189 -- 233	4 -- 51	phosphatidylglycerophosphatase C membrane bound		_____________188_________________________________________________234\n_____________\|___________________________________________________\|\n5'-UCG...GUCCA______UA__________CA__UCACG_____CG_________________GACUU...GCC-3'\n______________GAGGAG__UGGUU__UGG__AC_____AGCGU__UGUGG____UGUUUUUU\n______________:\|\|\|\|\|__\|\|\|\|\|__\|\|\|__\|\|_____\|\|\|:\|__\|:\|\|\|____\|\|\|\|\|\|\|:\n______________UUCCUC__ACCAA__ACC__UG_____UCGUA__AUACC____ACAAAAAG\n3'-UUU...UCCGA______C______GG___A___UCGA______AA_____CAAU________UCG-5'\n_____________\|___________________________________________________\|\n_____________52__________________________________________________3\n	227 -- 233	4 -- 10	-30.0966 kcal/mol	14.318 kcal/mol	4.69283 kcal/mol	188 234@LB@ \| \|@LB@5'-UCG...GUCCA UA CA UCACG CG GACUU...GCC-3'@LB@ GAGGAG UGGUU UGG AC AGCGU UGUGG UGUUUUUU@LB@ :\|\|\|\|\| \|\|\|\|\| \|\|\| \|\| \|\|\|:\| \|:\|\|\| \|\|\|\|\|\|\|:@LB@ UUCCUC ACCAA ACC UG UCGUA AUACC ACAAAAAG@LB@3'-UUU...UCCGA C GG A UCGA AA CAAU UCG-5'@LB@ \| \|@LB@ 52 3@LB@@LB@@LB@Energy -11.09 kcal/mol@LB@Hybridization Energy -30.0966 kcal/mol@LB@Unfolding Energy - mRNA 14.318 kcal/mol@LB@Unfolding Energy - sRNA 4.69283 kcal/mol@LB@@LB@Position - mRNA 189 -- 233@LB@Position - sRNA 4 -- 51@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 4 -- 10@LB@
167	0.00885	0.1781	b0241	phoE	-12.37	0.054121	1 -- 29	1 -- 31	outer membrane phosphoporin protein E	b0929 b2215 b1377	______________1____________________________________30\n______________\|____________________________________\|\n___________5'-___A___________UGCGC___A_____________AAGCC...AUG-3'\n______________AGC_UGGCGUUUUGU_____GGG_________UCAGC\n______________\|\|\|_\|:\|\|:\|\|\|\|:\|_____\|\|\|_________\|\|\|\|\|\n______________UCG_AUCGUAAAAUA_____CCC_________AGUCG\n3'-UUU...CCAUG_______________________AAUACAAAA_____-5'\n_____________\|____________________________________\|\n_____________32___________________________________1\n	9 -- 15	18 -- 24	-21.8929 kcal/mol	8.03382 kcal/mol	1.48722 kcal/mol	1 30@LB@ \| \|@LB@ 5'- A UGCGC A AAGCC...AUG-3'@LB@ AGC UGGCGUUUUGU GGG UCAGC@LB@ \|\|\| \|:\|\|:\|\|\|\|:\| \|\|\| \|\|\|\|\|@LB@ UCG AUCGUAAAAUA CCC AGUCG@LB@3'-UUU...CCAUG AAUACAAAA -5'@LB@ \| \|@LB@ 32 1@LB@@LB@@LB@Energy -12.37 kcal/mol@LB@Hybridization Energy -21.8929 kcal/mol@LB@Unfolding Energy - mRNA 8.03382 kcal/mol@LB@Unfolding Energy - sRNA 1.48722 kcal/mol@LB@@LB@Position - mRNA 1 -- 29@LB@Position - sRNA 1 -- 31@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 18 -- 24@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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