Input and runtime details for job 6860187 (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 6860187 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:29:33 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:29:58 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 01:36:19 CET 2018
	Post-Processing Finished		@ Sat Feb 17 01:36:26 CET 2018
	Job Completed		@ Sat Feb 17 01:36:50 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6860187&toolName=CopraRNA ( 30 days expiry )

Description of the job

SgrS

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
11	0.0006963	0.1842	b1739	osmE	-13.14	0.065080	250 -- 260	194 -- 204	osmotically-inducible lipoprotein	_____________249_________261\n_____________\|___________\|\n5'-GAA...AACCA___________UGUAC...AGC-3'\n______________UGCUGGCGGGU\n______________\|\|\|\|\|\|\|\|\|\|\|\n______________ACGACCGCCCA\n3'-UUU...AUUAG___________CUAAA...UAG-5'\n_____________\|___________\|\n_____________205_________193\n	254 -- 260	194 -- 200	-22.742 kcal/mol	5.67651 kcal/mol	8.00138 kcal/mol	249 261@LB@ \| \|@LB@5'-GAA...AACCA UGUAC...AGC-3'@LB@ UGCUGGCGGGU@LB@ \|\|\|\|\|\|\|\|\|\|\|@LB@ ACGACCGCCCA@LB@3'-UUU...AUUAG CUAAA...UAG-5'@LB@ \| \|@LB@ 205 193@LB@@LB@@LB@Energy -13.14 kcal/mol@LB@Hybridization Energy -22.742 kcal/mol@LB@Unfolding Energy - mRNA 5.67651 kcal/mol@LB@Unfolding Energy - sRNA 8.00138 kcal/mol@LB@@LB@Position - mRNA 250 -- 260@LB@Position - sRNA 194 -- 204@LB@Position Seed - mRNA 254 -- 260@LB@Position Seed - sRNA 194 -- 200@LB@
189	0.02188	0.3833	b4033	malF	-11.66	0.130598	273 -- 284	194 -- 205	maltose transporter subunit	_____________272__________285\n_____________\|____________\|\n5'-CUG...UCGGC____________UACCU...UAA-3'\n______________CUGCUGGUGGGU\n______________\|\|\|\|\|\|\|:\|\|\|\|\n______________GACGACCGCCCA\n3'-UUU...UAUUA____________CUAAA...UAG-5'\n_____________\|____________\|\n_____________206__________193\n	278 -- 284	194 -- 200	-24.1506 kcal/mol	7.59361 kcal/mol	9.05892 kcal/mol	272 285@LB@ \| \|@LB@5'-CUG...UCGGC UACCU...UAA-3'@LB@ CUGCUGGUGGGU@LB@ \|\|\|\|\|\|\|:\|\|\|\|@LB@ GACGACCGCCCA@LB@3'-UUU...UAUUA CUAAA...UAG-5'@LB@ \| \|@LB@ 206 193@LB@@LB@@LB@Energy -11.66 kcal/mol@LB@Hybridization Energy -24.1506 kcal/mol@LB@Unfolding Energy - mRNA 7.59361 kcal/mol@LB@Unfolding Energy - sRNA 9.05892 kcal/mol@LB@@LB@Position - mRNA 273 -- 284@LB@Position - sRNA 194 -- 205@LB@Position Seed - mRNA 278 -- 284@LB@Position Seed - sRNA 194 -- 200@LB@
74	0.007724	0.3458	b1261	trpB	-16.40	0.014006	36 -- 47	195 -- 206	tryptophan synthase beta subunit	_____________35___________48\n_____________\|____________\|\n5'-UGG...AACGU____________GGGCU...UCA-3'\n______________UCUGCUGGCGGG\n______________\|\|\|\|\|\|\|\|\|\|\|\|\n______________AGACGACCGCCC\n3'-UUU...AUAUU____________ACUAA...UAG-5'\n_____________\|____________\|\n_____________207__________194\n	41 -- 47	195 -- 201	-26.9412 kcal/mol	6.0368 kcal/mol	9.05854 kcal/mol	35 48@LB@ \| \|@LB@5'-UGG...AACGU GGGCU...UCA-3'@LB@ UCUGCUGGCGGG@LB@ \|\|\|\|\|\|\|\|\|\|\|\|@LB@ AGACGACCGCCC@LB@3'-UUU...AUAUU ACUAA...UAG-5'@LB@ \| \|@LB@ 207 194@LB@@LB@@LB@Energy -16.40 kcal/mol@LB@Hybridization Energy -26.9412 kcal/mol@LB@Unfolding Energy - mRNA 6.0368 kcal/mol@LB@Unfolding Energy - sRNA 9.05854 kcal/mol@LB@@LB@Position - mRNA 36 -- 47@LB@Position - sRNA 195 -- 206@LB@Position Seed - mRNA 41 -- 47@LB@Position Seed - sRNA 195 -- 201@LB@
39	0.003509	0.2912	b1293	sapB	-10.75	0.197427	9 -- 16	196 -- 203	antimicrobial peptide transport ABC transporter permease	_____________8____________17\n_____________\|____________\|\n5'-UCG...UAUUU_______CA___GC-3'\n______________CACCCCU__UGC\n______________\|\|\|\|\|\|:__\|\|\|\n______________GUGGGGG__ACG\n3'-UUU...ACCCC_______A____AAGUAG-5'\n_____________\|____________\|\n_____________204__________195\n	287 -- 293	11 -- 17	-15.5024 kcal/mol	0.267702 kcal/mol	6.55606 kcal/mol	8 17@LB@ \| \|@LB@5'-UCG...UAUUU CA GC-3'@LB@ CACCCCU UGC@LB@ \|\|\|\|\|\|: \|\|\|@LB@ GUGGGGG ACG@LB@3'-UUU...ACCCC A AAGUAG-5'@LB@ \| \|@LB@ 204 195@LB@@LB@@LB@Energy -10.75 kcal/mol@LB@Hybridization Energy -15.5024 kcal/mol@LB@Unfolding Energy - mRNA 0.267702 kcal/mol@LB@Unfolding Energy - sRNA 6.55606 kcal/mol@LB@@LB@Position - mRNA 9 -- 16@LB@Position - sRNA 196 -- 203@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 11 -- 17@LB@
47	0.004619	0.3205	b4142	groS	-15.85	0.018169	259 -- 271	196 -- 208	Cpn10 chaperonin GroES small subunit of GroESL	_____________258_______________________________272\n_____________\|_________________________________\|\n5'-UGA...AACUA_____________CAUCGUUCUG__________UGCAG...CUA-3'\n______________AAUCUGCUGGCGG__________ACCG__GCUC\n______________\|\|\|\|\|\|\|\|\|\|\|\|\|__________\|\|\|:__:\|\|\|\n______________UUAGACGACCGCC__________UGGU__UGAG\n3'-UUU...CCAUA_____________CACUAAAAUG____UA____UCAGU...UAG-5'\n_____________\|_________________________________\|\n_____________209_______________________________195\n	265 -- 271	196 -- 202	-33.1058 kcal/mol	10.148 kcal/mol	14.8106 kcal/mol	258 272@LB@ \| \|@LB@5'-UGA...AACUA CAUCGUUCUG UGCAG...CUA-3'@LB@ AAUCUGCUGGCGG ACCG GCUC@LB@ \|\|\|\|\|\|\|\|\|\|\|\|\| \|\|\|: :\|\|\|@LB@ UUAGACGACCGCC UGGU UGAG@LB@3'-UUU...CCAUA CACUAAAAUG UA UCAGU...UAG-5'@LB@ \| \|@LB@ 209 195@LB@@LB@@LB@Energy -15.85 kcal/mol@LB@Hybridization Energy -33.1058 kcal/mol@LB@Unfolding Energy - mRNA 10.148 kcal/mol@LB@Unfolding Energy - sRNA 14.8106 kcal/mol@LB@@LB@Position - mRNA 259 -- 271@LB@Position - sRNA 196 -- 208@LB@Position Seed - mRNA 265 -- 271@LB@Position Seed - sRNA 196 -- 202@LB@
96	0.01055	0.3575	b1953	yodD	-11.39	0.147949	264 -- 273	196 -- 205	uncharacterized protein	_____________263_____274\n_____________\|_______\|\n5'-CCA...UUCAC_______GUUUU...AAG-3'\n______________CUUCAUC\n______________\|\|\|\|\|\|\|\n______________GAAGUAG\n3'-UUU...GGAAC_______-5'\n_____________\|______\|\n_____________206____196\n	33 -- 39	1 -- 7	-8.82286 kcal/mol	0.690587 kcal/mol	0.701705 kcal/mol	263 274@LB@ \| \|@LB@5'-CCA...UUCAC GUUUU...AAG-3'@LB@ CUUCAUC@LB@ \|\|\|\|\|\|\|@LB@ GAAGUAG@LB@3'-UUU...GGAAC -5'@LB@ \| \|@LB@ 206 196@LB@@LB@@LB@Energy -11.39 kcal/mol@LB@Hybridization Energy -8.82286 kcal/mol@LB@Unfolding Energy - mRNA 0.690587 kcal/mol@LB@Unfolding Energy - sRNA 0.701705 kcal/mol@LB@@LB@Position - mRNA 264 -- 273@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 33 -- 39@LB@Position Seed - sRNA 1 -- 7@LB@
149	0.01599	0.3612	b3236	mdh	-10.77	0.195799	223 -- 232	196 -- 205	malate dehydrogenase NAD(P)-binding	_____________222_____233\n_____________\|_______\|\n5'-GUU...AUGAA_______GUCCU...AUG-3'\n______________AGUCGCA\n______________\|\|\|\|:\|\|\n______________UCAGUGU\n3'-UUU...AUGAG_______GUACU...UAG-5'\n_____________\|_______\|\n_____________206_____195\n	206 -- 212	169 -- 175	-8.87418 kcal/mol	1.40028 kcal/mol	0.26566 kcal/mol	222 233@LB@ \| \|@LB@5'-GUU...AUGAA GUCCU...AUG-3'@LB@ AGUCGCA@LB@ \|\|\|\|:\|\|@LB@ UCAGUGU@LB@3'-UUU...AUGAG GUACU...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -8.87418 kcal/mol@LB@Unfolding Energy - mRNA 1.40028 kcal/mol@LB@Unfolding Energy - sRNA 0.26566 kcal/mol@LB@@LB@Position - mRNA 223 -- 232@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 206 -- 212@LB@Position Seed - sRNA 169 -- 175@LB@
166	0.01886	0.3812	b3300	secY	-11.48	0.141920	168 -- 177	196 -- 205	preprotein translocase membrane subunit	_____________167_______________178\n_____________\|_________________\|\n5'-CCU...UCGAA____C_G__________CGAGG...UCC-3'\n______________GCUG_U_GCGGUAAAAU\n______________\|\|\|\|_\|_\|\|\|\|\|\|\|\|\|\|\n______________CGAC_A_CGCCAUUUUA\n3'-UUU...UGAAG______G__________UCACG...UAG-5'\n_____________\|_________________\|\n_____________206_______________195\n	177 -- 183	44 -- 50	-20.9884 kcal/mol	6.84834 kcal/mol	6.15722 kcal/mol	167 178@LB@ \| \|@LB@5'-CCU...UCGAA C G CGAGG...UCC-3'@LB@ GCUG U GCGGUAAAAU@LB@ \|\|\|\| \| \|\|\|\|\|\|\|\|\|\|@LB@ CGAC A CGCCAUUUUA@LB@3'-UUU...UGAAG G UCACG...UAG-5'@LB@ \| \|@LB@ 206 195@LB@@LB@@LB@Energy -11.48 kcal/mol@LB@Hybridization Energy -20.9884 kcal/mol@LB@Unfolding Energy - mRNA 6.84834 kcal/mol@LB@Unfolding Energy - sRNA 6.15722 kcal/mol@LB@@LB@Position - mRNA 168 -- 177@LB@Position - sRNA 196 -- 205@LB@Position Seed - mRNA 177 -- 183@LB@Position Seed - sRNA 44 -- 50@LB@
185	0.02128	0.3833	b2276	nuoN	-8.72	0.461673	62 -- 81	196 -- 211	NADH:ubiquinone oxidoreductase membrane subunit N	_____________61______________82\n_____________\|_______________\|\n5'-GUA...UAUGA__________U____GUGCU...AUC-3'\n______________UC_CUGUUGC_GGUG\n______________\|\|_\|\|\|\|:\|\|_\|\|\|:\n______________AG_GACAGCG_CCAU\n3'-UUU...GUUGA__C____________UUUAU...UAG-5'\n_____________\|_______________\|\n_____________212_____________195\n	69 -- 75	52 -- 58	-15.8669 kcal/mol	5.2118 kcal/mol	5.88061 kcal/mol	61 82@LB@ \| \|@LB@5'-GUA...UAUGA U GUGCU...AUC-3'@LB@ UC CUGUUGC GGUG@LB@ \|\| \|\|\|\|:\|\| \|\|\|:@LB@ AG GACAGCG CCAU@LB@3'-UUU...GUUGA C UUUAU...UAG-5'@LB@ \| \|@LB@ 212 195@LB@@LB@@LB@Energy -8.72 kcal/mol@LB@Hybridization Energy -15.8669 kcal/mol@LB@Unfolding Energy - mRNA 5.2118 kcal/mol@LB@Unfolding Energy - sRNA 5.88061 kcal/mol@LB@@LB@Position - mRNA 62 -- 81@LB@Position - sRNA 196 -- 211@LB@Position Seed - mRNA 69 -- 75@LB@Position Seed - sRNA 52 -- 58@LB@
173	0.0197	0.3812	b3210	arcB	-10.66	0.206219	214 -- 224	197 -- 207	aerobic respiration control sensor histidine protein kinase cognate to two-component response regulators ArcA and RssB	_____________213_________________225\n_____________\|___________________\|\n5'-UGC...UAACG_____G_____________AUUAU...UUC-3'\n______________UAACU_UCAGAAUUG_GGU\n______________:\|\|\|\|_\|\|\|\|\|\|\|\|\|_\|\|\|\n______________GUUGA_AGUCUUAAC_CCA\n3'-UUU...GUUCA_____A_________G___GUAGG...UAG-5'\n_____________\|___________________\|\n_____________208_________________196\n	156 -- 162	138 -- 144	-19.5528 kcal/mol	4.59493 kcal/mol	5.63708 kcal/mol	213 225@LB@ \| \|@LB@5'-UGC...UAACG G AUUAU...UUC-3'@LB@ UAACU UCAGAAUUG GGU@LB@ :\|\|\|\| \|\|\|\|\|\|\|\|\| \|\|\|@LB@ GUUGA AGUCUUAAC CCA@LB@3'-UUU...GUUCA A G GUAGG...UAG-5'@LB@ \| \|@LB@ 208 196@LB@@LB@@LB@Energy -10.66 kcal/mol@LB@Hybridization Energy -19.5528 kcal/mol@LB@Unfolding Energy - mRNA 4.59493 kcal/mol@LB@Unfolding Energy - sRNA 5.63708 kcal/mol@LB@@LB@Position - mRNA 214 -- 224@LB@Position - sRNA 197 -- 207@LB@Position Seed - mRNA 156 -- 162@LB@Position Seed - sRNA 138 -- 144@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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