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	Additional homologs
138	0.007886	0.2012	b3991	thiG	-13.21	0.033127	237 -- 259	64 -- 85	thiamine biosynthesis ThiGH complex subunit		_____________236______________________260\n_____________\|________________________\|\n5'-GCA...CACAU____UUA_________________CGCUU...CCG-3'\n______________CUGU___CCGGCA_CAGGGAAAUU\n______________\|\|\|:___\|\|::\|\|_\|\|\|\|\|\|\|\|\|:\n______________GACG___GGUUGU_GUCCCUUUAG\n3'-UUU...CUUAU____C________G__________AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	253 -- 259	64 -- 70	-25.8634 kcal/mol	5.26561 kcal/mol	7.38387 kcal/mol	236 260@LB@ \| \|@LB@5'-GCA...CACAU UUA CGCUU...CCG-3'@LB@ CUGU CCGGCA CAGGGAAAUU@LB@ \|\|\|: \|\|::\|\| \|\|\|\|\|\|\|\|\|:@LB@ GACG GGUUGU GUCCCUUUAG@LB@3'-UUU...CUUAU C G AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -13.21 kcal/mol@LB@Hybridization Energy -25.8634 kcal/mol@LB@Unfolding Energy - mRNA 5.26561 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 237 -- 259@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 253 -- 259@LB@Position Seed - sRNA 64 -- 70@LB@
105	0.005654	0.1855	b0004	thrC	-10.56	0.108775	227 -- 299	1 -- 79	L-threonine synthase		_____________226_____________________________________________________________________________________300\n_____________\|_______________________________________________________________________________________\|\n5'-CGC...GAUCA____G_G____UCAG____U__GCAA_______CCCAG____________________AAAAU___GG___________________G-3'\n______________CAAC_A_CAGG_____CUU_GC____GCCGUAA___________GGGUU____GGGCA_____CAG__GCUGUUUUUU___CCGCAC\n______________\|\|\|\|_\|_\|\|\|\|_____\|\|\|_\|\|____\|\|\|\|\|\|\|___________\|:\|\|\|____\|\|\|\|\|_____\|\|\|__:\|\|\|\|\|\|\|\|:___\|\|\|\|\|\|\n______________GUUG_U_GUCC_____GAA_CG____CGGCAUU___________CUCAA____CCCGU_____GUC__UGACAAAAAG___GGCGUG\n3'-UUU...ACGCG______G____CUUUA___C__ACG________UAAUAAUACUA_____UGUU_____________G___________UCC______-5'\n_____________\|______________________________________________________________________________________\|\n_____________80_____________________________________________________________________________________1\n	287 -- 293	10 -- 16	-55.9039 kcal/mol	22.5864 kcal/mol	22.7537 kcal/mol	226 300@LB@ \| \|@LB@5'-CGC...GAUCA G G UCAG U GCAA CCCAG AAAAU GG G-3'@LB@ CAAC A CAGG CUU GC GCCGUAA GGGUU GGGCA CAG GCUGUUUUUU CCGCAC@LB@ \|\|\|\| \| \|\|\|\| \|\|\| \|\| \|\|\|\|\|\|\| \|:\|\|\| \|\|\|\|\| \|\|\| :\|\|\|\|\|\|\|\|: \|\|\|\|\|\|@LB@ GUUG U GUCC GAA CG CGGCAUU CUCAA CCCGU GUC UGACAAAAAG GGCGUG@LB@3'-UUU...ACGCG G CUUUA C ACG UAAUAAUACUA UGUU G UCC -5'@LB@ \| \|@LB@ 80 1@LB@@LB@@LB@Energy -10.56 kcal/mol@LB@Hybridization Energy -55.9039 kcal/mol@LB@Unfolding Energy - mRNA 22.5864 kcal/mol@LB@Unfolding Energy - sRNA 22.7537 kcal/mol@LB@@LB@Position - mRNA 227 -- 299@LB@Position - sRNA 1 -- 79@LB@Position Seed - mRNA 287 -- 293@LB@Position Seed - sRNA 10 -- 16@LB@
195	0.01197	0.2159	b0738	tolR	-7.83	0.338188	180 -- 193	26 -- 40	membrane spanning protein in TolA-TolQ-TolR complex		_____________179_____________194\n_____________\|_______________\|\n5'-UGG...UUAGC______CA_______GUAAG...UGG-3'\n______________GA_GAG__ACAAGGG\n______________\|\|_\|\|\|__\|\|\|\|\|\|\|\n______________CU_CUC__UGUUCCC\n3'-UUU...UAAUA__A___AA_______GUGUC...GUG-5'\n_____________\|_______________\|\n_____________41______________25\n	187 -- 193	26 -- 32	-14.5104 kcal/mol	3.98616 kcal/mol	2.69022 kcal/mol	179 194@LB@ \| \|@LB@5'-UGG...UUAGC CA GUAAG...UGG-3'@LB@ GA GAG ACAAGGG@LB@ \|\| \|\|\| \|\|\|\|\|\|\|@LB@ CU CUC UGUUCCC@LB@3'-UUU...UAAUA A AA GUGUC...GUG-5'@LB@ \| \|@LB@ 41 25@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -14.5104 kcal/mol@LB@Unfolding Energy - mRNA 3.98616 kcal/mol@LB@Unfolding Energy - sRNA 2.69022 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 26 -- 40@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 26 -- 32@LB@
20	0.001165	0.1727	b1763	topB	-8.06	0.310309	3 -- 10	34 -- 41	DNA topoisomerase III		_____________2________11\n_____________\|________\|\n_________5'-UC________GAAAU...GUA-3'\n______________UGAUGGGU\n______________\|\|\|\|\|:\|\|\n______________ACUACUCA\n3'-UUU...AUAAU________AUGUU...GUG-5'\n_____________\|________\|\n_____________42_______33\n	4 -- 10	34 -- 40	-9.5271 kcal/mol	0.324007 kcal/mol	1.14413 kcal/mol	2 11@LB@ \| \|@LB@ 5'-UC GAAAU...GUA-3'@LB@ UGAUGGGU@LB@ \|\|\|\|\|:\|\|@LB@ ACUACUCA@LB@3'-UUU...AUAAU AUGUU...GUG-5'@LB@ \| \|@LB@ 42 33@LB@@LB@@LB@Energy -8.06 kcal/mol@LB@Hybridization Energy -9.5271 kcal/mol@LB@Unfolding Energy - mRNA 0.324007 kcal/mol@LB@Unfolding Energy - sRNA 1.14413 kcal/mol@LB@@LB@Position - mRNA 3 -- 10@LB@Position - sRNA 34 -- 41@LB@Position Seed - mRNA 4 -- 10@LB@Position Seed - sRNA 34 -- 40@LB@
32	0.001707	0.1727	b3606	trmL	-13.76	0.025837	263 -- 277	71 -- 85	tRNA Leu mC34 mU34 2'-O-methyltransferase SAM-dependent		_____________262_____________278\n_____________\|_______________\|\n5'-UAG...CGUCU_______________CUUUC...AAC-3'\n______________UUGCGCUAAUACCGG\n______________:\|\|\|\|\|:\|\|:\|\|\|:\|\n______________GACGCGGUUGUGGUC\n3'-UUU...CUUAU_______________CCUUU...GUG-5'\n_____________\|_______________\|\n_____________86______________70\n	271 -- 277	71 -- 77	-23.7581 kcal/mol	2.7368 kcal/mol	7.26103 kcal/mol	262 278@LB@ \| \|@LB@5'-UAG...CGUCU CUUUC...AAC-3'@LB@ UUGCGCUAAUACCGG@LB@ :\|\|\|\|\|:\|\|:\|\|\|:\|@LB@ GACGCGGUUGUGGUC@LB@3'-UUU...CUUAU CCUUU...GUG-5'@LB@ \| \|@LB@ 86 70@LB@@LB@@LB@Energy -13.76 kcal/mol@LB@Hybridization Energy -23.7581 kcal/mol@LB@Unfolding Energy - mRNA 2.7368 kcal/mol@LB@Unfolding Energy - sRNA 7.26103 kcal/mol@LB@@LB@Position - mRNA 263 -- 277@LB@Position - sRNA 71 -- 85@LB@Position Seed - mRNA 271 -- 277@LB@Position Seed - sRNA 71 -- 77@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@
166	0.009748	0.2068	b1261	trpB	-12.89	0.038353	88 -- 97	52 -- 61	tryptophan synthase beta subunit		_____________87_________98\n_____________\|__________\|\n5'-UGG...AAACC__________GACUU...UCA-3'\n______________GGCUGCGCCG\n______________\|\|\|\|\|\|\|\|\|\|\n______________CCGACGCGGC\n3'-UUU...UAGAA__________AUUUA...GUG-5'\n_____________\|__________\|\n_____________62_________51\n	91 -- 97	52 -- 58	-23.3299 kcal/mol	5.56351 kcal/mol	4.87533 kcal/mol	87 98@LB@ \| \|@LB@5'-UGG...AAACC GACUU...UCA-3'@LB@ GGCUGCGCCG@LB@ \|\|\|\|\|\|\|\|\|\|@LB@ CCGACGCGGC@LB@3'-UUU...UAGAA AUUUA...GUG-5'@LB@ \| \|@LB@ 62 51@LB@@LB@@LB@Energy -12.89 kcal/mol@LB@Hybridization Energy -23.3299 kcal/mol@LB@Unfolding Energy - mRNA 5.56351 kcal/mol@LB@Unfolding Energy - sRNA 4.87533 kcal/mol@LB@@LB@Position - mRNA 88 -- 97@LB@Position - sRNA 52 -- 61@LB@Position Seed - mRNA 91 -- 97@LB@Position Seed - sRNA 52 -- 58@LB@
97	0.005188	0.1855	b3060	ttdR	-16.80	0.006462	125 -- 147	67 -- 90	transcriptional activator of ttdABT	b1799	_____________124______________________148\n_____________\|________________________\|\n5'-UCC...AGAAU________________G_______UGGCA...CGC-3'\n______________GAAUAUUGCGCCAG_A_CAGGGAA\n______________\|\|\|\|\|:\|\|\|\|\|\|\|:_\|_\|\|\|\|\|\|\|\n______________CUUAUGACGCGGUU_U_GUCCCUU\n3'-UUU...ACGCG______________G_G_______UAGAA...GUG-5'\n_____________\|________________________\|\n_____________91_______________________66\n	141 -- 147	67 -- 73	-34.0784 kcal/mol	7.10756 kcal/mol	10.1694 kcal/mol	124 148@LB@ \| \|@LB@5'-UCC...AGAAU G UGGCA...CGC-3'@LB@ GAAUAUUGCGCCAG A CAGGGAA@LB@ \|\|\|\|\|:\|\|\|\|\|\|\|: \| \|\|\|\|\|\|\|@LB@ CUUAUGACGCGGUU U GUCCCUU@LB@3'-UUU...ACGCG G G UAGAA...GUG-5'@LB@ \| \|@LB@ 91 66@LB@@LB@@LB@Energy -16.80 kcal/mol@LB@Hybridization Energy -34.0784 kcal/mol@LB@Unfolding Energy - mRNA 7.10756 kcal/mol@LB@Unfolding Energy - sRNA 10.1694 kcal/mol@LB@@LB@Position - mRNA 125 -- 147@LB@Position - sRNA 67 -- 90@LB@Position Seed - mRNA 141 -- 147@LB@Position Seed - sRNA 67 -- 73@LB@
192	0.01187	0.2159	b2600	tyrA	-9.34	0.184498	136 -- 155	70 -- 86	fused chorismate mutase T/prephenate dehydrogenase		_____________135__________________156\n_____________\|____________________\|\n5'-UCG...GCCUU_______G__AUU_______AUCUG...UGG-3'\n______________GCUGCGU_AA___CAUCAGG\n______________:\|\|\|\|\|:_\|\|___\|\|:\|\|\|\|\n______________UGACGCG_UU___GUGGUCC\n3'-UUU...GCUUA_______G____________CUUUA...GUG-5'\n_____________\|____________________\|\n_____________87___________________69\n	149 -- 155	70 -- 76	-22.0981 kcal/mol	5.48162 kcal/mol	7.27772 kcal/mol	135 156@LB@ \| \|@LB@5'-UCG...GCCUU G AUU AUCUG...UGG-3'@LB@ GCUGCGU AA CAUCAGG@LB@ :\|\|\|\|\|: \|\| \|\|:\|\|\|\|@LB@ UGACGCG UU GUGGUCC@LB@3'-UUU...GCUUA G CUUUA...GUG-5'@LB@ \| \|@LB@ 87 69@LB@@LB@@LB@Energy -9.34 kcal/mol@LB@Hybridization Energy -22.0981 kcal/mol@LB@Unfolding Energy - mRNA 5.48162 kcal/mol@LB@Unfolding Energy - sRNA 7.27772 kcal/mol@LB@@LB@Position - mRNA 136 -- 155@LB@Position - sRNA 70 -- 86@LB@Position Seed - mRNA 149 -- 155@LB@Position Seed - sRNA 70 -- 76@LB@
185	0.01108	0.2089	b0662	ubiF	-8.33	0.279302	272 -- 292	6 -- 27	2-octaprenyl-3-methyl-6-methoxy-1 4-benzoquinol oxygenase		_____________271____________________293\n_____________\|______________________\|\n5'-AAU...GGGCU____________GA___GC___AACGGUGA-3'\n______________GGCACAGCAC_G__UUU__GGU\n______________\|\|\|\|\|\|\|\|\|\|_\|__\|\|\|__\|\|:\n______________CCGUGUCGUG_C__AAA__CCG\n3'-UUU...UGUUC__________A_AA___GU___GCGUG-5'\n_____________\|______________________\|\n_____________28_____________________5\n	275 -- 281	18 -- 24	-24.5826 kcal/mol	6.14687 kcal/mol	10.1088 kcal/mol	271 293@LB@ \| \|@LB@5'-AAU...GGGCU GA GC AACGGUGA-3'@LB@ GGCACAGCAC G UUU GGU@LB@ \|\|\|\|\|\|\|\|\|\| \| \|\|\| \|\|:@LB@ CCGUGUCGUG C AAA CCG@LB@3'-UUU...UGUUC A AA GU GCGUG-5'@LB@ \| \|@LB@ 28 5@LB@@LB@@LB@Energy -8.33 kcal/mol@LB@Hybridization Energy -24.5826 kcal/mol@LB@Unfolding Energy - mRNA 6.14687 kcal/mol@LB@Unfolding Energy - sRNA 10.1088 kcal/mol@LB@@LB@Position - mRNA 272 -- 292@LB@Position - sRNA 6 -- 27@LB@Position Seed - mRNA 275 -- 281@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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