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
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@
129	0.007194	0.1964	b3401	hslO	-8.25	0.287762	98 -- 107	1 -- 10	heat shock protein Hsp33		_____________97_________108\n_____________\|__________\|\n5'-GCC...UUAAC__U_______CCGGA...AGA-3'\n______________CA_GCCGCAC\n______________\|\|_\|\|\|\|\|\|\|\n______________GU_CGGCGUG\n3'-UUU...AAAAA__C_______-5'\n_____________\|_________\|\n_____________11________1\n	101 -- 107	1 -- 7	-14.7655 kcal/mol	1.13179 kcal/mol	5.44172 kcal/mol	97 108@LB@ \| \|@LB@5'-GCC...UUAAC U CCGGA...AGA-3'@LB@ CA GCCGCAC@LB@ \|\| \|\|\|\|\|\|\|@LB@ GU CGGCGUG@LB@3'-UUU...AAAAA C -5'@LB@ \| \|@LB@ 11 1@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -14.7655 kcal/mol@LB@Unfolding Energy - mRNA 1.13179 kcal/mol@LB@Unfolding Energy - sRNA 5.44172 kcal/mol@LB@@LB@Position - mRNA 98 -- 107@LB@Position - sRNA 1 -- 10@LB@Position Seed - mRNA 101 -- 107@LB@Position Seed - sRNA 1 -- 7@LB@
142	0.00825	0.2033	b3457	livH	-8.25	0.287512	56 -- 64	3 -- 11	branched-chain amino acid ABC transporter permease		_____________55________65\n_____________\|_________\|\n5'-GAU...CGUGA_________UGAAC...ACG-3'\n______________UUGGGCCGC\n______________\|::\|\|\|\|\|\|\n______________AGUCCGGCG\n3'-UUU...CAAAA_________UG-5'\n_____________\|_________\|\n_____________12________2\n	58 -- 64	3 -- 9	-16.0849 kcal/mol	2.23282 kcal/mol	5.54194 kcal/mol	55 65@LB@ \| \|@LB@5'-GAU...CGUGA UGAAC...ACG-3'@LB@ UUGGGCCGC@LB@ \|::\|\|\|\|\|\|@LB@ AGUCCGGCG@LB@3'-UUU...CAAAA UG-5'@LB@ \| \|@LB@ 12 2@LB@@LB@@LB@Energy -8.25 kcal/mol@LB@Hybridization Energy -16.0849 kcal/mol@LB@Unfolding Energy - mRNA 2.23282 kcal/mol@LB@Unfolding Energy - sRNA 5.54194 kcal/mol@LB@@LB@Position - mRNA 56 -- 64@LB@Position - sRNA 3 -- 11@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 3 -- 9@LB@
75	0.003854	0.1809	b0606	ahpF	-8.17	0.297536	59 -- 82	64 -- 85	alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding		_____________58_______________________83\n_____________\|________________________\|\n5'-UCA...UUGCU___A___GA______UC_______CACCU...CGG-3'\n______________CUG_CGC__AAUACU__GGAAAUU\n______________\|\|\|_\|\|\|__\|\|:\|\|:__\|\|\|\|\|\|:\n______________GAC_GCG__UUGUGG__CCUUUAG\n3'-UUU...CUUAU_______G_______UC_______AACCG...GUG-5'\n_____________\|________________________\|\n_____________86_______________________63\n	76 -- 82	64 -- 70	-19.6667 kcal/mol	4.11652 kcal/mol	7.38387 kcal/mol	58 83@LB@ \| \|@LB@5'-UCA...UUGCU A GA UC CACCU...CGG-3'@LB@ CUG CGC AAUACU GGAAAUU@LB@ \|\|\| \|\|\| \|\|:\|\|: \|\|\|\|\|\|:@LB@ GAC GCG UUGUGG CCUUUAG@LB@3'-UUU...CUUAU G UC AACCG...GUG-5'@LB@ \| \|@LB@ 86 63@LB@@LB@@LB@Energy -8.17 kcal/mol@LB@Hybridization Energy -19.6667 kcal/mol@LB@Unfolding Energy - mRNA 4.11652 kcal/mol@LB@Unfolding Energy - sRNA 7.38387 kcal/mol@LB@@LB@Position - mRNA 59 -- 82@LB@Position - sRNA 64 -- 85@LB@Position Seed - mRNA 76 -- 82@LB@Position Seed - sRNA 64 -- 70@LB@
153	0.009069	0.2059	b3529	yhjK	-8.15	0.299018	186 -- 212	47 -- 74	cyclic-di-GMP phosphodiesterase		_____________185__________________________213\n_____________\|____________________________\|\n5'-AGC...GAUUU_________GACAAU_____________CGCUC...AUC-3'\n______________CCGGGGGGA______UUGCG_CGUAAGU\n______________\|\|:\|\|\|::\|______:\|\|\|\|_\|\|\|\|\|:\|\n______________GGUCCCUUU______GACGC_GCAUUUA\n3'-UUU...GUUGU_________AGAACC_____G_______AUAAU...GUG-5'\n_____________\|____________________________\|\n_____________75___________________________46\n	187 -- 193	67 -- 73	-27.1977 kcal/mol	10.2409 kcal/mol	8.80319 kcal/mol	185 213@LB@ \| \|@LB@5'-AGC...GAUUU GACAAU CGCUC...AUC-3'@LB@ CCGGGGGGA UUGCG CGUAAGU@LB@ \|\|:\|\|\|::\| :\|\|\|\| \|\|\|\|\|:\|@LB@ GGUCCCUUU GACGC GCAUUUA@LB@3'-UUU...GUUGU AGAACC G AUAAU...GUG-5'@LB@ \| \|@LB@ 75 46@LB@@LB@@LB@Energy -8.15 kcal/mol@LB@Hybridization Energy -27.1977 kcal/mol@LB@Unfolding Energy - mRNA 10.2409 kcal/mol@LB@Unfolding Energy - sRNA 8.80319 kcal/mol@LB@@LB@Position - mRNA 186 -- 212@LB@Position - sRNA 47 -- 74@LB@Position Seed - mRNA 187 -- 193@LB@Position Seed - sRNA 67 -- 73@LB@
66	0.003275	0.1727	b0394	mak	-8.12	0.303293	18 -- 92	5 -- 77	manno(fructo)kinase		_____________17_______________________________________________________________________________93\n_____________\|________________________________________________________________________________\|\n5'-GUU...CUUCU____G___C_______CGC____AA_A_G_____CC____AAUUUUUGA_______________GAUAA____CAC____UUGUC...GUG-3'\n______________GCAC_CAG_GAAAUCU___GGCU__G_C_GUAAA__AUUA_________AC_____CACAGCAU_____UUUC___GGCC\n______________:\|\|\|_\|\|\|_\|\|\|\|\|\|\|___\|\|\|\|__\|_\|_\|\|\|\|\|__\|\|\|\|_________\|\|_____\|\|\|\|\|\|\|:_____\|\|\|\|___\|\|\|\|\n______________UGUG_GUC_CUUUAGA___CCGA__C_G_CAUUU__UAAU_________UG_____GUGUCGUG_____AAAG___CCGG\n3'-UUU...GCGGU________C_______A______CG___G_____AA____ACUACUCAA__UUCCC________ACAA_____U______CGUG-5'\n_____________\|________________________________________________________________________________\|\n_____________78_______________________________________________________________________________4\n	70 -- 76	18 -- 24	-46.4183 kcal/mol	15.5654 kcal/mol	22.7286 kcal/mol	17 93@LB@ \| \|@LB@5'-GUU...CUUCU G C CGC AA A G CC AAUUUUUGA GAUAA CAC UUGUC...GUG-3'@LB@ GCAC CAG GAAAUCU GGCU G C GUAAA AUUA AC CACAGCAU UUUC GGCC@LB@ :\|\|\| \|\|\| \|\|\|\|\|\|\| \|\|\|\| \| \| \|\|\|\|\| \|\|\|\| \|\| \|\|\|\|\|\|\|: \|\|\|\| \|\|\|\|@LB@ UGUG GUC CUUUAGA CCGA C G CAUUU UAAU UG GUGUCGUG AAAG CCGG@LB@3'-UUU...GCGGU C A CG G AA ACUACUCAA UUCCC ACAA U CGUG-5'@LB@ \| \|@LB@ 78 4@LB@@LB@@LB@Energy -8.12 kcal/mol@LB@Hybridization Energy -46.4183 kcal/mol@LB@Unfolding Energy - mRNA 15.5654 kcal/mol@LB@Unfolding Energy - sRNA 22.7286 kcal/mol@LB@@LB@Position - mRNA 18 -- 92@LB@Position - sRNA 5 -- 77@LB@Position Seed - mRNA 70 -- 76@LB@Position Seed - sRNA 18 -- 24@LB@
160	0.009416	0.2062	b2095	gatZ	-8.10	0.305092	155 -- 170	18 -- 33	D-tagatose 1 6-bisphosphate aldolase 2 subunit	b3132	_____________154______________171\n_____________\|________________\|\n5'-AAU...GUGGC__________G_____AACGC...UUG-3'\n______________UGCGAGGGCA_GGCAU\n______________\|:\|:\|\|\|\|\|\|_:\|\|\|:\n______________AUGUUCCCGU_UCGUG\n3'-UUU...ACUCA__________G_____ACAAA...GUG-5'\n_____________\|________________\|\n_____________34_______________17\n	158 -- 164	24 -- 30	-26.3287 kcal/mol	9.40457 kcal/mol	8.82204 kcal/mol	154 171@LB@ \| \|@LB@5'-AAU...GUGGC G AACGC...UUG-3'@LB@ UGCGAGGGCA GGCAU@LB@ \|:\|:\|\|\|\|\|\| :\|\|\|:@LB@ AUGUUCCCGU UCGUG@LB@3'-UUU...ACUCA G ACAAA...GUG-5'@LB@ \| \|@LB@ 34 17@LB@@LB@@LB@Energy -8.10 kcal/mol@LB@Hybridization Energy -26.3287 kcal/mol@LB@Unfolding Energy - mRNA 9.40457 kcal/mol@LB@Unfolding Energy - sRNA 8.82204 kcal/mol@LB@@LB@Position - mRNA 155 -- 170@LB@Position - sRNA 18 -- 33@LB@Position Seed - mRNA 158 -- 164@LB@Position Seed - sRNA 24 -- 30@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@
134	0.007678	0.1993	b3139	agaC	-7.83	0.338422	255 -- 275	57 -- 74	N-acetylgalactosamine-specific enzyme IIC component of PTS		_____________254___________________276\n_____________\|_____________________\|\n5'-AAC...UUGUU_______UUGAU_________GAAGC...CGA-3'\n______________CUGGGGA_____UUUUGGCUG\n______________\|::\|\|\|\|_____\|:\|\|\|\|\|\|\|\n______________GGUCCCU_____AGAACCGAC\n3'-UUU...GUUGU_______UU____________GCGGC...GUG-5'\n_____________\|_____________________\|\n_____________75____________________56\n	269 -- 275	57 -- 63	-21.9136 kcal/mol	6.09668 kcal/mol	7.9843 kcal/mol	254 276@LB@ \| \|@LB@5'-AAC...UUGUU UUGAU GAAGC...CGA-3'@LB@ CUGGGGA UUUUGGCUG@LB@ \|::\|\|\|\| \|:\|\|\|\|\|\|\|@LB@ GGUCCCU AGAACCGAC@LB@3'-UUU...GUUGU UU GCGGC...GUG-5'@LB@ \| \|@LB@ 75 56@LB@@LB@@LB@Energy -7.83 kcal/mol@LB@Hybridization Energy -21.9136 kcal/mol@LB@Unfolding Energy - mRNA 6.09668 kcal/mol@LB@Unfolding Energy - sRNA 7.9843 kcal/mol@LB@@LB@Position - mRNA 255 -- 275@LB@Position - sRNA 57 -- 74@LB@Position Seed - mRNA 269 -- 275@LB@Position Seed - sRNA 57 -- 63@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@

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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