Input and runtime details for job 1786318 (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 1786318 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:20:27 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:20:56 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 22:01:46 CET 2018
	Post-Processing Finished		@ Fri Feb 16 22:01:53 CET 2018
	Job Completed		@ Fri Feb 16 22:02:22 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

Description of the job

ArcZ

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
69	0.003463	0.1727	b2346	mlaA	-10.50	0.111973	167 -- 195	66 -- 86	ABC transporter maintaining OM lipid asymmetry OM lipoprotein component	_____________166___________________________196\n_____________\|_____________________________\|\n5'-GCG...GGCAA_____AUAA____UAAAAAAA________CAUUU...AAG-3'\n______________ACUGC____GCCA________CAGGGAGA\n______________\|\|\|\|\|____\|\|\|\|________\|\|\|\|\|\|:\|\n______________UGACG____CGGU________GUCCCUUU\n3'-UUU...GCUUA_____________UGUG____________AGAAC...GUG-5'\n_____________\|_____________________________\|\n_____________87____________________________65\n	189 -- 195	66 -- 72	-21.8219 kcal/mol	3.94189 kcal/mol	7.38216 kcal/mol	166 196@LB@ \| \|@LB@5'-GCG...GGCAA AUAA UAAAAAAA CAUUU...AAG-3'@LB@ ACUGC GCCA CAGGGAGA@LB@ \|\|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ UGACG CGGU GUCCCUUU@LB@3'-UUU...GCUUA UGUG AGAAC...GUG-5'@LB@ \| \|@LB@ 87 65@LB@@LB@@LB@Energy -10.50 kcal/mol@LB@Hybridization Energy -21.8219 kcal/mol@LB@Unfolding Energy - mRNA 3.94189 kcal/mol@LB@Unfolding Energy - sRNA 7.38216 kcal/mol@LB@@LB@Position - mRNA 167 -- 195@LB@Position - sRNA 66 -- 86@LB@Position Seed - mRNA 189 -- 195@LB@Position Seed - sRNA 66 -- 72@LB@
162	0.009519	0.2068	b4167	nnr	-8.70	0.240671	167 -- 176	76 -- 85	bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase	_____________166________177\n_____________\|__________\|\n5'-ACU...AUUUU__________UGAUU...UGC-3'\n______________UUGCGCUAAC\n______________:\|\|\|\|\|:\|\|\|\n______________GACGCGGUUG\n3'-UUU...CUUAU__________UGGUC...GUG-5'\n_____________\|__________\|\n_____________86_________75\n	170 -- 176	76 -- 82	-14.3794 kcal/mol	0.586298 kcal/mol	5.09564 kcal/mol	166 177@LB@ \| \|@LB@5'-ACU...AUUUU UGAUU...UGC-3'@LB@ UUGCGCUAAC@LB@ :\|\|\|\|\|:\|\|\|@LB@ GACGCGGUUG@LB@3'-UUU...CUUAU UGGUC...GUG-5'@LB@ \| \|@LB@ 86 75@LB@@LB@@LB@Energy -8.70 kcal/mol@LB@Hybridization Energy -14.3794 kcal/mol@LB@Unfolding Energy - mRNA 0.586298 kcal/mol@LB@Unfolding Energy - sRNA 5.09564 kcal/mol@LB@@LB@Position - mRNA 167 -- 176@LB@Position - sRNA 76 -- 85@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 76 -- 82@LB@
178	0.01053	0.208	b3582	sgbU	-5.91	0.640260	169 -- 196	65 -- 84	putative L-xylulose 5-phosphate 3-epimerase	_____________168__________________________197\n_____________\|____________________________\|\n5'-UCU...UUCCA_____AAAU_______AUCU________GCGCG...UUG-3'\n______________UGCGC____CGACGCU____GGGGAGGU\n______________\|\|\|\|\|____\|:\|\|:\|:____:\|\|\|\|::\|\n______________ACGCG____GUUGUGG____UCCCUUUA\n3'-UUU...UUAUG____________________________GAACC...GUG-5'\n_____________\|____________________________\|\n_____________85___________________________64\n	190 -- 196	65 -- 71	-23.9168 kcal/mol	10.6467 kcal/mol	7.36194 kcal/mol	168 197@LB@ \| \|@LB@5'-UCU...UUCCA AAAU AUCU GCGCG...UUG-3'@LB@ UGCGC CGACGCU GGGGAGGU@LB@ \|\|\|\|\| \|:\|\|:\|: :\|\|\|\|::\|@LB@ ACGCG GUUGUGG UCCCUUUA@LB@3'-UUU...UUAUG GAACC...GUG-5'@LB@ \| \|@LB@ 85 64@LB@@LB@@LB@Energy -5.91 kcal/mol@LB@Hybridization Energy -23.9168 kcal/mol@LB@Unfolding Energy - mRNA 10.6467 kcal/mol@LB@Unfolding Energy - sRNA 7.36194 kcal/mol@LB@@LB@Position - mRNA 169 -- 196@LB@Position - sRNA 65 -- 84@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 65 -- 71@LB@
116	0.006112	0.1855	b1260	trpA	-12.39	0.048115	172 -- 199	63 -- 89	tryptophan synthase alpha subunit	_____________171__________________________200\n_____________\|____________________________\|\n5'-GCC...UUCAC______U__AA_____GA__________GAUGG...CAU-3'\n______________GAUAUU_UG__AGCAC__GGGGAAAUCU\n______________:\|\|\|:\|_:\|__\|:\|\|\|__:\|\|\|\|\|\|\|\|\|\n______________UUAUGA_GC__UUGUG__UCCCUUUAGA\n3'-UUU...CGCGC______C__GG_____G___________ACCGA...GUG-5'\n_____________\|____________________________\|\n_____________90___________________________62\n	193 -- 199	63 -- 69	-25.3377 kcal/mol	5.06327 kcal/mol	7.88429 kcal/mol	171 200@LB@ \| \|@LB@5'-GCC...UUCAC U AA GA GAUGG...CAU-3'@LB@ GAUAUU UG AGCAC GGGGAAAUCU@LB@ :\|\|\|:\| :\| \|:\|\|\| :\|\|\|\|\|\|\|\|\|@LB@ UUAUGA GC UUGUG UCCCUUUAGA@LB@3'-UUU...CGCGC C GG G ACCGA...GUG-5'@LB@ \| \|@LB@ 90 62@LB@@LB@@LB@Energy -12.39 kcal/mol@LB@Hybridization Energy -25.3377 kcal/mol@LB@Unfolding Energy - mRNA 5.06327 kcal/mol@LB@Unfolding Energy - sRNA 7.88429 kcal/mol@LB@@LB@Position - mRNA 172 -- 199@LB@Position - sRNA 63 -- 89@LB@Position Seed - mRNA 193 -- 199@LB@Position Seed - sRNA 63 -- 69@LB@
4	3.471e-06	0.003055	b2099	yegU	-19.38	0.001997	173 -- 198	64 -- 88	ADP-ribosylglycohydrolase family protein	_____________172________________________199\n_____________\|__________________________\|\n5'-GUG...UCGCG_______________AA_________AAAUG...CAC-3'\n______________AUAUUGCGUUGACAC__GGGGAAGUU\n______________\|\|\|:\|\|\|\|:::\|\|\|\|__:\|\|\|\|\|:\|:\n______________UAUGACGCGGUUGUG__UCCCUUUAG\n3'-UUU...GCGCU_______________G__________AACCG...GUG-5'\n_____________\|__________________________\|\n_____________89_________________________63\n	192 -- 198	64 -- 70	-32.1286 kcal/mol	5.35868 kcal/mol	7.38555 kcal/mol	172 199@LB@ \| \|@LB@5'-GUG...UCGCG AA AAAUG...CAC-3'@LB@ AUAUUGCGUUGACAC GGGGAAGUU@LB@ \|\|\|:\|\|\|\|:::\|\|\|\| :\|\|\|\|\|:\|:@LB@ UAUGACGCGGUUGUG UCCCUUUAG@LB@3'-UUU...GCGCU G AACCG...GUG-5'@LB@ \| \|@LB@ 89 63@LB@@LB@@LB@Energy -19.38 kcal/mol@LB@Hybridization Energy -32.1286 kcal/mol@LB@Unfolding Energy - mRNA 5.35868 kcal/mol@LB@Unfolding Energy - sRNA 7.38555 kcal/mol@LB@@LB@Position - mRNA 173 -- 198@LB@Position - sRNA 64 -- 88@LB@Position Seed - mRNA 192 -- 198@LB@Position Seed - sRNA 64 -- 70@LB@
158	0.009324	0.2062	b3574	yiaJ	-10.56	0.109206	175 -- 190	70 -- 85	transcriptional repressor for the yiaKLMNO-lyxK-sgbHUE operon	_____________174______________191\n_____________\|________________\|\n5'-CCC...ACACU________C_______ACGCG...UUG-3'\n______________UUGCGCUA_CAUCAGG\n______________:\|\|\|\|\|:\|_\|\|:\|\|\|\|\n______________GACGCGGU_GUGGUCC\n3'-UUU...CUUAU________U_______CUUUA...GUG-5'\n_____________\|________________\|\n_____________86_______________69\n	184 -- 190	70 -- 76	-22.9924 kcal/mol	5.16069 kcal/mol	7.27689 kcal/mol	174 191@LB@ \| \|@LB@5'-CCC...ACACU C ACGCG...UUG-3'@LB@ UUGCGCUA CAUCAGG@LB@ :\|\|\|\|\|:\| \|\|:\|\|\|\|@LB@ GACGCGGU GUGGUCC@LB@3'-UUU...CUUAU U CUUUA...GUG-5'@LB@ \| \|@LB@ 86 69@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -22.9924 kcal/mol@LB@Unfolding Energy - mRNA 5.16069 kcal/mol@LB@Unfolding Energy - sRNA 7.27689 kcal/mol@LB@@LB@Position - mRNA 175 -- 190@LB@Position - sRNA 70 -- 85@LB@Position Seed - mRNA 184 -- 190@LB@Position Seed - sRNA 70 -- 76@LB@
67	0.003373	0.1727	b0723	sdhA	-10.29	0.122560	175 -- 204	36 -- 70	succinate dehydrogenase flavoprotein subunit	_____________174_________________________________205\n_____________\|___________________________________\|\n5'-GGU...UUUAU___U____________G______GUG_________AAUUG...GUG-3'\n______________GGA__UC___GUUGUG_UGUGGG____UGUGAUGA\n______________\|\|\|__\|\|___\|:\|\|:\|_:\|\|:::____\|:\|\|\|\|\|\|\n______________CCU__AG___CGACGC_GCAUUU____AUACUACU\n3'-UUU...UGGUC___UU__AAC______G______AAUA________CAAUG...GUG-5'\n_____________\|___________________________________\|\n_____________71__________________________________35\n	198 -- 204	36 -- 42	-24.7755 kcal/mol	5.81881 kcal/mol	8.66537 kcal/mol	174 205@LB@ \| \|@LB@5'-GGU...UUUAU U G GUG AAUUG...GUG-3'@LB@ GGA UC GUUGUG UGUGGG UGUGAUGA@LB@ \|\|\| \|\| \|:\|\|:\| :\|\|::: \|:\|\|\|\|\|\|@LB@ CCU AG CGACGC GCAUUU AUACUACU@LB@3'-UUU...UGGUC UU AAC G AAUA CAAUG...GUG-5'@LB@ \| \|@LB@ 71 35@LB@@LB@@LB@Energy -10.29 kcal/mol@LB@Hybridization Energy -24.7755 kcal/mol@LB@Unfolding Energy - mRNA 5.81881 kcal/mol@LB@Unfolding Energy - sRNA 8.66537 kcal/mol@LB@@LB@Position - mRNA 175 -- 204@LB@Position - sRNA 36 -- 70@LB@Position Seed - mRNA 198 -- 204@LB@Position Seed - sRNA 36 -- 42@LB@
126	0.006849	0.1914	b2930	yggF	-13.28	0.032133	176 -- 191	68 -- 83	fructose 1 6 bisphosphatase isozyme	_____________175______________192\n_____________\|________________\|\n5'-AUC...AUUUG________________GGCCG...GCC-3'\n______________GCGUUGAUAUCGGGGA\n______________\|\|\|:::\|:\|:\|:\|\|\|\|\n______________CGCGGUUGUGGUCCCU\n3'-UUU...UAUGA________________UUAGA...GUG-5'\n_____________\|________________\|\n_____________84_______________67\n	185 -- 191	68 -- 74	-24.7766 kcal/mol	4.1491 kcal/mol	7.34657 kcal/mol	175 192@LB@ \| \|@LB@5'-AUC...AUUUG GGCCG...GCC-3'@LB@ GCGUUGAUAUCGGGGA@LB@ \|\|\|:::\|:\|:\|:\|\|\|\|@LB@ CGCGGUUGUGGUCCCU@LB@3'-UUU...UAUGA UUAGA...GUG-5'@LB@ \| \|@LB@ 84 67@LB@@LB@@LB@Energy -13.28 kcal/mol@LB@Hybridization Energy -24.7766 kcal/mol@LB@Unfolding Energy - mRNA 4.1491 kcal/mol@LB@Unfolding Energy - sRNA 7.34657 kcal/mol@LB@@LB@Position - mRNA 176 -- 191@LB@Position - sRNA 68 -- 83@LB@Position Seed - mRNA 185 -- 191@LB@Position Seed - sRNA 68 -- 74@LB@
16	0.0007867	0.1666	b2178	yejB	-12.57	0.044336	179 -- 196	66 -- 82	microcin C ABC transporter permease	_____________178________________197\n_____________\|__________________\|\n5'-UGG...CCGUC________AA________GUAGA...GUC-3'\n______________CGCCAGCA__CAGGGAGA\n______________\|\|\|\|\|:\|\|__\|\|\|\|\|\|:\|\n______________GCGGUUGU__GUCCCUUU\n3'-UUU...AUGAC________G_________AGAAC...GUG-5'\n_____________\|__________________\|\n_____________83_________________65\n	190 -- 196	66 -- 72	-25.5869 kcal/mol	5.97553 kcal/mol	7.04029 kcal/mol	178 197@LB@ \| \|@LB@5'-UGG...CCGUC AA GUAGA...GUC-3'@LB@ CGCCAGCA CAGGGAGA@LB@ \|\|\|\|\|:\|\| \|\|\|\|\|\|:\|@LB@ GCGGUUGU GUCCCUUU@LB@3'-UUU...AUGAC G AGAAC...GUG-5'@LB@ \| \|@LB@ 83 65@LB@@LB@@LB@Energy -12.57 kcal/mol@LB@Hybridization Energy -25.5869 kcal/mol@LB@Unfolding Energy - mRNA 5.97553 kcal/mol@LB@Unfolding Energy - sRNA 7.04029 kcal/mol@LB@@LB@Position - mRNA 179 -- 196@LB@Position - sRNA 66 -- 82@LB@Position Seed - mRNA 190 -- 196@LB@Position Seed - sRNA 66 -- 72@LB@
23	0.001421	0.1727	b1234	rssA	-12.55	0.044848	179 -- 192	61 -- 74	putative patatin-like family phospholipase	_____________178____________193\n_____________\|______________\|\n5'-GAU...GCAUU______________CGGGA...AAA-3'\n______________CCAGGGGAAUCUUG\n______________\|\|\|\|\|\|:\|\|\|\|\|\|\|\n______________GGUCCCUUUAGAAC\n3'-UUU...GUUGU______________CGACG...GUG-5'\n_____________\|______________\|\n_____________75_____________60\n	186 -- 192	61 -- 67	-22.3239 kcal/mol	6.14875 kcal/mol	3.62869 kcal/mol	178 193@LB@ \| \|@LB@5'-GAU...GCAUU CGGGA...AAA-3'@LB@ CCAGGGGAAUCUUG@LB@ \|\|\|\|\|\|:\|\|\|\|\|\|\|@LB@ GGUCCCUUUAGAAC@LB@3'-UUU...GUUGU CGACG...GUG-5'@LB@ \| \|@LB@ 75 60@LB@@LB@@LB@Energy -12.55 kcal/mol@LB@Hybridization Energy -22.3239 kcal/mol@LB@Unfolding Energy - mRNA 6.14875 kcal/mol@LB@Unfolding Energy - sRNA 3.62869 kcal/mol@LB@@LB@Position - mRNA 179 -- 192@LB@Position - sRNA 61 -- 74@LB@Position Seed - mRNA 186 -- 192@LB@Position Seed - sRNA 61 -- 67@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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