Input and runtime details for job 2727377 (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 2727377 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:09 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:28 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:18:35 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:18:43 CET 2018
	Job Completed		@ Fri Feb 16 20:19:11 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2727377&toolName=CopraRNA ( 30 days expiry )

Description of the job

RyhB

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
189	0.02313	0.4113	b2438	eutK	-12.08	0.086588	220 -- 243	37 -- 62	putative ethanol utilization carboxysome structural protein	_____________219________________________244\n_____________\|__________________________\|\n5'-CGA...GGGAU____________AC______UG____CCGCG...GUC-3'\n______________UGCUGGAAGUGG____GGCA__GUCG\n______________\|:\|\|\|\|\|\|\|:::____:\|\|\|__\|\|\|\|\n______________AUGACCUUCGUU____UCGU__CAGC\n3'-UUU...UCAUU____________ACAC____UA____ACGAA...GCG-5'\n_____________\|__________________________\|\n_____________63_________________________36\n	224 -- 230	52 -- 58	-25.7957 kcal/mol	10.4122 kcal/mol	3.3026 kcal/mol	219 244@LB@ \| \|@LB@5'-CGA...GGGAU AC UG CCGCG...GUC-3'@LB@ UGCUGGAAGUGG GGCA GUCG@LB@ \|:\|\|\|\|\|\|\|::: :\|\|\| \|\|\|\|@LB@ AUGACCUUCGUU UCGU CAGC@LB@3'-UUU...UCAUU ACAC UA ACGAA...GCG-5'@LB@ \| \|@LB@ 63 36@LB@@LB@@LB@Energy -12.08 kcal/mol@LB@Hybridization Energy -25.7957 kcal/mol@LB@Unfolding Energy - mRNA 10.4122 kcal/mol@LB@Unfolding Energy - sRNA 3.3026 kcal/mol@LB@@LB@Position - mRNA 220 -- 243@LB@Position - sRNA 37 -- 62@LB@Position Seed - mRNA 224 -- 230@LB@Position Seed - sRNA 52 -- 58@LB@
195	0.0249	0.4226	b1476	fdnI	-9.91	0.194140	190 -- 212	37 -- 58	formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible	_____________189______________________213\n_____________\|________________________\|\n5'-CGU...GACGA_____AU__UCA____________AAAAU...UUU-3'\n______________GGAGG__CA___UGAGUAA_GUCG\n______________\|\|\|:\|__\|\|___\|\|\|\|:\|\|_\|\|\|\|\n______________CCUUC__GU___ACUCGUU_CAGC\n3'-UUU...UAUGA_________UAC_______A____ACGAA...GCG-5'\n_____________\|________________________\|\n_____________59_______________________36\n	202 -- 208	42 -- 48	-19.5397 kcal/mol	6.39857 kcal/mol	3.22699 kcal/mol	189 213@LB@ \| \|@LB@5'-CGU...GACGA AU UCA AAAAU...UUU-3'@LB@ GGAGG CA UGAGUAA GUCG@LB@ \|\|\|:\| \|\| \|\|\|\|:\|\| \|\|\|\|@LB@ CCUUC GU ACUCGUU CAGC@LB@3'-UUU...UAUGA UAC A ACGAA...GCG-5'@LB@ \| \|@LB@ 59 36@LB@@LB@@LB@Energy -9.91 kcal/mol@LB@Hybridization Energy -19.5397 kcal/mol@LB@Unfolding Energy - mRNA 6.39857 kcal/mol@LB@Unfolding Energy - sRNA 3.22699 kcal/mol@LB@@LB@Position - mRNA 190 -- 212@LB@Position - sRNA 37 -- 58@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
196	0.02499	0.4226	b3098	yqjD	-9.33	0.238834	67 -- 86	37 -- 57	membrane-anchored ribosome-binding protein	_____________66____________________87\n_____________\|_____________________\|\n5'-UCA...GAGGC_______AAA________C__AUAAG...AAG-3'\n______________GAAGCAA____GGCGAUG_CG\n______________\|\|\|\|\|\|\|____:\|\|:\|\|\|_\|\|\n______________CUUCGUU____UCGUUAC_GC\n3'-UUU...AUGAC_______ACAC_______A__ACGAA...GCG-5'\n_____________\|_____________________\|\n_____________58____________________36\n	77 -- 83	40 -- 46	-18.4137 kcal/mol	5.85817 kcal/mol	3.2267 kcal/mol	66 87@LB@ \| \|@LB@5'-UCA...GAGGC AAA C AUAAG...AAG-3'@LB@ GAAGCAA GGCGAUG CG@LB@ \|\|\|\|\|\|\| :\|\|:\|\|\| \|\|@LB@ CUUCGUU UCGUUAC GC@LB@3'-UUU...AUGAC ACAC A ACGAA...GCG-5'@LB@ \| \|@LB@ 58 36@LB@@LB@@LB@Energy -9.33 kcal/mol@LB@Hybridization Energy -18.4137 kcal/mol@LB@Unfolding Energy - mRNA 5.85817 kcal/mol@LB@Unfolding Energy - sRNA 3.2267 kcal/mol@LB@@LB@Position - mRNA 67 -- 86@LB@Position - sRNA 37 -- 57@LB@Position Seed - mRNA 77 -- 83@LB@Position Seed - sRNA 40 -- 46@LB@
200	0.02516	0.4226	b2566	era	-10.17	0.177109	195 -- 210	37 -- 61	membrane-associated 16S rRNA-binding GTPase	_____________194_______________________211\n_____________\|_________________________\|\n5'-UUG...CUGGA_________________________AUAAA...UCU-3'\n______________GCUGGAA______UGAGCA___UCG\n______________:\|\|\|\|\|\|______\|\|\|\|\|\|___\|\|\|\n______________UGACCUU______ACUCGU___AGC\n3'-UUU...CAUUA_______CGUUAC______UAC___ACGAA...GCG-5'\n_____________\|_________________________\|\n_____________62________________________36\n	195 -- 201	55 -- 61	-17.979 kcal/mol	4.50899 kcal/mol	3.30158 kcal/mol	194 211@LB@ \| \|@LB@5'-UUG...CUGGA AUAAA...UCU-3'@LB@ GCUGGAA UGAGCA UCG@LB@ :\|\|\|\|\|\| \|\|\|\|\|\| \|\|\|@LB@ UGACCUU ACUCGU AGC@LB@3'-UUU...CAUUA CGUUAC UAC ACGAA...GCG-5'@LB@ \| \|@LB@ 62 36@LB@@LB@@LB@Energy -10.17 kcal/mol@LB@Hybridization Energy -17.979 kcal/mol@LB@Unfolding Energy - mRNA 4.50899 kcal/mol@LB@Unfolding Energy - sRNA 3.30158 kcal/mol@LB@@LB@Position - mRNA 195 -- 210@LB@Position - sRNA 37 -- 61@LB@Position Seed - mRNA 195 -- 201@LB@Position Seed - sRNA 55 -- 61@LB@
2	1.064e-05	0.01787	b1683	sufB	-21.37	0.002185	208 -- 233	38 -- 66	component of SufBCD Fe-S cluster assembly scaffold	_____________207___________________________234\n_____________\|_____________________________\|\n5'-GUU...GUCUC________________C____________AAAAC...AGC-3'\n______________GUAAUACU_GAAGCAA__UGA_CGAUGUC\n______________\|\|\|\|\|\|\|\|_\|\|\|\|\|\|\|__\|\|\|_\|:\|\|\|\|\|\n______________CAUUAUGA_CUUCGUU__ACU_GUUACAG\n3'-UUU...CGAUU________C_______AC___C_______CACGA...GCG-5'\n_____________\|_____________________________\|\n_____________67____________________________37\n	227 -- 233	38 -- 44	-29.4313 kcal/mol	4.7571 kcal/mol	3.30527 kcal/mol	207 234@LB@ \| \|@LB@5'-GUU...GUCUC C AAAAC...AGC-3'@LB@ GUAAUACU GAAGCAA UGA CGAUGUC@LB@ \|\|\|\|\|\|\|\| \|\|\|\|\|\|\| \|\|\| \|:\|\|\|\|\|@LB@ CAUUAUGA CUUCGUU ACU GUUACAG@LB@3'-UUU...CGAUU C AC C CACGA...GCG-5'@LB@ \| \|@LB@ 67 37@LB@@LB@@LB@Energy -21.37 kcal/mol@LB@Hybridization Energy -29.4313 kcal/mol@LB@Unfolding Energy - mRNA 4.7571 kcal/mol@LB@Unfolding Energy - sRNA 3.30527 kcal/mol@LB@@LB@Position - mRNA 208 -- 233@LB@Position - sRNA 38 -- 66@LB@Position Seed - mRNA 227 -- 233@LB@Position Seed - sRNA 38 -- 44@LB@
5	0.0002772	0.1521	b3365	nirB	-15.55	0.022306	192 -- 212	38 -- 57	nitrite reductase large subunit NAD(P)H-binding	_____________191___________________213\n_____________\|_____________________\|\n5'-AUC...AAAUC_______AAA_______A___AGACU...UUA-3'\n______________GAGGCAA___UGAGCAA_GUC\n______________\|\|:\|\|\|\|___\|\|\|\|\|\|\|_\|\|\|\n______________CUUCGUU___ACUCGUU_CAG\n3'-UUU...AUGAC_______AC________A___CACGA...GCG-5'\n_____________\|_____________________\|\n_____________58____________________37\n	202 -- 208	42 -- 48	-22.0527 kcal/mol	3.28811 kcal/mol	3.2161 kcal/mol	191 213@LB@ \| \|@LB@5'-AUC...AAAUC AAA A AGACU...UUA-3'@LB@ GAGGCAA UGAGCAA GUC@LB@ \|\|:\|\|\|\| \|\|\|\|\|\|\| \|\|\|@LB@ CUUCGUU ACUCGUU CAG@LB@3'-UUU...AUGAC AC A CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -15.55 kcal/mol@LB@Hybridization Energy -22.0527 kcal/mol@LB@Unfolding Energy - mRNA 3.28811 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 192 -- 212@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 42 -- 48@LB@
10	0.0006218	0.2043	b1423	ydcJ	-15.65	0.021404	209 -- 256	38 -- 84	putative metalloenzyme	_____________208__________________________________________________257\n_____________\|____________________________________________________\|\n5'-GAA...GCGAA_______A_______A____AUUCG___________UUUC_CA_________AGCCA...UGG-3'\n______________CAGCAUC_CGGC_GG_UGAG_______GGAA_CAGU____G__GGCAAUGUC\n______________\|\|\|\|\|:\|_\|\|\|\|_\|\|_\|:\|\|_______\|\|\|\|_\|\|:\|____\|__:\|\|\|\|\|\|\|\|\n______________GUCGUGG_GCCG_CC_AUUC_______CCUU_GUUA____C__UCGUUACAG\n_____3'-UUUUCG____________A__G____AUUAUGA____C_________AC_________CACGA...GCG-5'\n_____________\|____________________________________________________\|\n_____________85___________________________________________________37\n	250 -- 256	38 -- 44	-41.5422 kcal/mol	10.9926 kcal/mol	14.897 kcal/mol	208 257@LB@ \| \|@LB@5'-GAA...GCGAA A A AUUCG UUUC CA AGCCA...UGG-3'@LB@ CAGCAUC CGGC GG UGAG GGAA CAGU G GGCAAUGUC@LB@ \|\|\|\|\|:\| \|\|\|\| \|\| \|:\|\| \|\|\|\| \|\|:\| \| :\|\|\|\|\|\|\|\|@LB@ GUCGUGG GCCG CC AUUC CCUU GUUA C UCGUUACAG@LB@ 3'-UUUUCG A G AUUAUGA C AC CACGA...GCG-5'@LB@ \| \|@LB@ 85 37@LB@@LB@@LB@Energy -15.65 kcal/mol@LB@Hybridization Energy -41.5422 kcal/mol@LB@Unfolding Energy - mRNA 10.9926 kcal/mol@LB@Unfolding Energy - sRNA 14.897 kcal/mol@LB@@LB@Position - mRNA 209 -- 256@LB@Position - sRNA 38 -- 84@LB@Position Seed - mRNA 250 -- 256@LB@Position Seed - sRNA 38 -- 44@LB@
13	0.000833	0.2153	b1531	marA	-8.74	0.292618	190 -- 205	38 -- 57	multiple antibiotic resistance transcriptional regulator	_____________189__________________206\n_____________\|____________________\|\n5'-AAG...AAAAA____________________CAGAC...AGC-3'\n______________GAGGUA___UGA_CGAUGUC\n______________\|\|:\|:\|___\|\|\|_\|:\|\|\|\|\|\n______________CUUCGU___ACU_GUUACAG\n3'-UUU...AUGAC______UAC___C_______CACGA...GCG-5'\n_____________\|____________________\|\n_____________58___________________37\n	199 -- 205	38 -- 44	-15.3925 kcal/mol	3.44101 kcal/mol	3.2161 kcal/mol	189 206@LB@ \| \|@LB@5'-AAG...AAAAA CAGAC...AGC-3'@LB@ GAGGUA UGA CGAUGUC@LB@ \|\|:\|:\| \|\|\| \|:\|\|\|\|\|@LB@ CUUCGU ACU GUUACAG@LB@3'-UUU...AUGAC UAC C CACGA...GCG-5'@LB@ \| \|@LB@ 58 37@LB@@LB@@LB@Energy -8.74 kcal/mol@LB@Hybridization Energy -15.3925 kcal/mol@LB@Unfolding Energy - mRNA 3.44101 kcal/mol@LB@Unfolding Energy - sRNA 3.2161 kcal/mol@LB@@LB@Position - mRNA 190 -- 205@LB@Position - sRNA 38 -- 57@LB@Position Seed - mRNA 199 -- 205@LB@Position Seed - sRNA 38 -- 44@LB@
20	0.001583	0.2659	b4547	ypfN	-17.32	0.011014	197 -- 242	38 -- 88	putative membrane protein UPF0370 family	_____________196_________________________________________________243\n_____________\|___________________________________________________\|\n5'-UGA...GAAAU____AU_G______________A__U__G____UUCUG_____U_______UUUUU...AGA-3'\n______________AAGC__G_A_CUGGCUGGCUAA_UA_UG_UGGA______GUGA____UGUC\n______________\|\|\|\|__\|_\|_\|:\|\|\|\|\|\|\|\|\|\|_\|\|_\|:_\|\|\|\|______\|\|\|\|____\|\|\|\|\n______________UUCG__C_U_GGCCGACCGAUU_AU_AU_ACCU______CACU____ACAG\n_________3'-UU____GU_G_G____________C__U__G____UCGUUA____CGUU____CACGA...GCG-5'\n_____________\|___________________________________________________\|\n_____________89__________________________________________________37\n	211 -- 217	67 -- 73	-42.3158 kcal/mol	10.0822 kcal/mol	14.9106 kcal/mol	196 243@LB@ \| \|@LB@5'-UGA...GAAAU AU G A U G UUCUG U UUUUU...AGA-3'@LB@ AAGC G A CUGGCUGGCUAA UA UG UGGA GUGA UGUC@LB@ \|\|\|\| \| \| \|:\|\|\|\|\|\|\|\|\|\| \|\| \|: \|\|\|\| \|\|\|\| \|\|\|\|@LB@ UUCG C U GGCCGACCGAUU AU AU ACCU CACU ACAG@LB@ 3'-UU GU G G C U G UCGUUA CGUU CACGA...GCG-5'@LB@ \| \|@LB@ 89 37@LB@@LB@@LB@Energy -17.32 kcal/mol@LB@Hybridization Energy -42.3158 kcal/mol@LB@Unfolding Energy - mRNA 10.0822 kcal/mol@LB@Unfolding Energy - sRNA 14.9106 kcal/mol@LB@@LB@Position - mRNA 197 -- 242@LB@Position - sRNA 38 -- 88@LB@Position Seed - mRNA 211 -- 217@LB@Position Seed - sRNA 67 -- 73@LB@
21	0.001761	0.2682	b2988	gss	-16.20	0.017239	12 -- 42	38 -- 68	glutathionylspermidine amidase and glutathionylspermidine synthetase	_____________11________________________________43\n_____________\|_________________________________\|\n5'-AGU...CUUCU________G__UU____________________ACUUG...UCG-3'\n______________GAGUGGUA_UG__GAAGCAGUGU_AGCAG_GUC\n______________:\|\|\|::\|\|_\|\|__\|\|\|\|\|\|:\|\|\|_\|\|\|\|:_\|\|\|\n______________UUCAUUAU_AC__CUUCGUUACA_UCGUU_CAG\n3'-UUU...ACCGA________G______________C_____A___CACGA...GCG-5'\n_____________\|_________________________________\|\n_____________69________________________________37\n	28 -- 34	48 -- 54	-32.4779 kcal/mol	12.9749 kcal/mol	3.30528 kcal/mol	11 43@LB@ \| \|@LB@5'-AGU...CUUCU G UU ACUUG...UCG-3'@LB@ GAGUGGUA UG GAAGCAGUGU AGCAG GUC@LB@ :\|\|\|::\|\| \|\| \|\|\|\|\|\|:\|\|\| \|\|\|\|: \|\|\|@LB@ UUCAUUAU AC CUUCGUUACA UCGUU CAG@LB@3'-UUU...ACCGA G C A CACGA...GCG-5'@LB@ \| \|@LB@ 69 37@LB@@LB@@LB@Energy -16.20 kcal/mol@LB@Hybridization Energy -32.4779 kcal/mol@LB@Unfolding Energy - mRNA 12.9749 kcal/mol@LB@Unfolding Energy - sRNA 3.30528 kcal/mol@LB@@LB@Position - mRNA 12 -- 42@LB@Position - sRNA 38 -- 68@LB@Position Seed - mRNA 28 -- 34@LB@Position Seed - sRNA 48 -- 54@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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